# hmmscan :: search sequence(s) against a profile database
# HMMER 3.2.1 (June 2018); http://hmmer.org/
# Copyright (C) 2018 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query sequence file:             /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Neorickettsia_helminthoeca_str._Oregon-ASM63298v1/GCA_000632985.1_ASM63298v1_protein.faa
# target HMM database:             /oak/stanford/groups/akundaje/marinovg/genomes/PFam/PFam32.0/Pfam-A.hmm
# output directed to file:         /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Neorickettsia_helminthoeca_str._Oregon-ASM63298v1/GCA_000632985.1_ASM63298v1_protein.PFam32-A
# per-seq hits tabular output:     /oak/stanford/groups/akundaje/marinovg/genomes/Bacteria/Neorickettsia_helminthoeca_str._Oregon-ASM63298v1/GCA_000632985.1_ASM63298v1_protein.PFam32-A.tblout
# number of worker threads:        20
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       AHX10978.1  [L=290]
Description: uroporphyrinogen decarboxylase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-79  266.1   0.0    5.4e-79  265.8   0.0    1.0  1  URO-D     Uroporphyrinogen decarboxylase (URO-D)


Domain annotation for each model (and alignments):
>> URO-D  Uroporphyrinogen decarboxylase (URO-D)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.8   0.0     3e-83   5.4e-79      45     344 ..       1     287 [.       1     288 [. 0.95

  Alignments for each domain:
  == domain 1  score: 265.8 bits;  conditional E-value: 3e-83
                 HHH-HHHHHHHHHHHHHHH--S-EE-S--TTGGGGGGT-EEEEETTTEEEEE--S-....GGGS----GGG.G..HHHHHHHHHHHHH.--SS-EEEEE CS
       URO-D  45 lcknpelaaevtlqpvrrfglDaailfsdilveaealGlevefeegegPvvekpvrtaedveklevpddveegrlpyvleaikllkkelggevpligfv 143
                 +c +pe aae+t+qp++rf++Daai+fsdilv + alG+ +e +++ gPv+e     +++ve l+ ++  + ++++ +l+ai++++  l +e  ligf+
  AHX10978.1   1 MCDSPEIAAEITMQPIKRFDFDAAIIFSDILVLPRALGCNIEVKKDIGPVIET----IDKVESLNYDEF-A-KKISGTLDAIRITRGLLSKEKKLIGFA 93 
                 699************************************************98....68999**87765.4.68************************* PP

                 E-HHHHHHHHHCTT.-SS-HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEETTGGGS-HHHHHHHTHHHHHHHHHHHHH.H--S-EE CS
       URO-D 144 gaPftlasylveGg.skgfekllkllykdpeevhklldkltdvvieylkaqieagAdaiqifDswagllspedfeefvlpylkrivdevkaegpkvpvi 241
                 g+P+t+a y++eG+  k+f k++++++k+  +++ ++d+ltd++i+ylk+qie gAd+iqif+s a++ s   feef+++++k+iv+ +       pvi
  AHX10978.1  94 GGPWTIALYIIEGKwDKTFLKTKSFINKRYSDFKNIIDILTDATISYLKKQIECGADIIQIFESFASAASFTEFEEFIIEPTKKIVSSIDV-----PVI 187
                 *****************************************************************************************97.....*** PP

                 EEESSHH.HHHHHHTTS--SEEE--TTS-HHHHHHSS....EEE--B-G.GGGGS-HHHHHHHHHHHHT.T---SSSEEB-BSS---TTS-HHHHHHHH CS
       URO-D 242 lfikgagaeiledlaelgadvlsldwtvdlkeaarevgdkvalqGnldPialLlgspeeiekevkeilekgaggkkgyilnlGhgippetppenvkalv 340
                  f+kgaga++l++++++ +d++s d + +l   ++++++ +++qGnldP  lL  ++++   ++ +il+    +++ +i+nlGhgi  etp++n++ ++
  AHX10978.1 188 GFPKGAGASYLNYVRDTSVDIISTDYSLSLDWIVQNLQQYATIQGNLDP-YLLAFNKDKALYQTGKILDS--LSGEDFIFNLGHGIYKETPIANIESVL 283
                 *******99*********************555669999**********.58889999999********4..56899*******************999 PP

                 HHHH CS
       URO-D 341 eavk 344
                 + ++
  AHX10978.1 284 DKIR 287
                 8765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.43
# Mc/sec: 2045.28
//
Query:       AHX10979.1  [L=115]
Description: quinolinate synthetase A family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-36  126.0   0.0    1.8e-36  125.9   0.0    1.0  1  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.9   0.0     1e-40   1.8e-36      55     155 ..       2     103 ..       1     109 [. 0.96

  Alignments for each domain:
  == domain 1  score: 125.9 bits;  conditional E-value: 1e-40
                 HHHHHHHHHHSTTSEEE-SSTT---HHHCT--HHHHHHHHHHSTTS-EEEESSS-HHHHTT-SEEE-TTTHHHHHHHSS.-SEEEEES-HHHHHHHHHH CS
        NadA  55 hFMaetakiLspekkvllpdleagCsladmitaeeveelkeelpdaavvtYvNssaevKalsdivcTSsnavkvvealk.ekkilflPDqnLgryvakk 152
                 +FM+e akiLsp+kkvl+pdl+agCsl+++++   ++++ +++++  v+tY+Nss+evKa+sd +cTSs+a+k++++++ +k+i+f PD++Lg+y++kk
  AHX10979.1   2 KFMGEVAKILSPSKKVLMPDLDAGCSLEKSCKVGPFKHFISKVDNPFVLTYINSSVEVKAVSDSICTSSSAEKIIRNIPaDKTIVFGPDRYLGDYLQKK 100
                 7*****************************************************************************77*****************99 PP

                 H.S CS
        NadA 153 lge 155
                   e
  AHX10979.1 101 NRE 103
                 755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (115 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 868.46
//
Query:       AHX10980.1  [L=149]
Description: quinolinate synthetase A family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.5e-39  134.8   0.0    3.8e-39  134.6   0.0    1.0  1  NadA         Quinolinate synthetase A protein
  ------ inclusion threshold ------
      0.049   13.6   0.1      0.082   12.8   0.1    1.3  1  Mob_synth_C  Molybdenum Cofactor Synthesis C


Domain annotation for each model (and alignments):
>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.6   0.0   4.3e-43   3.8e-39     158     298 ..       1     143 [.       1     144 [. 0.93

  Alignments for each domain:
  == domain 1  score: 134.6 bits;  conditional E-value: 4.3e-43
                 EEESSSS-GCGGG--CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSEEE.......ECS. CS
        NadA 158 iilwkgaCsvHeefkaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapekefials.a.eaae. 253
                 + +w+g+C+vHe+f++++v +lk ++pdakv++HPEck+++++ ad++gSTsq++++vk+s   efii Te g+++++kk  p+ +f+++  +   ++ 
  AHX10980.1   1 MEIWNGTCIVHENFSEKHVISLKMSNPDAKVIAHPECKDTLLNYADFIGSTSQLLSYVKSSGFMEFIILTEPGIIHQMKKVLPGGRFYEVGaSgG-VCe 98 
                 679*************************************************************************************9886334.442 PP

                 .SSSSTTGGG--HHHHHHHHHHT-S.B----HHHHHHHHHHHHHHH CS
        NadA 254 .eavCetMkkitleklleaLeeleeeeikvdeevaekAkkalerml 298
                     C++M+ +t+ekl+++L+++e+  i++d+++a++A+ ++++m+
  AHX10980.1  99 mCSKCPYMRLNTIEKLYNCLKKEEP-YITIDQSIAHAARSSIDKMF 143
                 3445*******************99.9******************7 PP

>> Mob_synth_C  Molybdenum Cofactor Synthesis C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   9.1e-06     0.082      71     106 ..      99     135 ..      95     145 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9.1e-06
                  -GGG--EEEE-TTSEEESSSS-SS-.EEHHHHHHTT- CS
  Mob_synth_C  71 FCasCnRlRltadGklktCLfaeee.idlrdllrega 106
                   C++C  +Rl +  kl++CL +ee  i + + + + a
   AHX10980.1  99 MCSKCPYMRLNTIEKLYNCLKKEEPyITIDQSIAHAA 135
                  6**********************99888888877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       526  (0.0293379); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1113.07
//
Query:       AHX10981.1  [L=161]
Description: pantetheine-phosphate adenylyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-17   62.0   0.0    8.2e-17   61.7   0.0    1.1  1  CTP_transf_like  Cytidylyltransferase-like
  ------ inclusion threshold ------
      0.078   13.4   0.1        2.3    8.7   0.0    2.3  2  HMA              Heavy-metal-associated domain
        0.1   12.9   0.0       0.13   12.5   0.0    1.2  1  RGS              Regulator of G protein signaling domain


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   1.4e-20   8.2e-17       1     142 [.       5     134 ..       5     135 .. 0.90

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 1.4e-20
                      EEEE--TT--HHHHHHHHHHHHHSSESEEEEEESSTHCSST-SCSSTHHHHHHHHHHH.TTCTTEEEEE.EESEHHHHHHHTTTTEEEEEEEHH CS
  CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleedlivgvpsdeppkkkkkplasaeeRlemlela.kevdevisvd.pweltrevlkklkpdklylvigad 92 
                      ++ GtFDp++lGHl+++++a+  +++ li+g++ + +++    p +s+ eRl+ + +   e +  i+v+ ++ l  +++++ ++   ++++g +
       AHX10981.1   5 VYAGTFDPVTLGHLDIIKRALLIVDK-LIIGIAEKSSKN----PTFSSIERLDFVTESiSEISGNIEVKiFDGLLVNFMRNENCR--IIIRGLR 91 
                      589***********************.***999988888....88********99998866665566551555677*********..******* PP

                      HHHHHHCHHHHHHHHHHHHHEEEEEEHTTCEEEEEEECCTTTCSHHHHHH CS
  CTP_transf_like  93 vledfsewkeleeilgnvklvvvsrpekqanvllkaekrtngiSstkire 142
                      +++df  ++e++    n kl++   +     ++l+a+++t++ Sst +++
       AHX10981.1  92 AVSDF--EYEFQISWLNHKLAGDIMT-----IFLPASNETQFLSSTLVKQ 134
                      *****..****************999.....99**************997 PP

>> HMA  Heavy-metal-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0      0.04   2.4e+02      16      31 ..      54      69 ..      52      70 .. 0.91
   2 ?    8.7   0.0   0.00039       2.3      33      58 ..     131     156 ..     126     160 .. 0.91

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.04
         HMA 16 vekvLselpgVesvkv 31
                v++++se++g+ +vk+
  AHX10981.1 54 VTESISEISGNIEVKI 69
                89*********99987 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.00039
         HMA  33 latktvtVegdaestklrkiieaiek 58 
                 l+++ +t +gd +++++++ii++++k
  AHX10981.1 131 LVKQVATLNGDLSQLLPSQIINKVRK 156
                 7899**********999*******99 PP

>> RGS  Regulator of G protein signaling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   2.2e-05      0.13      14      78 ..      73     137 ..      65     160 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.2e-05
                 HHHHHHHHTTCTHHHHHHHHHHHHHTSSHHHHHHHH.HHHHHHHHTSTTSTTSSTS-HHHHHHHHH CS
         RGS  14 lFreFlesefseenlsFwlaveefkkakeqeelkkk.akeIyneylapsspkelnidkklreelek 78 
                 l+ +F+++e++   ++ + av++f+ + + + l+ k a +I+  +l p+s++  ++++ l++++++
  AHX10981.1  73 LLVNFMRNENCRIIIRGLRAVSDFEYEFQISWLNHKlAGDIMTIFL-PASNETQFLSSTLVKQVAT 137
                 6779***********************6666666668*********.9999999******999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      338  (0.0188521); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1168.56
//
Query:       AHX10982.1  [L=274]
Description: hypothetical protein NHE_0005 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.04   14.2   0.5        4.3    7.7   0.1    2.4  2  FKBP_C    FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0024        43      33      67 ..     116     149 ..      89     170 .. 0.85
   2 ?    7.7   0.1   0.00024       4.3       7      66 ..     201     253 ..     195     258 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0024
                 SEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEG CS
      FKBP_C  33 kplefkvGsgqvikGfeealegmkvGekrtltipp 67 
                 ++le +vG  + i+ f  a  gmk+ e++t+ +  
  AHX10982.1 116 QQLEYQVGM-HNIPVFNIAPIGMKKTEEATIGVSN 149
                 677888884.679*****************98865 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.00024
                 TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEE CS
      FKBP_C   7 egdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltip 66 
                  gd+++++yk +  +gk++ s+     ++++k+G   +   fe+ + gm+   krt++  
  AHX10982.1 201 CGDRAEIKYKVYDLQGKKIISD-----KANIKIGG--KSALFENFVIGMQPSTKRTVIMN 253
                 58999*****999999999999.....89999995..6667****************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       465  (0.0259356); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2128.62
//
Query:       AHX10983.1  [L=258]
Description: parB/RepB/Spo0J family partition domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-23   81.5   1.1    5.6e-23   81.0   0.3    1.7  2  ParBc     ParB-like nuclease domain
    1.1e-11   44.3   2.3    1.6e-11   43.9   0.4    2.2  2  HTH_ParB  HTH domain found in ParB protein
    0.00036   20.5   0.1      0.015   15.3   0.0    2.4  2  KorB      KorB domain
  ------ inclusion threshold ------
      0.014   15.4   0.3       0.17   11.9   0.0    2.9  2  HTH_19    Helix-turn-helix domain
      0.026   13.7   2.1      0.027   13.7   0.6    1.7  2  DUF561    Protein of unknown function (DUF561)
      0.052   13.4   0.1       0.17   11.8   0.1    1.8  1  TrmB      Sugar-specific transcriptional regulator TrmB


Domain annotation for each model (and alignments):
>> ParBc  ParB-like nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.0   0.3   1.9e-26   5.6e-23       3      89 ..      10      96 ..       8      97 .. 0.97
   2 ?   -3.5   0.0       4.4   1.3e+04      16      27 ..     187     197 ..     179     208 .. 0.54

  Alignments for each domain:
  == domain 1  score: 81.0 bits;  conditional E-value: 1.9e-26
       ParBc  3 vplseirpnplqprkd.spekieelvasIkkkGllqPiivrktrqgryeiiaGerRlrAakrlglkevpvivleiddeeamalslien 89
                ++++ei+ n++qpr+  ++ ++ el++sIkk+G+ qPi+vr++  +ry+++ GerRlrAak lglk +p i++e +d+  +++++ien
  AHX10983.1 10 LNTDEIDANENQPRRSfDEASLLELSESIKKNGIVQPIVVRRKG-NRYQLVVGERRLRAAKKLGLKVIPGIIKEFTDQSSLEIAIIEN 96
                6799***************************************6.******************************************9 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.4
       ParBc  16 rkdspekieelv 27 
                 r++ ++ i++++
  AHX10983.1 187 RQT-EDLIRKII 197
                 333.33333332 PP

>> HTH_ParB  HTH domain found in ParB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.69     2e+03      27      43 ..      88     104 ..      80     104 .. 0.78
   2 !   43.9   0.4   5.2e-15   1.6e-11       2      52 .]     148     195 ..     147     195 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.69
    HTH_ParB  27 elqlqlaekiieegLsV 43 
                  l +++ e +++e+L++
  AHX10983.1  88 SLEIAIIENVQREDLNS 104
                 56678899999999995 PP

  == domain 2  score: 43.9 bits;  conditional E-value: 5.2e-15
    HTH_ParB   2 evqeavsegkiseGHARaLlslkdeelqlqlaekiieegLsVRetEklvre 52 
                  v+ +++++kis GHA+ L+s+++    + +a+++++  L+VR+tE+l+r+
  AHX10983.1 148 NVKILLRDKKISLGHAKLLISVENN---EYIADEVVRLSLNVRQTEDLIRK 195
                 57889*******************8...9********************96 PP

>> KorB  KorB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   4.9e-06     0.015       6      37 ..     122     153 ..     119     159 .. 0.90
   2 ?    2.7   0.0     0.044   1.3e+02      22      61 ..     182     222 ..     176     250 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 4.9e-06
        KorB   6 qadIAkaLGksksfvslylklldvpdylrely 37 
                  +++A + G+s+s+++ +  +l +pd ++ l+
  AHX10983.1 122 HEEVASIVGRSRSYITNHVRILSLPDNVKILL 153
                 689*************************9876 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.044
        KorB  22 lylklldvpdylrelyds.eviadirtLyeLrraaekhpae 61 
                 l l + + +d +r+++++ + ++di+   eL  + +k  ++
  AHX10983.1 182 LSLNVRQTEDLIRKIINKkQSCSDIKKSSELLMLERKVSER 222
                 56778899*******99625799999988888887776655 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   5.9e-05      0.17       5      31 ..     112     138 ..     112     140 .. 0.94
   2 ?   -0.5   0.1      0.42   1.3e+03      31      31 ..     195     195 ..     157     228 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5.9e-05
      HTH_19   5 keaReelgltqeelaerlgisrskisa 31 
                 ++++ee+++t ee+a+ +g srs+i++
  AHX10983.1 112 NRLIEEFKYTHEEVASIVGRSRSYITN 138
                 5899*********************86 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.42
      HTH_19  31 a 31 
                 +
  AHX10983.1 195 K 195
                 1 PP

>> DUF561  Protein of unknown function (DUF561)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.34     1e+03      12      46 ..      70     107 ..      65     131 .. 0.51
   2 ?   13.7   0.6   8.9e-06     0.027      99     190 ..     136     228 ..     129     244 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.34
      DUF561  12 kkaikvisGl.nnfnveqvl..kiaraaekakatyvDi 46 
                 k  +kvi G+ + f  +  l  +i++  ++     +D 
  AHX10983.1  70 KLGLKVIPGIiKEFTDQSSLeiAIIENVQREDLNSIDE 107
                 55567777752445444333013344455555555553 PP

  == domain 2  score: 13.7 bits;  conditional E-value: 8.9e-06
      DUF561  99 klsseeilalvkevrkLlPktdlsvtiPyiL.kleeqvkLakkLeslgvdliqteGkitsiskakkvndliekslstlastyeiskkvslPvi 190
                   +   il+l ++v+ Ll + ++s     +L ++e+  ++a+++++l +++ qte  i +i ++k+    i+ks + l    ++s+++ + v+
  AHX10983.1 136 ITNHVRILSLPDNVKILLRDKKISLGHAKLLiSVENNEYIADEVVRLSLNVRQTEDLIRKIINKKQSCSDIKKSSELLMLERKVSERLGMRVV 228
                 5567789******************98876637889999***********************99999999****9999999999888777665 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   5.6e-05      0.17       9      47 ..     106     144 ..     103     157 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                 HCCCHCHHHHHHCCCHHCHHCCCTTSSCHCHHHHHHHHH CS
        TrmB   9 yEakvYlaLlklgpatadeiaeelgvprskvYevLrsLe 47 
                  Ea +Y  L+++ + t +e+a+++g++rs + + +r L+
  AHX10983.1 106 DEAIAYNRLIEEFKYTHEEVASIVGRSRSYITNHVRILS 144
                 5999*************************9998888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2092.67
//
Query:       AHX10984.1  [L=479]
Description: hypothetical protein NHE_0007 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (479 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 3591.27
//
Query:       AHX10985.1  [L=413]
Description: his Kinase A domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.3e-27   93.8   0.3    1.8e-26   92.8   0.3    1.5  1  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
      4e-18   65.2   0.0    7.9e-18   64.3   0.0    1.5  1  HisKA          His Kinase A (phospho-acceptor) domain
    3.4e-06   26.9   0.5    7.3e-06   25.9   0.1    1.9  2  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.023   14.7   0.0    1.3  1  HATPase_c_2    Histidine kinase-like ATPase domain
      0.016   14.4   0.2      0.026   13.7   0.2    1.3  1  Peptidase_M56  BlaR1 peptidase M56
      0.039   13.9   0.0        1.5    8.8   0.0    2.4  2  GRIP           GRIP domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.8   0.3   6.1e-30   1.8e-26       2     110 ..     298     407 ..     297     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: 92.8 bits;  conditional E-value: 6.1e-30
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHTGTCSTTCH.HCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETT CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveikaseddlvisveDnGiGipkedlkklfekfsq.ddstkrggggtGlGlsivkklvelmgGeiwvesepg 99 
                 d kr++q+i n+++Navkf+ ++g+i ++i++   +++i+++DnG Gip++d+ k    f q + + +r++ gtG+Gl ++kklvelmgG ++++s++g
  AHX10985.1 298 DHKRVKQVILNILSNAVKFTDENGDINISIRKLPSEIEIEISDNGVGIPEKDIAKALSVFGQsNTELSRKYDGTGIGLPLSKKLVELMGGVFEINSKEG 396
                 7899***************88**********63379******************8888888877789999***************************** PP

                 TEEEEEEEEES CS
   HATPase_c 100 rGttftftlpl 110
                  Gt + ++lp 
  AHX10985.1 397 SGTIVKIRLPH 407
                 ********996 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.0   2.6e-21   7.9e-18       2      65 ..     188     251 ..     187     253 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 2.6e-21
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA   2 lgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                 +++fla+v+HEL+tPL+ai+g++++++  + ++ e k+y ++i  ++++l++l++d+Ld+s+ e
  AHX10985.1 188 KSQFLANVSHELKTPLNAIIGFSDLIRTADTASKEHKDYANDIYYSGNHLLNLINDILDFSKSE 251
                 89************************7777899****************************987 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.1       2.5   7.5e+03     103     124 ..     168     189 ..     158     198 .. 0.55
   2 !   25.9   0.1   2.4e-09   7.3e-06       4      77 ..     303     375 ..     299     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.5
  HATPase_c_3 103 ldvdkidkenekvleeltveei 124
                  ++++   k+ ++++ee++ ++ 
   AHX10985.1 168 FSINTKLKKAKENIEEISLQKS 189
                  4444444445555666666554 PP

  == domain 2  score: 25.9 bits;  conditional E-value: 2.4e-09
  HATPase_c_3   4 ekAlaelvdNsldAdaen..vkievnknrgktgeivieDdGkGmseeelknalr.latsskeakrkstslGkkGiGl 77 
                  +++++ ++ N++    en  ++i++ k + ++ ei i D+G G++e+++ +al+ +++s++e    s+++   GiGl
   AHX10985.1 303 KQVILNILSNAVKFTDENgdINISIRKLP-SEIEIEISDNGVGIPEKDIAKALSvFGQSNTEL---SRKYDGTGIGL 375
                  78999*******98777766888888876.799********************7477777775...55555556665 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   7.6e-06     0.023      24     123 ..     294     403 ..     276     405 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 7.6e-06
  HATPase_c_2  24 lseelldeirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeep........keslkegGrGlalikglvDev. 112
                  l +++ ++++ ++  +++Nav+   ++   g+++++++  + ++++e++D+G g + +++++              + + +  G+Gl l k+lv+ + 
   AHX10985.1 294 LIKSDHKRVKQVILNILSNAVKFTDEN---GDINISIRKLPSEIEIEISDNGVGIPEKDIAKALS--VfgqsntelSRKYDGTGIGLPLSKKLVELMg 386
                  555566677777777899999999874...88999999****************77777666533..13456777789999999********998776 PP

  HATPase_c_2 113 ...ey...dgegnvvtm 123
                     e+   +g g++v +
   AHX10985.1 387 gvfEInskEGSGTIVKI 403
                  64555655555666665 PP

>> Peptidase_M56  BlaR1 peptidase M56
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.2   8.8e-06     0.026      83     166 ..     109     190 ..      75     202 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.8e-06
  Peptidase_M56  83 ddkasalatdvkkvewktilkillliWivgalilllyliaallvlkkrfvrklgklrae.elkeaLkeakeemqlkrnikirlss 166
                    d+  +       +++ ++i+  +  +Wi   l+++l +ia + +  +++++ ++ l+++ +++ +Lk+ake+ +   +i++++s+
     AHX10985.1 109 DADEETPSIMEITYNANNIVGPIRFLWISFTLVVILVCIAIFAWSVRKIIKGSRVLNEQfSINTKLKKAKENIE---EISLQKSQ 190
                    444444444556789999**********999997777777777666668888888876547899********99...77776665 PP

>> GRIP  GRIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00049       1.5      21      42 ..     232     253 ..     222     255 .. 0.83
   2 ?    2.4   0.0      0.05   1.5e+02      18      39 ..     298     319 ..     292     321 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00049
        GRIP  21 serkqLvpVlstlLkfspeEeq 42 
                  + ++L++ +  +L+fs++E +
  AHX10985.1 232 YSGNHLLNLINDILDFSKSELN 253
                 5679***************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.05
        GRIP  18 keaserkqLvpVlstlLkfspe 39 
                 + + +++ ++++ls   kf++e
  AHX10985.1 298 DHKRVKQVILNILSNAVKFTDE 319
                 4477899999**********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1268  (0.0707234); expected 358.6 (0.02)
Passed bias filter:                      667  (0.0372023); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3278.79
//
Query:       AHX10986.1  [L=411]
Description: FAD dependent oxidoreductase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.7e-08   32.7   0.1    1.6e-07   31.3   0.0    1.7  2  DAO       FAD dependent oxidoreductase


Domain annotation for each model (and alignments):
>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   2.5      0.46   8.3e+03       1       9 [.       3      11 ..       3      11 .. 0.92
   2 !   31.3   0.0   8.7e-12   1.6e-07     103     321 ..     155     376 ..      75     397 .. 0.59

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.46
                EEEEECTSH CS
         DAO  1 dvviiGGGi 9 
                d v+iGGG+
  AHX10986.1  3 DYVVIGGGV 11
                89******7 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 8.7e-12
                 HHHHHHTTTTE.EEEEHHHHHHHSTTSTTTSEEEEETTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEE..TCEEEEEEECT.EEEEEEEEEE CS
         DAO 103 lallleaglda.elldaeevrelepalpgllgalfypdtgqvdpakltaalaraaealGveilegtevtgleeed..gkvwgverttp.gendaadavV 197
                 +++  +++l   e +d+  v++ +p    l+ga++++ +  ++  k+++ +++ ++++Gv+++ +te+ +l+      k++ v  +++ g +++ +   
  AHX10986.1 155 AEE--KNDLSPiE-IDG--VEKDSP---FLRGAIYDDRSFSFNSLKFCRKILNFLRSNGVDFFCNTEISKLNF-TleRKLKSV--VSSsGKVFTGRNYF 242
                 222..23332201.333..334444...446***************************************933.123456667..56669886658899 PP

                 E--GGGHHHHHTTCTTTSEEEEEEEEEEEEEECCTHSTGSGCSEEEEE........EEETTTTEEEEEETTSEEEEEESSE.EETTCSSTSCSHH.HHH CS
         DAO 198 naaGawsdllgllkeldlpispvrgqvlvlkplseklvspaailpvpe........tdddgrgvyvtprkdgrvlvGgtad.eesgdddpevdee.did 286
                 +a Ga s  l+ +  l+  ++p+ g  + ++ +  +  +++ ++ +          ++    + + + + d+ ++vG+    + ++    +++ +  ++
  AHX10986.1 243 IAIGANSFGLNDFFGLKYLTQPILGLWFLIDGVRAENPFKYHHYVNSNlafcqsytPISSISDGFGYSTGDNALVVGTGCAwT-RSLYGKSCSGNaFVQ 340
                 99999984333332333344666666655555444333333222222233333344222222235566678889998876533.333333554442566 PP

                 HHHHHHHHHSGGGCGEEE.EEEEEEE.ETTSSEEEEE CS
         DAO 287 ellealrklfPqlgdvlr.kwaGlrp.lpdglplige 321
                    + lrklfP++ ++++ +  ++r    +glp++  
  AHX10986.1 341 MNEKLLRKLFPGK-KIVQiHGNCIRNfSYNGLPIVFS 376
                 6999999*****5.55543888999944799998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (411 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       444  (0.0247643); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3244.16
//
Query:       AHX10987.1  [L=350]
Description: iron uptake protein A1 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-17   63.9   0.2    1.9e-17   63.5   0.2    1.1  1  SBP_bac_6   Bacterial extracellular solute-binding protein
    2.3e-16   60.5   0.0      3e-16   60.1   0.0    1.1  1  SBP_bac_8   Bacterial extracellular solute-binding protein
    3.7e-16   59.6   0.0    7.3e-16   58.6   0.0    1.4  1  SBP_bac_11  Bacterial extracellular solute-binding protein
      2e-13   51.0   0.0    4.3e-13   49.9   0.0    1.5  1  SBP_bac_1   Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_6  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.5   0.2   4.2e-21   1.9e-17       3     222 ..      87     310 ..      85     324 .. 0.85

  Alignments for each domain:
  == domain 1  score: 63.5 bits;  conditional E-value: 4.2e-21
   SBP_bac_6   3 lpdlilsfdkdflekfieeglfqpldpanlpnvnkdfaeeglkdpdgkyypygvgplvlavnkdrlkgrpvPksWaDLldPeykgkvalpgnngsdlfe 101
                  +d++++ d   l+ +  e+l+q + +a l++  +    ++l+    ++ +++  + ++++ kdr++  ++ k+++DL +P++k++  l++ n   +++
  AHX10987.1  87 SADVFIAADVVNLAFAERENLLQCISSAVLESAIP----SNLRNC--YWFGLTRRTRLIVYSKDRVNPSEI-KDYEDLSNPKWKDRLLLRSSNS-PYNQ 177
                 68999999999999999999998666666655543....555554..888*****************9999.*******************998.**** PP

   SBP_bac_6 102 alllalykdfgedgvkkllrnlkanlhpaq...mvkaagslesgepavsvvpyff.adilpekkkgk......nlkvvwPed...Galvspifmlvkkg 187
                  l++ +   +g+++ + +++ +  n+         ++++ ++sge+ + vv  ++ a+il+++k +       ++ v+ P++   Ga v++  + v ++
  AHX10987.1 178 SLIASMIFANGLEKTESWIKGVVRNMARPPyggDIDQIKGVASGEGDLAVVNSYYvARILASDK-NVykkvaeKIGVIFPNQdnrGAMVNISGAGVTRY 275
                 **********************999988888998899999*****8888887655156666665.54589999*******87788************** PP

   SBP_bac_6 188 .kkkelakafidfllspevqailakaggvfPvvtnp 222
                  k+ke a +f+ f++s+++q+++a ++ ++P+ ++ 
  AHX10987.1 276 aKNKENAIKFLQFMVSRKAQEMYATENHEYPI-LAS 310
                 *******************************8.433 PP

>> SBP_bac_8  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.1   0.0   6.7e-20     3e-16       2     278 ..      53     321 ..      52     324 .. 0.79

  Alignments for each domain:
  == domain 1  score: 60.1 bits;  conditional E-value: 6.7e-20
                 HHHHHHHH-TEEEEEEE--SSSHHHHHHHHHHTT---SEE.EEE-HHHHHHHHHTTSB--GGGSTTHHH-HHHHHTT--TS.----EEEEEEE-EEEEE CS
   SBP_bac_8   2 lakefekktgvkvnvvtaasndleqklkaalaagtapdidvvwanedalatlaeeglladlsdldnlddltdalaavgydgklygvPyasetpyvliyn 100
                 + ++f+++tg+kvn++t +  +l++ +k++ +  +a d++ + a+  +la +  e+ll+ +s+      +++ l+        y++ ++  t  +++y 
  AHX10987.1  53 VFAAFTEETGIKVNYITDDAIKLISRMKSEGKNTSA-DVF-IAADVVNLAFAERENLLQCISSAVLESAIPSNLRN------CYWFGLTRRT-RLIVYS 142
                 6799***********999888999999997644433.444.333345666666699******87777778887774......4*****9997.9***** PP

                 HHHHHHS.---BHHHHHHHHHHHHHH-SE..GG---G.GGGGGTHHETTEE---H..HHH.HHHHHHHHHHHHTT-EE-S....--SSTTTTTSBSEEE CS
   SBP_bac_8 101 kdllekaedpktwdellaaakklkgkfgl..pdpasg.wlqaallakdgksldddggkdglkealellkklkdngktydtga..davsefanGevafti 194
                 kd +     +k++++l    +k+k +  l  ++++++ +l+a +++++           gl+++  ++k  + n+  ++ g   d+++ +a+Ge   ++
  AHX10987.1 143 KDRVNPS-EIKDYEDLSN--PKWKDRLLLrsSNSPYNqSLIASMIFAN-----------GLEKTESWIKGVVRNMARPPYGGdiDQIKGVASGEGDLAV 227
                 ****987.9*********..***9888776567776536666666644...........556666799999999998865541367779****999999 PP

                 E-TTHHHHHH........-TTTSEEEE--S-...-EEEEEEEEEEBTTS-HHHHHHHHHHHHHTTSHHHHHHHHHH---BS-S-TTTHHHHHH-H CS
   SBP_bac_8 195 ngswdiaaaq........kagkklgaivpkq...gsfaggkglavpknaknedlaAldFlkwltspenqaalaektgyipvnksaalspevkkdp 278
                   s  +a +         k  +k+g+i+p+q   g++++++g  v+  akn++  A++Fl++++s  +q+++a+     p++ s+++s+ +k++ 
  AHX10987.1 228 VNSYYVARILasdknvykKVAEKIGVIFPNQdnrGAMVNISGAGVTRYAKNKEN-AIKFLQFMVSRKAQEMYATENHEYPILASVENSEILKSWG 321
                 7665555433444666646689*******654459******************7.*******************************999988875 PP

>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.0   1.6e-19   7.3e-16       4     224 ..      41     298 ..      38     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1.6e-19
                 EE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH.....-SEEEESSH.HHHHHHHHGGGGG................GG-EEEEEEEEEE CS
  SBP_bac_11   4 aaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadga...rpDvwipassawlellaaaglvqa................esavplassplvi 83 
                 ++++ +++ +r++ aaF+++tg+kv++ + ++ kl+++++++     +Dv+i+a+   l+ +++++l+q                      l++ +  i
  AHX10987.1  41 VYSSRKEQMVRDVFAAFTEETGIKVNYITDDAIKLISRMKSEGkntSADVFIAADVVNLAFAERENLLQCissavlesaipsnlrnCYWFGLTRRTRLI 139
                 688889*********************************7765589**********99**********9899999988888777666666777777888 PP

                 EESTT-..TT---SHHHHHHSS-..-EEEE--T-TTTTHH.HHHHGGG--....HHHHHHHHHT.EEEEESSHHHHHHHHHTTT-SEEEEEHHHH.... CS
  SBP_bac_11  84 avpkgn..pkkikgwadLlkpgl..klavadPttspsGlaalalleaaga....qellkalekk.vvklgessrqlltaveageadagivyesea.... 169
                 ++ k++  p  ik+ +dL +p++  +l +   ++sp+ +  +a +  a++    + ++k + ++ ++   +++ + ++ v++ge d+++v+   +    
  AHX10987.1 140 VYSKDRvnPSEIKDYEDLSNPKWkdRLLLR-SSNSPYNQSLIASMIFANGlektESWIKGVVRNmARPPYGGDIDQIKGVASGEGDLAVVNSYYVaril 237
                 8888878899*************6544443.4689999966666665544477899********544557888999999************99997877 PP

                 .....H..HSTTSSEEEE--TTT--....EEEEEEEE-TT--HHHHHHHHHTTSHHHHHHH CS
  SBP_bac_11 170 .....kaaengdkleavylpeglnl.dpldypaavlkkaakreaAraFlafLrspeaqail 224
                       +++ ++k+ ++ + ++    +    +a+v++ a+++e A +Fl+f+ s++aq++ 
  AHX10987.1 238 asdknVYKKVAEKIGVIFPNQDNRGaMVNISGAGVTRYAKNKENAIKFLQFMVSRKAQEMY 298
                 7776644478888888888888877455588999************************975 PP

>> SBP_bac_1  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   9.6e-17   4.3e-13       9     315 .]      48     296 ..      42     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 9.6e-17
                 HHHHHHHHHHHHHHTTEEEEEEEECHHHHHHHHHHHHHTTSSSCSEEEE.CGGHHHHHHHTTSBECCHHHHHHTTECTTCCTEEEEHHHHTHHHHC.E. CS
   SBP_bac_1   9 alqalvakafekehpgikVeiesvgsgslaqkltlaiaaGdgpaDviav.dndwiarlakaglllpldpyvkaylapgvkdaadklsssvlpkild.s. 104
                  +   v +af++ ++gikV++++ +   l+   +   ++ +  aDv++  d   +a   +++ll+ +++ v + ++p +             ++++ + 
  AHX10987.1  48 QMVRDVFAAFTE-ETGIKVNYITDDAIKLIS--RMKSEGKNTSADVFIAaDVVNLAFAERENLLQCISSAVLESAIPSNL---------RNCYWFGlTr 134
                 566667799*99.8*******9997777777..33333444667*****777777766666*****************87.........4566777455 PP

                 EEESEEEEEEEEEEEETTTHHCTTGGG.....SHBHHHHHHHHHHHHHHCTCTHCCHCCEEHHHHHHHHHHHHHHHHTGGGEECCCTHHCSHHHHS..H CS
   SBP_bac_1 105 kvlyvPlyaargliYNkdlfekagldp.....pwtWdelveaakklkekgkkpiggarggsasgtayyfalalakslggkvfdkdgggldnpegvt..a 196
                 +        +r+++Y+kd + +++++       + W+     ++ l  + ++p      + +s  a+  +                   +n+  +t  +
  AHX10987.1 135 R--------TRLIVYSKDRVNPSEIKDyedlsNPKWK-----DRLLLRSSNSP------YNQSLIASMIF-------------------ANGLEKTesW 195
                 5........************9999887888888888.....66677777777......66666666655...................4444555567 PP

                 HHHHHHHHHHHHHHHHHHTTEEECSSHHHHHHHHHTTSCSEEEEEHHHHHHHHCEEEEECHHCHHHHTTSTEEEECEEBETTTTSEE..EEEEEEEEBT CS
   SBP_bac_1 197 atylvklyavanltkelkgkgaenkdgaaalalfeaGeaamaivglwaalaamkvapkvafaadkekpkeelgvaplPagkggkpgi..lgayglaipk 293
                 ++ +v  +            ++++ d ++ ++ +++Ge ++a+v ++++     + + + +++ ++k+ e++gv+  P      + +  ++ +g ++  
  AHX10987.1 196 IKGVVRNM----------ARPPYGGDIDQIKG-VASGEGDLAVVNSYYV-----ARILASDKNVYKKVAEKIGVIF-PNQ---DNRGamVNISGAGVTR 274
                 77777777..........88999999999655.779************6.....6678999999999999999975.433...333347********** PP

                 TCSTHHHHHHHHHHHTSHHHHH CS
   SBP_bac_1 294 gsknpeaAkkFldfllspeaqa 315
                  +kn+e A kFl+f+ s +aq+
  AHX10987.1 275 YAKNKENAIKFLQFMVSRKAQE 296
                 *******************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (350 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 2562.50
//
Query:       AHX10988.1  [L=157]
Description: hypothetical protein NHE_0011 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-22   79.0   0.0    4.7e-22   78.8   0.0    1.0  1  RuvX      Holliday junction resolvase


Domain annotation for each model (and alignments):
>> RuvX  Holliday junction resolvase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   2.6e-26   4.7e-22       3     133 ..      19     143 ..      17     145 .. 0.93

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 2.6e-26
                 EEEEEESSSEEEEEEE-S--SS---EEEEE---HHHHHHHHHHHHHHTT--EEEEE------SSS---SSTTHHHHHHHHHT..T-EEEEE--S----X CS
        RuvX   3 ilglDvGtkriGvAvsdplgilaspletierkskekdleelkelvkeeeveeiVvGlPlnldgsegesakkvrkfaeeLakrlkklpvelvDErlttve 101
                 i+++D+G+k iGvAvsdp+ ++ + +  ++++ ++ d+  ++++ ++++   iVvG P+++  +++     ++kf  +L++++ + p+ + DE+l+t++
  AHX10988.1  19 IIAVDLGRKSIGVAVSDPQLKYVQDYFQFDSRGRSCDAWYIQKIKQDYS--GIVVGTPFSH-TRNNGWLSFIDKFSAKLSDTT-GKPILMQDESLSTIK 113
                 89****************************887899999*****98885..*********9.66677999************8.*************** PP

                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        RuvX 102 aerilresglsrkkrkkvvDklaAviiLqsyL 133
                 a +i+   ++sr++++k +Dkl+A +iL++ L
  AHX10988.1 114 ALNII--GKTSRNRQRKWKDKLSAYCILEETL 143
                 ****9..68899*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1254.25
//
Query:       AHX10989.1  [L=50]
Description: hypothetical protein NHE_0012 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       273  (0.0152267); expected 358.6 (0.02)
Passed bias filter:                      193  (0.0107647); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 410.62
//
Query:       AHX10990.1  [L=180]
Description: CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-16   59.9   0.3    3.2e-16   59.9   0.3    2.6  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.9   0.3   1.8e-20   3.2e-16       2      66 .]       4      70 ..       4      70 .. 0.81
   2 ?   -0.1   1.7     0.092   1.7e+03      11      11 ..     129     129 ..      72     174 .. 0.55

  Alignments for each domain:
  == domain 1  score: 59.9 bits;  conditional E-value: 1.8e-20
                     -HHHHHHHHHHHHHHHHHGGGS-H....HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
  CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyp..lvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                     lPn++T+lr++l+ l +l +++ +   +++ +l++  asltD++DG+lAR l+ +s++Gkl+D++aD
       AHX10990.1  4 LPNLLTILRIILIPLFCLSFYIESKfsWLVTVLIFSSASLTDFFDGYLARTLEAQSKFGKLFDPIAD 70
                     6***********88888766444445444444444588**************999***********9 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.092
                      H CS
  CDP-OH_P_transf  11 l 11 
                       
       AHX10990.1 129 T 129
                      2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       519  (0.0289475); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1341.51
//
Query:       AHX10991.1  [L=188]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 6 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.5e-28   98.6  16.7    2.5e-28   98.6  16.7    1.5  2  Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.058   12.8  11.7       0.11   11.9  11.7    1.5  1  Ceramidase   Ceramidase
       0.16   12.3   0.3       0.16   12.3   0.3    3.1  3  ATP-synt_C   ATP synthase subunit C
       0.48   10.4  17.4       0.58   10.2  17.4    1.1  1  HisKA_7TM    N-terminal 7TM region of histidine kinase
       0.73    9.5   0.0       0.73    9.5   0.0    2.5  2  DUF2244      Integral membrane protein (DUF2244)


Domain annotation for each model (and alignments):
>> Oxidored_q3  NADH-ubiquinone/plastoquinone oxidoreductase chain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.2      0.46   1.7e+03      42      53 ..       3      14 ..       1      17 [. 0.61
   2 !   98.6  16.7   6.9e-32   2.5e-28       2     144 .]      16     152 ..      15     152 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.46
                 HHIIIIIHHHHH CS
  Oxidored_q3 42 ilvYvGAilvlf 53
                 +++Y+ A +v+f
   AHX10991.1  3 LIIYLLAFVVIF 14
                 566666666665 PP

  == domain 2  score: 98.6 bits;  conditional E-value: 6.9e-32
                  HHHHHH-SBHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHIIIIIHHHHHHHHHHHSSTTS----TTCHHHHHHHHHHHHHHHHHHHTT--..... CS
  Oxidored_q3   2 allvitsknpvysalfLilsfvgvaglfillgaeFlallqilvYvGAilvlflFvimllesaeeeepeslsrslalaalligllllalllllllesss 99 
                  ++ +++ +n v+s+l+L+l+f+ ++++++  gae +a+++++vYvGAi++lflFv+m+l  + +e   s + s +   + +g+l  a+ ++l+    s
   AHX10991.1  16 SIRAVSCRNAVHSVLYLVLTFFTASIVLLASGAEVIAFMLLIVYVGAIAILFLFVVMML--RIDEFDLSVKFSVRKC-VGCGILASAFCFWLVD---S 107
                  78899*****************************************************7..5677777777777777.7777777888888865...3 PP

                  .--------TT-HHHHHHHHTTTTHHHHHHHHHHHHHHHHHHHHC CS
  Oxidored_q3 100 savdaqvadvsnieaigsllftkyllpfelasllLLvaligaivl 144
                   +++  ++   +i+ +g +l+t+y+++f l ++lLL a+i+a+++
   AHX10991.1 108 YTFQGLERPHVSIKDVGLVLYTDYVYLFHLSGVLLLFAMIAAVII 152
                  55577778888*******************************986 PP

>> Ceramidase  Ceramidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9  11.7     3e-05      0.11      91     204 ..       5     119 ..       1     173 [. 0.61

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
  Ceramidase  91 atalvlyavfsekksrstrvllgvlltalavvvtllylvlk...epvlhqvafalltvlvllrsiyliekkvdksdeaakkevkklallgliifllgfl 186
                 + +l+++++fs  +  s r  +  +l ++ +++t+ +++l    e++ + ++   + ++++l  ++++  ++d+ d ++k +v+k++ +g  i++++f 
  AHX10991.1   5 IYLLAFVVIFSSIRAVSCRNAVHSVLYLVLTFFTASIVLLAsgaEVIAFMLLIVYVGAIAILFLFVVMMLRIDEFDLSVKFSVRKCVGCG--ILASAFC 101
                 34455566666666777777777777777777777777644122333444444444444555555666678899999********98776..5689*** PP

  Ceramidase 187 iWnlDnlfCstltrlrra 204
                 +W++D    + l+r   +
  AHX10991.1 102 FWLVDSYTFQGLERPHVS 119
                 *****9887777665544 PP

>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1       1.1   3.9e+03      48      59 ..       2      13 ..       1      15 [. 0.53
   2 ?   -2.4  10.3       1.7   6.2e+03      36      58 ..      50      73 ..       8      74 .. 0.66
   3 ?   12.3   0.3   4.6e-05      0.16       6      60 .]      90     152 ..      88     152 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 1.1
                HHHHHHHHHHHH CS
  ATP-synt_C 48 aialygLivali 59
                a+ +y L + +i
  AHX10991.1  2 ALIIYLLAFVVI 13
                455555555544 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
                HHHHHHHHHHHHHHHH.HHHHHHH CS
  ATP-synt_C 36 ftksliilafaeaial.ygLival 58
                 + ++++++ ++aia+ + ++v++
  AHX10991.1 50 VIAFMLLIVYVGAIAIlFLFVVMM 73
                455677778888888845555554 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 4.6e-05
                 HH.GGGHHHHHHHHHHHHHHHHHHHHSG.........HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ATP-synt_C   6 avGlsalgsGigiGkagsagiravarnp.........klftksliilafaeaialygLivalil 60 
                 +vG + l+s+++ + + s   +++ r p          l+t  + ++ +++++ l+++i a+i+
  AHX10991.1  90 CVGCGILASAFCFWLVDSYTFQGLER-PhvsikdvglVLYTDYVYLFHLSGVLLLFAMIAAVII 152
                 99**************9999999988.66999999999************************98 PP

>> HisKA_7TM  N-terminal 7TM region of histidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2  17.4   0.00016      0.58       3     162 ..       7     162 ..       1     170 [. 0.53

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00016
   HisKA_7TM   3 lisallslvlaiyawrrrskpgaraflllllavalwslgyalellattleakllwaklqylgivfipvlwllfaleytg.k.rrwltrrrlallll.vp 98 
                 l+++++++  +  +  r+++ +  +++l+++++++ +l++++e++    + +ll   + y+g+  i +l+++++l+    + + +++ r+ +   +   
  AHX10991.1   7 LLAFVVIFSSIRAVSCRNAVHSVLYLVLTFFTASIVLLASGAEVI----AFMLL---IVYVGAIAILFLFVVMMLRIDEfDlSVKFSVRKCVGCGIlAS 98 
                 333333333333333666677788999988888888999999988....44455...567888888888888888887744433344455555555244 PP

   HisKA_7TM  99 vltlilvltnplhhlfyvsagsfvvlef.ehGplfwvhlaysyllliagvvlli...rali....rssglyr 162
                 ++++ lv ++ + +l        +++++ + G++++  + y+yl+ + gv+ll+    a+i    r++++ r
  AHX10991.1  99 AFCFWLVDSYTFQGLER------PHVSIkDVGLVLY--TDYVYLFHLSGVLLLFamiAAVIitlaRKKNVKR 162
                 66666665566666632......2222235555554..3344444333443333111222233325555444 PP

>> DUF2244  Integral membrane protein (DUF2244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3  10.2      0.44   1.6e+03       5      56 ..      18      70 ..       3      79 .. 0.78
   2 ?    9.5   0.0    0.0002      0.73      22      67 ..     125     170 ..     122     184 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.44
     DUF2244  5 rSlsprgflllllalalvslvialafllaGawpvlpFa.glevlalalafrvs 56
                r++s r ++  +l l+l+++++++++l+ Ga +++  + ++ v a+a+ f  +
  AHX10991.1 18 RAVSCRNAVHSVLYLVLTFFTASIVLLASGAEVIAFMLlIVYVGAIAILFLFV 70
                67888889999999999999999999999998876554144556666666554 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0002
     DUF2244  22 vslvialafllaGawpvlpFaglevlalalafrvsarhardrEeit 67 
                 ++l +  + l++   ++l+Fa+++ ++++la + +++++  rE+i+
  AHX10991.1 125 LVLYTDYVYLFHLSGVLLLFAMIAAVIITLARKKNVKRQVIREQIS 170
                 56666677778888899***************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1397  (0.0779185); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.28s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 1406.67
//
Query:       AHX10992.1  [L=99]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      5e-15   55.0  11.3    7.8e-15   54.4  11.3    1.3  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
  ------ inclusion threshold ------
      0.042   13.8   9.5      0.053   13.5   9.5    1.2  1  NAD4L        NADH dehydrogenase subunit 4L (NAD4L)
        0.1   11.8   1.7       0.12   11.5   1.7    1.1  1  2-ph_phosp   2-phosphosulpholactate phosphatase


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4  11.3   1.3e-18   7.8e-15       3     103 ..       8      94 ..       6      98 .. 0.94

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 1.3e-18
                  HHHHHHHHHHHHHHHHH.SSCCHHHHHHHHHHHHHHHHHHHHHHHHC.............TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHHSSS-B CS
  Oxidored_q2   3 llliallfliGlygvll.rrnllkvliglelisnavnlllvlagvftegtlvitnpatefadplpqalvLtaivigaaetavgLallvrlyreygtdd 99 
                  ++++  lf +Gl+gvll +rnl++vl+++e i++++ l++++++ +                + +++ ++++i+++aae+a++La++v  +++ g +d
   AHX10992.1   8 FFIASCLFSVGLFGVLLsTRNLISVLVSIEAILLGAVLNFCAVATS---------------VLEGHVAAILVITVAAAEAAIALAIVVVYFKKSGAID 90 
                  577889*************************************885...............59*********************************** PP

                  CCG- CS
  Oxidored_q2 100 vqel 103
                  v+++
   AHX10992.1  91 VRSM 94 
                  *998 PP

>> NAD4L  NADH dehydrogenase subunit 4L (NAD4L)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   9.5   8.9e-06     0.053       5      81 ..      11      89 ..       3      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.9e-06
       NAD4L  5 lllfvllilislllsltrllNlLiilEnfNv..llLlvcllvsvedsriiFivlmvlfvvEvsvgLvvvtvvieisslr 81
                  +++++ l++ lls+ +l+ +L+ +E + +  +l ++++ +sv + ++  i ++ +   E+ ++L +v v ++ s  +
  AHX10992.1 11 ASCLFSVGLFGVLLSTRNLISVLVSIEAILLgaVLNFCAVATSVLEGHVAAILVITVAAAEAAIALAIVVVYFKKSGAI 89
                23445555677789999999999999987543155566788999*************************9999887665 PP

>> 2-ph_phosp  2-phosphosulpholactate phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   1.7   2.1e-05      0.12      93     141 ..      22      69 ..      18      80 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 2.1e-05
                 EEEE-CCHHHHHHHCCTSSEEEEE-STTHHHHHHHHHHHTSS..EEEEE-- CS
  2-ph_phosp  93 vvltTtNGTralekaasakrvligsllNakavaeklkelake..vvivcaG 141
                 v l+T N   +l  ++    +l+g++lN  ava+ ++e +     vi  a 
  AHX10992.1  22 VLLSTRNLISVLVSIE---AILLGAVLNFCAVATSVLEGHVAaiLVITVAA 69 
                 5678888888887777...7*****************99998754444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1143  (0.0637515); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 816.89
//
Query:       AHX10993.1  [L=654]
Description: proton-translocating NADH-quinone oxidoreductase, chain L family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.6e-90  300.9  21.0    8.6e-90  300.9  21.0    2.7  3  Proton_antipo_M  Proton-conducting membrane transporter
    3.8e-20   71.7   3.9    2.5e-19   69.1   3.9    2.6  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 
  ------ inclusion threshold ------
      0.031   14.4   0.0       0.11   12.7   0.0    1.8  2  Rad21_Rec8_N     N terminus of Rad21 / Rec8 like protein


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.2   0.7       1.3   7.5e+03     117     157 ..      83     121 ..      81     127 .. 0.61
   2 !  300.9  21.0   1.4e-93   8.6e-90       1     286 [.     130     416 ..     130     426 .. 0.95
   3 ?    1.9   1.5     0.018   1.1e+02     236     270 ..     448     484 ..     414     506 .. 0.76

  Alignments for each domain:
  == domain 1  score: -4.2 bits;  conditional E-value: 1.3
  Proton_antipo_M 117 sallAatlvkagvlllirlllllavssneisqlllilaiis 157
                      s+++ a++ +++  + +  +  ++ s++  s +++ l++ +
       AHX10993.1  83 SLMF-AVVNTVSFVVHCYSIGYMK-SDPHKSRFFAYLSLFT 121
                      5556.6666666666664444444.7777777777777666 PP

  == domain 2  score: 300.9 bits;  conditional E-value: 1.4e-93
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskal.....elglnslelllllllll 89 
                      a+d l+l+lg+E+v++++ylLig+w+kk++++ As+k+f+++++g++ +L+gi+++y++ gtl+f+++ + +     ++ l+  +++++ l+l+
       AHX10993.1 130 AGDFLQLFLGWEGVGVCSYLLIGFWFKKESANLASMKAFIVNRIGDFCFLVGIFAVYKIFGTLDFTDVTSSIelhldTKILGFDAISFICLMLF 223
                      7899****************************************************************99999999999999************ PP

  Proton_antipo_M  90 vgllvKsaqvplhlWlpdayveaPtpvsall.AatlvkagvlllirlllllavssneisqlllilaiismllgslvalaqtdiKrllAySsish 182
                      +g + Ksaq+ lh+Wlpda +e+Ptpvsal+ Aat+v+agv+l+++l+ll++ s++ ++ql+++++i+++++g+++al q diK+ +AyS++s+
       AHX10993.1 224 IGCMSKSAQLGLHTWLPDA-MEGPTPVSALIhAATMVTAGVFLVAKLSLLFE-SAPLVRQLIMWIGIATAIFGGVIALYQDDIKKTIAYSTCSQ 315
                      *******************.********************************.***************************************** PP

  Proton_antipo_M 183 lGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaav 276
                      lGym+ a+++    ++ aa++hl tha+fkallFl+ag+vi++ + ++++ ++ggL+ +mP ++ ++l++ l+l+G+ p+agF+sk+li+ ++ 
       AHX10993.1 316 LGYMFAACGA---SAYVAAVFHLATHAFFKALLFLCAGNVIHSVHGEQNMHKMGGLRRRMPSTYYMMLIGSLALCGIFPFAGFYSKDLIILSLS 406
                      **********...6779**********************************************************************9988776 PP

  Proton_antipo_M 277 avslillvla 286
                        ++ +++ +
       AHX10993.1 407 FSEVPFILSI 416
                      6666666555 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.018
  Proton_antipo_M 236 ggLakkmPilalvllvlllslaGlPpt..agFlskfl 270
                       +++++ P+  lv++ ++ ++ G P++   +F++   
       AHX10993.1 448 PSISMTLPLSLLVFFSVTSGYFGAPFLleGNFWANTG 484
                      46899*********************97779998764 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   3.9   4.2e-23   2.5e-19       1      58 []      61     118 ..      61     118 .. 0.98

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4.2e-23
  Proton_antipo_N   1 lftWlsvgglsieigfllDklsalmllvvtfvsllvhlYSigYMaddegyqRFfayls 58 
                      ++tW+svg l+ ++++ +D++  lm +vv +vs++vh YSigYM++d++++RFfayls
       AHX10993.1  61 VYTWISVGFLESNFSLHVDRFISLMFAVVNTVSFVVHCYSIGYMKSDPHKSRFFAYLS 118
                      69******************************************************97 PP

>> Rad21_Rec8_N  N terminus of Rad21 / Rec8 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   1.8e-05      0.11      40      82 ..      16      58 ..      15      78 .. 0.88
   2 ?   -3.0   0.0       1.3   8.1e+03      37      60 ..     613     636 ..     611     637 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.8e-05
  Rad21_Rec8_N 40 aveeIlnpeaplaLrlsgqLllGvvriyskkvkyllsDceeal 82
                  +++ +++ ++++ L l ++Ll+Gv+ i s k+ y l D e++ 
    AHX10993.1 16 SCSLLIKFRESICLQLWSSLLVGVAAILSWKLFYSLGDGETLS 58
                  5888899899***************************988876 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.3
  Rad21_Rec8_N  37 iekaveeIlnpeaplaLrlsgqLl 60 
                   i+  + +I++++++++L  ++ L+
    AHX10993.1 613 IPGLCAKIVDKTSSVTLSWQTGLI 636
                   788999***999999998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (654 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.24s 00:00:00.85 Elapsed: 00:00:00.42
# Mc/sec: 4726.05
//
Query:       AHX10994.1  [L=205]
Description: ankyrin repeat family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-18   67.0   8.6    2.2e-09   37.8   0.5    2.9  3  Ank_2          Ankyrin repeats (3 copies)
    6.5e-18   64.8   1.0     0.0014   19.2   0.0    4.1  4  Ank_4          Ankyrin repeats (many copies)
    3.9e-15   54.4   0.7    0.00024   21.3   0.0    4.3  4  Ank_3          Ankyrin repeat
    4.7e-15   55.5   1.6    0.00032   20.9   0.0    3.2  3  Ank_5          Ankyrin repeats (many copies)
    3.6e-14   52.5   3.1     0.0016   18.8   0.2    4.5  5  Ank            Ankyrin repeat
  ------ inclusion threshold ------
      0.098   13.1   0.1       0.32   11.4   0.0    1.8  2  Ribosomal_S11  Ribosomal protein S11


Domain annotation for each model (and alignments):
>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.5   7.2e-13   2.2e-09       8      80 ..      19     105 ..      12     108 .. 0.74
   2 !   31.3   0.7   7.5e-11   2.2e-07      21      65 ..      69     123 ..      61     139 .. 0.76
   3 !   14.9   0.0     1e-05     0.031      26      73 ..     111     172 ..     110     181 .. 0.70

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 7.2e-13
       Ank_2   8 gnlelvklLl...egadpn..k..ngktaLhyAakngnleivklLleh...ad....ndgrtpLhyAarsghleivklLlekgadin 80 
                  n+el+  Ll   e +d+   +  +g+t+Lh+A+ +gn+++v   le+   ++     d  tpLh+Aar+++l i+  Ll++ga++ 
  AHX10994.1  19 QNTELFSDLLdssEVTDIFkmTdiQGETILHIACGAGNVKAVISALEYdadLNaknkVDSDTPLHIAARNDNLVILMHLLNSGASVI 105
                 4567888888643335544441579************998888888877562254567799*********99999999999999875 PP

  == domain 2  score: 31.3 bits;  conditional E-value: 7.5e-11
       Ank_2  21 dpn..k..ngktaLhyAakngnleivklLleh......adndgrtpLhyAarsgh 65 
                 d+n  +  +  t+Lh+Aa+n+nl i+  Ll+        + +g+tpLh A+ ++ 
  AHX10994.1  69 DLNakNkvDSDTPLHIAARNDNLVILMHLLNSgasvieKNAKGNTPLHEAVLFNA 123
                 44453257789**********99999****966678666699*********9874 PP

  == domain 3  score: 14.9 bits;  conditional E-value: 1e-05
       Ank_2  26 gktaLhyAakng.nleivklLleh.............adndgrtpLhyAarsghleivklLl 73 
                 g+t+Lh A+  + +++++  ++e              ++ndg+tpL +A +s +  +++ L 
  AHX10994.1 111 GNTPLHEAVLFNaKRKVLNKMVECcittkgrgiacdmLNNDGKTPLDLALESLNVGAIEALA 172
                 89****999986333554555552344467777767777**********9986666666665 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   4.5e-07    0.0014      25      51 ..      34      60 ..      16      63 .. 0.78
   2 !   16.4   0.1   3.5e-06      0.01      12      47 ..      55      90 ..      54      94 .. 0.88
   3 !   15.4   0.0   6.8e-06      0.02      20      46 ..      97     122 ..      90     129 .. 0.87
   4 !   13.1   0.0   3.8e-05      0.11      23      54 ..     141     171 ..     129     172 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.5e-07
       Ank_4 25 adinaqdnrsGetalhiAakrgnveil 51
                 di + ++++Get lhiA+  gnv+++
  AHX10994.1 34 TDIFKMTDIQGETILHIACGAGNVKAV 60
                5677778*****************998 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.5e-06
       Ank_4 12 grlelvrlLlekgadinaqdn.rsGetalhiAakrgn 47
                g++++v + le++ad+na  n  + +t+lhiAa++ n
  AHX10994.1 55 GNVKAVISALEYDADLNAK-NkVDSDTPLHIAARNDN 90
                888999999*********9.76889*********987 PP

  == domain 3  score: 15.4 bits;  conditional E-value: 6.8e-06
       Ank_4  20 LlekgadinaqdnrsGetalhiAakrg 46 
                 Ll++ga++ +  n+ G+t+lh A++++
  AHX10994.1  97 LLNSGASVIEK-NAKGNTPLHEAVLFN 122
                 89********8.************997 PP

  == domain 4  score: 13.1 bits;  conditional E-value: 3.8e-05
       Ank_4  23 kgadinaqdnrsGetalhiAakrgnveilklL 54 
                 +g+ +++  n++G t+l+ A+   nv +++ L
  AHX10994.1 141 RGIACDML-NNDGKTPLDLALESLNVGAIEAL 171
                 68889**9.*****************999987 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   8.1e-08   0.00024       2      31 .]      44      72 ..      43      72 .. 0.96
   2 !   13.1   0.1   3.6e-05      0.11       3      26 ..      79     101 ..      77     104 .. 0.74
   3 !   12.2   0.0   7.3e-05      0.22       2      23 ..     111     137 ..     110     146 .. 0.74
   4 ?    3.3   0.0     0.058   1.7e+02       1      21 [.     151     171 ..     151     177 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 8.1e-08
       Ank_3  2 GetpLhlAarsgnleivkfLlenkgadvna 31
                Get+Lh+A+ +gn++ v+  le + ad+na
  AHX10994.1 44 GETILHIACGAGNVKAVISALE-YDADLNA 72
                9*********************.*****96 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 3.6e-05
       Ank_3   3 etpLhlAarsgnleivkfLlenkg 26 
                  tpLh+Aar++nl i+  Ll+  g
  AHX10994.1  79 DTPLHIAARNDNLVILMHLLN-SG 101
                 59***********76555554.45 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 7.3e-05
       Ank_3   2 GetpLhlAarsgnl.....eivkfLle 23 
                 G+tpLh+A++++       ++v+ ++ 
  AHX10994.1 111 GNTPLHEAVLFNAKrkvlnKMVECCIT 137
                 9***********996554336777666 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.058
       Ank_3   1 nGetpLhlAarsgnleivkfL 21 
                 +G tpL lA++s n+  +++L
  AHX10994.1 151 DGKTPLDLALESLNVGAIEAL 171
                 699******999777666666 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   1.1e-07   0.00032      13      47 ..      41      75 ..      39      76 .. 0.93
   2 !   20.9   0.2   1.1e-07   0.00032      13      56 .]      79     118 ..      74     118 .. 0.91
   3 !   11.8   0.0   7.8e-05      0.23      37      56 .]     140     159 ..     123     159 .. 0.83

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.1e-07
       Ank_5 13 dgggntpLhvAakygaadvvrlLlargadlnltds 47
                d  g+t+Lh+A+ +g+   v+  l++ adln++++
  AHX10994.1 41 DIQGETILHIACGAGNVKAVISALEYDADLNAKNK 75
                66799***************************995 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 1.1e-07
       Ank_5  13 dgggntpLhvAakygaadvvrlLlargadlnltdsrGltaldlA 56 
                 d    tpLh+Aa++ ++ ++  Ll+ ga+   +++ G+t+l+ A
  AHX10994.1  79 D----TPLHIAARNDNLVILMHLLNSGASVIEKNAKGNTPLHEA 118
                 3....************************************866 PP

  == domain 3  score: 11.8 bits;  conditional E-value: 7.8e-05
       Ank_5  37 argadlnltdsrGltaldlA 56 
                  rg ++++ +++G+t+ldlA
  AHX10994.1 140 GRGIACDMLNNDGKTPLDLA 159
                 68999**************9 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0         6   1.8e+04      16      24 ..      22      30 ..      19      34 .. 0.63
   2 !   17.1   0.1   1.9e-06    0.0056       2      32 .]      44      75 ..      43      75 .. 0.87
   3 !   18.8   0.2   5.2e-07    0.0016       3      30 ..      79     107 ..      77     109 .. 0.86
   4 !    9.4   0.0    0.0005       1.5       2      11 ..     111     122 ..     110     145 .. 0.75
   5 ?    4.6   0.0     0.016        49       1      10 [.     151     160 ..     151     180 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6
                HHHHHHHTT CS
         Ank 16 riiklLLhG 24
                +  ++LL++
  AHX10994.1 22 ELFSDLLDS 30
                566788844 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.9e-06
                SBBHHHHHHHHTT.HHHHHHHHTTTSTTCBTT CS
         Ank  2 GnTPLHlAatngk.kriiklLLhGAnlnaldn 32
                G T LH+A+  g+ k +i++L + A+lna+++
  AHX10994.1 44 GETILHIACGAGNvKAVISALEYDADLNAKNK 75
                99*******7787999****6468*****995 PP

  == domain 3  score: 18.8 bits;  conditional E-value: 5.2e-07
                 BBHHHHHHHHTTHHHHHHHH.TTTSTTCB CS
         Ank   3 nTPLHlAatngkkriiklLL.hGAnlnal 30 
                 +TPLH+Aa+n+++ i+  LL +GA++  +
  AHX10994.1  79 DTPLHIAARNDNLVILMHLLnSGASVIEK 107
                 7**********9999999**889*98655 PP

  == domain 4  score: 9.4 bits;  conditional E-value: 0.0005
                 SBBHHHHHH..H CS
         Ank   2 GnTPLHlAa..t 11 
                 GnTPLH A+  +
  AHX10994.1 111 GNTPLHEAVlfN 122
                 9******98541 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.016
                 TSBBHHHHHH CS
         Ank   1 dGnTPLHlAa 10 
                 dG TPL lA 
  AHX10994.1 151 DGKTPLDLAL 160
                 8*******85 PP

>> Ribosomal_S11  Ribosomal protein S11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.32      11      54 ..      34      77 ..      27      88 .. 0.87
   2 ?   -1.2   0.0      0.91   2.7e+03      29      69 ..     100     110 ..      78     143 .. 0.51

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
  Ribosomal_S11 11 ntiititdlkGaevlvksaGglgvkasrkssPyaaqlaaekaae 54
                     i ++td++G+++l  ++G+ +vka   +  y a l a++ ++
     AHX10994.1 34 TDIFKMTDIQGETILHIACGAGNVKAVISALEYDADLNAKNKVD 77
                   56899****************************99999988765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.91
  Ribosomal_S11  29 aGglgvkasrkssPyaaqlaaekaaekvldkGikavevkvk 69 
                    +G++++ +                              + k
     AHX10994.1 100 SGASVIEK------------------------------NAK 110
                    33333322..............................222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 1660.39
//
Query:       AHX10995.1  [L=402]
Description: queuine tRNA-ribosyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-100  337.2   0.1   3.9e-100  335.4   0.1    1.7  1  TGT       Queuine tRNA-ribosyltransferase


Domain annotation for each model (and alignments):
>> TGT  Queuine tRNA-ribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.4   0.1  2.1e-104  3.9e-100       3     345 ..      20     401 ..      17     402 .] 0.94

  Alignments for each domain:
  == domain 1  score: 335.4 bits;  conditional E-value: 2.1e-104
                 EEEEEEEETTEEEEESEEEEBETTSSBTTB-HHHHH.HTTES-EEEEHHHHHHTTTHHHHHHTTHHHHHHT--S-EEEE-SHHHHHHH........... CS
         TGT   3 aRlGklelphgtietPafmpvgtqgtvkgltpdelkeelgaqiilsntyhlelrpgeelvakagglhkflgwdkpiltdsggfqvfsl........... 90 
                  R+G+++++hg+++tPaf+  +t+gt+kgl ++++k e+g+qiilsntyhl+l+pg e +++agg+++f+gwd+p+ltdsggfq fsl           
  AHX10995.1  20 SRIGTITTKHGVVHTPAFIFCATRGTIKGLGTHQVK-EAGSQIILSNTYHLMLKPGGEYIENAGGIQRFTGWDGPMLTDSGGFQAFSLnskdtakvdel 117
                 6**********************************6.88*************************************************99999999888 PP

                 ......E.......EEESSEEEEE-TTTS-EEEE-HHHHHHHHHHHT-SEEE-------SS--HHHHHHHHHHHHHHHHHHHHHH.......SEEEEEE CS
         TGT  91 ......k.......kiteegvsfqsridGskvlltpeesieiqeklgsDiimalddvvpspaskkrveksverTlrwldrcleah.......qalfgiv 169
                       k       +i+eeg++ +s +dG +++l+pe+si++q klg+D+i+ ld++++ +++k ++ k+++r +rw+dr+l++        q l gi+
  AHX10995.1 118 krkyscKqnksgiiEISEEGIECKSYYDGTRFFLSPEKSIDVQIKLGADLIVVLDECTKFSKDKTYNTKALRRNERWADRSLAYAkmhkkrwQGLYGII 216
                 8777651566888899******************************************************************665677999999***** PP

                 --TT-HHHHHHHHHHHHHH--SEEEE-SSSSSSHHHHHHHHHHHHGGGS-TTS-EEETTB-SHHHHHHHHHTT--EEEESHHHHHHHTTEEEETTE... CS
         TGT 170 qGglyedlreesaeelakrdfdgyaigGlsvgeekeellevveavtellpedkprylmGvgtPedlleavalGvDmfdcvyptrtarngraltseg... 265
                 +Gg+++dlr+esa    +r+f g aigG s+g +k+e+++vve ++e l +++p++l G+g  +d+  +va+G+D fdcv ptr+ar+g al++++   
  AHX10995.1 217 HGGTFNDLRRESAAFNNSREFFGHAIGG-SLGRDKKEMMDVVEMSMEDLSKERPVHLLGIGGISDIFMGVARGIDTFDCVHPTRIARHGGALVKHSssl 314
                 ****************************.9***************************************************************664444 PP

                 ......EEETTSGGGTT--SBSSSS--SHHHHH-BHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTT.-HHHHHHHHH CS
         TGT 266 ......elnlknakyaedfspldegCsCytCknytraylhhllktkemlgaiLltiHNlhyylelfkriReaIkeg.tfeefveefa 345
                        +nl n+ +++   p++e+C+C +Ck+y+r yl+ ll  ke +  +L+t+HN+++++ l+++iR  +k++ ++++++++++
  AHX10995.1 315 eyinreYINLGNSVFKRCDLPIEESCDCKICKTYSRGYLNYLLSVKENIVFSLITYHNVYFMNVLMEKIRYTLKNNlDLKQLQKHYC 401
                 4555549********************************************************************988999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.23s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2951.60
//
Query:       AHX10996.1  [L=39]
Description: hypothetical protein NHE_0021 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.024   14.4   0.1       0.27   11.0   0.0    1.9  2  L27       L27 domain


Domain annotation for each model (and alignments):
>> L27  L27 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0    0.0075   1.4e+02      38      48 ..       2      12 ..       1      17 [. 0.77
   2 ?   11.0   0.0   1.5e-05      0.27      15      37 ..      16      38 ..      13      39 .] 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0075
         L27 38 evHDrVaetvy 48
                +++  V+e+v+
  AHX10996.1  2 SLYNNVYEKVF 12
                67888999987 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 1.5e-05
         L27 15 sdvnedlaeLqkvLqsphlqaLl 37
                ++v++ +a Lqk+++s+ l +++
  AHX10996.1 16 PGVDNMAAVLQKLFSSRMLSSCR 38
                678889***********999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 318.88
//
Query:       AHX10997.1  [L=213]
Description: carbonic anhydrase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-46  157.9   0.0    2.7e-46  157.7   0.0    1.0  1  Pro_CA    Carbonic anhydrase
  ------ inclusion threshold ------
      0.011   15.8   0.1      0.026   14.6   0.1    1.6  1  DUF1290   Protein of unknown function (DUF1290)


Domain annotation for each model (and alignments):
>> Pro_CA  Carbonic anhydrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.7   0.0     3e-50   2.7e-46       1     156 []      41     197 ..      41     197 .. 0.92

  Alignments for each domain:
  == domain 1  score: 157.7 bits;  conditional E-value: 3e-50
                 EEEEEETTTTS-HHHHTTS-TTSEEEEEETTG---TT......-HHHHHHHHHHHHTS--SEEEEEEETT-HHHHHHHSHHCCSTTSSHHHHHHHHHHH CS
      Pro_CA   1 alvigCsDSRvppelitdagpGdlFvvrnvgnlvppa......dssvlaaleyAvevlkvkhivVlGHskCGavkaalkaekseeeagaidkwlekire 93 
                 +l+igCsDSRv+p+++tda+pGd+Fv+rn++nlvp++       ++v+aa+e+Av+ l+v++ivV+GHs CG+++ ++++ +  +++++i+ w++ + +
  AHX10997.1  41 TLFIGCSDSRVDPAILTDANPGDIFVIRNIANLVPKYepewstCHGVSAAIEFAVQILNVSDIVVMGHSCCGGIRSLIDN-D-FKKNSFIAGWIDIASP 137
                 69****************************************99*******************************88875.4.5668************ PP

                 HHHHCHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHTTS-EEEEEEEETTTTEE CS
      Pro_CA  94 alekveeelesekekearerlleeenVaeqlenLlekpvvreavekgklkvhGlvydletGev 156
                 ++++  + +++    e +  l e+++++ +l+nLl++p v+++ve+g++k+hG++++++tGe+
  AHX10997.1 138 VKTAIPDIMKK---GECKYSLSEQLAIKLSLKNLLTFPYVSSRVETGTVKLHGWYFSINTGEL 197
                 *9998865444...5677777799*************************************86 PP

>> DUF1290  Protein of unknown function (DUF1290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.1   2.9e-06     0.026      13      42 ..     103     132 ..      91     136 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2.9e-06
     DUF1290  13 ilaaldsvfGgiraslekkFdekvfisgff 42 
                 i+ +  s +Ggir+ ++++F+++ fi g++
  AHX10997.1 103 IVVMGHSCCGGIRSLIDNDFKKNSFIAGWI 132
                 56677899*******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1588.60
//
Query:       AHX10998.1  [L=643]
Description: chaperone protein DnaK [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.9e-260  865.2  14.3   2.3e-260  864.9  14.3    1.1  1  HSP70          Hsp70 protein
    5.5e-19   68.2   1.6    1.7e-14   53.4   0.1    2.7  2  MreB_Mbl       MreB/Mbl protein
    0.00097   19.0   0.2     0.0036   17.1   0.1    2.0  2  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
  ------ inclusion threshold ------
      0.014   15.1   0.0      0.032   14.0   0.0    1.6  1  FGGY_C         FGGY family of carbohydrate kinases, C-termina
       0.02   15.0   7.0      0.075   13.2   7.0    2.0  1  DUF1090        Protein of unknown function (DUF1090)
        3.8    6.9   6.4         22    4.3   0.0    2.3  2  XRN_N          XRN 5'-3' exonuclease N-terminus


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  864.9  14.3  7.8e-264  2.3e-260       1     599 []       6     600 ..       6     600 .. 0.99

  Alignments for each domain:
  == domain 1  score: 864.9 bits;  conditional E-value: 7.8e-264
                 EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTT.SEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSHHHHHHHTTXSSEEEEETTSBEE CS
       HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkk.erlvGeaAkrqavtnpkntvfsvKrliGrkfsdpevqkeikelpykvvkkengkav 98 
                 +iGiDLGttns+va+ +    +vi+n+eg+rttPsvvaFt + + lvG++A+rqavtn+kntv++ KrliGr+fsd+ v++  k  pyk+ +++ng+a+
  AHX10998.1   6 AIGIDLGTTNSCVAIKD----KVIENAEGARTTPSVVAFTADnQILVGAPAQRQAVTNAKNTVMASKRLIGRRFSDEAVKAAQKDYPYKIAEAKNGDAW 100
                 59************965....7******************997889***************************************************** PP

                 EEEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSX CS
       HSP70  99 veveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggt 197
                 +e+   g+ ++p+qi+a +L klke aea+ g k+t+avitvPaYf+daqRqatkdAgkiAGL+vlRi+NepTAaalaYGldk+++ +n++v+DlGggt
  AHX10998.1 101 IEAG--GKVYSPSQIGANILIKLKEAAEAHSGSKITKAVITVPAYFDDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKTSTTKNIAVFDLGGGT 197
                 **99..********************************************************************************************* PP

                 EEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTT.EEEEEEEEH CS
       HSP70 198 fdvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedg.kdlseklsR 295
                 fdvSilel++GvfevkaT+gDthlGGedfD++++++lveefkk++g+dl++d+ alqrlkea ekaKkeLSs+++t+inl+++t+d++g k+l++k++R
  AHX10998.1 198 FDVSILELGDGVFEVKATNGDTHLGGEDFDRVILNFLVEEFKKENGMDLRTDPLALQRLKEASEKAKKELSSTQETDINLPYITADASGpKHLNIKFTR 296
                 *************************************************************************************************** PP

                 HHHHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCHHBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-E CS
       HSP70 296 akfeelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgkepsktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLsl 394
                 ak+e+lv+dl++rt+ep++kalkd++lk eei++vvlvGG+tR+P+v ++v e+fgkep+k+vnpDe+va+GAA+qa++l+g ++ +d++llDvtpLsl
  AHX10998.1 297 AKLESLVSDLVDRTIEPCKKALKDSGLKREEIHDVVLVGGMTRMPAVIKKVTEFFGKEPHKGVNPDEVVAVGAAIQANILAGGSDAQDIVLLDVTPLSL 395
                 *************************************************************************************************** PP

                 EEEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEE CS
       HSP70 395 gietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeee 493
                 gietlggv+tkli+rnttiptkksq+fsta+d+q+av+i+v+qger++++dnkllg+f+l+gippaprGvpqieV+fdidanGi++vsakdk+tgke++
  AHX10998.1 396 GIETLGGVFTKLIDRNTTIPTKKSQTFSTAEDSQSAVTIRVFQGERQMANDNKLLGQFSLEGIPPAPRGVPQIEVSFDIDANGIVHVSAKDKGTGKEQT 494
                 *************************************************************************************************** PP

                 EEEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHH CS
       HSP70 494 itieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkvvek 592
                 ++i+as gl++eei+kmv +a + a+ed+kk+e +eakn+ae+l++s+ek+l+e ++k+ +++++++e+ai++Lke + +e+  +i+++t++l+k+++k
  AHX10998.1 495 VKIQASGGLTDEEIKKMVDEAAAKADEDRKKRELVEAKNNAESLIHSTEKSLSEYGSKIGASDRQNIEEAIKALKEVMGNEDPVAIKERTDALSKASMK 593
                 *************************************************************************************************** PP

                 HHHHHHH CS
       HSP70 593 iaeklye 599
                 ++e++y+
  AHX10998.1 594 LGEAMYK 600
                 ****995 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.1   9.9e-06      0.03       3      47 ..       6      53 ..       4      95 .. 0.78
   2 !   53.4   0.1   5.7e-18   1.7e-14      78     317 ..     118     371 ..     105     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-06
                EEEEEE-SSEEEEEETTTEEEEEE.....ES-EEEETTT--EEEESHHHH CS
    MreB_Mbl  3 dlgiDLGtantlvyvkgkgivlne.....psvvAikkktkkvlavGeeAk 47
                 +giDLGt+n  v +k+k i   e     psvvA++ +++    vG  A+
  AHX10998.1  6 AIGIDLGTTNSCVAIKDKVIENAEgarttPSVVAFTADNQI--LVGAPAQ 53
                69****************996544344449****9887653..3666654 PP

  == domain 2  score: 53.4 bits;  conditional E-value: 5.7e-18
                 HHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EE.EEEE-SS-EEEEEEETTEEEEEEE... CS
    MreB_Mbl  78 lkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnm.vvdiGggttevavislggivtsks... 172
                 l ++ + ++ ++  + ++ vi+vP   ++ +r+A k+a k aG +   +i+ep aAA+  gl+ + ++ n+ v d+Gggt +v+++ lg+ v       
  AHX10998.1 118 LIKLKEAAEAHSGSKITKAVITVPAYFDDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKTSTTKNIaVFDLGGGTFDVSILELGDGVFEVKatn 216
                 5555555666677788999********************************************99988887478***************9775432112 PP

                 ..ES-SHHHHHHHHHHHHHHHHSEE--HH..HHHHHHHHH-BSS--HHHH.....EEEEEEEETTT..TCEEEEEEE..HHHHHHHHHHHHHHHHHHHH CS
    MreB_Mbl 173 ..vrvaGdeldeaiikyirkkynlliGer..taekikieigsavkeeeee.....kmeikGrdlvt..glpkevevs..seevrealkepvsaiveavk 258
                    +++G+++d  i++++ ++++   G    t     +++ +a +++++e     +++i+   ++     pk+++++   +++++ +++ v + +e  k
  AHX10998.1 217 gdTHLGGEDFDRVILNFLVEEFKKENGMDlrTDPLALQRLKEASEKAKKElsstqETDINLPYITAdaSGPKHLNIKftRAKLESLVSDLVDRTIEPCK 315
                 22689****************998877641132222223333333332222222455555444443113456555431156667777777777777777 PP

                 HHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE-SSTTTHHHHHHHH CS
    MreB_Mbl 259 evLektppeLaadivdrgivltGGgallkgldkllseetglpvkvaedpltcvakGtgk 317
                 ++L++    L  + ++  +vl+GG + +  + k ++e +g + + + +p ++va G+++
  AHX10998.1 316 KALKDSG--LKREEIH-DVVLVGGMTRMPAVIKKVTEFFGKEPHKGVNPDEVVAVGAAI 371
                 7777653..4444333.478999999999999999999999999999999999999876 PP

>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       1.3   3.9e+03      24      47 ..     122     145 ..     111     168 .. 0.61
   2 !   17.1   0.1   1.2e-06    0.0036      13      73 ..     304     372 ..     301     390 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
                    HHHHHHCTTSSCCEEEEEESSCCC CS
  DMRL_synthase  24 ldelkeagvaeenidvvtVPGafE 47 
                    +++++++  ++ +  v+tVP  f+
     AHX10998.1 122 KEAAEAHSGSKITKAVITVPAYFD 145
                    555555555545555566665543 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.2e-06
                    HHHHHHHHHHHHHHHHHCTTS.SCCEEEEEESSCCCHHHHHHHHCT......STT-..SEEEEEEEEE- CS
  DMRL_synthase  13 eeitdkllegaldelkeagva.eenidvvtVPGafElplaakklae......ssky.ldavialGvvir 73 
                    ++++d+ +e ++++lk+ g + ee  dvv V G   +p ++kk++e      +++   d v+a+G+ i+
     AHX10998.1 304 SDLVDRTIEPCKKALKDSGLKrEEIHDVVLVGGMTRMPAVIKKVTEffgkepHKGVnPDEVVAVGAAIQ 372
                    57899**************88467779*******************665544244448*******9887 PP

>> FGGY_C  FGGY family of carbohydrate kinases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.0   1.1e-05     0.032      72     196 ..     249     375 ..     226     377 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.1e-05
      FGGY_C  72 eslaelaaaeavadaggvvfvpafsglrapywdpdargtitglsssttlahiarAaleavalqlrailealekd.......sgkpldrlavdGGgsknd 163
                 ++la+++  ea+++a+  +  +  +    py  +da+g       ++    ++rA le++   l +++ +  k+       ++ ++  ++++GG+++ +
  AHX10998.1 249 DPLALQRLKEASEKAKKELSSTQETDINLPYITADASG------PKHLNIKFTRAKLESLVSDLVDRTIEPCKKalkdsglKREEIHDVVLVGGMTRMP 341
                 66666666666666666666666666666666666666......33335778899999999888888766644456665666666************** PP

      FGGY_C 164 llmqllAdilg.vpVerpktaeatalGaAilAav 196
                 ++ +   + +g  p + + ++e +a+GaAi A++
  AHX10998.1 342 AVIKKVTEFFGkEPHKGVNPDEVVAVGAAIQANI 375
                 ***********989899999***********986 PP

>> DUF1090  Protein of unknown function (DUF1090)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   7.0   2.5e-05     0.075      23     108 ..     506     594 ..     504     596 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
     DUF1090  23 qaIekqieaAkah.gnqkrvagLekaLkevka..nCtdeklkaerqekv.eekeeeVaereaeLaeakekgdkdkiakrqekLaeakeeL 108
                 ++I+k +++A a+ +++++ ++L +a +++++  + t+++l + + +k+ ++ +++++e  + L+e + ++d+  i++r + L +a  +L
  AHX10998.1 506 EEIKKMVDEAAAKaDEDRKKRELVEAKNNAESliHSTEKSLSE-YGSKIgASDRQNIEEAIKALKEVMGNEDPVAIKERTDALSKASMKL 594
                 5788888777665155667789*******99855777777765.555665999*********************************9998 PP

>> XRN_N  XRN 5'-3' exonuclease N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0    0.0075        22      37      77 ..     474     514 ..     461     520 .. 0.77
   2 ?    1.2   5.6     0.068     2e+02      99     198 ..     517     631 ..     512     641 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.0075
                 EETHHHHHHHHS-SSS-......--SSHHHHHHHHHHHHHH CS
       XRN_N  37 lDmNgiihkcshkedkeekelskkpkteeeifkkifkyidr 77 
                 +D Ngi+h +++++ + +++++k +++     ++i k++d+
  AHX10998.1 474 IDANGIVHVSAKDKGTGKEQTVKIQASGGLTDEEIKKMVDE 514
                 8**********998877777777777666666666666665 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.068
                 HHHHHHHHHHHHHHHHHHHH..............HHH.HHHHHHHHHHHT-BB--------GGGSSTTSHHHHHHHHHHHHHH.HHHHHH-GGGGG-EE CS
       XRN_N  99 aKmnqqRsRRfrsakeakee..............kee.keelkeelekeekeeeeeeekfdsnvitpGtefmeklsealkafi.kkklkedpawknlkv 181
                 aK  + R++R   +++++ e              + +  ++ ++++e++ k+ +e   + d  +i   t+ ++k s +l + + k++++++++  ++  
  AHX10998.1 517 AKADEDRKKRELVEAKNNAEslihstekslseygS-KiGASDRQNIEEAIKALKEVMGNEDPVAIKERTDALSKASMKLGEAMyKDSQSQNQQSTSTGA 614
                 77777777765444444444366665444333221.223333344444444444777888999****************76550556666666678999 PP

                 EEE-TTS-S-HHHHHHH CS
       XRN_N 182 ilsdaevpGEGEhKime 198
                   sd+e + EGE K+++
  AHX10998.1 615 GSSDNEKKSEGEEKVVD 631
                 9**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (643 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1560  (0.0870099); expected 358.6 (0.02)
Passed bias filter:                      639  (0.0356406); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.34s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 4298.19
//
Query:       AHX10999.1  [L=243]
Description: tRNA pseudouridine(38-40) synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-37  127.9   0.0    9.1e-25   87.2   0.0    2.1  2  PseudoU_synth_1  tRNA pseudouridine synthase


Domain annotation for each model (and alignments):
>> PseudoU_synth_1  tRNA pseudouridine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   0.0   5.2e-14   9.3e-10       1     107 [.       5     104 ..       5     105 .. 0.94
   2 !   87.2   0.0   5.1e-29   9.1e-25       2     107 ..     145     243 .]     144     243 .] 0.95

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 5.2e-14
  PseudoU_synth_1   1 AakelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvl.favgqgklspedvkellnakkrkk.iav 92 
                      A  e+ G+ ++g +  q+q++ ++++  le  ++ + +e     ++t++++g++d++V+a+++v+ f+v+  +l+p ++ +++n ++r++ ia+
       AHX10999.1   5 ATIEYNGSEFSG-W--QRQKDARSIQGELEKILQLLFRE-----EITITAAGRTDSGVHALGQVIhFDVEYPRLQPFQIMNAVNNHLRDSlIAI 90 
                      6679********.9..899999************99999.....9******************************************9988999 PP

  PseudoU_synth_1  93 etapavglvlfhvrY 107
                      + ++ v++  f++r+
       AHX10999.1  91 TNVEIVDE-TFDARF 104
                      99999999.889888 PP

  == domain 2  score: 87.2 bits;  conditional E-value: 5.1e-29
  PseudoU_synth_1   2 akelvGthdfgsfckqkqekkntvrtileaaieevsgeekellvvtvkgsgFldhqVRamvgvlfavgqgklspedvkellnakkrkkiaveta 95 
                      ak+l+G+hdf+sf+++k++++n  rt+ +++i     +++e + +++++++Fl++qVR+mvg+l+a+  g    + v+e+l +++r   a++ta
       AHX10999.1 145 AKYLIGKHDFQSFRSAKCSASNALRTLDQFDIV----KNGEEILFSISARSFLHNQVRIMVGTLVAIALGA--QSSVPEILLKRNRCY-AGPTA 231
                      89*******************************....778889*********************9998775..578***********9.***** PP

  PseudoU_synth_1  96 pavglvlfhvrY 107
                      pa+gl+l++++Y
       AHX10999.1 232 PAHGLYLVKIDY 243
                      *********998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1792.47
//
Query:       AHX11000.1  [L=38]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       173  (0.00964917); expected 358.6 (0.02)
Passed bias filter:                       46  (0.00256568); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 290.12
//
Query:       AHX11001.1  [L=1388]
Description: ankyrin repeat family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-34  118.2   3.8    6.1e-07   29.9   0.0    9.2 11  Ank_2     Ankyrin repeats (3 copies)
    1.8e-34  117.6   9.7    9.7e-09   35.6   0.0   10.2 10  Ank_4     Ankyrin repeats (many copies)
    6.1e-19   66.1  21.2       0.72   10.6   0.0   14.0 15  Ank_3     Ankyrin repeat
    8.7e-16   57.8  12.4     0.0042   17.4   0.1    9.0  9  Ank_5     Ankyrin repeats (many copies)
    3.2e-15   55.8  21.6       0.88   10.1   0.1   11.9 10  Ank       Ankyrin repeat
  ------ inclusion threshold ------
      0.083   12.3   0.5       0.17   11.4   0.5    1.4  1  DUF3087   Protein of unknown function (DUF3087)
       0.65    9.9   3.4        1.6    8.6   3.4    1.6  1  DUF2975   Protein of unknown function (DUF2975)


Domain annotation for each model (and alignments):
>> Ank_2  Ankyrin repeats (3 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   5.3e+03      24      59 ..      36      75 ..      20      75 .. 0.64
   2 ?    3.4   0.0     0.046   1.2e+02       5      73 ..     416     507 ..     411     522 .. 0.60
   3 ?    5.1   0.0     0.014        35      19      59 ..     484     537 ..     450     552 .. 0.70
   4 !   13.3   0.1   3.7e-05     0.094      16      73 ..     572     639 ..     492     646 .. 0.75
   5 !   15.2   0.0   9.5e-06     0.024      20      73 ..     612     678 ..     598     687 .. 0.71
   6 !   20.5   0.8   2.1e-07   0.00054       6      64 ..     706     784 ..     662     793 .. 0.50
   7 !   23.6   0.0   2.3e-08   5.9e-05      20      73 ..     769     835 ..     750     842 .. 0.76
   8 !   29.9   0.0   2.4e-10   6.1e-07      25      78 ..     854     920 ..     841     924 .. 0.81
   9 !   13.8   0.2   2.7e-05     0.068      25      74 ..     991    1013 ..     929    1051 .. 0.54
  10 !    9.0   0.2    0.0008         2       1      41 [.     996    1047 ..     996    1069 .. 0.72
  11 ?   -2.5   0.0       3.3   8.4e+03      40      56 ..    1155    1169 ..    1122    1208 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
       Ank_2 24 kngktaLhyAakngnleivklLleh....adndgrtpLhy 59
                ++g  +L + a+ g++e ++    +        g +pLh+
  AHX11001.1 36 SDGSCVLDHIARTGDTEGLRQVAVAiaqgKQTGGVSPLHI 75
                3788899999999999886655544432433568899985 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.046
       Ank_2   5 akngnlelvklLl..egadpn.....k.ngktaLhyAakngnlei.vklLle..h.....adnd..........grtpLhyAarsghleivklLl 73 
                 a+ gn +l++l l   g+ ++     + ng  ++ +A  +g++ + v+ L +  +     +  +          g  pL +Aa +g+ +++  L+
  AHX11001.1 416 ARTGNIQLLELYLrcPGVQLDvfdvrDdNGYGPVGAALVGGHEGLaVRVLGAlvQcsdqrL--NvgeilcgpgpGSAPLLVAAMQGQ-NAALALM 507
                 5567677777777765544433333225888899989888887443777766331434342..023444455568899999998887.4444443 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.014
       Ank_2  19 gadpnkngktaLhyAakngnleivklLle....h............adndgrtpLhy 59 
                 g      g  +L +Aa++g++ ++ l+le    +             ++ g+t Lh+
  AHX11001.1 484 GPG---PGSAPLLVAAMQGQNAALALMLElirrKcpdaqvrdlmtsSNSAGQTTLHI 537
                 333...468999999999998888888885544155556655544333669999997 PP

  == domain 4  score: 13.3 bits;  conditional E-value: 3.7e-05
       Ank_2  16 LlegadpnkngktaLhyAakngnleivklLle..h..........adndgrtpLhyAarsghleivklLl 73 
                 Ll+  d+  +g+t+Lh+  ++gn  +v  Ll+              ++ g ++L++A  +g+ +++klL 
  AHX11001.1 572 LLCARDA--DGNTPLHLGLQRGNGGLVLSLLKllSpgdllevcktSNSGGVSVLQAALLCGNRQVLKLLQ 639
                 2233444..5899999999999877776666644133555555544577889999999999999999885 PP

  == domain 5  score: 15.2 bits;  conditional E-value: 9.5e-06
       Ank_2  20 adpnk.ngktaLhyAakngnleivklLleh...........ad.ndgrtpLhyAarsghleivklLl 73 
                 ++ ++  g ++L++A   gn++++klL +             +  + rtpLh+A  sg  e++ l l
  AHX11001.1 612 CKTSNsGGVSVLQAALLCGNRQVLKLLQKSlnpdqlgeilvCEdHTSRTPLHAATLSGDVELFSLVL 678
                 333323789999*******99999999985455556555542257799*******999999888776 PP

  == domain 6  score: 20.5 bits;  conditional E-value: 2.1e-07
       Ank_2   6 kngnlelvklLl..eg......adpnkngktaLhyAakngnleivklLleh............adndgrtpLhyAarsg 64 
                  +gn  +v+  l  +       +d n++g+++Lh+A+ +g+  i+ l+l +             d++ +tpLh+A+   
  AHX11001.1 706 GSGNGGMVRAVLaaFPdflketHDHNNEGQNILHAAVGSGDPAILHLILGQlsansvvqlcccSDRYANTPLHMAVAMR 784
                 2233335555554311222212222236666666666666666666666433333444444444466666666666555 PP

  == domain 7  score: 23.6 bits;  conditional E-value: 2.3e-08
       Ank_2  20 adpnkngktaLhyAakngnleivklLleh...............adndgrtpLhyAarsghleivklLl 73 
                 +d     +t+Lh A+   n+ +++l+l++               +d++g t+Lh+A+  g  e+vkl  
  AHX11001.1 769 SDR--YANTPLHMAVAMRNIALLRLMLQKvkqcslgdrdgifctTDSSGSTVLHLAVALGDVEMVKLVA 835
                 231..347********9989999****955667777777777766699*********99*******876 PP

  == domain 8  score: 29.9 bits;  conditional E-value: 2.4e-10
       Ank_2  25 ngktaLhyAakngnleivklLleh............adndgrtpLhyAarsghleivklLlek.gad 78 
                 + + +Lh+Aa  gn+eivk L+e             +d +g+tp  +Aa +g+ eivkl++++ g +
  AHX11001.1 854 QARGPLHTAAVFGNVEIVKCLVERlspeqlfkvlsrVDLSGNTPFCLAAAHGNVEIVKLFIKRlGKE 920
                 4567******************944555677788777788********************9655655 PP

  == domain 9  score: 13.8 bits;  conditional E-value: 2.7e-05
       Ank_2   25 ngktaLhyAakngnleivklLlehadndgrtpLhyAarsghleivklLle 74  
                  +                             tpLh+A+ +++l++++ Ll 
  AHX11001.1  991 C---------------------------AFTPLHMAVLHNNLDCANALLR 1013
                  2...........................3455555555555555555552 PP

  == domain 10  score: 9.0 bits;  conditional E-value: 0.0008
       Ank_2    1 LhlAakngnlelvklLl.....egadpn...k......ngktaLhyAakngnlei 41  
                  Lh+A++++nl++ + Ll     +g d +           g+t+Lh+ ++ +   +
  AHX11001.1  996 LHMAVLHNNLDCANALLrslmlSGGDSSyvcAilaqpvSGLTPLHCVTSVN---A 1047
                  899999988999999997666666554444313445789999999988764...3 PP

  == domain 11  score: -2.5 bits;  conditional E-value: 3.3
       Ank_2   40 eivklLleh.adndgrtp 56  
                   + ++L++h ++    t+
  AHX11001.1 1155 RMFSYLVQHdVN---VTA 1169
                  455666665422...222 PP

>> Ank_4  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.055   1.4e+02       4      41 ..     491     537 ..     488     537 .. 0.83
   2 !   12.1   0.0   8.8e-05      0.22      27      53 ..     573     602 ..     550     603 .. 0.78
   3 !    9.5   0.0   0.00059       1.5      17      54 ..     600     638 ..     596     639 .. 0.84
   4 ?    3.7   0.0     0.038        98      34      53 ..     657     676 ..     647     678 .. 0.81
   5 ?    4.9   0.0     0.016        41       2      52 ..     659     714 ..     658     717 .. 0.72
   6 !    6.4   0.0    0.0054        14       5      54 ..     701     753 ..     697     754 .. 0.69
   7 !   20.4   0.2   2.2e-07   0.00056       4      55 .]     737     793 ..     735     793 .. 0.85
   8 !   24.8   0.0   9.6e-09   2.5e-05       2      53 ..     774     833 ..     773     834 .. 0.93
   9 !   35.6   0.0   3.8e-12   9.7e-09       2      55 .]     856     914 ..     855     914 .. 0.92
  10 !   16.4   0.2   3.9e-06    0.0099       3      42 ..     994    1042 ..     992    1051 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.055
       Ank_4   4 aLhyaaisgrlelvrlLlek..gadinaq.......dnrsGetalhi 41 
                 +L  aa++g+  +++l le   ++ ++aq       +n+ G+t lhi
  AHX11001.1 491 PLLVAAMQGQNAALALMLELirRKCPDAQvrdlmtsSNSAGQTTLHI 537
                 7999**************96548999999777777777889999986 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 8.8e-05
       Ank_4  27 inaqdnrsGetalhiAakrgn....veilkl 53 
                 ++a+ +++G+t+lh +++rgn    ++ lkl
  AHX11001.1 573 LCAR-DADGNTPLHLGLQRGNgglvLSLLKL 602
                 5688.9***************6665555555 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00059
       Ank_4  17 vrlLl.ekgadinaqdnrsGetalhiAakrgnveilklL 54 
                 ++lL      ++++++n+ G + l+ A++ gn ++lklL
  AHX11001.1 600 LKLLSpGDLLEVCKTSNSGGVSVLQAALLCGNRQVLKLL 638
                 55555445678999***********************98 PP

  == domain 4  score: 3.7 bits;  conditional E-value: 0.038
       Ank_4  34 sGetalhiAakrgnveilkl 53 
                   +t+lh A + g+ve + l
  AHX11001.1 657 TSRTPLHAATLSGDVELFSL 676
                 578************98765 PP

  == domain 5  score: 4.9 bits;  conditional E-value: 0.016
       Ank_4   2 ltaLhyaaisgrlelvrlLlek.gad....inaqdnrsGetalhiAakrgnveilk 52 
                 +t+Lh+a  sg++el  l l   g +    +   ++++G+ +l  A+  gn  +++
  AHX11001.1 659 RTPLHAATLSGDVELFSLVLGLlGSEaaagLASLCDINGNGLLTAAVGSGNGGMVR 714
                 57888888888888888888655666666655556888888888888888877776 PP

  == domain 6  score: 6.4 bits;  conditional E-value: 0.0054
       Ank_4   5 LhyaaisgrlelvrlLlekgad....inaqdnrsGetalhiAakrgnveilklL 54 
                 L +a+ sg+  +vr  l+  +d     +   n++G++ lh A+  g++ il+l 
  AHX11001.1 701 LTAAVGSGNGGMVRAVLAAFPDflkeTHD-HNNEGQNILHAAVGSGDPAILHLI 753
                 55555566666777777666664332222.3899****************9986 PP

  == domain 7  score: 20.4 bits;  conditional E-value: 2.2e-07
       Ank_4   4 aLhyaaisgrlelvrlLl.....ekgadinaqdnrsGetalhiAakrgnveilklLl 55 
                 +Lh+a+ sg+  +++l+l     ++ ++++++++r+ +t+lh+A+ + n+  l+l l
  AHX11001.1 737 ILHAAVGSGDPAILHLILgqlsaNSVVQLCCCSDRYANTPLHMAVAMRNIALLRLML 793
                 69****************655533446688888*******************99875 PP

  == domain 8  score: 24.8 bits;  conditional E-value: 9.6e-09
       Ank_4   2 ltaLhyaaisgrlelvrlLlekgad........inaqdnrsGetalhiAakrgnveilkl 53 
                 +t+Lh+a+++ ++ l+rl l+k ++        i +++++sG t lh A+  g+ve++kl
  AHX11001.1 774 NTPLHMAVAMRNIALLRLMLQKVKQcslgdrdgIFCTTDSSGSTVLHLAVALGDVEMVKL 833
                 79*******************966669******88888********************96 PP

  == domain 9  score: 35.6 bits;  conditional E-value: 3.8e-12
       Ank_4   2 ltaLhyaaisgrlelvrlLlek.gad.....inaqdnrsGetalhiAakrgnveilklLl 55 
                 +++Lh aa +g++e+v+ L+e+  ++     + ++ + sG+t++  Aa +gnvei+kl++
  AHX11001.1 856 RGPLHTAAVFGNVEIVKCLVERlSPEqlfkvLSRV-DLSGNTPFCLAAAHGNVEIVKLFI 914
                 789*****************985566999978888.**********************97 PP

  == domain 10  score: 16.4 bits;  conditional E-value: 3.9e-06
       Ank_4    3 taLhyaaisgrlelvrlLl....ekgad.........inaqdnrsGetalhiA 42  
                  t+Lh+a+ +++l+++  Ll        +         i aq + sG+t+lh++
  AHX11001.1  994 TPLHMAVLHNNLDCANALLrslmL---SggdssyvcaILAQ-PVSGLTPLHCV 1042
                  79************9999955442...1444667777***9.*********97 PP

>> Ank_3  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0         7   1.8e+04       8      17 ..      87      96 ..      87     105 .. 0.72
   2 ?   -3.7   0.0         7   1.8e+04       4      23 ..     410     429 ..     409     432 .. 0.80
   3 ?    0.3   0.0      0.65   1.7e+03       5      22 ..     491     511 ..     488     518 .. 0.68
   4 ?    4.4   0.0     0.029        75       1      23 [.     579     601 ..     579     606 .. 0.83
   5 ?    0.1   0.0      0.74   1.9e+03       2      22 ..     619     639 ..     618     645 .. 0.75
   6 ?    3.1   0.0     0.077     2e+02       3      18 ..     659     674 ..     657     682 .. 0.82
   7 ?   -0.1   0.0      0.84   2.1e+03       1      26 [.     696     720 ..     696     724 .. 0.85
   8 !    7.9   0.0    0.0021       5.5       1      23 [.     733     755 ..     733     761 .. 0.86
   9 !    8.3   0.1    0.0016         4       3      23 ..     774     794 ..     772     800 .. 0.91
  10 !    7.4   0.0    0.0031       7.9       2      20 ..     815     833 ..     814     838 .. 0.90
  11 !   10.6   0.0   0.00028      0.72       5      23 ..     858     876 ..     856     881 .. 0.91
  12 !   10.3   0.0   0.00034      0.88       2      28 ..     894     920 ..     893     923 .. 0.88
  13 !    9.1   0.4   0.00087       2.2       4      23 ..     994    1013 ..     992    1016 .. 0.93
  14 ?    1.2   0.0      0.32   8.3e+02       2      15 ..    1035    1048 ..    1034    1065 .. 0.81
  15 ?   -2.9   0.0       6.9   1.8e+04      16      29 ..    1154    1167 ..    1135    1168 .. 0.54

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 7
       Ank_3  8 lAarsgnlei 17
                +Aar+gn++ 
  AHX11001.1 87 IAARAGNVDF 96
                69*****974 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 7
       Ank_3   4 tpLhlAarsgnleivkfLle 23 
                 ++L l ar gn+ ++++ l+
  AHX11001.1 410 SLLQLTARTGNIQLLELYLR 429
                 67777899999999999887 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.65
       Ank_3   5 pLhlAarsgnle...ivkfLl 22 
                 pL +Aa++g  +   ++  L+
  AHX11001.1 491 PLLVAAMQGQNAalaLMLELI 511
                 9*********97222355444 PP

  == domain 4  score: 4.4 bits;  conditional E-value: 0.029
       Ank_3   1 nGetpLhlAarsgnleivkfLle 23 
                 +G+tpLhl +  gn  +v  Ll+
  AHX11001.1 579 DGNTPLHLGLQRGNGGLVLSLLK 601
                 69*******99999987766665 PP

  == domain 5  score: 0.1 bits;  conditional E-value: 0.74
       Ank_3   2 GetpLhlAarsgnleivkfLl 22 
                 G + L  A+++gn  ++k+L 
  AHX11001.1 619 GVSVLQAALLCGNRQVLKLLQ 639
                 6688999********666664 PP

  == domain 6  score: 3.1 bits;  conditional E-value: 0.077
       Ank_3   3 etpLhlAarsgnleiv 18 
                 +tpLh A +sg++e+ 
  AHX11001.1 659 RTPLHAATLSGDVELF 674
                 8**********99854 PP

  == domain 7  score: -0.1 bits;  conditional E-value: 0.84
       Ank_3   1 nGetpLhlAarsgnleivkfLlenkg 26 
                 nG+ +L  A+ sgn  +v++ l    
  AHX11001.1 696 NGNGLLTAAVGSGNGGMVRAVLA-AF 720
                 7999999***********99987.45 PP

  == domain 8  score: 7.9 bits;  conditional E-value: 0.0021
       Ank_3   1 nGetpLhlAarsgnleivkfLle 23 
                 +G+++Lh A+ sg+++i++++l 
  AHX11001.1 733 EGQNILHAAVGSGDPAILHLILG 755
                 599*************9999886 PP

  == domain 9  score: 8.3 bits;  conditional E-value: 0.0016
       Ank_3   3 etpLhlAarsgnleivkfLle 23 
                 +tpLh+A+   n+++++++l+
  AHX11001.1 774 NTPLHMAVAMRNIALLRLMLQ 794
                 8****************9998 PP

  == domain 10  score: 7.4 bits;  conditional E-value: 0.0031
       Ank_3   2 GetpLhlAarsgnleivkf 20 
                 G t LhlA+  g++e+vk+
  AHX11001.1 815 GSTVLHLAVALGDVEMVKL 833
                 88*************9986 PP

  == domain 11  score: 10.6 bits;  conditional E-value: 0.00028
       Ank_3   5 pLhlAarsgnleivkfLle 23 
                 pLh+Aa +gn+eivk L+e
  AHX11001.1 858 PLHTAAVFGNVEIVKCLVE 876
                 9****************99 PP

  == domain 12  score: 10.3 bits;  conditional E-value: 0.00034
       Ank_3   2 GetpLhlAarsgnleivkfLlenkgad 28 
                 G+tp+ lAa +gn+eivk++++  g +
  AHX11001.1 894 GNTPFCLAAAHGNVEIVKLFIKRLGKE 920
                 9********************977765 PP

  == domain 13  score: 9.1 bits;  conditional E-value: 0.00087
       Ank_3    4 tpLhlAarsgnleivkfLle 23  
                  tpLh+A++++nl+ + +Ll+
  AHX11001.1  994 TPLHMAVLHNNLDCANALLR 1013
                  9************9999997 PP

  == domain 14  score: 1.2 bits;  conditional E-value: 0.32
       Ank_3    2 GetpLhlAarsgnl 15  
                  G tpLh++ + + +
  AHX11001.1 1035 GLTPLHCVTSVNAV 1048
                  89****99887766 PP

  == domain 15  score: -2.9 bits;  conditional E-value: 6.9
       Ank_3   16 e.ivkfLlenkgadv 29  
                    +  +L++ + ++v
  AHX11001.1 1154 RrMFSYLVQ-HDVNV 1167
                  236889999.66665 PP

>> Ank_5  Ankyrin repeats (many copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   8.2e+03      46      56 .]     140     150 ..     136     150 .. 0.85
   2 ?    2.5   0.0     0.078     2e+02      10      36 ..     574     600 ..     571     626 .. 0.80
   3 ?   -3.7   0.0       6.9   1.8e+04      13      23 ..     655     665 ..     649     666 .. 0.66
   4 ?    0.7   0.1      0.29   7.3e+02      12      32 ..     730     750 ..     724     760 .. 0.76
   5 !   10.8   0.1   0.00019      0.48       8      46 ..     765     805 ..     759     807 .. 0.86
   6 !    8.8   0.0   0.00082       2.1      11      35 ..     810     834 ..     808     842 .. 0.88
   7 ?    2.6   0.0      0.07   1.8e+02      19      37 ..     858     876 ..     848     883 .. 0.88
   8 !   13.2   0.0   3.4e-05     0.088      11      37 ..     889     915 ..     886     921 .. 0.89
   9 !   17.4   0.1   1.6e-06    0.0042       7      36 ..     983    1012 ..     977    1024 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
       Ank_5  46 dsrGltaldlA 56 
                 ++ Gl+++d+A
  AHX11001.1 140 TGKGLSPVDYA 150
                 6789******9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.078
       Ank_5  10 nrldgggntpLhvAakygaadvvrlLl 36 
                 +++d +gntpLh+   +g+  +v+ Ll
  AHX11001.1 574 CARDADGNTPLHLGLQRGNGGLVLSLL 600
                 567778999999988888888888888 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 6.9
       Ank_5  13 dgggntpLhvA 23 
                 d  + tpLh A
  AHX11001.1 655 DHTSRTPLHAA 665
                 44455899866 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.29
       Ank_5  12 ldgggntpLhvAakygaadvv 32 
                  +++g+++Lh A+  g + ++
  AHX11001.1 730 HNNEGQNILHAAVGSGDPAIL 750
                 478899******987766655 PP

  == domain 5  score: 10.8 bits;  conditional E-value: 0.00019
       Ank_5   8 dvnrldgggntpLhvAakygaadvvrlLl..argadlnltd 46 
                  ++++d++ ntpLh+A+  ++  ++rl+l    +++l+ +d
  AHX11001.1 765 LCCCSDRYANTPLHMAVAMRNIALLRLMLqkVKQCSLGDRD 805
                 68999*********************999877777777666 PP

  == domain 6  score: 8.8 bits;  conditional E-value: 0.00082
       Ank_5  11 rldgggntpLhvAakygaadvvrlL 35 
                 ++d  g t+Lh+A+  g  ++v+l 
  AHX11001.1 810 TTDSSGSTVLHLAVALGDVEMVKLV 834
                 68999*****************975 PP

  == domain 7  score: 2.6 bits;  conditional E-value: 0.07
       Ank_5  19 pLhvAakygaadvvrlLla 37 
                 pLh+Aa  g+ ++v+ L++
  AHX11001.1 858 PLHTAAVFGNVEIVKCLVE 876
                 9*************98884 PP

  == domain 8  score: 13.2 bits;  conditional E-value: 3.4e-05
       Ank_5  11 rldgggntpLhvAakygaadvvrlLla 37 
                 r d  gntp+++Aa +g+ ++v+l+++
  AHX11001.1 889 RVDLSGNTPFCLAAAHGNVEIVKLFIK 915
                 67899*******************994 PP

  == domain 9  score: 17.4 bits;  conditional E-value: 1.6e-06
       Ank_5    7 advnrldgggntpLhvAakygaadvvrlLl 36  
                  +   ++ g+ +tpLh+A+ ++++d+++ Ll
  AHX11001.1  983 ILAHYTYGCAFTPLHMAVLHNNLDCANALL 1012
                  56678999*********************9 PP

>> Ank  Ankyrin repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.2      0.11   2.7e+02       2      21 ..      69     103 ..      68     169 .. 0.82
   2 !    9.8   0.2   0.00044       1.1       1      19 [.     579     636 ..     579     648 .. 0.64
   3 ?    2.5   0.1     0.092   2.4e+02       3      20 ..     659     676 ..     659     695 .. 0.69
   4 ?    2.1   0.1      0.12   3.1e+02       2      26 ..     734     760 ..     733     765 .. 0.78
   5 ?    5.0   0.1     0.015        38       3      13 ..     774     785 ..     774     801 .. 0.71
   6 !    7.2   0.0    0.0029       7.4       2      21 ..     815     833 ..     814     842 .. 0.87
   7 ?    5.2   0.0     0.012        31       5      22 ..     858     875 ..     857     881 .. 0.90
   8 !   10.1   0.0   0.00035      0.88       2      22 ..     894     914 ..     893     921 .. 0.88
   9 !   10.1   0.1   0.00035      0.88       3      22 ..     993    1012 ..     993    1021 .. 0.89
  10 ?    4.0   0.0      0.03        78       2      21 ..    1035    1065 ..    1034    1087 .. 0.74

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.11
                 SBBHHHH............HHHHTT...HHHHHHH CS
         Ank   2 GnTPLHl............Aatngk...kriiklL 21 
                 G +PLH+            Aa+ g+   ++ i++L
  AHX11001.1  69 GVSPLHIlfvflsarsvpiAARAGNvdfLSTISAL 103
                 899***88899998888887888875554444444 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00044
                 TSBBHHHH......................................HH.HHTTHHHHH CS
         Ank   1 dGnTPLHl......................................Aa.tngkkriik 19 
                 dGnTPLHl                                      Aa  +g+ +++k
  AHX11001.1 579 DGNTPLHLglqrgngglvlsllkllspgdllevcktsnsggvsvlqAAlLCGNRQVLK 636
                 9*******66666666666666666666666666666666555555334555566666 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.092
                 BBHHHHHHHHTTHHHHHH CS
         Ank   3 nTPLHlAatngkkriikl 20 
                 +TPLH A   g+++  +l
  AHX11001.1 659 RTPLHAATLSGDVELFSL 676
                 5*****876676666555 PP

  == domain 4  score: 2.1 bits;  conditional E-value: 0.12
                 SBBHHHHHHHHTTHHHHHHHH.T.TTS CS
         Ank   2 GnTPLHlAatngkkriiklLL.h.GAn 26 
                 G   LH A+  g++ i++l+L + +An
  AHX11001.1 734 GQNILHAAVGSGDPAILHLILgQlSAN 760
                 6777****9778899***999444465 PP

  == domain 5  score: 5.0 bits;  conditional E-value: 0.015
                 BBHHHHHH.HHT CS
         Ank   3 nTPLHlAa.tng 13 
                 nTPLH+A+ +++
  AHX11001.1 774 NTPLHMAVaMRN 785
                 8*****986433 PP

  == domain 6  score: 7.2 bits;  conditional E-value: 0.0029
                 SBBHHHHHHHHTTHHHHHHH CS
         Ank   2 GnTPLHlAatngkkriiklL 21 
                 G T+LHlA+  g+++++k L
  AHX11001.1 815 GSTVLHLAVALGDVEMVK-L 833
                 88*******99*999*99.5 PP

  == domain 7  score: 5.2 bits;  conditional E-value: 0.012
                 HHHHHHHHTTHHHHHHHH CS
         Ank   5 PLHlAatngkkriiklLL 22 
                 PLH Aa +g+++i+k L+
  AHX11001.1 858 PLHTAAVFGNVEIVKCLV 875
                 9**9999********987 PP

  == domain 8  score: 10.1 bits;  conditional E-value: 0.00035
                 SBBHHHHHHHHTTHHHHHHHH CS
         Ank   2 GnTPLHlAatngkkriiklLL 22 
                 GnTP  lAa  g+++i+kl++
  AHX11001.1 894 GNTPFCLAAAHGNVEIVKLFI 914
                 9********99*********9 PP

  == domain 9  score: 10.1 bits;  conditional E-value: 0.00035
                  BBHHHHHHHHTTHHHHHHHH CS
         Ank    3 nTPLHlAatngkkriiklLL 22  
                  +TPLH+A+  ++++++ +LL
  AHX11001.1  993 FTPLHMAVLHNNLDCANALL 1012
                  7*******99*******998 PP

  == domain 10  score: 4.0 bits;  conditional E-value: 0.03
                  SBBHHHH.....HH......HHTTHHHHHHH CS
         Ank    2 GnTPLHl.....Aa......tngkkriiklL 21  
                  G TPLH+     A+      ++g ++++++L
  AHX11001.1 1035 GLTPLHCvtsvnAVqtiarcNIGRPDMCEML 1065
                  89****9343332254444577778888876 PP

>> DUF3087  Protein of unknown function (DUF3087)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.5   6.6e-05      0.17       5      65 ..    1217    1278 ..    1214    1288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
     DUF3087    5 eidkerYrkklnrvivalvallavlsllfstllialfgeeevsnfhln.llGvvlalvltaa 65  
                  +id    r+++  ++  l+++ +vl l +++l+++  + ++++ + +n l+Gvv+a+vl+a+
  AHX11001.1 1217 HIDIPARRRRIEVSTCLLLSTALVLTLGVAALAVSHASRDKSDMLLVNvLIGVVVAAVLCAL 1278
                  56666779999***************************9999999998468*******9986 PP

>> DUF2975  Protein of unknown function (DUF2975)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.4   0.00063       1.6      62     114 ..    1229    1284 ..    1221    1285 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00063
     DUF2975   62 iglaliaa.alllaagivalallae.lelap.gvvllllgvafaslvigllvlvla 114 
                  ++ +l+++ al+l++g+ ala++ + ++ +  ++v++l+gv++a+++++l++lv++
  AHX11001.1 1229 VSTCLLLStALVLTLGVAALAVSHAsRDKSDmLLVNVLIGVVVAAVLCALFALVVS 1284
                  344555555788888888888888866666689999999***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.90u 0.27s 00:00:01.17 Elapsed: 00:00:00.43
# Mc/sec: 9583.85
//
Query:       AHX11002.1  [L=166]
Description: hypothetical protein NHE_0027 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.12   12.2   0.0       0.24   11.3   0.0    1.5  1  Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)


Domain annotation for each model (and alignments):
>> Phage_AlpA  Prophage CP4-57 regulatory protein (AlpA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   1.3e-05      0.24       2      25 ..      94     117 ..      93     129 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 1.3e-05
  Phage_AlpA   2 rilrlreVeqktglsrstiYrlik 25 
                 r l+++e  +k+gl rs+ Y+ i+
  AHX11002.1  94 RKLNMEEFLTKIGLDRSQCYDCIR 117
                 6799*****************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1285.87
//
Query:       AHX11003.1  [L=292]
Description: hypothetical protein NHE_0028 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       656  (0.0365888); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 2334.76
//
Query:       AHX11004.1  [L=39]
Description: hypothetical protein NHE_0029 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 315.07
//
Query:       AHX11005.1  [L=262]
Description: conserved hypothetical integral membrane family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-29  102.6  17.0    2.3e-29  102.6  17.0    1.7  2  Vut_1     Putative vitamin uptake transporter


Domain annotation for each model (and alignments):
>> Vut_1  Putative vitamin uptake transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.9      0.21   3.7e+03       8      24 ..      44      60 ..      35      78 .. 0.44
   2 !  102.6  17.0   1.3e-33   2.3e-29       2     149 ..      92     253 ..      91     254 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.21
       Vut_1  8 pltflitdiisevyGkk 24
                 l ++++ i  +++Gk 
  AHX11005.1 44 LLCMTMMMISFKYFGKM 60
                33333333333333332 PP

  == domain 2  score: 102.6 bits;  conditional E-value: 1.3e-33
       Vut_1   2 aGvllfpltflitdiisevyGkkaarkvvllgflanllalillllalllpa......ealesvfgltprivlasliaylvsqlldvyvfhrlkkltkgk 94 
                 +G+++f+++fl+++i++e yG   a+  v+l+f++ +++++ ++++l +++        ++++f++++ +++ +++ayl+sq+ d+y+f+ lk +   +
  AHX11005.1  92 LGTIAFSTIFLANNILTERYGIGVAKGNVFLSFALYAFFILAMIITLSYKPktdayyPCMQKLFQNSATLLISGVTAYLISQFSDIYIFAGLK-HLLPR 189
                 79***********************************************9988766666*********************************9.44558 PP

       Vut_1  95 klwlrnigStlvsqlvdtlifvtiaflg.........eqlleiilsqylikllialldtplvyl 149
                 +lwlr+++  ++s+lvd++if t+a+++         + ++++il++y i +li l+ tp++y+
  AHX11005.1 190 FLWLRSLIGVMISSLVDNIIFSTLAWYVlttnpveisALIFTYILGTYWIRVLIGLFGTPFLYI 253
                 9************************9779**********************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1943.63
//
Query:       AHX11006.1  [L=39]
Description: hypothetical protein NHE_0031 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       164  (0.00914719); expected 358.6 (0.02)
Passed bias filter:                      153  (0.00853366); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 320.82
//
Query:       AHX11007.1  [L=322]
Description: phosphoribosylformylglycinamidine cyclo-ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-29  101.8   0.0    5.3e-29  101.4   0.0    1.2  1  AIRS_C    AIR synthase related protein, C-terminal domain
    2.4e-15   56.9   0.2    4.5e-15   56.1   0.2    1.5  1  AIRS      AIR synthase related protein, N-terminal domain


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.4   0.0   5.9e-33   5.3e-29       3     145 ..     174     321 ..     172     322 .] 0.95

  Alignments for each domain:
  == domain 1  score: 101.4 bits;  conditional E-value: 5.9e-33
                 TEEEEEEETSSCTCCHHHHHHHCHHHCTSHTT....TSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECG...TH CS
      AIRS_C   3 GdvliltgslGlggagtslkrkileeegldds....avqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidld...kv 94 
                 Gdv++ ++s+G++++g+sl+rk++++ g  ++    ++  g+ ll+pt+iyvk+ l a+ +  ka++++TgGG+l++l +++p+    ++i+++    +
  AHX11007.1 174 GDVIVALKSSGFHSNGFSLIRKVFKTLGITYDtihhGRSWGEILLTPTRIYVKQVLEAR-KFLKAIAHITGGGILENLRRVVPEE---LRIHMKpykFP 268
                 9**************************99999***8888*******************8.99**********************7...888888889** PP

                 HHHHHHH.....HHHHHHHCSTTTEEEEEEEHGGH.HHHHHHHHHTTCCCEEEEEEE CS
      AIRS_C  95 pifdele.....splemllsensGrllvavppeea.davlaileeeglpeaavIGev 145
                  ifd+l+     +++eml+++n+G+++++v+++e+ d+v++i++     ea+++G++
  AHX11007.1 269 DIFDWLMvngriEREEMLRTFNCGIGMILVVAQENvDTVMKIFDT----EASILGHL 321
                 ********************************************5....58888875 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.2     5e-19   4.5e-15       6      94 .]      58     161 ..      28     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 5e-19
                 EEEEEEEE.EECC....TCCCC...HHHHHHHHHHHHHHTTTEEEEEEEEEEEEC.....HHHHHHHHHHHHHHHTT-EEEEEEEEEESS......EEE CS
        AIRS   6 vvttdshnrpvlv....epvhf...iGakavavnlsDlaamGArPlalllslalp.....wleevvrglaeaaeelgvplvgGdtsfsne......pti 86 
                 + +td++++++l+    +       iG  +va++++Dl++ GA+Pl++l+++a +     + +++++g+ ++++e+ ++l+gG+t+++++      + +
  AHX11007.1  58 ASSTDGVGTKLLIanelN---NhatIGIDLVAMCVNDLICHGAEPLFFLDYYATGkldleTSKAIISGITDGCREACISLIGGETAEMPGlysksdYDL 153
                 679999999999944333...14469*********************************999************************9999889999999 PP

                 EEEEEEEE CS
        AIRS  87 svtavGlv 94 
                 + +avG+v
  AHX11007.1 154 AGFAVGIV 161
                 99999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 2205.46
//
Query:       AHX11008.1  [L=93]
Description: NADH-ubiquinone/plastoquinone oxidoreductase chain 4L family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-19   69.2   7.3    2.1e-19   69.1   7.3    1.0  1  Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase cha
     0.0064   16.4   1.7     0.0064   16.4   1.7    2.1  2  DUF2108      Predicted membrane protein (DUF2108)
  ------ inclusion threshold ------
       0.35   11.1   4.7       0.13   12.6   1.6    1.8  2  DUF1430      Protein of unknown function (DUF1430)
        2.4    7.8  10.4       0.45   10.1   3.2    2.3  2  SPW          SPW repeat


Domain annotation for each model (and alignments):
>> Oxidored_q2  NADH-ubiquinone/plastoquinone oxidoreductase chain 4L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.1   7.3   4.7e-23   2.1e-19       7      94 ..       3      91 ..       1      93 [] 0.96

  Alignments for each domain:
  == domain 1  score: 69.1 bits;  conditional E-value: 4.7e-23
                 HHHHHHHHHHHHHSSCCHHHHHHHHHHHHHHHHHHHHHHHHC..............TTSCGGHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Oxidored_q2  7 allfliGlygvllrrnllkvliglelisnavnlllvlagvftegtlvi.tnpatefadplpqalvLtaivigaaetavgLallvrlyre 94
                 + l+++Gly ++++  ++k+ligl++ +++v l+++ +++  +g+++i   +++++++plp++l+Ltaiv+g+a++a+gLal+v ++++
   AHX11008.1  3 VWLMMVGLYIIMASPRAIKKLIGLSVFQSSVLLFYISLSYIDGGAVPIiASQTQHYVNPLPHVLMLTAIVVGVATLALGLALVVLINKS 91
                 6799*****************************************99999999*******************************99986 PP

>> DUF2108  Predicted membrane protein (DUF2108)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   1.7   1.4e-06    0.0064       7      48 ..       3      44 ..       1      54 [. 0.91
   2 !    5.7   2.1    0.0031        14      28      66 ..      38      82 ..      38      86 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
     DUF2108  7 lalaliGaigvillkkpldKlimlalleaGlillivakgYLD 48
                + l+++G   ++ + + ++Kli l++ ++ ++l+ ++  Y+D
  AHX11008.1  3 VWLMMVGLYIIMASPRAIKKLIGLSVFQSSVLLFYISLSYID 44
                578999*9*********************************9 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0031
     DUF2108 28 imlalleaGlillivak..gYLD....VaiavallePvstiilll 66
                i+l+ +++G +++i+++   Y+     V +++a++  v+t+ l l
  AHX11008.1 38 ISLSYIDGGAVPIIASQtqHYVNplphVLMLTAIVVGVATLALGL 82
                78999**********853379855555999999999999997755 PP

>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.1      0.58   2.6e+03      49      61 ..       2      14 ..       1      18 [. 0.66
   2 ?   12.6   1.6   2.8e-05      0.13      27      83 ..      19      75 ..      15      92 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.58
     DUF1430 49 ivllillvlifil 61
                +v+l++++l +i+
  AHX11008.1  2 VVWLMMVGLYIIM 14
                5677777776665 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 2.8e-05
     DUF1430 27 likkihGyslfkrhkeyliiqlivllillvlifiltkekiillvvlvlllielllil 83
                +ikk+ G+s+f+++  +++i+l  +  ++v i+ ++ + ++  +  vl+l+ +++ +
  AHX11008.1 19 AIKKLIGLSVFQSSVLLFYISLSYIDGGAVPIIASQTQHYVNPLPHVLMLTAIVVGV 75
                7********************999888888888888888888888888888877765 PP

>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.7      0.04   1.8e+02       5      14 ..       6      15 ..       4      17 .. 0.79
   2 ?   10.1   3.2    0.0001      0.45      25      44 ..      65      84 ..      61      87 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.04
         SPW  5 lllGlwlivS 14
                +++Gl++i++
  AHX11008.1  6 MMVGLYIIMA 15
                678****987 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0001
         SPW 25 gaawnnvivGavvavLalaf 44
                 +++++++vG+++++L+la 
  AHX11008.1 65 VLMLTAIVVGVATLALGLAL 84
                589***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 707.03
//
Query:       AHX11009.1  [L=146]
Description: Na+/H+ antiporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-23   83.3  14.8    1.9e-23   83.1  14.8    1.0  1  MnhB      Domain related to MnhB subunit of Na+/H+ antiporter


Domain annotation for each model (and alignments):
>> MnhB  Domain related to MnhB subunit of Na+/H+ antiporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.1  14.8     1e-27   1.9e-23       2     123 ..       7     128 ..       6     129 .. 0.88

  Alignments for each domain:
  == domain 1  score: 83.1 bits;  conditional E-value: 1e-27
        MnhB   2 lrtvarllvplillvslylllrGhnsPGGGFqgGlilaaalillylafgleelekllrvklaprileglglllavltgllglllg..fltslflelel. 97 
                 l++v+  +vp+i+l+++y+ ++G+ +PGGGFq+G++laaa+i + lafg++   +l r ++      ++g+l+++++gl+++l g  fl+++++  ++ 
  AHX11009.1   7 LKVVVSGMVPIIILFAIYVQMHGEITPGGGFQAGVLLAAAFIGYSLAFGRKPILRLFRLTTL-IHYGAIGALIYLFVGLAPVLRGgnFLQHSHIIEGMp 104
                 799*************************************************5555555533.58899****************99*****99966665 PP

        MnhB  98 llgevelgtallfdlgVylvVvggll 123
                 ll ++e+g+ +l  lgV+l+V++++l
  AHX11009.1 105 LL-SQEIGIFILE-LGVGLTVFSSIL 128
                 44.5789988777.*******99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1154.14
//
Query:       AHX11010.1  [L=180]
Description: hypothetical protein NHE_0035 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      9e-13   48.2  12.0      9e-13   48.2  12.0    2.3  3  DUF4040         Domain of unknown function (DUF4040)
     0.0021   17.2   4.6      0.003   16.7   4.6    1.2  1  Acyl_transf_3   Acyltransferase family
  ------ inclusion threshold ------
        1.6    7.3   9.5       0.11   11.2   2.3    2.3  1  DUF2298         Uncharacterized membrane protein (DUF2298)


Domain annotation for each model (and alignments):
>> DUF4040  Domain of unknown function (DUF4040)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2  12.0   1.5e-16     9e-13       2      61 ..      13      72 ..      12      76 .. 0.96
   2 ?   -3.1   0.1       1.5   9.1e+03      26      32 ..      97     103 ..      90     109 .. 0.44
   3 ?   -1.0   0.5      0.34     2e+03      23      34 ..     159     170 ..     141     174 .. 0.62

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.5e-16
     DUF4040  2 llvlaalaavlardrlaavillgvvGllvallfvllgAPDvAlTqaavveglttvlllla 61
                +lvl+++a+++++d+l+ v+++g+++ll++l++++++A DvA+T+ av++ +ttv++ll+
  AHX11010.1 13 GLVLISIALAATEDLLTEVVYSGIISLLLTLMYMTMNAADVAITESAVGSYVTTVFILLV 72
                6899******************************************************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.5
     DUF4040  26 vGllval 32 
                 v  ++al
  AHX11010.1  97 VTAGCAL 103
                 3333333 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.34
     DUF4040  23 lgvvGllvallf 34 
                 + v+  + +l+f
  AHX11010.1 159 VVVFTAAFSLIF 170
                 333444444444 PP

>> Acyl_transf_3  Acyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   4.6     5e-07     0.003     139     271 ..      10     146 ..       8     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-07
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Acyl_transf_3 139 alfvlylllplllrllrkvrkshlllllilllllslvfirhelfgpatsvgllplpsvlallfflfGalladaddrdrnlsrglkislllslllla 234
                    +l++l+l++  l++    +  ++   ++ lll+l++++++++ +    s++ + +     ++ +l+G+++ + +d    +s +++++l+   ++ a
     AHX11010.1  10 LLLGLVLISIALAATEDLLTEVVYSGIISLLLTLMYMTMNAADVAITESAVGSYVTT---VFILLVGMVIDKKNDPTPTRSDKWLALLASVTAGCA 102
                    57788888888888888888888888999999999999*999988888877765555...9*********************************** PP

                    xxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx RF
  Acyl_transf_3 235 lillalfgqtdg.......gglvasvliqsaslllvslgimlll 271
                    l ++ + + t+g       ++ ++++l ++ sl+ +   + ++l
     AHX11010.1 103 LVCVTYDLPTYGllaapanNEIYKYYLENTESLFGFPNVVTAIL 146
                    **********9999999995555555555555544444443333 PP

>> DUF2298  Uncharacterized membrane protein (DUF2298)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.3   1.9e-05      0.11     254     311 ..      64     121 ..      59     177 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 1.9e-05
     DUF2298 254 pllllalalllallrrpaskrrrrrsllllllalvlGalaatNtWdfptyllllllal 311
                   ++++l++ + + +++    +r+ ++l ll+++++G+ ++  t d+pty+ll++ a 
  AHX11010.1  64 VTTVFILLVGMVIDKKNDPTPTRSDKWLALLASVTAGCALVCVTYDLPTYGLLAAPAN 121
                 45666666677776777777777777899999*********************98664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 1296.21
//
Query:       AHX11011.1  [L=89]
Description: monovalent cation/proton antiporter, MnhG/PhaG subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.4e-21   74.9   6.0    4.8e-21   74.8   6.0    1.0  1  PhaG_MnhG_YufB  Na+/H+ antiporter subunit


Domain annotation for each model (and alignments):
>> PhaG_MnhG_YufB  Na+/H+ antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   6.0   2.7e-25   4.8e-21       2      77 ..       3      79 ..       2      81 .. 0.96

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 2.7e-25
  PhaG_MnhG_YufB  2 lllGalfvllgaigllrlpdvytRlhaatkadtlGlllillGlllrf.slaaslkllliilfllltaPvaahliara 77
                    +l+G++++l g+ig++r+p +++++haa+++d++G+ l++lG++l+f  +++slk++lii +l++t++v+++l+ ++
      AHX11011.1  3 MLAGTFIMLSGTIGIVRFPYFFSKVHAASMTDSFGAPLTILGCALKFgISMTSLKVILIIPILWITSSVGSYLLCKS 79
                    799********************************************98889*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (89 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      188  (0.0104858); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 676.34
//
Query:       AHX11012.1  [L=232]
Description: RNA methyltransferase, RsmE family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-42  145.8   0.0    1.4e-42  145.6   0.0    1.0  1  Methyltrans_RNA  RNA methyltransferase
  ------ inclusion threshold ------
       0.11   12.9   0.1       0.46   10.8   0.1    1.9  2  DUF4468          Domain of unknown function (DUF4468) with TB


Domain annotation for each model (and alignments):
>> Methyltrans_RNA  RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  145.6   0.0   1.5e-46   1.4e-42       3     225 ..      21     221 ..      19     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 145.6 bits;  conditional E-value: 1.5e-46
                      EEHHHHHHHHTTTT--TT-EEEEEESSSEEEEEEEEEEESSEEEEEEEEEEE---SSSSEEEEEEE--SSHHHHHHHHHHHHTT-SEEEEEE-T CS
  Methyltrans_RNA   3 ltdeeahHlvkVlRlkegdeiklfdgdgkeyeaeieeiskkkvtvkilekeeenkespekitlaqalpkgdklelilqkatElGvseivplise 96 
                      l++ + h+l +V Rl +++ + +f+ +++e++a+ e+   + v +  ++++ + +e + +it+++a+pk+++l+ i++++tElG+++++p++s+
       AHX11012.1  21 LNQGQQHYLSNVIRLPKNSDVLIFNSKDGEWLAKFEK---DYV-IPHQQSRIQVQEYSYEITVCFAIPKSKTLKTIIRQSTELGATTLQPIHSD 110
                      677899***************************9964...444.4444444444455555********************************** PP

                      TSSS...HHHHHHHHHHHHHHHHHHHHHHT-SS--EEEEEEEHHHHHHHCSCCEEEEEEETTSSEBGGGSSHCCHTHHCSEEEEEE--TT---H CS
  Methyltrans_RNA  97 rsvvkldekkkdkklerwqkilieAaeQsgrtrlpevkepislkelleelkeadlklildeeekksleelsekkkelkevkvlliiGPEGGfse 190
                      ++v      + +k +++++   ieAa+Q++r ++p + +pis++e+  ++k+    +i+de++++++    +  +     + +++iGPEGGfs+
       AHX11012.1 111 HTV------NRIKDTDKLELWSIEAAQQCRRMSIPRILSPISFQEISIQYKNV---IICDETSEDATVCDIPILN-----SYTIVIGPEGGFSP 190
                      **7......5569999999999*************************999995...******9999888888887.....79************ PP

                      HHHHHHHHTTCEEEB-SSS---HHHHHHHHHHHHH CS
  Methyltrans_RNA 191 kEiellkeagfkpvsLgpriLRteTAalaalsalq 225
                      +E++l    + + +sLg+ +LR++TA++aa+s + 
       AHX11012.1 191 AELSL----EGHRISLGKMVLRCDTAVVAAISQIR 221
                      **994....457********************986 PP

>> DUF4468  Domain of unknown function (DUF4468) with TBP-like fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1   5.1e-05      0.46      11      73 ..      17      79 ..       9      87 .. 0.86
   2 ?   -1.0   0.0      0.25   2.2e+03      61      87 ..     146     172 ..     137     174 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.1e-05
                -HHHHHHHHHHHHHHHHSS-TTEEEE.EETTTTEEEEEEEEEEE-SS....S-EEEEEEEEEE CS
     DUF4468 11 skdeiYdrakkwaakrfkdenqsriqledkeegviaakgeewlvfsssalsldrtkirYtlii 73
                +k  + +  + ++++  +  ++s + + + ++g+  ak+e+++v+ +++   +  + +Y++++
  AHX11012.1 17 KKILLNQGQQHYLSNVIRLPKNSDVLIFNSKDGEWLAKFEKDYVIPHQQSRIQVQEYSYEITV 79
                5555666667788888888888*************************9999999999999987 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.25
                 .S-EEEEEEEEEEEEETTEEEEEEEEE CS
     DUF4468  61 sldrtkirYtliievkdgkyrvtltni 87 
                 s ++ +i+Y+ +i + +   ++t+++i
  AHX11012.1 146 SFQEISIQYKNVIICDETSEDATVCDI 172
                 566788999999999999888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1683.10
//
Query:       AHX11013.1  [L=99]
Description: helix-turn-helix domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-14   54.0   0.0    1.4e-14   53.8   0.0    1.1  1  HTH_37    Helix-turn-helix domain
     0.0026   17.7   0.1     0.0039   17.2   0.1    1.3  1  HTH_19    Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.8   0.0   1.6e-18   1.4e-14      11      79 ..      28      97 ..      19      98 .. 0.91

  Alignments for each domain:
  == domain 1  score: 53.8 bits;  conditional E-value: 1.6e-18
                HHHH.HHHHHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTTEEEEEEE CS
      HTH_37 11 eelk.aKaqlalaiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalGqkveivv 79
                 +l+  ++ l+++i ++i+ +++sq+ aa ll+i+qPk+s++++ k + fsl++Ll++   lG kv +++
  AHX11013.1 28 SQLSdVRSILVKRISQIIAYNNWSQKYAASLLKIDQPKISQIKNFKTEGFSLERLLKFFILLGWKVDVRL 97
                5555589***********************************************************9875 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.3e-07    0.0039       3      48 ..      40      85 ..      39      98 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.3e-07
      HTH_19  3 rLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllki 48
                r+ +++  ++++q+  a+ l+i++ kis+i n k++ +s e+llk+
  AHX11013.1 40 RISQIIAYNNWSQKYAASLLKIDQPKISQIKNFKTEGFSLERLLKF 85
                888888899**********************99******9999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       595  (0.0331865); expected 358.6 (0.02)
Passed bias filter:                      448  (0.0249875); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 774.42
//
Query:       AHX11014.1  [L=128]
Description: DNA-directed RNA polymerase, omega subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.3e-06   27.4   0.0      4e-06   26.6   0.0    1.3  1  RNA_pol_Rpb6  RNA polymerase Rpb6


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb6  RNA polymerase Rpb6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.0   2.2e-10     4e-06       8      46 ..      15      58 ..      14      60 .. 0.80

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.2e-10
                  -HHHHHHHHHHHHHHH..........HTSS-SSSSTTCHHHHTT- CS
  RNA_pol_Rpb6  8 trYelvriaakRArQieeg.e.....sletqkpvviAlrEiaegk 46
                  +++elv++ ++RA  +++g       + e++k   iAl+E++ + 
    AHX11014.1 15 SKFELVVLTSQRAYDLQSGaLaeiehD-ESDKSPIIALKELYSKT 58
                  8***************77642344343.689**********9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (128 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1073.91
//
Query:       AHX11015.1  [L=304]
Description: riboflavin biosynthesis protein RibF [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-31  108.3   0.0    5.1e-31  107.7   0.0    1.3  1  FAD_syn          FAD synthetase
    6.4e-29  100.5   0.0    1.1e-28   99.8   0.0    1.3  1  Flavokinase      Riboflavin kinase
  ------ inclusion threshold ------
       0.03   14.5   0.4      0.083   13.1   0.4    1.9  1  CTP_transf_like  Cytidylyltransferase-like
       0.18   11.9   0.1        1.1    9.3   0.0    2.2  3  Fis1_TPR_C       Fis1 C-terminal tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> FAD_syn  FAD synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.7   0.0   1.1e-34   5.1e-31       4     157 ..      10     160 ..       7     161 .. 0.95

  Alignments for each domain:
  == domain 1  score: 107.7 bits;  conditional E-value: 1.1e-34
     FAD_syn   4 edegavvtlGnFDGvHlGHqallkkaveaakekglpsvvvtFephPrevlakekaparLttleeklelleelgvdavlvvdFtkefaelsaeeFiekll 102
                  + ++vvt+GnFDGvHlGH al++ + ++a+ ++l  v++tF+phP+ +l+  k+++ + +   k+ell+ +  d +++++F+++f++ls+++F+  ll
  AHX11015.1  10 IQYPSVVTFGNFDGVHLGHAALFSVVCDLARVHSLHRVIITFDPHPSCYLE-GKDDFLILDKMSKIELLAPY-TDSLYFIRFDQSFSKLSPRDFLA-LL 105
                 67889**********************************************.99****************98.6*********************6.58 PP

     FAD_syn 103 veklkvkavvvGfdfrfGkkregdvellkelgaklgfevevvpkveleeekisst 157
                  + + +k++v  ++ rfG++++g+++++++++++++++  v++  + ++ k sst
  AHX11015.1 106 SSYIDIKYLVNAENCRFGNGGSGSIQDVRDYQETFSYKSVVLEVESNGGAKYSST 160
                 88***********************************999999999999999998 PP

>> Flavokinase  Riboflavin kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.8   0.0   2.4e-32   1.1e-28       1     107 [.     178     297 ..     178     300 .. 0.94

  Alignments for each domain:
  == domain 1  score: 99.8 bits;  conditional E-value: 2.4e-32
                  HTS-EEEEEEEES-SSCHTTTT--EEEEE-.S-B-.GTSEEEEEEEE.......EEEEEEEETTTSSE....EEEEETT--S--TTSEEEEEEEEEEE CS
  Flavokinase   1 LgrpyslsgkVvkGkkrGrelgfpTaNlel.ekll.pkkGVYavrvk.......gvaniGvrptfknk....vEvhildfsedlygkelrvellkflR 85 
                  Lgr +s++g + kG++++ ++gfpT+N+++ ++++ pk GVY ++v        g++niG rpt  ++    +E+hi+df +++yg+  rv l +flR
   AHX11015.1 178 LGRFHSIRGVIEKGRGLAATIGFPTINISIpDEIIkPKLGVYLAEVVlgpevhqGIVNIGKRPTTCSSgkviLEMHIFDFAAEVYGEIARVYLKSFLR 275
                  7999*************************99888889***************************866456778************************* PP

                  E----SSHHHHHHHHHHHHHHH CS
  Flavokinase  86 pekkFdsleaLkaqikkDveka 107
                  +e++Fdsl +Lk+qi++D+ +a
   AHX11015.1 276 EERQFDSLAQLKEQISRDIGAA 297
                  ******************9877 PP

>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.4   1.9e-05     0.083       2      36 ..      17      53 ..      16     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.9e-05
                     EEE--TT--HHHHHHHHHHHHHSSES..EEEEEESST CS
  CTP_transf_like  2 agGtFDpiHlGHlrlleqakklleed..livgvpsde 36
                     + G+FD +HlGH++l+ ++ +l        v+++ d+
       AHX11015.1 17 TFGNFDGVHLGHAALFSVVCDLARVHslHRVIITFDP 53
                     68***************99998776665334455555 PP

>> Fis1_TPR_C  Fis1 C-terminal tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.58   2.6e+03      15      48 ..     134     166 ..     133     172 .. 0.73
   2 ?   -2.3   0.0       1.1   4.7e+03      12      25 ..     166     179 ..     164     181 .. 0.83
   3 ?    9.3   0.0   0.00025       1.1      20      48 ..     266     294 ..     264     295 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.58
                 T-HHHHHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
  Fis1_TPR_C  15 geYseArryvdalLeiEPenrQaqsLkeliedki 48 
                 ++Y+e   y   +Le+E +n  a+  ++li ++i
  AHX11015.1 134 RDYQETFSYKSVVLEVE-SNGGAKYSSTLIRNAI 166
                 68999999999999999.6766665555666555 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.1
                 HHHT-HHHHHHHHH CS
  Fis1_TPR_C  12 yklgeYseArryvd 25 
                 +k g+ + Ar+++ 
  AHX11015.1 166 IKNGDLTGARQFLG 179
                 59999*****9985 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.00025
                 HHHHHHHHHHHTTS-HHHHHHHHHHHHHH CS
  Fis1_TPR_C  20 ArryvdalLeiEPenrQaqsLkeliedki 48 
                 Ar y++ +L+ E ++   ++Lke i + i
  AHX11015.1 266 ARVYLKSFLREERQFDSLAQLKEQISRDI 294
                 899********************998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2605.11
//
Query:       AHX11016.1  [L=364]
Description: hypothetical protein NHE_0041 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0033   16.9   1.3     0.0055   16.2   1.3    1.2  1  HMMR_N          Hyaluronan mediated motility receptor N-termi
     0.0065   16.6   1.9       0.56   10.3   0.8    2.2  2  DUF848          Gammaherpesvirus protein of unknown function 
  ------ inclusion threshold ------
      0.018   14.9   0.2      0.035   14.0   0.2    1.4  1  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.022   15.0   1.7        1.1    9.5   0.2    2.7  2  DUF3216         Protein of unknown function (DUF3216)
      0.036   14.2   0.0      0.078   13.1   0.0    1.6  1  DUF3898         Domain of unknown function (DUF3898)
      0.053   12.3   0.8      0.074   11.8   0.8    1.2  1  BshC            Bacillithiol biosynthesis BshC
      0.064   13.0   0.7      0.099   12.3   0.7    1.2  1  mRNA_triPase    mRNA capping enzyme, beta chain
       0.11   12.7   0.8        0.3   11.3   0.3    2.0  2  Fib_alpha       Fibrinogen alpha/beta chain family
       0.12   11.8   3.7       0.42   10.1   0.8    2.6  3  DUF2884         Protein of unknown function (DUF2884)
       0.17   11.7   3.2        1.9    8.2   1.0    2.9  2  Lectin_N        Hepatic lectin, N-terminal domain
       0.19   11.8   0.1        0.6   10.2   0.1    1.7  1  Spore_III_AB    Stage III sporulation protein AB (spore_III_A
       0.29   11.2   5.2        1.1    9.3   0.6    2.7  3  ApoLp-III       Apolipophorin-III precursor (apoLp-III)
       0.35   10.9   2.5        4.6    7.2   0.8    2.7  2  DUF4446         Protein of unknown function (DUF4446)


Domain annotation for each model (and alignments):
>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   1.3     4e-06    0.0055     178     275 ..     157     256 ..     153     264 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4e-06
      HMMR_N 178 kevsvkQedmeaklqvtqknLeeskakvaqLkeklvslekekieekseteklleyieelsn.vseqlekykldiaqleellkekndei.esLkssLeek 274
                 k v+++ e++ a   vtq  +++    v++Lke+++    +k++ k+ +ek  +  ++l   ++e+ e  + ++++++e +k + +e  e++k +L  k
  AHX11016.1 157 KDVAARKEELKAVAGVTQSTFDALDRVVRELKERNKGDDSLKAKIKYSNEKVKAAFSKLGDkIAESNENLRTKVKYSNEKVKGALNEFgEKIKDTLTTK 255
                 789999999**************************************************761566679*************988666537788888877 PP

      HMMR_N 275 e 275
                 +
  AHX11016.1 256 K 256
                 6 PP

>> DUF848  Gammaherpesvirus protein of unknown function (DUF848)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.0     0.017        23      78     135 ..      30      83 ..      16      91 .. 0.88
   2 !   10.3   0.8    0.0004      0.56      61     133 ..     179     253 ..     157     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.017
      DUF848  78 lLkklnrkkvarveeLtdkvlelkeevsleldsleeaqeeyqegessetsipDtltqW 135
                  L kl++  + +++  +dkv++   + s+ ++ l++   e+     s+ +++D++ +W
  AHX11016.1  30 ALGKLDPFTLSDLQVYVDKVMNFSSNDSVVMQLLNAVSAEKG----SQEKLQDLIARW 83 
                 5778999999999999**********9999999999887776....5558******** PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.0004
      DUF848  61 lveavdteieakkkelslLkk...lnrkkv.arveeLtdkvlelkeevsleldsleeaqeeyqegessetsipDtlt 133
                  +  v +e+++++k  ++Lk+      +kv a+  +L dk++e +e+++ ++   +e+ +   ++ +++  i+Dtlt
  AHX11016.1 179 ALDRVVRELKERNKGDDSLKAkikYSNEKVkAAFSKLGDKIAESNENLRTKVKYSNEKVKGALNEFGEK--IKDTLT 253
                 56677788888999888887553344556615679*****************99999888888555554..999987 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.2   2.5e-05     0.035      62     163 ..     157     252 ..     149     263 .. 0.43

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.5e-05
                     HCCCHHHHHHHHHCCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHH CS
  Apolipoprotein  62 eqlgqnleelrqrlapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrv 156
                     + ++++ eel++  a  t+   + l++ ++el+e+ +   + l+ +++ + e++ka ++    +l +k+ae+ e+l+ +++ + e+v+ +l++  
      AHX11016.1 157 KDVAARKEELKAV-AGVTQSTFDALDRVVRELKERNKG-DDSLKAKIKYSNEKVKAAFS----KLGDKIAESNENLRTKVKYSNEKVKGALNEFG 245
                     4444444444443.444444445555555555555332.44455555544444444444....23333333333333333333333333333333 PP

                     HHHHHTS CS
  Apolipoprotein 157 eelrekl 163
                     e ++++l
      AHX11016.1 246 EKIKDTL 252
                     3333333 PP

>> DUF3216  Protein of unknown function (DUF3216)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.2    0.0008       1.1      55      82 ..     200     227 ..     195     229 .. 0.92
   2 ?    4.4   0.2     0.031        43      55      73 ..     229     247 ..     227     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0008
                 TTT---HHHHHHHHHHHHHHHHHH---- CS
     DUF3216  55 kekydeekvkellekvkakreeleellr 82 
                 k ky++ekvk  + k+  k +e +e lr
  AHX11016.1 200 KIKYSNEKVKAAFSKLGDKIAESNENLR 227
                 89***********************999 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.031
                 TTT---HHHHHHHHHHHHH CS
     DUF3216  55 kekydeekvkellekvkak 73 
                 k ky++ekvk  l++   k
  AHX11016.1 229 KVKYSNEKVKGALNEFGEK 247
                 89********999986544 PP

>> DUF3898  Domain of unknown function (DUF3898)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.7e-05     0.078       5      48 ..     202     249 ..     196     260 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.7e-05
     DUF3898   5 kleteqvieaaa....qiveqkPeielklkldeievkalladfGeklh 48 
                 k+++e+v  a +    +i e + ++ +k+k  + +vk+ l +fGek+ 
  AHX11016.1 202 KYSNEKVKAAFSklgdKIAESNENLRTKVKYSNEKVKGALNEFGEKIK 249
                 566667766654122268999999*********************995 PP

>> BshC  Bacillithiol biosynthesis BshC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.8   5.4e-05     0.074     404     482 ..     176     255 ..     131     260 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.4e-05
                 HHH-SHHHHHHHHH.HTS-HHHHHHHHHHHHHHHHHHHHHHHHHHTT-GGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        BshC 404 lfekleelkkklve.easeleldelfeeakeeleeafealkelaakidktleklveanekkilkqlekLekkllkaekrk 482
                  f  l+ + ++l e ++ + +l+++++  +e++++af++l +++a+ +++l+  v+ +++k++ +l+++ +k+++    k
  AHX11016.1 176 TFDALDRVVRELKErNKGDDSLKAKIKYSNEKVKAAFSKLGDKIAESNENLRTKVKYSNEKVKGALNEFGEKIKDTLTTK 255
                 4444444444444304446678899*********************************************9999876665 PP

>> mRNA_triPase  mRNA capping enzyme, beta chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.7   7.2e-05     0.099      60     125 ..     165     236 ..     154     251 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.2e-05
                   TEEEEE-B-HHHHHHHHHHHHHHHH..HTTCCCTTTEEEEEEEEEEEEEE-S......-SSS--EEEEEEET CS
  mRNA_triPase  60 dskfesgvdedqfkelnnfLnelsrrneeenskrekvslkeskevDkfYelk......kkeekskirvskds 125
                   + k + gv+++ f++l ++++el++rn+ ++s + k++++++k +  f +l       +++ ++k++ s+++
    AHX11016.1 165 ELKAVAGVTQSTFDALDRVVRELKERNKGDDSLKAKIKYSNEKVKAAFSKLGdkiaesNENLRTKVKYSNEK 236
                   6677889***********************************999999999888664333333444444443 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.9   2.6e+03      37      73 ..      39      75 ..      27      83 .. 0.69
   2 ?   11.3   0.3   0.00022       0.3      31     106 ..     153     228 ..     149     254 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.9
                HCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH CS
   Fib_alpha 37 lekleneleeisnstkeaeelvkeikdslrekqkskk 73
                l++l+  ++++ n +++ + +++ ++ + +ek +++k
  AHX11016.1 39 LSDLQVYVDKVMNFSSNDSVVMQLLNAVSAEKGSQEK 75
                5667777777777777777777766666666665555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00022
                 CCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
   Fib_alpha  31 kdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdndnvikksskeleeeilrlketidaqesnirv 106
                 ++v kd++  ++el+ ++  t+++++   ++   l+e++k ++  +  ik s+++++   ++l ++i +  +n+r 
  AHX11016.1 153 HEVPKDVAARKEELKAVAGVTQSTFDALDRVVRELKERNKGDDSLKAKIKYSNEKVKAAFSKLGDKIAESNENLRT 228
                 678899999999******************************999************9999999999999988874 PP

>> DUF2884  Protein of unknown function (DUF2884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1       0.4   5.6e+02     110     173 ..      15      77 ..       2      84 .. 0.67
   2 ?   10.1   0.8    0.0003      0.42      77     128 ..     177     227 ..     167     255 .. 0.80
   3 ?    1.4   0.0      0.14   1.9e+02      93     123 ..     232     262 ..     222     265 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.4
     DUF2884 110 kekfykdgdklvlgaqslesldeafdkefeqeieelvee.siGsilsalgsemlesegdnleafe 173
                  ek++ + d + + +++l +ld  + ++++ ++ ++++  s  s++++l +++ +++g++ e+++
  AHX11016.1  15 AEKLKLNLD-VGVFQDALGKLDPFTLSDLQVYVDKVMNFsSNDSVVMQLLNAVSAEKGSQ-EKLQ 77 
                 444444445.44556677779999999999999998886367789999999999999996.3333 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
     DUF2884  77 sdaldevltellgedsevaeklktkldelkarvkekfykdgdklvlgaqsle 128
                  dald+v++el  e ++  ++lk+k++  +++vk+ f+k gdk+  ++++l 
  AHX11016.1 177 FDALDRVVREL-KERNKGDDSLKAKIKYSNEKVKAAFSKLGDKIAESNENLR 227
                 589********.7788888***********************9875555544 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.14
     DUF2884  93 evaeklktkldelkarvkekfykdgdklvlg 123
                  + ek+k +l+e+ +++k+++ +++++++l+
  AHX11016.1 232 YSNEKVKGALNEFGEKIKDTLTTKKGSFTLP 262
                 5678999999999999999999999999987 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.24   3.3e+02      56      90 ..      41      77 ..      38      86 .. 0.71
   2 ?    8.2   1.0    0.0014       1.9      52     123 ..     154     228 ..      96     230 .. 0.76

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.24
    Lectin_N 56 eLetLketfsnfssstlaeiqalss..qggslsekvt 90
                +L+   +++ nfss+  + +q l++  + +  +ek++
  AHX11016.1 41 DLQVYVDKVMNFSSNDSVVMQLLNAvsAEKGSQEKLQ 77
                7888889999****99999998886223444455554 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0014
    Lectin_N  52 qLqreLetLketfsnfssstlaeiqalssqggslsekvt...sleaklekkqqdlkadhselllhvkqlvkdLrt 123
                 ++ +++ + ke+++ ++  t++ + al+   ++l+e+ +   sl+ak++  ++++ka  s+l +++ +  ++Lrt
  AHX11016.1 154 EVPKDVAARKEELKAVAGVTQSTFDALDRVVRELKERNKgddSLKAKIKYSNEKVKAAFSKLGDKIAESNENLRT 228
                 566889999999999999999999999997777665543333************************999999986 PP

>> Spore_III_AB  Stage III sporulation protein AB (spore_III_AB)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.1   0.00043       0.6      25      73 ..     182     230 ..     176     261 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00043
                   HHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHHHHHCS-TTHHHHHHHH CS
  Spore_III_AB  25 rrlkeleelkralellegeirygatpLpealeklaeksesplseffeev 73 
                   r ++el+e  +    l+++i+y+++  + a++kl+ k+ ++ +++  +v
    AHX11016.1 182 RVVRELKERNKGDDSLKAKIKYSNEKVKAAFSKLGDKIAESNENLRTKV 230
                   667888888888899********************77777444332222 PP

>> ApoLp-III  Apolipophorin-III precursor (apoLp-III)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.1      0.22     3e+02       4      27 ..      39      62 ..      37      81 .. 0.85
   2 ?    8.9   0.6    0.0011       1.5      96     144 ..     183     231 ..     152     233 .. 0.80
   3 ?    9.3   0.6    0.0008       1.1      24      71 ..     205     252 ..     202     256 .. 0.90

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.22
   ApoLp-III  4 ieelqksvkkqlnlpsqeevveti 27
                +++lq  v k++n+ s++ vv  +
  AHX11016.1 39 LSDLQVYVDKVMNFSSNDSVVMQL 62
                6899999***********999776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0011
   ApoLp-III  96 vqslvkesqklaeslkensqeakeklakaikqayddaveaaqklakqLk 144
                 v   +ke +k + slk++++  +ek+++a  ++ d+++e+ ++l +++k
  AHX11016.1 183 VVRELKERNKGDDSLKAKIKYSNEKVKAAFSKLGDKIAESNENLRTKVK 231
                 4455788999999999999999999999999999999999999999987 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0008
   ApoLp-III  24 vetiKensenlvdqlkqvikslqeelkkksdeleealkevkkkieeta 71 
                 +e +K   ++l d++ +  ++l+ ++k  +++++ al+e+ +ki+ t 
  AHX11016.1 205 NEKVKAAFSKLGDKIAESNENLRTKVKYSNEKVKGALNEFGEKIKDTL 252
                 5788999999999*******************************9986 PP

>> DUF4446  Protein of unknown function (DUF4446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.8    0.0033       4.6       5      76 ..     117     188 ..     114     218 .. 0.57
   2 ?    4.0   0.6     0.034        47      45      83 ..     178     216 ..     172     253 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0033
     DUF4446   5 vlavlvvillillivllvklkklkkkykklmkgkdgksleellkekleeveelkeeseelekeieeleeklk 76 
                 + ++ +v+l+i++ +++++++kl+k  +     k g+++ + ++ + ee++++   ++++ + ++++ ++lk
  AHX11016.1 117 ISGISIVLLMIAVTFTIYQTHKLNKLENVWPGAKGGHEVPKDVAARKEELKAVAGVTQSTFDALDRVVRELK 188
                 445555566666666666666666555555555566666666666666666665555554444444443333 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.034
     DUF4446  45 ellkekleeveelkeeseelekeieeleeklkkslqkvg 83 
                 ++l + ++e++e ++  ++l+++i+  +ek+k++++k+g
  AHX11016.1 178 DALDRVVRELKERNKGDDSLKAKIKYSNEKVKAAFSKLG 216
                 556666777777777777777777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (364 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1112  (0.0620224); expected 358.6 (0.02)
Passed bias filter:                      839  (0.0467957); expected 358.6 (0.02)
Passed Vit filter:                       111  (0.00619109); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.37
# Mc/sec: 2941.30
//
Query:       AHX11017.1  [L=336]
Description: ABC transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.6e-31  108.2   0.0      7e-31  107.6   0.0    1.3  1  ABC_tran    ABC transporter
  ------ inclusion threshold ------
      0.016   14.5   0.1      0.027   13.7   0.1    1.2  1  Zeta_toxin  Zeta toxin
      0.038   13.7   0.0       0.06   13.1   0.0    1.3  1  PRK         Phosphoribulokinase / Uridine kinase family
       0.39    9.5   1.7         17    4.1   0.9    2.0  2  ABC_ATPase  Predicted ATPase of the ABC class


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   1.6e-34     7e-31       2     136 ..     108     255 ..     107     256 .. 0.89

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 1.6e-34
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTC... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxx... RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............esdee... 84 
                 k vs+++ +g++v++vG++ aGKSt++kl+ g lkp++G  +ldg+d+ + e++++ +++g+lpq+ +lf+ + ++en              + ++   
  AHX11017.1 108 KGVSFTVPAGKIVGVVGSSAAGKSTIAKLIVGVLKPAAGVARLDGADTYTWERQHFGRHVGYLPQDIELFNAT-IKENisrfdpnmdpaevVKAAKiag 205
                 78*********************************************************************99.********99888776633333333 PP

                 HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  85 iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +++++ ++ + +  dtv++ ++s LSgGq+qr+ +ara+  + kll+lDEp 
  AHX11017.1 206 VHEMILRFPDGY--DTVIGAGGSVLSGGQRQRIGIARAFYGNVKLLVLDEPN 255
                 556665555555..*************************************6 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.1   6.1e-06     0.027      17      52 ..     118     153 ..     111     162 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6.1e-06
  Zeta_toxin  17 klillgGqpGAGKselaellkdelerqgnvvrldpD 52 
                 k++ ++G+++AGKs++a+l+   l+++ +v rld+ 
  AHX11017.1 118 KIVGVVGSSAAGKSTIAKLIVGVLKPAAGVARLDGA 153
                 567799***************************974 PP

>> PRK  Phosphoribulokinase / Uridine kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.3e-05      0.06       1      25 [.     119     143 ..     119     172 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.3e-05
         PRK   1 vIgvagsSGaGkttvarklekifgr 25 
                 ++gv gsS+aGk+t+a+ ++ +++ 
  AHX11017.1 119 IVGVVGSSAAGKSTIAKLIVGVLKP 143
                 79*****************999983 PP

>> ABC_ATPase  Predicted ATPase of the ABC class
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.9    0.0038        17     236     263 ..     106     136 ..      94     146 .. 0.82
   2 ?    4.0   0.0    0.0038        17     303     421 ..     207     327 ..     195     333 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0038
                 EEEEE..EE-SS.EEEEEE-TTSSHHHHHHH CS
  ABC_ATPase 236 kvsGm..gipkG.vtlIvGggfhGKsTLLeA 263
                 +++G+   +p G ++ +vG+ + GKsT+ + 
  AHX11017.1 106 TIKGVsfTVPAGkIVGVVGSSAAGKSTIAKL 136
                 5666522589999**************9774 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.0038
                 TTTB---CCC--ST.TEEESS--HHHHHHHHHHHHHHTT-SEEEEEGGGS-HHHH---HHHHHHS-GGG--B--HHHCHHHHHHHH--EEEEEESS-GC CS
  ABC_ATPase 303 spFinnLPegkdtt.kfstedASGStsqAanimealeagakllLiDEDtsAtNlmirDermqelvskekepitplvdrvrelykklgvstilvvggsgd 400
                   +i + P g dt   +  +  SG   q   i++a   + kll++DE ++    +   +++ +l   ++  it++v   +    +  + +++v  g+ +
  AHX11017.1 207 HEMILRFPDGYDTViGAGGSVLSGGQRQRIGIARAFYGNVKLLVLDEPNANLDSVGEAHLIMALRYAKEMKITTFVMTHKFSLLSEVDWLMMVKDGMIA 305
                 56677777777777556666679999999*********************999999999999999999999****987765544444556677788888 PP

                 CTTT-SEEE.EEETTEEEE-HH CS
  ABC_ATPase 401 yldvAdtvi.lmeeykpkdvte 421
                 +l   d +i ++ e++ ++ t+
  AHX11017.1 306 LLGEKDDIIaQLSEHHKQEKTD 327
                 8877666663799999888884 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       647  (0.0360868); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 2849.96
//
Query:       AHX11018.1  [L=267]
Description: madB domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (267 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2005.21
//
Query:       AHX11019.1  [L=42]
Description: hypothetical protein NHE_0044 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       441  (0.024597); expected 358.6 (0.02)
Passed bias filter:                      286  (0.0159518); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 334.44
//
Query:       AHX11020.1  [L=266]
Description: enoyl-[acyl-carrier-protein] reductase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-79  267.3   0.0    1.2e-79  267.2   0.0    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    4.9e-17   62.0   0.0    6.5e-17   61.6   0.0    1.1  1  adh_short        short chain dehydrogenase
  ------ inclusion threshold ------
      0.018   14.4   0.1        2.5    7.4   0.0    2.1  2  Enoyl_reductase  Trans-2-enoyl-CoA reductase catalytic region
      0.064   13.5   0.0      0.094   13.0   0.0    1.4  1  DUF5625          Domain of unknown function (DUF5625)


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.2   0.0   2.7e-83   1.2e-79       1     234 []      11     250 ..      11     250 .. 0.98

  Alignments for each domain:
  == domain 1  score: 267.2 bits;  conditional E-value: 2.7e-83
                   TTT..TSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.EEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EG..CSS-GGGH-H CS
  adh_short_C2   1 Gaa..sgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.vlecDVtdeeqvealveevvekfgklDilvnnagiapk..lkgpfletsr 92 
                   G+a  ++I++ i k ++e+Ga+++lt+  ++ kkr+ ++aee+g + ++ cDV++ee ++ l+  ++ek+gklD++v+++++++k  l+g++++ts 
    AHX11020.1  11 GIAndRSIAYSIGKICNENGANLILTYPVDQFKKRLVPIAEEFGGAeLVCCDVSKEEGIAGLFHIIAEKYGKLDFIVHSVAFSDKeeLQGEYINTSL 107
                   88999**************************************96559************************************************* PP

                   HHHHHHHHHHTHHHHHHHHHHHHHCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHH CS
  adh_short_C2  93 eefdraldvnlyslfllakaalplmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdel 188
                   ++f + +++++ysl++++++alplmke+ gs+++ls++gae+v+p+yn++g++Kaalea+++yl v+lg++ iR+N++s+gpikTlaas+i +f+ +
    AHX11020.1 108 ANFLNSMHISCYSLTAICRYALPLMKENgGSVLTLSYYGAEKVIPHYNVMGVCKAALEASVKYLSVDLGKYSIRINTISAGPIKTLAASAIGKFSYI 204
                   ***********************999888******************************************************************** PP

                   HHHHHHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTGG CS
  adh_short_C2 189 leelearaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGlt 234
                   l+++++++p++r++t e+va aal+++sd++s++tG+tl+vD+G++
    AHX11020.1 205 LKWSKHNSPIKRNTTKEDVAGAALYFLSDLSSGTTGSTLHVDCGYH 250
                   *********************************************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   1.4e-20   6.5e-17       9     188 ..      15     196 ..       8     201 .. 0.88

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.4e-20
                 TSHHHHHHHHHHHHTT-EEEE...EESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S....S--SSGGGCSHHH CS
   adh_short   9 ssGIGraiakelakeGakvvv...vdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGi....tgsgpfselseee 100
                 ++ I + i k + ++Ga++++   vd+ +++l  +a+e++     a  + +Dv+++e +  l+  +++k+gkld +v+ ++     + +g+  ++s ++
  AHX11020.1  15 DRSIAYSIGKICNENGANLILtypVDQFKKRLVPIAEEFGG----AELVCCDVSKEEGIAGLFHIIAEKYGKLDFIVHSVAFsdkeELQGEYINTSLAN 109
                 56788889999999999999854455666666666666665....99***********************************88776677888999999 PP

                 HHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHH CS
   adh_short 101 wervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmak 188
                 + +++++   ++  ++r +lp m+ +++G++ + s   +++  +++ + +  Kaa+++ ++ l+ +l +++ir+n++  G+++T  a 
  AHX11020.1 110 FLNSMHISCYSLTAICRYALPLMK-ENGGSVLTLSYYGAEKVIPHYNVMGVCKAALEASVKYLSVDLGKYSIRINTISAGPIKTLAAS 196
                 **********************77.999***99999999********************************************97665 PP

>> Enoyl_reductase  Trans-2-enoyl-CoA reductase catalytic region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.0   0.00057       2.5      40      76 ..      72     107 ..      50     122 .. 0.77
   2 ?    5.0   0.2     0.003        14     139     204 ..     139     202 ..     131     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00057
                      HHHHHHHCTT-EEEEEE----SEEE-TTTS-EEE--- CS
  Enoyl_reductase  40 vielikeelgkvDlvvYslAsprRtdpktgevyrsvl 76 
                        + i e++gk+D++v s+A + +++ + ge ++ +l
       AHX11020.1  72 LFHIIAEKYGKLDFIVHSVAFSDKEELQ-GEYINTSL 107
                      567899**************99988877.55555444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.003
                      EEEEEE---GGGHHHHTSSHHHHHHHHHHHHHHHHHHHCCCHSEEEEEEEE-----CTCCCSTTHH CS
  Enoyl_reductase 139 tvaysYiGpeltapiYregtiGkAKedlektakelneklkelggkAyvsvnkalvtqasaaiPvvp 204
                       +++sY G e   p Y+   +G  K+ le+++k l+ +l +++++ ++  +  + t a++ai  ++
       AHX11020.1 139 VLTLSYYGAEKVIPHYN--VMGVCKAALEASVKYLSVDLGKYSIRINTISAGPIKTLAASAIGKFS 202
                      5789******9999996..7999*********************9999999999999999998776 PP

>> DUF5625  Domain of unknown function (DUF5625)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.1e-05     0.094      76     116 ..     148     188 ..      76     196 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.1e-05
                 EEEEEE-S--SSTTE...EEEEEEEE-SEEEEEEEEE-S-- CS
     DUF5625  76 dkkinakglgsgaateyereIktlsLkkGkYsirietledv 116
                 +k i + +  +  + + e  +k ls++ GkYsiri+t+ + 
  AHX11020.1 148 EKVIPHYNVMGVCKAALEASVKYLSVDLGKYSIRINTISAG 188
                 6777777888888889999******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1987.94
//
Query:       AHX11021.1  [L=66]
Description: thiamine biosynthesis protein ThiS [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-10   41.4   0.0    1.9e-10   41.2   0.0    1.1  1  ThiS            ThiS family
    0.00098   19.1   0.0     0.0049   16.9   0.0    1.9  2  ThiS-like       ThiS-like ubiquitin
  ------ inclusion threshold ------
       0.12   12.3   0.1         11    5.9   0.0    2.1  2  B3              B3 DNA binding domain
       0.13   12.2   0.0       0.24   11.4   0.0    1.4  1  MazE_antitoxin  Antidote-toxin recognition MazE, bacterial an


Domain annotation for each model (and alignments):
>> ThiS  ThiS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.0   4.3e-14   1.9e-10      13      77 .]       7      66 .]       2      66 .] 0.90

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 4.3e-14
                CEEEEESSTSBHHHHHHHHHHHTCHHGTTTTEEEEETTEEEGC.CTTTSB--TTCEEEEEESTTC- CS
        ThiS 13 eeelelaegstvaelleaLgerypelalerrvavavNgeivpr.lwldtelkdgDevailppVaGG 77
                ++ le+a+  t+ +l+  L+ +        ++a++vN  i+p+  +++++lk+gD ++i+ +V+GG
  AHX11021.1  7 DKNLEVADSCTLFDLVIRLDLDT------SQLAIEVNRAIIPKsMYKEHALKAGDSIEIVEFVGGG 66
                4566677799***********99......**************88********************9 PP

>> ThiS-like  ThiS-like ubiquitin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.1e-06    0.0049       1      22 [.       1      22 [.       1      34 [. 0.90
   2 ?    0.2   0.0      0.17   7.7e+02      41      53 ..      47      59 ..      44      61 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
   ThiS-like  1 MkIklNekeveveegttlealk 22
                M Ik+N k++ev + +tl++l 
  AHX11021.1  1 MIIKVNDKNLEVADSCTLFDLV 22
                99*****************986 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.17
   ThiS-like 41 eDteLkegDevfl 53
                ++ +Lk gD++ +
  AHX11021.1 47 KEHALKAGDSIEI 59
                5678999999966 PP

>> B3  B3 DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.004        18      70      83 ..       5      18 ..       4      39 .. 0.90
   2 ?    5.9   0.0    0.0026        11      16      36 ..      39      58 ..      26      62 .. 0.66

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.004
                HHHTT--TTSEEEE CS
          B3 70 vkangLkegDfvvF 83
                v++++L++ D++++
  AHX11021.1  5 VNDKNLEVADSCTL 18
                89**********97 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0026
                EEE-HHHHHHHTSTCEECECE CS
          B3 16 lviPkkfaeensglkkeeske 36
                 +iPk+  +e+ +lk + s+e
  AHX11021.1 39 AIIPKSMYKEH-ALKAGDSIE 58
                56666666666.555555544 PP

>> MazE_antitoxin  Antidote-toxin recognition MazE, bacterial antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   5.4e-05      0.24      11      30 ..      41      60 ..      38      64 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.4e-05
                    E-CCCHHHCCEECTCEEEEE CS
  MazE_antitoxin 11 iPkevrfelgireGdevele 30
                    iPk + +e+ +++Gd++e++
      AHX11021.1 41 IPKSMYKEHALKAGDSIEIV 60
                    9*****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (66 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      250  (0.0139439); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 486.43
//
Query:       AHX11022.1  [L=170]
Description: hexapeptide transferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.4e-15   54.2   4.8    2.7e-06   26.9   0.4    4.0  3  Hexapep     Bacterial transferase hexapeptide (six repeats)
    8.2e-05   22.3   5.3      0.014   15.1   0.0    3.7  3  Hexapep_2   Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
       0.13   11.2   0.3       0.98    8.3   0.0    1.9  2  Fucokinase  L-fucokinase


Domain annotation for each model (and alignments):
>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.4   4.5e-10   2.7e-06       1      36 []      10      45 ..      10      45 .. 0.96
   2 !    7.5   1.2    0.0006       3.6       1      34 [.      55      88 ..      49      94 .. 0.66
   3 !   17.8   0.0   3.3e-07     0.002       2      35 ..      91     124 ..      90     125 .. 0.92

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.5e-10
                TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
     Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36
                s++IG+ ++I  +a i g+V+IG ++ +++g++i+g
  AHX11022.1 10 SPIIGELTFIAQNAFIIGDVTIGADSSVWHGCTIRG 45
                579*******************************97 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0006
                TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
     Hexapep  1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34
                st I ++++I+ +++  g ++IG  v++g+ + +
  AHX11022.1 55 STNIQDGTTIHVGSHKDGSTIIGQCVTVGHSCLL 88
                5677788888886666666666666666665544 PP

  == domain 3  score: 17.8 bits;  conditional E-value: 3.3e-07
                 EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                 +++ +n+++g+++ i++++ I +n+ +gag+ ++
  AHX11022.1  91 CTLMDNTFVGMGSLIMDGALIEENAMLGAGSLLT 124
                 67789*************************9876 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   0.3    0.0023        14       3      29 ..      12      40 ..      12      44 .. 0.77
   2 ?    1.2   0.0     0.053   3.2e+02       2      12 ..      80      90 ..      79      91 .. 0.90
   3 !   15.1   0.0   2.3e-06     0.014       6      33 ..      95     124 ..      95     125 .. 0.95

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0023
                EE-TT-EE-TT-EE.S.EEE-TT-EE-TT CS
   Hexapep_2  3 iIGdnCliGanagi.G.vslGdncvvgaG 29
                iIG+ ++i  na i G v++G ++ v  G
  AHX11022.1 12 IIGELTFIAQNAFIiGdVTIGADSSVWHG 40
                79999999999996666999999877555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.053
                EEE-TT-EE-T CS
   Hexapep_2  2 viIGdnCliGa 12
                v++G  Cl++a
  AHX11022.1 80 VTVGHSCLLHA 90
                789999***98 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.3e-06
                 TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
   Hexapep_2   6 dnCliGanagi..GvslGdncvvgaGvvit 33 
                 dn+++G  + i  G  +++n+ +gaG+ +t
  AHX11022.1  95 DNTFVGMGSLImdGALIEENAMLGAGSLLT 124
                 8*********99***************998 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.029   1.8e+02     278     308 ..      22      56 ..      15      70 .. 0.74
   2 ?    8.3   0.0   0.00016      0.98     279     330 ..      74     123 ..      71     134 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.029
  Fucokinase 278 nSvlessvsvg.egsviehsslkgnvs...igsns 308
                 n+++ ++v++g ++sv+  ++++g+v+   ig+ +
  AHX11022.1  22 NAFIIGDVTIGaDSSVWHGCTIRGDVNrivIGEST 56 
                 67777888888677888889999776655577765 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00016
  Fucokinase 279 Svlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtil 330
                 +++ + v+vg ++++  ++l +n+ +g +s++ +  l ++++  +l   ++l
  AHX11022.1  74 TIIGQCVTVGHSCLLHACTLMDNTFVGMGSLIMDGALIEENA--MLGAGSLL 123
                 6888999*************************9999888755..66665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       257  (0.0143343); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1200.04
//
Query:       AHX11023.1  [L=127]
Description: succinate dehydrogenase, cytochrome b556 subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-21   74.4   7.6    9.3e-21   74.1   7.6    1.1  1  Sdh_cyt   Succinate dehydrogenase/Fumarate reductase transmem


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.1   7.6   5.2e-25   9.3e-21       5     120 ..       3     118 ..       1     120 [. 0.88

  Alignments for each domain:
  == domain 1  score: 74.1 bits;  conditional E-value: 5.2e-25
     Sdh_cyt   5 rplsphlqlyrlplgawlsilhritGvallvglllllvwlllalslsspesfarvvallas.piklilllllllallyHllnGiRhllwDlglgleles 102
                  p+sphlq+yrlp +a+lsi+hritG++l + ll+ ++w+++a +   ++ f  +  ++ s +i  +  + +ll ++yH++ G+Rhl+ D+  g+++ +
  AHX11023.1   3 PPISPHLQIYRLPFAALLSISHRITGFLLSL-LLISFIWYVFAFLYFPSSFFCSILGFFFSgLIGRFFSFSFLLFFCYHFCSGLRHLFCDYCGGFSQLA 100
                 599****************************.9999999999999999999999987777777777777*********************656677777 PP

     Sdh_cyt 103 arksalavlalavalvlv 120
                 ++   ++v+a +++l+l+
  AHX11023.1 101 VKLGNFFVVASSILLFLF 118
                 778889999999988875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       996  (0.0555525); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1007.23
//
Query:       AHX11024.1  [L=109]
Description: succinate dehydrogenase, hydrophobic membrane anchor protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-07   31.9   6.4    1.5e-07   31.5   6.3    1.3  1  Sdh_cyt       Succinate dehydrogenase/Fumarate reductase tran
    0.00012   21.8   2.3    0.00012   21.8   2.3    1.7  1  Yip1          Yip1 domain
     0.0018   18.0   7.4     0.0072   16.0   7.4    1.8  1  CybS          CybS, succinate dehydrogenase cytochrome B smal
  ------ inclusion threshold ------
       0.03   13.8   0.1      0.046   13.2   0.1    1.2  1  zn-ribbon_14  Zinc-ribbon
        2.1    8.2  12.9      0.064   13.1   4.9    1.9  2  DUF2721       Protein of unknown function (DUF2721)


Domain annotation for each model (and alignments):
>> Sdh_cyt  Succinate dehydrogenase/Fumarate reductase transmembrane subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   6.3   4.1e-11   1.5e-07      20      94 ..       5      77 ..       1     104 [. 0.78

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 4.1e-11
     Sdh_cyt 20 awlsilhritGvallvglllllvwlllalslsspesfarvvallaspiklilllllllallyHllnGiRhllwD.l 94
                   + ++r+t+++l++++l+ll+ l+l+  ++ p + + + + +   + l  +ll++l+ lyH + G+R++++D +
  AHX11024.1  5 VRFWQMQRLTAFLLIPLFLFLLISLTLSIEGVLPLDLEILKDRF---FVLSAILLFALVSLYHSMLGLRVIVEDyI 77
                56799***********8888887767666677999999998888...7777779999*****************43 PP

>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   2.3   3.5e-08   0.00012      93     152 ..       3      73 ..       1      90 [. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 3.5e-08
        Yip1  93 gkgsfkqtlsvvgyallPlilgaliaillllllgt...........llllvgllaliWslvllylglkaah 152
                  +++f q+ +++++ l+Pl+l++li++ l++ +              +l+++ll+++ sl+  +lgl++ +
  AHX11024.1   3 ADVRFWQMQRLTAFLLIPLFLFLLISLTLSIEGVLpldleilkdrfFVLSAILLFALVSLYHSMLGLRVIV 73 
                 6789***********************99888777********************************9875 PP

>> CybS  CybS, succinate dehydrogenase cytochrome B small subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   7.4     2e-06    0.0072      35     115 ..       7     106 ..       2     109 .] 0.84

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2e-06
        CybS  35 hwtleRivavglvpltvvplvagsl................spvlDavl..avlllihshlgfesciiDYipkrvygklhklahylLalgtvlslvGl. 114
                  w+++R++a  l+pl +  l++ +l                + vl a+l  a++ l+hs lg+  ++ DYi++  + kl  l   l  +++v++++G+ 
  AHX11024.1   7 FWQMQRLTAFLLIPLFLFLLISLTLsiegvlpldleilkdrFFVLSAILlfALVSLYHSMLGLRVIVEDYISSVFLCKLCLLLVNLFVGFSVFAVIGIi 105
                 6**************999988866445788899998888886666665423777899****************9999********************72 PP

        CybS 115 Y 115
                 Y
  AHX11024.1 106 Y 106
                 5 PP

>> zn-ribbon_14  Zinc-ribbon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.3e-05     0.046       8      24 ..      76      92 ..      75      96 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
  zn-ribbon_14  8 ylSSqkiCkACvLLegL 24
                  y+SS  +Ck C+LL +L
    AHX11024.1 76 YISSVFLCKLCLLLVNL 92
                  9*************887 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   4.9   1.8e-05     0.064      58     114 ..       5      61 ..       2      73 .. 0.88
   2 ?   -0.5   1.8      0.29     1e+03      73      86 ..      79      92 ..      66     107 .. 0.51

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
     DUF2721  58 rRarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvsll 114
                  R   ++r  ++l + ++l++l++l+l ++ +l ldl++l   +fvl+ +ll++ + 
  AHX11024.1   5 VRFWQMQRLTAFLLIPLFLFLLISLTLSIEGVLPLDLEILKDRFFVLSAILLFALVS 61 
                 5788899999***************************************99986444 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.29
     DUF2721 73 sallvvlvvlllfl 86
                s++l+ l+ ll+ l
  AHX11024.1 79 SVFLCKLCLLLVNL 92
                33333333333322 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (109 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       751  (0.0418874); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 828.87
//
Query:       AHX11025.1  [L=568]
Description: arginine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-22   80.0   0.0    3.1e-22   79.0   0.0    1.6  1  DALR_1           DALR anticodon binding domain
    6.4e-14   51.7   0.1    1.5e-13   50.4   0.1    1.5  1  tRNA-synt_1d     tRNA synthetases class I (R)
    4.8e-12   46.3   0.0    1.2e-11   45.0   0.0    1.7  1  Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
    8.8e-06   24.7   0.0       0.88    8.2   0.0    3.4  3  tRNA-synt_1g     tRNA synthetases class I (M)
    3.9e-05   23.2   0.0       0.26   10.6   0.0    2.3  2  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
     0.0055   15.7   0.0      0.086   11.7   0.0    2.6  3  tRNA-synt_1f     tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.0   0.0   1.1e-25   3.1e-22       1     119 []     448     568 .]     448     568 .] 0.92

  Alignments for each domain:
  == domain 1  score: 79.0 bits;  conditional E-value: 1.1e-25
                 HHHHHHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHH......HCTSTTSCTHHH.HHH CS
      DALR_1   1 vqyahaRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYn......kervlkeeeeelaaaR 93 
                 vqyahaR++s+l+k++ +ge     + +l+++  e+eL+k l ++p++ ++++ + ++hkl++yl+e+a++fh+ +n      + r++ ee++ l+++R
  AHX11025.1 448 VQYAHARCASLLTKHKMSGE----CNVSLMQSGYELELMKVLSKLPSLFKSIVGSGDVHKLTFYLQEVAEKFHALWNagmkdkQLRFIVEENPSLTNSR 542
                 8*************998883....344444778*******************************************988877666************** PP

                 HHHHHHHHHHHHHHHHHTT----S-- CS
      DALR_1  94 LaLvkavrqvLangLdlLGieapekm 119
                 L Lv+av++++a+ L +L i++ e m
  AHX11025.1 543 LFLVSAVKNTIASVLGVLKIQPAESM 568
                 ************************99 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   5.2e-17   1.5e-13      19     299 ..     115     411 ..      99     432 .. 0.76

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 5.2e-17
                   T-EEEEE----BTTS--BHHHHHHHHHHHHHHHHHHHCT-EEEEEE--B-SSTCHHHHHHHHHHHTTTTTTS-----SCCCHHH.HHHHHCCCSHCC CS
  tRNA-synt_1d  19 kkkvvvdfssPniakemhvGhLrstiiGdavsrlleflGydvirlnhvGDWGtqfGlLiaylekkqdekllqeqelqdLeafyk.eakkdydeeeif 114
                   +  v ++f s n   ++h Gh+r +ii d+ ++ll    ++v+r  ++ D G+q  lL+  +  +  e+++++   +   + y  +  k+ + e ++
    AHX11025.1 115 NTPVNLEFVSANPTGPLHLGHVRGAIIFDVFAELLSKFNFSVTREYYINDAGKQIDLLLLSVFIRCTEQVTGKSVENFPAGCYAgDYIKEIAAELQL 211
                   5567899*************************************************99988888888887755544444567753677889999888 PP

                   CHHHHHHHH.HHHCT-HHHHHHHHH.HHHHHHHHHHHHHHHCT---EC--CCCCCC.CHHHHHHHHHCTT-EEECT.....T........CEEEEEC CS
  tRNA-synt_1d 115 aerarnyvv.kLqsgdedirklwkl.lvditrtelqklydrldvtlierGeslyke.slneivkelkkkglvkesd.....G........alvvfld 195
                        +y + +L++  e ++++    +++++r +l+kl++ +d  +  r + l+k+  +++++ +l ++g +ke++     G        +++vfl+
    AHX11025.1 212 VCPGVDYGKlNLDEFIESFKEIVLDlMMKMIRVDLEKLNISYDCYV--REQDLHKDgYIESAISILAERGCIKEEElpapkGkvadwverKQLVFLS 306
                   8888888652555555555554433256666666677777777666..44557776368999********999986444433221122214567776 PP

                   CC.TSSCCEECC-TTS-B-HHHHHHHHHHHHHHTT--SEEEEEEECCCHHHHHHHHHHHHCTTSSTTTSEEEEEEE--EE-TTSSB..SBCSSSTC- CS
  tRNA-synt_1d 196 ef.gkrlgvvvqksDGgylytttDiaaakerkeelkadkvlyvidsrqslhlqqiflilkkigyvpeskdlehanfGmvlgkdkkk..fktrkGetv 289
                   ++ g+   + ++k DG+++y ++Dia   ++ +   ++ +++ + +    +++++  i+  ++ +  s+ ++  n+   l +++k+  ++ r+G+ +
    AHX11025.1 307 KHfGDDENRALKKADGSWTYFASDIAYHFHKIQRGFMN-MIVGLGADHAGYVKRLSGIVEALSKNTASIYVKLYNLVN-LFRNGKPvkLSKRNGNLI 401
                   43499999*****************9988887766665.55667788899**********999877777777666644.577787612568****** PP

                   BHHHHHHHHH CS
  tRNA-synt_1d 290 kLadlLdeal 299
                    ++d+L+ ++
    AHX11025.1 402 TIEDVLESGI 411
                   ******9887 PP

>> Arg_tRNA_synt_N  Arginyl tRNA synthetase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   4.2e-15   1.2e-11      29      85 .]      31      88 ..       6      88 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4.2e-15
                     .SSGGG-SEEEEGGGG--TT-..-HHHHHHHHHHT---TTT.EEEEEEETT.EEEEEE CS
  Arg_tRNA_synt_N 29 pknpkfGDyatnvamqlakklkknPreiAeeiaekleksei.iekvevagpGFiNffL 85
                     +k+ ++GD++tnv + lak+l ++ +e+A++ia +le++++ i+ v va  GFiN+ L
       AHX11025.1 31 AKKREHGDFSTNVVFFLAKELIMPLEELAQRIAIALEERGNlIKVVAVASGGFINIVL 88
                     5899***********************************999*************986 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.6   0.0    0.0038        11      11      31 ..     128     148 ..     123     158 .. 0.86
   2 !    8.2   0.0   0.00029      0.88      68     117 ..     236     285 ..     228     290 .. 0.90
   3 !    7.4   0.0   0.00052       1.6     324     373 ..     389     438 ..     372     443 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0038
                   SS---HHHHHHHHHHHHHHHH CS
  tRNA-synt_1g  11 ngklHlGhllevisaDifaRy 31 
                   +g+lHlGh++ +i+ D+fa  
    AHX11025.1 128 TGPLHLGHVRGAIIFDVFAEL 148
                   699***************965 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00029
                   HHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEE CS
  tRNA-synt_1g  68 ekvheeikelfkklnisfdkygrttseehkelvqeifkklkekgliyeke 117
                   + + ++i+ +++klnis+d y r ++ ++    ++ ++ l e+g i+e+e
    AHX11025.1 236 DLMMKMIRVDLEKLNISYDCYVREQDLHKDGYIESAISILAERGCIKEEE 285
                   567789999*************************************9987 PP

  == domain 3  score: 7.4 bits;  conditional E-value: 0.00052
                   --------------HHHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHH CS
  tRNA-synt_1g 324 egkKlSkSrgvvvkakealer.ldadllRYylaaeapekkDldfswedfve 373
                   +  KlSk +g++++++++le+ ++++ +R+ ++++++e   ldf ++ fv+
    AHX11025.1 389 KPVKLSKRNGNLITIEDVLESgITVNEIRFAMLTKSSEV-VLDFDLDRFVN 438
                   5569**************************999987765.46777777776 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   8.8e-05      0.26      23      49 ..     131     157 ..     117     210 .. 0.91
   2 !   10.3   0.0   0.00011      0.33     252     292 ..     391     432 ..     368     440 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 8.8e-05
                   -BHHHHHHHHHHHHHHHHHHHTT-EEE CS
  tRNA-synt_1e  23 shlGhaRslvafDilrrilqalgYdvq 49 
                    hlGh+R +++fD+++ +l ++++ v+
    AHX11025.1 131 LHLGHVRGAIIFDVFAELLSKFNFSVT 157
                   7*********************99997 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00011
                   BE--TTTT---BHHHHHTT.S-HHHHHHHHHSS-TTS-EEE- CS
  tRNA-synt_1e 252 ekmsksLknfitikdvlkk.fdprqlRllllsahyrsqldfk 292
                    k+sk  +n+iti+dvl++  + +++R+++l++  +  ldf+
    AHX11025.1 391 VKLSKRNGNLITIEDVLESgITVNEIRFAMLTKSSEVVLDFD 432
                   59***************974799*****************97 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.25   7.4e+02      33      61 ..     127     155 ..     124     165 .. 0.78
   2 ?   -0.2   0.0      0.12   3.6e+02     111     149 ..     238     277 ..     228     302 .. 0.77
   3 !   11.7   0.0   2.9e-05     0.086     269     331 ..     377     443 ..     348     465 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.25
  tRNA-synt_1f  33 pSGliHiGnlrevltadlvaralrkrgee 61 
                   p G++H+G +r  +  d+ a+ l+k   +
    AHX11025.1 127 PTGPLHLGHVRGAIIFDVFAELLSKFNFS 155
                   89*********999999988888877666 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.12
  tRNA-synt_1f 111 fnaelvesLdelgievef.isatelYksglydeaikeale 149
                   + ++++  L++l+i +++ +++++l k+g  ++ai ++ e
    AHX11025.1 238 MMKMIRVDLEKLNISYDCyVREQDLHKDGYIESAISILAE 277
                   6678888899999999962567778888887777765444 PP

  == domain 3  score: 11.7 bits;  conditional E-value: 2.9e-05
  tRNA-synt_1f 269 vvYelillkgge...kmssSkGnvltledwlev.aepevlrflilrrkPkkakkldldleilrlvde 331
                     Y+l+ l  ++   k+s+ +Gn +t+ed+le  ++ + +rf +l +  +  +++dld  +   +d+
    AHX11025.1 377 KLYNLVNLFRNGkpvKLSKRNGNLITIEDVLESgITVNEIRFAMLTKSSEVVLDFDLDRFVNTSYDN 443
                   3688887754444789***************97357899*******888888999999777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3873.54
//
Query:       AHX11026.1  [L=206]
Description: inhibitor of apoptosis-promoting Bax1 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-51  173.7  36.3    4.9e-51  173.5  36.3    1.0  1  Bax1-I    Inhibitor of apoptosis-promoting Bax1


Domain annotation for each model (and alignments):
>> Bax1-I  Inhibitor of apoptosis-promoting Bax1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.5  36.3   2.7e-55   4.9e-51      11     207 .]       1     202 [.       1     202 [. 0.94

  Alignments for each domain:
  == domain 1  score: 173.5 bits;  conditional E-value: 2.7e-55
      Bax1-I  11 lalgllltalvaavvlsspaqlflslhivlflvvilaplalvflslsaarlkkkssalalallllftlleGlslspillvytgaiilqaflltaaifgg 109
                 +a++l++t+++a++v++sp+ l l  +++l +vv++ap+++vf+++++    +++s  a +l+++f++l+Glsls i+++ytg+++ ++f++ a +fg+
  AHX11026.1   1 MAIALGITGVTAYLVSTSPSMLSLLYQTPLQWVVMFAPIVFVFIFSAK--VSSMTSDSAKLLFWGFSVLMGLSLSWIFVAYTGTSVSRVFFISASMFGA 97 
                 899*****************88888889**************966554..455666666**************************************** PP

      Bax1-I 110 lslyalttkrdlsglggflfagligliiaslvnlFlpssalelaisylgvllfsglilyDtqkiierageygee.......dailaalsLyldfinlFl 201
                 ++l++  tk dl+ +g+fl++g++g++ias+vn+Fl+s a+++a+s+lgv++f+gl++yD+q+i+  ++   +         ail+al+Ly+dfin+F+
  AHX11026.1  98 MALFGNNTKADLTAMGSFLIMGVVGILIASIVNIFLQSAAVYFAVSFLGVIIFTGLTAYDVQRIKDSYYLASNAgesalskVAILGALTLYFDFINIFI 196
                 *****************************************************************988877777************************* PP

      Bax1-I 202 slLril 207
                 slL+++
  AHX11026.1 197 SLLNLM 202
                 ***998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1145  (0.063863); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.28s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1491.15
//
Query:       AHX11027.1  [L=841]
Description: hypothetical protein NHE_0053 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-16   59.1   6.7         18    5.9   0.0   10.2 16  DUF1843   Domain of unknown function (DUF1843)


Domain annotation for each model (and alignments):
>> DUF1843  Domain of unknown function (DUF1843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.0   0.00099        18      12      46 ..     451     485 ..     448     487 .. 0.87
   2 !    5.7   0.0    0.0012        22      12      46 ..     471     505 ..     467     505 .. 0.87
   3 !    5.8   0.0    0.0011        19      12      46 ..     491     525 ..     487     527 .. 0.87
   4 !    5.8   0.0    0.0011        20      12      46 ..     511     545 ..     508     547 .. 0.87
   5 !    5.8   0.0    0.0011        19      12      46 ..     531     565 ..     527     567 .. 0.87
   6 !    5.8   0.0    0.0011        19      12      46 ..     551     585 ..     547     587 .. 0.87
   7 !    5.7   0.0    0.0012        21      12      46 ..     571     605 ..     567     606 .. 0.87
   8 !    5.8   0.0    0.0011        20      12      46 ..     591     625 ..     588     627 .. 0.87
   9 !    5.8   0.0    0.0011        20      12      46 ..     611     645 ..     608     647 .. 0.87
  10 !    5.7   0.0    0.0012        22      12      46 ..     631     665 ..     627     665 .. 0.87
  11 !    5.8   0.0    0.0011        19      12      46 ..     651     685 ..     647     687 .. 0.87
  12 !    5.7   0.0    0.0012        22      12      46 ..     671     705 ..     667     705 .. 0.87
  13 !    5.8   0.0    0.0011        19      12      46 ..     691     725 ..     687     727 .. 0.87
  14 !    5.8   0.0    0.0011        19      12      46 ..     711     745 ..     707     747 .. 0.87
  15 !    5.8   0.0    0.0011        19      12      46 ..     731     765 ..     727     767 .. 0.87
  16 !    5.9   0.0    0.0011        19      12      46 ..     751     785 ..     747     787 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.00099
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 451 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 485
                 68******999999999999999999999998766 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0012
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 471 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 505
                 68******999999999999999999999998765 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 491 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 525
                 68******999999999999999999999998766 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 511 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 545
                 67******999999999999999999999998766 PP

  == domain 5  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 531 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 565
                 68******999999999999999999999998766 PP

  == domain 6  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 551 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 585
                 68******999999999999999999999998766 PP

  == domain 7  score: 5.7 bits;  conditional E-value: 0.0012
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 571 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 605
                 68******999999999999999999999998766 PP

  == domain 8  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 591 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 625
                 67******999999999999999999999998766 PP

  == domain 9  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 611 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 645
                 67******999999999999999999999998766 PP

  == domain 10  score: 5.7 bits;  conditional E-value: 0.0012
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 631 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 665
                 68******999999999999999999999998765 PP

  == domain 11  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 651 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 685
                 68******999999999999999999999998766 PP

  == domain 12  score: 5.7 bits;  conditional E-value: 0.0012
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 671 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 705
                 68******999999999999999999999998765 PP

  == domain 13  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 691 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 725
                 68******999999999999999999999998766 PP

  == domain 14  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 711 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 745
                 68******999999999999999999999998766 PP

  == domain 15  score: 5.8 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 731 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 765
                 68******999999999999999999999998766 PP

  == domain 16  score: 5.9 bits;  conditional E-value: 0.0011
     DUF1843  12 asGDLakMKalaaqaeqqLaeygdiasaleqLkaE 46 
                 + GDL +M++ +++  +   ++gd++ + ++L  E
  AHX11027.1 751 SHGDLTEMRKALSREPSPTRSHGDLTEMRKALSRE 785
                 679*****999999999999999999999998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (841 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       813  (0.0453455); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 5813.13
//
Query:       AHX11028.1  [L=71]
Description: hypothetical protein NHE_0054 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 567.08
//
Query:       AHX11029.1  [L=680]
Description: NADH dehydrogenase (quinone), G subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-49  167.5   0.0    6.6e-24   84.6   0.0    2.7  3  Molybdopterin    Molybdopterin oxidoreductase
    9.3e-20   70.5   0.1    2.2e-19   69.2   0.1    1.7  1  Fer2_4           2Fe-2S iron-sulfur cluster binding domain
    8.7e-17   60.4   0.1    8.7e-17   60.4   0.1    2.0  2  NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur
    3.8e-10   40.3   0.8    7.3e-10   39.4   0.8    1.4  1  NADH_dhqG_C      NADH-ubiquinone oxidoreductase subunit G, C-
    6.5e-08   32.4   2.1    1.4e-07   31.4   0.3    2.4  2  Fer2             2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.098   12.5   1.3        4.1    7.4   0.4    2.8  2  Fer4             4Fe-4S binding domain


Domain annotation for each model (and alignments):
>> Molybdopterin  Molybdopterin oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.28   8.3e+02      64     124 ..     179     234 ..     175     249 .. 0.72
   2 !   84.6   0.0   2.2e-27   6.6e-24       1     178 [.     272     429 ..     272     435 .. 0.90
   3 !   79.8   0.0   6.7e-26     2e-22     236     431 ..     440     594 ..     430     595 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.28
                    HHHHHTT-EEE-BEECCGGGTTHHHHCHHCCCCCTTTS-SS-CCGGGG-SEEEEESS-HHH CS
  Molybdopterin  64 kllsllggknlsfydwyadlppasaqqtigsdsrsnyessnpledlensdliilwGsNvre 124
                    +++++ ++  ++  ++  dl+p  a     s+  +  + s++l++++  d+  ++GsN+r 
     AHX11029.1 179 TYIKKAIS--SEISGNIIDLCPVGAL---TSKPYAFTARSWELNKIDSVDVLDAVGSNIRV 234
                    56666666..5666677777764432...222233346699999**************996 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 2.2e-27
                    B--S-EEECTTTTTSEEEE--HHHHHHHHHHHHHHHHHHCSGGGEEEEEBTSSCSHHHHHHHHHHHHHTT-EEE-BEECCGGGTTHHHHCHHCCCC CS
  Molybdopterin   1 RlkyPmvRkqargeGkFvrvsWdeAleliaaslkytikkygpdrvagfssgplmsmeslaslkkllsllggknlsfydwyadlppasaqqtigsds 96 
                    Rl++ ++R     +Gk+++ +Wd Al +i +++  +      +++a +++g+l+++es ++lk+++ +lg + l++++++a +p        +sd 
     AHX11029.1 272 RLDRCYIR---V-NGKLEECTWDRALSEIVKRIDIV----SREEIA-AIAGNLIDVESAFLLKRMMDKLGVSKLECRQDGATYP--------VSD- 349
                    88899999...6.9*********************3....333455.9***********************************7........566. PP

                    CTTTS-SS-CCGGGG-SEEEEESS-HHHHSHHHHHHHHHHHHTTC-EEEEECS.SB-HCGGGCSEEEEEHTTTHHHHHHHHHH CS
  Molybdopterin  97 rsnyessnpledlensdliilwGsNvreerpilnarirkaalkkkakvivigp.ryaellkfadewlaikpgtdaalalamgh 178
                    rs y ++++++++e+sdl++l+G+N+r  +p+ nar+rk++l ++ kvi +g  +++   +f++ +l+ +  t++++  +++h
     AHX11029.1 350 RSLYTFNSTISGIEKSDLCFLVGANLRVDAPLINARLRKRWLAGDYKVIGLGCgDVK--HTFDVHDLGDSVSTLVDI-KEGKH 429
                    999**********************************************99962555..689999999999999998.77766 PP

  == domain 3  score: 79.8 bits;  conditional E-value: 6.7e-26
                    SSEEEEECHHHHTSTTHHHHHHHHHHHHHHCTHCSSTTCEEEEESSCTTHHHCHHHHTCCTTCCCCCCCTTHHHHHCCCTTTCSTSS--ECGGCHH CS
  Molybdopterin 236 gksmiivGaglnhrqdgdaiyravinLallvgnvgqpgGgwahlnGqlilagaaekvgalpvllsvkslkeekikfaaeqpgnlgnfprnlfvers 331
                     ++m+i+G  ++ r d + ++  + ++a     ++    + +++    +l+++   vgal                      ++g++ +  ++   
     AHX11029.1 440 MNPMMIIGPDMLARPDASYVLFLLRSIAEQFSFIRD---DCNNFS---VLQRHSGTVGAL----------------------DIGFHHQGGLS--- 504
                    468888899999999999999999999999999988...677777...888888899999......................88888888886... PP

                    HHHHTTSSSEEEEESH.HHHHSTTSCCCHCHHHCSSEEEEEESCS.SHHHHTSSEEEEBE-CCGSEEEEE-TTSEEEEEEESSS-STT-BEHHHHH CS
  Molybdopterin 332 nllkssgkkvlyllgnnpevdhadenevekalekldlvvvldgrl.tstalyaDiiLPaatwyEkedlytndegrfqhlkqavsppgeaksdwkIl 426
                     +l+ ++ kv+yllg       ade        + d++v+++g++ +++a +aD iLP+++++Ek+ +y+n+egr q + +a++ppgeak+d +I+
     AHX11029.1 505 SVLC-GDTKVVYLLG-------ADECVD---SIPEDAFVIYQGHHgDRGAGRADAILPGCSYVEKDAIYVNTEGRAQLAFRAIFPPGEAKDDREII 589
                    5677.89********.......777766...569************************************************************** PP

                    HHHHH CS
  Molybdopterin 427 kaLak 431
                     +La+
     AHX11029.1 590 ADLAQ 594
                    ***97 PP

>> Fer2_4  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.2   0.1   7.5e-23   2.2e-19       3      82 .]       1      78 [.       1      78 [. 0.93

  Alignments for each domain:
  == domain 1  score: 69.2 bits;  conditional E-value: 7.5e-23
      Fer2_4  3 pvtltfDGkevtvpeGdtvasAllangvdvprsckygrprgelcaggeCrnClVevegepn..vracstpvedGlkvetqtg 82
                ++++t++Gk+++v++G +v+++++ +gv++pr c++    + l+  g+Cr ClVe+eg p   +++c +pv+dG++v+t+t+
  AHX11029.1  1 MISVTINGKKLSVEPGYSVIQVCQMAGVEIPRFCYH----ERLKIAGNCRMCLVEIEGGPPkpIASCAMPVADGMVVHTDTP 78
                5899********************************....89***************7554346***************985 PP

>> NADH-G_4Fe-4S_3  NADH-ubiquinone oxidoreductase-G iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.1   2.9e-20   8.7e-17       1      37 [.      84     120 ..      84     123 .. 0.94
   2 ?   -4.7   0.7         6   1.8e+04      14      21 ..     145     152 ..     140     153 .. 0.75

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 2.9e-20
  NADH-G_4Fe-4S_3   1 RktilellLanHpldCltCdknGnCeLQdlayelgve 37 
                      R +++e+lLanHpldC++Cd++G+C+LQd a+ +g  
       AHX11029.1  84 REGVMEFLLANHPLDCPICDQGGECDLQDQAMLYGKG 120
                      899*******************************965 PP

  == domain 2  score: -4.7 bits;  conditional E-value: 6
  NADH-G_4Fe-4S_3  14 ldCltCdk 21 
                      + C  C++
       AHX11029.1 145 NRCILCSR 152
                      56999987 PP

>> NADH_dhqG_C  NADH-ubiquinone oxidoreductase subunit G, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.8   2.4e-13   7.3e-10      34      51 .]     652     669 ..     625     669 .. 0.86

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 2.4e-13
  NADH_dhqG_C  34 dFYmTDpISRASaTMAkC 51 
                   FYmTDpISRAS TMAkC
   AHX11029.1 652 SFYMTDPISRASSTMAKC 669
                  7***************** PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.4   0.3   4.6e-11   1.4e-07       1      76 [.       4      66 ..       4      69 .. 0.81
   2 ?   -0.5   0.1      0.42   1.2e+03      17      40 ..      86     108 ..      73     110 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.4 bits;  conditional E-value: 4.6e-11
                EETTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSS......SSSSTTEEEEEESCECTTSSSSTHHHHHTTEEEEGGGSE CS
        Fer2  1 itidgkevevevadgettlldaaeenggidipysCgg......ggCgtClvevlegevqsdetelegeeldegklrlaCqti 76
                +ti+gk+ +ve    ++++ ++++ + g++ip +C++      g+C++Clve++ g            +    k +++C+++
  AHX11029.1  4 VTINGKKLSVEP---GYSVIQVCQMA-GVEIPRFCYHerlkiaGNCRMCLVEIEGG-----------PP----KPIASCAMP 66
                6899**888876...777******99.***************777*******9844...........22....345666665 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.42
                 HBHHHHHHHTTTTTSTTSSSSSS.S CS
        Fer2  17 ttlldaaeenggidipysCgggg.C 40 
                   +++++  n+ +d p  C +gg C
  AHX11029.1  86 G-VMEFLLANHPLDCP-ICDQGGeC 108
                 3.78999999999999.9***9999 PP

>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   0.4    0.0014       4.1       6      16 ..     145     155 ..     141     156 .. 0.88
   2 ?    2.9   0.0     0.035     1e+02      16      24 .]     195     203 ..     194     203 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0014
                 TTSSS-THHHH CS
        Fer4   6 ekCigCGaCve 16 
                 ++Ci C +Cv 
  AHX11029.1 145 NRCILCSRCVR 155
                 79*******96 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.035
                 HHSTTTEEE CS
        Fer4  16 evCPvgAIt 24 
                 + CPvgA+t
  AHX11029.1 195 DLCPVGALT 203
                 67*****86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (680 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       550  (0.0306766); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.38
# Mc/sec: 5349.40
//
Query:       AHX11030.1  [L=318]
Description: NADH-ubiquinone oxidoreductase chain 1 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   1.1e-117  392.6  24.3   1.3e-117  392.4  24.3    1.0  1  NADHdh    NADH dehydrogenase


Domain annotation for each model (and alignments):
>> NADHdh  NADH dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  392.4  24.3  7.1e-122  1.3e-117      11     298 ..       2     309 ..       1     310 [. 0.97

  Alignments for each domain:
  == domain 1  score: 392.4 bits;  conditional E-value: 7.1e-122
                 HHHHHHHHHHHHHHHHHHTTS--S-SSTTTTTTHHHHHHHHHCCS-----TTS-HHHHHHHHHHHHHHHHCTTTTS-SSS..........SSS--TTHH CS
      NADHdh  11 llvvalltlleRkvlAriqdRlGPnrvGplGllqplaDalKlllKediipkkadkllfllapvlalilallafaviPfge..........vladlnvgl 99 
                 +l va+lt++eRkv+A+ q R+GP  vGp+Gllqp+aDa+K+llKe +ip++a   lfllapv++++lal+ +aviP+g+          v+ad+n+g+
  AHX11030.1   2 ILSVAYLTYAERKVIAATQLRIGPDLVGPFGLLQPIADAMKVLLKEIVIPRAAGAKLFLLAPVIVFVLALVGWAVIPLGTsevagvevptVIADINLGV 100
                 68999**************************************************************************44567788999********* PP

                 HHHHHHHHHCHHHHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-HHHHHHCCCTT..-CCCCHHHHHHHHHHHHHHCCTCTTBT CS
      NADHdh 100 llilalsslgvygillaGwasnskYallGalRsaaqmisyEvalglsllavvllagslslseiveaqeei..wfillqllafiifliallaetnraPFD 196
                 +++la+++l+vygi++aGw+s+s+Y++lGalRsa+qmisyE++++ ++++v+llagsl+l eiv a+++   w+ +l+l++++if++++laetnr+PFD
  AHX11030.1 101 MYLLAIAALEVYGIIIAGWSSKSTYSFLGALRSASQMISYEIVIAPVIISVILLAGSLNLAEIVIAKHNLpyWVDILMLPMAFIFFVSILAETNRHPFD 199
                 *****************************************************************99988889966679******************** PP

                 TTTSTTSSSSCCCTT-HCHHHHHHHHHHHHHHHHHHHHHHHHCT.SS-HCCS........HHHHHHHHHHHHHHHHHHHHHC----TCHHHHHHHCCTC CS
      NADHdh 197 lpeaesELvaGfhtEYsgmkfalfflaeyanmvlvsalavllFlgGwllpfs........gllwfllKvllllflfiwiratlpRlRydqlmklgwkvl 287
                 lpeae+ELv+G+++EYs++ falffl+eyanm+l s+++++lFlgGw +p+         g++wf++Kv ++lf fi++ratlpR+Rydqlm+lgwk++
  AHX11030.1 200 LPEAEAELVSGYNVEYSSIPFALFFLGEYANMILSSSIMTVLFLGGWYPPIDsyffsfipGFVWFIAKVSFVLFWFIIVRATLPRYRYDQLMRLGWKIF 298
                 **************************************************999********************************************** PP

                 HHHHHHHHHHH CS
      NADHdh 288 lplalanlllt 298
                 lp++++++l++
  AHX11030.1 299 LPVTFLWILIV 309
                 ********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (318 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      240  (0.0133861); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2398.64
//
Query:       AHX11031.1  [L=191]
Description: BON domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-25   87.1   3.1      2e-12   47.2   0.1    2.1  2  BON              BON domain
  ------ inclusion threshold ------
      0.017   15.6   1.2      0.026   15.0   1.2    1.5  1  Phage_sheath_1N  Phage tail sheath protein beta-sandwich doma


Domain annotation for each model (and alignments):
>> BON  BON domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.8   0.4   2.3e-14   2.1e-10       9      68 ..      52     109 ..      44     110 .. 0.84
   2 !   47.2   0.1   2.3e-16     2e-12       3      68 ..     119     184 ..     117     185 .. 0.96

  Alignments for each domain:
  == domain 1  score: 40.8 bits;  conditional E-value: 2.3e-14
                 HHHHHHHHCHTTGCCCEEEEETTCEEEECEEECHHHHHHHHHHHHCCTTEEEEEEEEEEE CS
         BON   9 vkaalakdggldaadinVevenGvVtLsGtVdseaekekAveiarnvaGVkkVvnelkvr 68 
                 v +al +  g+   +i+++v++G+V++sG V+s  ++ ++ +++++ +GV++V nel+v 
  AHX11031.1  52 VVRALSNK-GF-GKNITISVNEGRVLVSGSVPSSMDRIAVSKVIWTQEGVREVMNELQVE 109
                 55555544.33.389*******************************************96 PP

  == domain 2  score: 47.2 bits;  conditional E-value: 2.3e-16
                 HCCHHHHHHHHHHHCHTTGCCCEEEEETTCEEEECEEECHHHHHHHHHHHHCCTTEEEEEEEEEEE CS
         BON   3 aeiaakvkaalakdggldaadinVevenGvVtLsGtVdseaekekAveiarnvaGVkkVvnelkvr 68 
                 a+i+a++k  ++  +++++++ +Ve+++G V+L G ++s +e  k+++i+r+v+GVk+Vv +++++
  AHX11031.1 119 AWITAQIKLSMLLKSSVKSFNYTVETHDGTVYLLGIAQSKDELKKVYDIVRRVDGVKQVVSHVRLK 184
                 89*********9999**********************************************99986 PP

>> Phage_sheath_1N  Phage tail sheath protein beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   1.2   2.9e-06     0.026       1      78 [.      23     126 ..      23     180 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.9e-06
                      CE-SCEEEEE.TTSS.T..............EEESSSSGGGGGEEEEEEEHSS................STTSEEEEEEETTEEEEEEEEES.S CS
  Phage_sheath_1N   1 Gtaatatltltstasea..............igakypgerGnritvevtsgad................dsnqfdvivregdrivdaqilvt.g 63 
                      Gt+a atl +tst++++              ++a++   +G++it++v++g +                +     + + eg r v  +  v+  
       AHX11031.1  23 GTTA-ATLAVTSTQEKSigaiiddkaiwfrvVRALSNKGFGKNITISVNEGRVlvsgsvpssmdriavsK----VIWTQEGVREVMNELQVEkR 111
                      5666.79*******99669*********************************999999888776644331....34466666666333335556 PP

                      CCCTT-BSSEEEEHH CS
  Phage_sheath_1N  64 ekdvvgniavaaklv 78 
                      e+++ ++++++a+++
       AHX11031.1 112 EQSFAKSAWITAQIK 126
                      666677777777754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1431.07
//
Query:       AHX11032.1  [L=463]
Description: fumarate hydratase, class II [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   3.9e-105  351.7   0.0   4.9e-105  351.4   0.0    1.1  1  Lyase_1      Lyase
    7.3e-23   80.7   0.2    1.6e-22   79.7   0.2    1.6  1  FumaraseC_C  Fumarase C C-terminus


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.4   0.0  5.4e-109  4.9e-105       1     312 []      11     341 ..      11     341 .. 0.97

  Alignments for each domain:
  == domain 1  score: 351.4 bits;  conditional E-value: 5.4e-109
                 CEEEEETCHHHHHHHHHHHHHGGGHHHHHC.....HHHHHHHHHHHTTSST....HHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHH CS
     Lyase_1   1 grftvkadklmgiftersrenfrlseedik.....alaalkkaaakanvdl....keeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnev 90 
                 g+++v+   ++g++t+rs+enf+++ e+i      a a++k aaa +n+      ke +  i+++++e+++  klddqf+l v+q+gsgt++nmn+nev
  AHX11032.1  11 GEINVPKKSYWGAQTQRSIENFKIGTEKIPievirAIAVIKLAAARVNANEgllrKEYLPVIEEVCNEIIS-EKLDDQFPLSVWQTGSGTQTNMNVNEV 108
                 78999********************888879999988889999998888888899****************.9************************** PP

                 HH....HHTT......HSSGIIIIITTT--HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHH CS
     Lyase_1  91 ig....ellg......ekvepndkvhtgqSsnDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaeal 179
                 i+    e+l+       +++pnd+++++qSsnD++pTa+r+a++k + e L+p l  L+d+l+ek   f+ ++kiGrTh qdAtP+ l+qe+s++ ++l
  AHX11032.1 109 IAnraiEKLNgvlgskSPIHPNDHINMCQSSNDTFPTAMRIAAVKMIGESLIPSLSYLMDVLSEKITDFEGIIKIGRTHMQDATPIPLAQEFSCFRAQL 207
                 **999977778999*999********************************************************************************* PP

                 HHHHHHHHHHHHHHTCEETTTTTTTSSTTTSCCTHHHHHHHHHHHHHCST.EESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSS CS
     Lyase_1 180 erdrerlkellkrllvellgggtavgtglnadpefaelvakelakvtglp.vkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.agl 276
                  +++erl+e l + l+e  +ggtavgtgln+++ f++++++e++k+tg+  ++a n+ e ++++D +vel+g l++latsL+k+++D+rll+sg+ +g+
  AHX11032.1 208 AKSKERLNENL-NRLYEIPQGGTAVGTGLNTKKGFDKKIVDEISKITGVSfFPAGNKCEMIAAHDVLVELSGNLNVLATSLMKIGNDIRLLASGPrCGI 305
                 ***********.999************************************************************************************ PP

                 EEEEGCCTSSC-TTSTTTEBTHHHHHHHHHHHHHHH CS
     Lyase_1 277 velslaesepGSSiMPgKvNPvqlElltgvagrvvG 312
                 +el l+++epGSSiMPgKvNP+q+E+lt+v+++v+G
  AHX11032.1 306 GELTLPANEPGSSIMPGKVNPTQCEALTMVCTQVMG 341
                 ***********************************9 PP

>> FumaraseC_C  Fumarase C C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.7   0.2   1.7e-26   1.6e-22       1      53 [.     407     459 ..     407     460 .. 0.98

  Alignments for each domain:
  == domain 1  score: 79.7 bits;  conditional E-value: 1.7e-26
                  GGGGGHHHHHHHHHHHHHHHHHHHT--HHHHHHHTT-.-HHHHHHHT-HHHHH CS
  FumaraseC_C   1 LVTaLnphIGYekAakIAkeAlkegktlreavlelgllteeeldelldpekMt 53 
                  LVTaLn+hIGY+kAa+IAk A+ ++ tl+ea++el+l++ ee+d+++dpe+M+
   AHX11032.1 407 LVTALNKHIGYDKAASIAKLAYSKDCTLKEAAVELKLISGEEFDKIVDPETMV 459
                  8***************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (463 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3524.26
//
Query:       AHX11033.1  [L=397]
Description: aspartate kinase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    6.4e-39  134.0   0.4    8.5e-39  133.6   0.4    1.2  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.6   0.4   4.7e-43   8.5e-39       1     240 [.      10     235 ..      10     236 .. 0.93

  Alignments for each domain:
  == domain 1  score: 133.6 bits;  conditional E-value: 4.7e-43
                 TEEEEEE-TTCCCCTCCHHHHHHHHHHHHHHHHTTEEEEEE--.HHHHHHHHHH..TCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHHHHT CS
   AA_kinase   1 krvVvKlGGssltdkeeaslrrlaeqiaalkesgnklvvVhGg.gsftdgllal..ksglssgelaaglrstleeagevatrdalaslgerlvaallaa 96 
                 k+ V K+GGssl++ +   +rr++ ++++++++g  +vvV+++ gs+td l++   + +++++ +                 d ++s ge+++  l++ 
  AHX11033.1  10 KVKVQKFGGSSLSSLKH--IRRCVSIVERAVSEGFSVVVVVSAmGSYTDSLVDYieAFDVQDNDSS----------------DVVLSAGEQVSCGLFTL 90 
                 5789*************..***********************************99999*999999................***************** PP

                 THGEEEE-GGGTCEECCCE.....HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTE..EEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTT CS
   AA_kinase  97 glpavglsaaaldateagr...degsdgnvesvdaeaieelleagvvpvltgfigldeege..lgrgssDtiaallAealgAdkliiltdVdGVydadp 190
                 +l ++g++a +l   +  +    ++s+++++sv  e+i +++++++v+v++gf+g+       lgrg+sD +a++lA+ l+A +++i+tdV+GV++ dp
  AHX11033.1  91 ALGEIGIKAISLMGWQLPIetdGFHSKARIRSVCVEKILDYINQKYVVVVAGFQGVYLGRLttLGRGGSDITATALAKSLNAISCEIYTDVEGVFSTDP 189
                 **8888888877766666677777******************************776665577************************************ PP

                 TTC.CTTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
   AA_kinase 191 kkv.pdarllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvIt 240
                 + + + a+ lp+i +++++e      +   kv+h +al++ar+g+ ++ I+
  AHX11033.1 190 RAHaKEAEHLPQIGYSQLLE-----MSLKEKVLHSRALDIARKGVSNILIK 235
                 ***9999*************.....6677789************9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       547  (0.0305092); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2892.58
//
Query:       AHX11034.1  [L=769]
Description: polyribonucleotide nucleotidyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-39  133.5   0.4    1.5e-19   70.8   0.0    2.9  3  RNase_PH    3' exoribonuclease family, domain 1
    4.8e-13   49.2   1.0    4.8e-13   49.2   1.0    2.1  2  S1          S1 RNA binding domain
    9.9e-12   45.2   0.6      3e-11   43.7   0.6    1.9  1  PNPase      Polyribonucleotide nucleotidyltransferase, RNA bi
    1.6e-09   37.7   3.4    7.8e-06   25.8   0.4    2.8  2  RNase_PH_C  3' exoribonuclease family, domain 2
      7e-05   22.6   0.2    0.00019   21.2   0.2    1.8  1  KH_1        KH domain


Domain annotation for each model (and alignments):
>> RNase_PH  3' exoribonuclease family, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.8   0.1     1e-19   3.7e-16       3     132 .]      14     150 ..      12     150 .. 0.88
   2 ?   -3.0   0.0       2.8     1e+04      47      89 ..     178     217 ..     159     233 .. 0.63
   3 !   70.8   0.0   4.3e-23   1.5e-19       1     132 []     327     460 ..     327     460 .. 0.93

  Alignments for each domain:
  == domain 1  score: 59.8 bits;  conditional E-value: 1e-19
                 EEEEEEES.SSSTTSEEEEEEECCEEEEEEEEEEEEE..E-TCCG--CCEEEECCCCECCCCEC-C........S...HHHHHHHHHHHHHHCCTC-CC CS
    RNase_PH   3 Rslsietg.vlsqanGSaylelGdtkvlasvtgpiee..rpseerddaegaldveveyapfasger.....rregrpsdeeielsrlleralrpsille 93 
                 ++l+i+tg v++q  G a +++G t +la+vt+++ +   ++++ d ++ al++++  +++a g++     +reg+ +++ei+ sr+++ra+rp+i  +
  AHX11034.1  14 KDLHIKTGeVARQTAGVASVSYGGTVILAAVTVQKDSavAGKPS-DLSGLALVTNFLAKSYALGRIptgffKREGKLTEREILASRVIDRAIRPLIQEN 111
                 6899*******************************884333333.444577***********9999*****999***********************99 PP

                 GCCTCEEEEEEEEEECCCS-CHH..HCHHHHHHHHHCTCEE CS
    RNase_PH  94 kkpkstididitvlssdggslld..alinaaslALadagip 132
                     ++++i++ +l +d +s+l    + +aas+AL+ +gip
  AHX11034.1 112 LV--NEVNIVCKLLAHDSKSVLPevPALIAASVALKLSGIP 150
                 98..8*************66654226789***********9 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 2.8
                 CCEEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCT CS
    RNase_PH  47 aegaldveveyapfasgerrregrpsdeeielsrlleralrps 89 
                 +  +l + ++  +++ +e      ++ +e e+ ++l++al++ 
  AHX11034.1 178 SVLELFAACTEDSVVMVES---EANEVSEPEMVSALKDALEST 217
                 3444555555556665555...445666667777777777765 PP

  == domain 3  score: 70.8 bits;  conditional E-value: 4.3e-23
                 EEEEEEEEESSSSTTSEEEEEEECCEEEEEEEEEEEEEE-TCCG--CC....EEEECCCCECCCCEC-C...S...HHHHHHHHHHHHHHCCTC-CCGC CS
    RNase_PH   1 elRslsietgvlsqanGSaylelGdtkvlasvtgpieerpseerddae....galdveveyapfasgerrregrpsdeeielsrlleralrpsillekk 95 
                 e+R++si+ + l+  +GSa+++ G t+ l++ t+++ ++++ + dd +    + + +++++ p+a ge      p+++ei   rl  +al+++++++  
  AHX11034.1 327 EIRPISISLDYLPGTHGSALFTRGGTQSLVVTTLGSYQDEQIM-DDIDgerrESVLLHYNFLPYAVGEVGALRAPGRREIGHGRLALKALKAMLPTKAT 424
                 79**********************************8866666.66666787889**************66667**********************999 PP

                 CTCEEEEEEEEEECCCS-CHHHCHHHHHHHHHCTCEE CS
    RNase_PH  96 pkstididitvlssdggslldalinaaslALadagip 132
                   +ti+i+ ++++sdg s  +a ++++slAL+d+g+p
  AHX11034.1 425 FPYTIRIVSEITESDG-SSSMATVCGSSLALMDTGVP 460
                 99**************.******************99 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.1         2   7.3e+03       9      27 ..      20      37 ..      18      41 .. 0.85
   2 !   49.2   1.0   1.3e-16   4.8e-13       3      75 .]     634     704 ..     632     704 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 2
                EEEEEEEETTEEEEEETTT CS
          S1  9 eGeVtsvtkgGafVelgng 27
                +GeV + t g a V +g g
  AHX11034.1 20 TGEVARQTAGVASVSYG-G 37
                799*********99999.4 PP

  == domain 2  score: 49.2 bits;  conditional E-value: 1.3e-16
                 TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                  +g+++eG+++s++++G+fV l n +eg+v++se+s + rv d+    ++G+ v v+v ++  d + i l+++
  AHX11034.1 634 SIGKIYEGKIVSIVDFGLFVLLPNRQEGLVHISEISKE-RVNDIRASHTEGQAVTVRVKDISPDGK-IKLTMR 704
                 689***********************************.*************************98.999875 PP

>> PNPase  Polyribonucleotide nucleotidyltransferase, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.7   0.6   8.3e-15     3e-11       1      82 [.     245     323 ..     245     324 .. 0.93

  Alignments for each domain:
  == domain 1  score: 43.7 bits;  conditional E-value: 8.3e-15
                 HHHHHHHTTTHHHHHHHTTS..SSHHHHHHHHHHHHHHHHHHHH...HHSTTS-HHHHHHHHHHHHHHHHHHHHHHTS-TTTS- CS
      PNPase   1 eleekvaelaeerisealti..teKqeRyaaldeikekvveafaaeleeedeedekeikeifkalekkvvRsrildegvRiDGR 82 
                 el+ kv+e  ee+++ ++ +  ++K+eRy+ ld i+ ++ ++f  e       + +e+  + k++ek++v ++ l++gvRiDGR
  AHX11034.1 245 ELYSKVKETYEESLKAVYDAqiKNKEERYTLLDVIYLDAYAKFG-E----MGFTDAEVRFFIKKVEKEIVKRNTLENGVRIDGR 323
                 5889**************76559*********************.2....37999***************************** PP

>> RNase_PH_C  3' exoribonuclease family, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.2     5e-05      0.18      23      65 ..     172     214 ..     153     216 .. 0.81
   2 !   25.8   0.4   2.2e-09   7.8e-06       3      66 ..     465     532 ..     463     533 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
                 HHHHSSEEEEEEEETTSEEEEEEEECSSC.EEHHHHHHHHHHHH CS
  RNase_PH_C  23 Eedlsegdltlavagtkevvtlmkeggsq.ldeetlleaielAk 65 
                 + + s+++l l+ a t+++ ++m e +++ ++e +++ a++ A+
  AHX11034.1 172 QSRESDSVLELFAACTEDS-VVMVESEANeVSEPEMVSALKDAL 214
                 444599*************.8888888888*********99776 PP

  == domain 2  score: 25.8 bits;  conditional E-value: 2.2e-09
                 -EEEEEEEETTE....EEES--HHHHHHSSEEEEEEEETTSEEEEEEEECSSC..EEHHHHHHHHHHHHH CS
  RNase_PH_C   3 viavtvgkvddq....fvlDptkeEedlsegdltlavagtkevvtlmkeggsq..ldeetlleaielAkk 66 
                 v+++++g++ d     ++ D + +E++l+  d+++ vagt++ +t ++++ +   ++ e +++a+  A++
  AHX11034.1 465 VAGIAMGLITDGekysILSDISGDEDALG--DMDFKVAGTGSGITALQMDMKVqgISVEIIEKALNQALE 532
                 89*******6555799*********7766..******************998889***********9987 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.2   5.4e-08   0.00019       5      65 ..     563     617 ..     560     618 .. 0.89

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 5.4e-08
                 EEGGGHHHHHHTGGGHHHHHHHHHHT-EEEEESSTT...T.-EEEEEE.SHHHHHHHHHHHH CS
        KH_1   5 lvPsslvgriIGkgGsnIkeIreetgakIkvpksedegsderevtisG.speavekAkelie 65 
                 +++++ v ++IG gG++Ik I  +t  kI+++        ++ v+i   s+e   kAk++i 
  AHX11034.1 563 EINKDVVHKVIGSGGKTIKGISCDTASKIDID-A------NNFVHIMAdSKETLMKAKARID 617
                 688999****************88******76.4......468***************9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (769 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       726  (0.0404931); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 5434.23
//
Query:       AHX11035.1  [L=86]
Description: ribosomal protein S15 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-30  105.0   1.2      2e-30  104.8   1.2    1.0  1  Ribosomal_S15  Ribosomal protein S15


Domain annotation for each model (and alignments):
>> Ribosomal_S15  Ribosomal protein S15
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.8   1.2   1.1e-34     2e-30       1      81 []       5      85 ..       5      85 .. 0.99

  Alignments for each domain:
  == domain 1  score: 104.8 bits;  conditional E-value: 1.1e-34
                   HHHHHHHHSSSTT-TSSHHHHHHHHHHHHHHHHHHHHCTTT-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCTST CS
  Ribosomal_S15  1 kkelikefqrhekDtGspevqiallterInnltehlkenkkDkhsrrgLlklvskRrkllkYLkrkdverYkklieklglr 81
                   k+e+ik+f+ +++DtGs+ vq+al+terInnlt+hl+e kkD++sr gLlk++skRr+ll+YL ++d +  k+li+ l++r
     AHX11035.1  5 KSEIIKKFRIADNDTGSAFVQVALFTERINNLTRHLQEFKKDYASRLGLLKIISKRRRLLNYLAKNDQQGCKNLIKMLNIR 85
                   789****************************************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 682.85
//
Query:       AHX11036.1  [L=44]
Description: hypothetical protein NHE_0062 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      198  (0.0110436); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.26s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 337.84
//
Query:       AHX11037.1  [L=428]
Description: adenylosuccinate lyase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-48  166.4   0.0    1.4e-48  165.9   0.0    1.2  1  Lyase_1   Lyase
    1.5e-23   83.1   0.0    3.6e-23   81.9   0.0    1.7  1  ADSL_C    Adenylosuccinate lyase C-terminus
  ------ inclusion threshold ------
      0.028   14.5   0.1      0.068   13.3   0.1    1.6  1  ASL_C     Adenylosuccinate lyase C-terminal


Domain annotation for each model (and alignments):
>> Lyase_1  Lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.9   0.0   2.3e-52   1.4e-48      12     310 ..      12     284 ..       4     286 .. 0.88

  Alignments for each domain:
  == domain 1  score: 165.9 bits;  conditional E-value: 2.3e-52
                 HHHHHHHHHHGGGHHHHHCHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHCHCHHCGGHHHBSSSSSHHHHHHHHHHHHHHHHTTHSSGIIIIITTT-- CS
     Lyase_1  12 giftersrenfrlseedikalaalkkaaakanvdlkeeaaaiikaldevleegklddqfvlkviqegsgtavnmnlnevigellgekvepndkvhtgqS 110
                  i++++ ++  +l+     ++ +++ka  k++ ++   ++ i++ +    + ++l++ ++++   +++  a+   + e +g        +++++h+g +
  AHX11037.1  12 SIWSDETKFSLWLE-----IELLVCKAHSKLGNIPSDSLEVILSKA----S-FNLERIAAVEATVKHDVIAFLTSVAESVG-------PASRYIHMGMT 93 
                 57777877777777.....899999******999955555555554....4.66668899999999999999999999999.......99********* PP

                 HHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHTTT-EEEEEETTEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTCEETTTTTTTSSTTT CS
     Lyase_1 111 snDqvpTalrlalkkalsekLlpaleqLidalkekakefkdvvkiGrThlqdAtPvtlgqelsayaealerdrerlkellkrllvellgggtavgtgln 209
                 s D+++T ++l+l+ka    Ll++l++   a+keka ++kd+  +Gr h+ +A+P+tlg +++ + ++++r+r rl ++ k+++v +++g  avg+ + 
  AHX11037.1  94 SSDVIDTCFSLQLRKAG-LLLLDDLDRVLGAIKEKALKYKDTTCVGRSHGIHAEPMTLGLKFARFYQEFKRNRARLLDAIKEISVCKISG--AVGQFAS 189
                 ****************9.67**********************************************************************..9****** PP

                 SCCTHHHHHHHHHHHHHCSTEESSSHHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT.TSSEEEEGCCTSSC-TTSTTTEBTHHHHHHHHHH CS
     Lyase_1 210 adpefaelvakelakvtglpvkapnsfeavsdrDavvellgalkllatsLskfaeDlrllssge.aglvelslaesepGSSiMPgKvNPvqlElltgva 307
                 +dp  +e++akel    +   + +   ++v +rD+++ ++g+l+++a s+  +a ++r l+ +e +    + +  +++GSS MP+K+NPv +E+ltg a
  AHX11037.1 190 IDPFIQEYIAKELD---L---VPEIPATQVIPRDRYAVFFGILAVIASSMENIATEIRHLQRTEvLECA-EFFSPGQKGSSAMPHKKNPVLSENLTGLA 281
                 **************...6...2333334789*********************************55555.55555666*******************99 PP

                 HHH CS
     Lyase_1 308 grv 310
                 + v
  AHX11037.1 282 RIV 284
                 765 PP

>> ADSL_C  Adenylosuccinate lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.9   0.0     6e-27   3.6e-23       1      73 []     350     425 ..     350     425 .. 0.96

  Alignments for each domain:
  == domain 1  score: 81.9 bits;  conditional E-value: 6e-27
                 TGGGHHHHHHHHH.HTH-HHHHHHHHHHHHHHHHHC....HHHHHHT-HHHHCHHCHHHHHT-GGGCCTTHHHHHHHH CS
      ADSL_C   1 GlifservllaLv.kglgReeAyelVqeaamkawee....llelLaadpevkkseeeldalfdpayylgsadeivdrv 73 
                 Glifs++vllaLv +g +ReeAye+Vqe+amk+w++    ++e L++d++v ++   +++lf ++ yl+++d i++ v
  AHX11037.1 350 GLIFSQKVLLALVeSGKTREEAYEIVQENAMKTWNDknssFIEHLKKDARVDLDN--IERLFCYEGYLKHVDYIFENV 425
                 9************66************************************9865..******************986 PP

>> ASL_C  Adenylosuccinate lyase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.1e-05     0.068       4      96 ..     300     394 ..     298     409 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.1e-05
                 T--TCHHHHHTTCHHHHHHHH.HHHHHHHHHHCCEEE-HHHHHHHHHT-G.GGGHHHHHHHHHHT..T-TTHHHHHHHHHTTS.---HHHHHHHHHCS CS
       ASL_C   4 QRDLtdStvlRnlgvalahsl.ialksllkglsklevneealaedLdenw.evlaEaiqtvlrre..giekpYeklkeltrgk.kitkeslkefiesl 96 
                  RD++ S+v R l+ + + +l  al++l k +s+l v e++++++L+     + +  +  +l ++    e++Ye ++e   ++ + +    ++fie+l
  AHX11037.1 300 ERDISHSSVERVLAPTACITLdFALDRLSKVVSELLVFEDNITDNLNLLRgLIFSQKVLLALVESgkTREEAYEIVQENAMKTwNDK---NSSFIEHL 394
                 6************9887776659************************8751566888888887661146789999988765552222...23444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       651  (0.0363099); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3121.69
//
Query:       AHX11038.1  [L=161]
Description: ribosomal protein L9 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      5e-20   71.8   0.1    8.4e-20   71.0   0.1    1.4  1  Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
    1.7e-18   65.9   0.4    4.1e-18   64.7   0.4    1.7  1  Ribosomal_L9_N  Ribosomal protein L9, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_L9_C  Ribosomal protein L9, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.0   0.1   9.3e-24   8.4e-20       1      84 [.      63     144 ..      63     146 .. 0.92

  Alignments for each domain:
  == domain 1  score: 71.0 bits;  conditional E-value: 9.3e-24
                     HHHHHHHHHHSS...-EEEE--B-TT-BBSS---HHHHHHHHHHHT-----GGGEE-TTT-SBSSEEEEEEESSSS-EEEEEEEE CS
  Ribosomal_L9_C   1 eeaealaekLea.kvkvtikakagedgklFGsVtakdIaealkkklgieidkkkieleepiktlGeyevtvkLhkevtakikveV 84 
                     e+a +lae  +a +v + i a+ +e g lFG+V+ak+I++al+kk gie+ +k+i+l +pik+lG +ev++ Lh+ev++ ++v+V
      AHX11038.1  63 EAASKLAESFSAiDV-LPIYAQ-AERGFLFGAVNAKHIVAALSKK-GIEVSQKNIVLGSPIKELGAHEVKIFLHPEVECLLRVHV 144
                     578999999996665.688888.7799******************.**************************************9 PP

>> Ribosomal_L9_N  Ribosomal protein L9, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.7   0.4   4.5e-22   4.1e-18       1      46 [.       1      46 [.       1      47 [. 0.97

  Alignments for each domain:
  == domain 1  score: 64.7 bits;  conditional E-value: 4.5e-22
                    -EEEESSCBTTTBSSS-EEE--HHHHHHTTTTTTSEEE-SHHHHHH CS
  Ribosomal_L9_N  1 MkVILlkdVkglGkkGdvveVkdGyaRNyLipqglAvyAtpenlke 46
                    M VIL++   +lG  Gdv +Vk+G+aRNyLip g+Av+At++nl+ 
      AHX11038.1  1 MLVILKETTRKLGSVGDVLTVKKGFARNYLIPLGKAVRATKANLAI 46
                    78******************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1203.93
//
Query:       AHX11039.1  [L=83]
Description: ribosomal protein S18 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.7e-15   56.3   0.1    3.3e-15   56.0   0.1    1.1  1  Ribosomal_S18  Ribosomal protein S18


Domain annotation for each model (and alignments):
>> Ribosomal_S18  Ribosomal protein S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.1   1.9e-19   3.3e-15       2      51 ..      25      74 ..      24      75 .. 0.97

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 1.9e-19
  Ribosomal_S18  2 kekidYkdvelLsqFiterGkIlprriTGlcakhQrklakaIkrARhlaL 51
                   +e++dYk+v ++++F+t+ G+ l+rr T l ak+Qrk+ak++k+ ++laL
     AHX11039.1 25 IENFDYKNVAFMKRFMTSAGRTLSRRFTSLPAKKQRKMAKEVKKMKFLAL 74
                   6899*********************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (83 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      330  (0.0184059); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.28s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 594.79
//
Query:       AHX11040.1  [L=106]
Description: ribosomal protein S6 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-15   57.6   0.0    1.3e-15   57.4   0.0    1.1  1  Ribosomal_S6  Ribosomal protein S6


Domain annotation for each model (and alignments):
>> Ribosomal_S6  Ribosomal protein S6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.0   7.3e-20   1.3e-15       5      89 ..       1      85 [.       1      86 [. 0.97

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 7.3e-20
                  EEEE-TTS-HHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEEEEEETTEEEEEEEEEEEEESCCHHHHHHHHHHCSTTEEEEEEE CS
  Ribosomal_S6  5 vfilrpelseeevkelvekvgklilenggvvrkveswGkrkLaypikkkteGyyvlmnfdaspevikelertlrldervlRyliv 89
                  +f+++ +l+e  v +l++++++++ en+ +v + eswG+   ay+ik++t++ y+++ ++a+p+ ++++e +l+ ++ vlRyl+ 
    AHX11040.1  1 MFLASSSLTEGGVCNLMDNFNAIFAENNIKVLRQESWGLLSPAYRIKNHTKANYFMFVISAEPSSLHKFEAKLKYNDLVLRYLLQ 85
                  78999999999***********************************************************************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (106 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 768.79
//
Query:       AHX11041.1  [L=41]
Description: hypothetical protein NHE_0067 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 316.70
//
Query:       AHX11042.1  [L=336]
Description: PBP superfamily domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      8e-20   71.7   0.0    1.1e-19   71.2   0.0    1.1  1  PBP_like_2  PBP superfamily domain
  ------ inclusion threshold ------
      0.024   13.8   0.0       0.04   13.0   0.0    1.4  1  PBP_like    PBP superfamily domain


Domain annotation for each model (and alignments):
>> PBP_like_2  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   1.2e-23   1.1e-19      10     282 .]      19     303 ..      15     303 .. 0.86

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 1.2e-23
  PBP_like_2  10 geifgaGsttpapalrkladafekaapgakvnyastGSgagikalrngd....vdfagsdrplteseiaagwaang..aggliqvpvaigaialvvnkd 102
                 ++++++Gs+t+ p++    + f++ +  +++ ++stG++ag k ++ g      d+a s+r++ e+e+ a ++  +  + ++ +++ + +a+++++   
  AHX11042.1  19 EHVQIVGSSTVFPFISVISEEFARTYRVQTPMVESTGTSAGFKLFCMGVgeahPDIAVSSRRIDETEL-ALCKVYSvdKADILEIKLGEDALVIASDAG 116
                 5699************99999****99999************************************99.6788888878******************99 PP

  PBP_like_2 103 npln..lsreaLakIfsgkI.......tnWnd......vlglpadgpIkvvhrsdgsgttflfstalaeq....gpwtasgigasgsegvasavsnnga 182
                 ++ +  +s +++    +  I       +n n         +   d  Ik++ + ++ gt++ +++ ++ +     p+++ + +  +  g++s+++ +g 
  AHX11042.1 117 SNFRyqFSSDDIFRAIAFYIpsgmsliKNPNKrwididS-KRFYDSEIKIYGPLKNTGTFESIKQLILFRhclsDPAFKLAYEKDKLRGACSVIRDDGV 214
                 888899777776666554435555566666666666954.5556**************************555555555444444477889999****9 PP

  PBP_like_2 183 igyvsvaywlavkgysladvtngagkfvlptaataasalkvakiasnplawslqpveeniadgayPlsrftyiivyqpyayhgnnaalakaFldyllsd 281
                   yv+++++++v +++l+ +  + g f  ++   +as+lk  ++     ++ +qp++e+i +g+y l+r++y++v+ p+       + +k+ l  +lsd
  AHX11042.1 215 --YVEASSDENVIVQKLVRNPDAFGLFSYSFFIRNASKLKSHQV-----DG-VQPSYESIMSGEYGLTRPIYLYVKIPHLDF---VPNLKGLLREVLSD 302
                 ..*****************************9999999999555.....55.*************************98644...89999999988888 PP

  PBP_like_2 282 e 282
                 +
  AHX11042.1 303 N 303
                 6 PP

>> PBP_like  PBP superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.5e-06      0.04       2     113 ..      38     182 ..      37     213 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.5e-06
                 HHHHHH-TTCEEEEEES-HHHHHHHHHTTS-....SEEEESS---CCCHHCCCCCEEEEEEEEEEEE-CC-HCHCCCCHCCHHHS.............. CS
    PBP_like   2 eelaeknpgvrvavanvGsggGlkalragea....diagshlldketeeynapalrkaldgievvlvnlarreqglvvakgnpkk.............. 82 
                 ee+a++ +  +  v  +G+++G+k ++ g      dia s++ ++ete + ++ +   +d++++ +++l +++  +   +g + +              
  AHX11042.1  38 EEFARTYRVQTPMVESTGTSAGFKLFCMGVGeahpDIAVSSRRIDETELALCKVYS--VDKADILEIKLGEDALVIASDAGSNFRyqfssddifraiaf 134
                 6777776666677999***********985322338*********99777777666..68889999***999999999999777677888889999999 PP

                 ............--BGGGC.....-S-B-EEEEE-TTSHHHHHHHHHH CS
    PBP_like  83 ............itnwkdl.....adaplrlvnRetGSGtrdlfdell 113
                              + w d+      d+++ ++++ + +Gt+  + +l+
  AHX11042.1 135 yipsgmsliknpNKRWIDIdskrfYDSEIKIYGPLKNTGTFESIKQLI 182
                 999999998888777888877665679999999999999999988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 2591.25
//
Query:       AHX11043.1  [L=400]
Description: drug resistance transporter, Bcr/CflA subfamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-40  139.7  43.4    1.1e-40  139.7  43.4    1.8  2  MFS_1     Major Facilitator Superfamily
    3.8e-08   32.6  18.1    3.8e-08   32.6  18.1    3.5  2  Sugar_tr  Sugar (and other) transporter
    0.00057   18.4  23.2    0.00081   17.9  23.2    1.2  1  MFS_3     Transmembrane secretion effector
    0.00073   18.9  25.8      0.057   12.7  15.3    2.3  2  MFS_4     Uncharacterised MFS-type transporter YbfB
     0.0022   16.5  12.0     0.0025   16.3  11.5    1.3  1  TRI12     Fungal trichothecene efflux pump (TRI12)
  ------ inclusion threshold ------
       0.27    9.5  15.1       0.35    9.1   5.0    3.0  2  OATP      Organic Anion Transporter Polypeptide (OATP) family


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7  43.4   3.6e-44   1.1e-40       2     352 ..      11     352 ..      10     353 .. 0.90
   2 ?   -0.3   0.0      0.13   3.9e+02     153     174 ..     369     388 ..     357     397 .. 0.47

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 3.6e-44
       MFS_1   2 llaaflsalarsilgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfasslwlllvlrvlqGlgag 100
                  l+++++ +a  i+ palp  +a  + +s+  i l ++   lg av+sl++G+lsd +Gr++ l+lgl +f++++ll++f++s+++l++ r++qG+g+g
  AHX11043.1  11 TLVVLVADIAVEIYVPALP-SIAAFFSASAEIIKLTMGSNILGIAVSSLFYGALSDAWGRKPALILGLSIFVVASLLCIFSTSVFVLIFWRFFQGVGQG 108
                 5788999999*********.9*****************************************************88888978888************** PP

       MFS_1 101 alfpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpa 199
                 +++ +g a + d +++e+ ++ i+ ls+ ++++++++pllg++++ ++ W+++f++la+++ ++++ +l++++++  ++k++ + +         +++ 
  AHX11043.1 109 VAMVVGFASVKDFYSGERCAQIISRLSTVVAVSPAFAPLLGSMILVHFTWHYIFLFLALIASICLL-MLIFFFQDTLKHKNPLSLRA-------IFASY 199
                 ***************************************************************977.56889999999999988777.......67777 PP

       MFS_1 200 wkallkdpvlwillialllfffgfsg..lltllplylqevlglsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallav 296
                  + +++++++   l++++++ +++++  + t  p++l e+++ +   + g+l+a+   +++i+ +l  r+++ +g r+++ ++l l ll+ ++l++l  
  AHX11043.1 200 MRVIRNKNYI---LYSFVVVITFMWLwnVITSAPFLLLEDMNVP-MTEYGYLVAINVSGFVIGTILNHRYLHYVGLRNFIRFGLTLPLLSEILLIILHY 294
                 8889999955...44444444444445699999999********.99999999999999999999********************************** PP

       MFS_1 297 tssavllll..vlvliGfglgfvfpsllalasdlappeeagtasglfntagslggalg 352
                 t+  ++lll  + ++  +gl+fv + +++l+ d + ++ +g+a++l  ++  + galg
  AHX11043.1 295 TTGFSALLLecIWFFSAMGLAFVIGNATTLVLDQVDERDNGKATALLVFFEMVFGALG 352
                 *44444444559999999**********************************999998 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.13
       MFS_1 153 vfyilaivsllafvlfllllpe 174
                 +f i ++++ ++++l  +l+++
  AHX11043.1 369 IFTIGCVLATMLMLL--ILFRV 388
                 222222222222222..33333 PP

>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6  18.1   1.3e-11   3.8e-08      48     194 ..      42     183 ..      32     195 .. 0.80
   2 ?   -6.7  10.9         6   1.8e+04      45     106 ..     241     302 ..     205     386 .. 0.67

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.3e-11
                 HHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHH CS
    Sugar_tr  48 sglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqla 146
                 + l++++ ++G +++slf g l+d +GRk++l+ +  +fv++++l+++++   sv vli+ R++ G+g G+a v+    ++ +   + + +++s   + 
  AHX11043.1  42 IKLTMGSNILGIAVSSLFYGALSDAWGRKPALILGLSIFVVASLLCIFST---SVFVLIFWRFFQGVGQGVAMVVGFASVKDFYSGERCAQIISRLSTV 137
                 56889999******************************************...*******************999888888877666655555555555 PP

                 HHHHHHHHHHHHHHH.HTSS-TTHHH.HHHHCCHHHHHHHHHHGGGS--- CS
    Sugar_tr 147 itfGilvaaifglgl.nktsnadgwr.illglqlvpallllilllflPES 194
                 +++   +a  +g  +  ++     w+ i+l+l+l+ ++ ll+l++f+ ++
  AHX11043.1 138 VAVSPAFAPLLGSMIlVHF-T---WHyIFLFLALIASICLLMLIFFFQDT 183
                 5555555555554442222.2...43168899999999999999999887 PP

  == domain 2  score: -6.7 bits;  conditional E-value: 6
                 ..HHHHHHHTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH-TTTTSS-TGGG CS
    Sugar_tr  45 svlsglivsiflvGaiiGslfagllgdrfGRkkslliaavlfvigavlqaaakgknsvevli 106
                  + +g +v+i + G +iG ++     +++G ++ + ++ +l + + +l ++ + ++ + +l+
  AHX11043.1 241 MTEYGYLVAINVSGFVIGTILNHRYLHYVGLRNFIRFGLTLPLLSEILLIILHYTTGFSALL 302
                 45667777777778888888888888888888888888888887777777777665555554 PP

>> MFS_3  Transmembrane secretion effector
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9  23.2   2.7e-07   0.00081      38     400 ..      33     393 ..       9     399 .. 0.81

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-07
       MFS_3  38 tdisasplmvAlvqaaatLPifllsilaGalaDnfdrRkvllavqlllalvsvlltvlaalgllspwlllaltlligiGaalndPaWqAsvgelvkrrd 136
                 +  sas   + l   +  L i + s++ Gal+D + r+  l+ + ++ +++s+l + +     +s+++l+   ++ g+G+ + +    Asv ++ + + 
  AHX11043.1  33 AFFSASAEIIKLTMGSNILGIAVSSLFYGALSDAWGRKPALILGLSIFVVASLLCIFS-----TSVFVLIFWRFFQGVGQGVAMVVGFASVKDFYSGER 126
                 567899999999999*******************************999988776555.....578999****************************** PP

       MFS_3 137 vpaAvaLnsvginiaRsvGPAlgGvlvaavGaalafavnal.sylalivallrwkrevr.ksslprEkllealraglRftaasreikavlvRaalFgls 233
                   + +   s  + ++ +  P lg +++  +   + f + al + + l++ +   + + + k++l    l++ +   +R  +  + i  ++v  + F   
  AHX11043.1 127 CAQIISRLSTVVAVSPAFAPLLGSMILVHFTWHYIFLFLALiASICLLMLIFFFQDTLKhKNPLS---LRAIFASYMRVIRNKNYILYSFVVVITFMW- 221
                 *******************************9999987655134444444444444333034444...444455556777777777777776555554. PP

       MFS_3 234 asavlaLLPlvardqldgdalvyGillgalGvGAilgalllsr......LRerlsse.rlvllaavalAlvllslalasslwvavlvlllgGaaWital 325
                    v++  P++  + ++   + yG+l++   +G ++g++l+ r      LR+++    +l ll+ + l +   +++++  l   +  +   G a+++  
  AHX11043.1 222 LWNVITSAPFLLLEDMNVPMTEYGYLVAINVSGFVIGTILNHRylhyvgLRNFIRFGlTLPLLSEILLIILHYTTGFSALLLECIWFFSAMGLAFVIGN 320
                 456667789999999************998889999998887733333366666654245567888888888899999999999999999********* PP

       MFS_3 326 stlnvavqlavPrWvvgRalavYltvlaGglaaGsllWGavaealsvtlaLlaaaaalllaaaillllklpelea 400
                 +t  v  q+   +  ++ al v+  +++G+l  G ++     + + v+la+ + ++ l    ++l+l+++ + e+
  AHX11043.1 321 ATTLVLDQVDERDNGKATALLVFFEMVFGAL--GVYINAPFYDGTIVPLAIFTIGCVLATMLMLLILFRVDRKEN 393
                 *****************************75..889999999999999999999999998888888888877665 PP

>> MFS_4  Uncharacterised MFS-type transporter YbfB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7  15.3   1.9e-05     0.057      12     216 ..      24     224 ..      19     231 .. 0.79
   2 !   11.9   2.7   3.5e-05       0.1      19     122 ..     233     341 ..     227     398 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 1.9e-05
       MFS_4  12 ytpiLPallaegqlslsqagllaaaNylGYLvGallaafalsagaeRlr.llagllatvllllamaltesfaaflliRflaGvasAvvlvfgsslvlah 109
                 y p LP + a  + s+  + l    N lG  v +l+   als    R   l  gl   v++ l + + +s+++++ +Rf  Gv+ +v++v+g + v   
  AHX11043.1  24 YVPALPSIAAFFSASAEIIKLTMGSNILGIAVSSLFY-GALSDAWGRKPaLILGLSIFVVASLLCIFSTSVFVLIFWRFFQGVGQGVAMVVGFASVKDF 121
                 99*********************************65.777777778776889999999***********************************99999 PP

       MFS_4 110 aaaarrervgallfaGvGlGiavsgllvllllqlglsasslWlalavlsavllllvalllpraalreasaaaeaakaeqkslpllalllaYglaGfGYi 208
                  +  r +++++ l   v +  a + ll +++l+++  ++ + l la+++ + ll+++   + + l++ ++++   +a  +s   ++    Y l+ f  +
  AHX11043.1 122 YSGERCAQIISRLSTVVAVSPAFAPLLGSMILVHF-TWHYIFLFLALIASICLLMLIFFFQ-DTLKH-KNPLSL-RAIFASYMRVIRNKNYILYSFVVV 216
                 99999999999998776666666666665555554.4555688888888888888888887.44444.455555.344555555666778999988777 PP

       MFS_4 209 itatFlva 216
                 it  +l +
  AHX11043.1 217 ITFMWLWN 224
                 77777665 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.5e-05
       MFS_4  19 llaegqlslsqagllaaaNylGYLvGallaafalsagaeRlrllagl...latvllllamaltesfaafll..iRflaGvasAvvlvfgsslvlahaaa 112
                 ll++ ++ +++ g+l a+N  G+ +G +l    l+    R  ++ gl   l++ +ll+    t++f+a+ll  i f + ++ A+v+  +++lvl ++ +
  AHX11043.1 233 LLEDMNVPMTEYGYLVAINVSGFVIGTILNHRYLHYVGLRNFIRFGLtlpLLSEILLIILHYTTGFSALLLecIWFFSAMGLAFVIGNATTLVLDQVDE 331
                 789999***********************9888888889999888883335688999999999999999875578888899999999999999999999 PP

       MFS_4 113 arrervgall 122
                   +++  all
  AHX11043.1 332 RDNGKATALL 341
                 9888877753 PP

>> TRI12  Fungal trichothecene efflux pump (TRI12)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3  11.5   8.3e-07    0.0025      65     218 ..      26     181 ..       8     225 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 8.3e-07
       TRI12  65 salpnilqdvgqs.ensslfstlwttgqavsilvmgrltdrfgrrpfvilthilglvgaivgctatkfntllaamtllgvaagpagaspl.fvgelmsn 161
                  alp i      s e   l      +g avs l  g l+d +gr+p +il   + +v +++   +t +  l+    + gv  g a    +  v ++ s 
  AHX11043.1  26 PALPSIAAFFSASaEIIKLTMGSNILGIAVSSLFYGALSDAWGRKPALILGLSIFVVASLLCIFSTSVFVLIFWRFFQGVGQGVAMVVGFaSVKDFYSG 124
                 566666666554414445555667789*********************************99999999999999999***9999987655157777777 PP

       TRI12 162 ktkflgllivsipvvvtsglspylgqrlaiqgswrwifyiyiitsaiavllivvwyy 218
                       +  +s  v v  + +p lg  + +  +w +if    ++++i++l+++ ++ 
  AHX11043.1 125 ERCAQIISRLSTVVAVSPAFAPLLGSMILVHFTWHYIFLFLALIASICLLMLIFFFQ 181
                 66665566667767777789******************9999999998877766554 PP

>> OATP  Organic Anion Transporter Polypeptide (OATP) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.0   0.00012      0.35     130     195 ..      91     156 ..      77     191 .. 0.88
   2 ?    6.2   1.3   0.00091       2.7     276     348 ..     188     259 ..     180     295 .. 0.80

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00012
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 130 klvllfflaqlllGiGatpiytlGisYidDnvkkknsplylgilyalrilGpalGfllGslllkly 195
                 + v+++++  +++G+G+ + + +G + + D+ + ++ +  ++ l+++ ++ pa++ llGs++l  +
  AHX11043.1  91 TSVFVLIFWRFFQGVGQGVAMVVGFASVKDFYSGERCAQIISRLSTVVAVSPAFAPLLGSMILVHF 156
                 4456899999**************************************************998654 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.00091
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        OATP 276 elkslkdfpkalkrllknpifllvilssvfeillvaGfitFlpkylEtqFslsaseAnlltGvvvipgaalGi 348
                    sl+ ++++++r+++n+ ++l+++  v++++ +  +it  p  l +  ++  +e   l+ ++++ g+++G+
  AHX11043.1 188 NPLSLRAIFASYMRVIRNKNYILYSFVVVITFMWLWNVITSAPFLLLEDMNVPMTEYGYLV-AINVSGFVIGT 259
                 4568999******************************999988777777666666655554.34555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (400 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1098  (0.0612416); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.67u 0.26s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 2766.42
//
Query:       AHX11044.1  [L=266]
Description: eamA-like transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-14   53.3  33.2    5.4e-11   42.8   6.8    2.0  2  EamA      EamA-like transporter family
  ------ inclusion threshold ------
       0.63    8.3  31.6       0.52    8.6  20.1    2.0  2  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> EamA  EamA-like transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   6.8     6e-15   5.4e-11      32     136 ..       5     106 ..       1     107 [. 0.91
   2 !   16.7  18.4   6.8e-07    0.0061       5     135 ..     118     246 ..     115     248 .. 0.91

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 6e-15
        EamA  32 tltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnaslitslePvftlilsvlllgekltlkqllgivlill 130
                  ++f+  +i++i+l+++al+k++ l     + w +++l + l t+  ++l++ya ++++ +++s it+l P++    s  +++ek++++   ++v +++
  AHX11044.1   5 VVAFYLNVIGFIFLIPFALWKRKEL--AQSTLWRIYMLRA-LLTASSQILLVYAYNNMEFAQVSAITLLYPLMCSAASCMIFREKVGIRRASALVTGFI 100
                 5789999******************..5555566666666.899******************************************************* PP

        EamA 131 Gvllil 136
                 G+++i+
  AHX11044.1 101 GAVIII 106
                 ***986 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 6.8e-07
        EamA   5 llallaalfwaiyfvlskillrkvspltltfvrfliagillliiallkegklaklslkdwllllllgllgtvlafllffyalkktsasnaslitslePv 103
                 l+++l++++w +y +++ +  ++ s +t +f+ +l+ +++  + a +k+ ++   s+  w  + ++gl+ ++ + + +   ++  + s+++++ +l+ v
  AHX11044.1 118 LYVILVTFLWVAYDLATSKWGKTESLITQSFFVMLFVTLFSALPASFKDFTN--VSPLFWENFHYFGLIVVFYFVSGIAAIMHANELSVVMPFYFLVLV 214
                 789**************999*********************99999999999..7888888888888877777777788888888999*********** PP

        EamA 104 ftlilsvlllgekltlkqllgivlillGvlli 135
                 +++ ++++++ e+++l++ +g+ +il ++ +i
  AHX11044.1 215 VSTAIGYYVFSESVSLSTSFGATIILGSTSYI 246
                 **************************998877 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   8.0     0.002        18      79     172 ..       7     106 ..       3     117 .. 0.80
   2 ?    8.6  20.1   5.7e-05      0.52      39     184 ..     115     258 ..      92     266 .] 0.73

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.002
     DUF2070  79 elivviisllaillsall......qalvllalvlslalvfalrllvlvavsdesllkavlpaliqpllailllvlyfspesfllllllslifalavylf 171
                 ++++ +i ++ ++ +al       q+ +   ++l   l+++ ++l+++a+ + ++ ++++++l++pl+  +++ ++f+++  ++ + ++++ +++++++
  AHX11044.1   7 AFYLNVIGFIFLIPFALWkrkelaQSTLWRIYMLRALLTASSQILLVYAYNNMEFAQVSAITLLYPLMCSAASCMIFREKVGIRRASALVTGFIGAVII 105
                 44444444445554444456678888999999999*****************************************88888888777777777777776 PP

     DUF2070 172 i 172
                 i
  AHX11044.1 106 I 106
                 5 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 5.7e-05
     DUF2070  39 fgillfglpalvaflltlpvlrilggrltykrslflalltelivviisllaillsall...qalvllalvlslalvfalrllvlvavsdesllkavlpa 134
                 + +l+++l +++ ++ +l + ++     +++  ++ +++ +l+v ++s l++ +  ++   + +  ++  ++l++vf ++  +  ++  ++l+ ++  +
  AHX11044.1 115 HYSLYVILVTFLWVAYDLATSKW----GKTESLITQSFFVMLFVTLFSALPASFKDFTnvsPLFWENFHYFGLIVVFYFVSGIAAIMHANELSVVMPFY 209
                 22233333344444444444444....45566688888889999999999999988888889999999******************************* PP

     DUF2070 135 liqpllailllvlyfspesfllllllslifalavylfivvvdrplkrnlg 184
                 ++ ++++ ++ +++f +es+ l   + ++++l++  +i + ++++k++++
  AHX11044.1 210 FLVLVVSTAIGYYVF-SESVSLSTSFGATIILGSTSYIAYREYQIKKSME 258
                 **********99997.566666777889999****************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1109  (0.0618551); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2009.59
//
Query:       AHX11045.1  [L=40]
Description: hypothetical protein NHE_0071 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       190  (0.0105974); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.21s 00:00:00.50 Elapsed: 00:00:00.34
# Mc/sec: 354.30
//
Query:       AHX11046.1  [L=183]
Description: SURF1 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-06   27.7   0.0    3.1e-06   27.5   0.0    1.0  1  SURF1     SURF1 family


Domain annotation for each model (and alignments):
>> SURF1  SURF1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.5   0.0   1.7e-10   3.1e-06      77     175 ..      36     167 ..       6     168 .. 0.59

  Alignments for each domain:
  == domain 1  score: 27.5 bits;  conditional E-value: 1.7e-10
       SURF1  77 GylvltplrleddgeavlVnrGWvpaea.eklpka........apegeevrevtGllr..kss.tp..apeeesgewqvqsidvaalaeal..gaq... 156
                 G + ++ +  ++d+e  lVn G+v++++ e   +a        +   ++ ++++G l   +s+ +p  ++ + ++  ++++++ ++l++    +     
  AHX11046.1  36 GEHFYVLISGATDKESFLVNIGYVKKSSkE---EAidiinqrlE--YPKEMNLVGHLIpmRSTkVPfiKN-DLTNL-ELYYLNSKELSNVFqlP-Msdy 126
                 54545444444459**********996632...22445666432..2333379**999665554557633.35665.79********9995331.0334 PP

       SURF1 157 ...................kvlpvvl........hlgYaltWfgla 175
                                                   hl Ya+ W++++
  AHX11046.1 127 viystsndliedspevfvqL-----PrpiikvimHLWYAIMWYSIS 167
                 44455555564444444333.....033444555*********997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1601.04
//
Query:       AHX11047.1  [L=497]
Description: transcription termination factor Rho [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.9e-26   91.2   0.0    1.1e-25   90.5   0.0    1.4  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind
    5.1e-24   83.9   0.1    1.2e-23   82.7   0.0    1.7  2  Rho_RNA_bind  Rho termination factor, RNA-binding domain
    0.00032   20.6   2.6    0.00035   20.4   0.6    2.2  2  Rho_N         Rho termination factor, N-terminal domain
     0.0018   17.9   0.1     0.0099   15.5   0.0    2.3  2  AAA_25        AAA domain
     0.0044   17.4   0.0      0.029   14.8   0.0    2.3  2  AAA           ATPase family associated with various cellular 
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.064   13.2   0.0    1.5  1  NACHT         NACHT domain
      0.078   13.2   0.7       0.32   11.3   0.0    2.3  3  AAA_22        AAA domain


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0   4.4e-29   1.1e-25       3     211 ..     235     438 ..     233     440 .. 0.93

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 4.4e-29
                  HHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS..S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHHHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   3 rvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd..d.aiiyvgiGergnevaevleefpegtimkrtvlvantsnepvaareasiytgitlA 97 
                  r++D + p+++Gqr li+++ ++Gkt ++q++++  +s+  d   i+ +i er +ev+++ ++++         +v +t +ep+ + + ++  +i  A
   AHX11047.1 235 RIIDIIAPLGRGQRALIVAQPKTGKTILLQNIAHSISSNypDiHLIILLIDERPEEVTDMRRSVNA-------EVVSSTFDEPADKHVYVAEFAIEKA 325
                  89********************************99888887899**************9988765.......589********************** PP

                  HHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETSSEEEEEEEEEEE-GGCS.TTSHHHHHHHHHSSEEEEB- CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  98 EyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapdrtGsvtivaavspaggD.fsdpvttatlgitdgfivLd 194
                    + +qgk+v++++ds++r a+A++ +  + g+  +  g  ++  +k  +l   a ++ +  Gs+ti+ +  ++ g  +++ + ++  g  ++ i+Ld
   AHX11047.1 326 KRLVEQGKHVVILLDSITRLARAYNSVVPSSGKLLS-GGVDSNALQKAKRLFGAARNI-EGGGSLTIIGTALVDTGSrMDELIYEEFKGTGNSEIILD 421
                  ********************************9875.799******************.568******9999987752788999************** PP

                  HHHHHTTBSSSBCTTTE CS
                  xxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 195 kklaqrkhfPainvlvS 211
                  +kla+++ fPai++ +S
   AHX11047.1 422 RKLAEKRLFPAIDITKS 438
                  **************998 PP

>> Rho_RNA_bind  Rho termination factor, RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.7   0.0   4.8e-27   1.2e-23       2      71 ..     121     192 ..     120     194 .. 0.97
   2 ?   -3.3   0.0       3.5   8.9e+03      22      36 ..     310     324 ..     308     326 .. 0.78

  Alignments for each domain:
  == domain 1  score: 82.7 bits;  conditional E-value: 4.8e-27
                   EEEEEE-TTS-EEEE-G..TT---TT-EEE-CCCCCCTT--TT-EEEEEEE---SSS-SEEECEECEETTEE CS
  Rho_RNA_bind   2 eGiLeilpdgygFlRts..nylpgpedvYVsasqirkfgLrtGDaveGkvrppkerekynaLlrvesvngee 71 
                   +G+ e+l++g++F+R+s  nyl++++dvY+s+ q+r++g+rtGD + G+vr+pk++e+y+aL +  ++n+++
    AHX11047.1 121 SGVAEVLNEGFAFMRSSayNYLASQDDVYISPGQVRRLGIRTGDSIYGEVRAPKKGERYFALAKALEINNNP 192
                   69*******************************************************************975 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
                   --TT-EEE-CCCCCC CS
  Rho_RNA_bind  22 pgpedvYVsasqirk 36 
                   p ++ vYV++  i k
    AHX11047.1 310 PADKHVYVAEFAIEK 324
                   66789***9988866 PP

>> Rho_N  Rho termination factor, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.6   1.4e-07   0.00035       1      36 [.      71     106 ..      71     110 .. 0.91
   2 ?   -3.3   0.1       3.5   8.9e+03      12      21 ..     181     190 ..     181     192 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.4e-07
                 HHHHS-HHHHHHHHHHTT-TTGGGS-HHHHHHHHHH CS
       Rho_N   1 eLkektlseLraiAkelgienysrlRKqdLIfaIlk 36 
                 eL +kt  eL++ A+ l++ n+++  KqdLI  I +
  AHX11047.1  71 ELRSKTACELLKRAENLNLQNLAGTSKQDLIVLIAQ 106
                 79*****************************77755 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.5
                 HHHHHTT-TT CS
       Rho_N  12 aiAkelgien 21 
                 a+Ak l+i n
  AHX11047.1 181 ALAKALEINN 190
                 689***9965 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   3.9e-06    0.0099      31     125 ..     244     337 ..     223     383 .. 0.68
   2 ?   -1.9   0.0      0.81   2.1e+03     134     159 ..     459     486 ..     448     487 .. 0.66

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 3.9e-06
      AAA_25  31 pagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal.......rddarllvldlagveslpLfakdrg 122
                  +g  al++++p+tGKt l+ ++a+++++  p  +     +   l+++ E +e+ +  R + v +++       ++d++++v   a ++  +L++++++
  AHX11047.1 244 GRGQRALIVAQPKTGKTILLQNIAHSISSNYP--D----IHLIILLID-ERPEEVTDMRRS-VNAEVvsstfdePADKHVYVAEFAIEKAKRLVEQGKH 334
                 6899***********************98654..3....334444444.444433333333.3333334455444455555555444444455555555 PP

      AAA_25 123 gtl 125
                   +
  AHX11047.1 335 VVI 337
                 554 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.81
      AAA_25 134 eaaieevegvrlv..viDplsralggde 159
                 ++ ++++ +++ +  viD l+r+ +++e
  AHX11047.1 459 RRILNQMTDADAIefVIDKLQRTKNNEE 486
                 4445555554444449999999988876 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.96   2.5e+03      10      33 ..     115     140 ..     114     158 .. 0.77
   2 !   14.8   0.0   1.1e-05     0.029       2      74 ..     250     349 ..     249     394 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.96
                 SHHHHHHHHHHHHT..HEEEEEETTT CS
         AAA  10 GKTllakavakelg..vefleisgse 33 
                 GKT++ + va+ l+  + f++ s+ +
  AHX11047.1 115 GKTIVSSGVAEVLNegFAFMRSSAYN 140
                 9*********9996447777776655 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.1e-05
                 EEESSTTSSHHHHHHHHHHHHTHE....................EEEEETTTCSSS..................STTHHHHHHHHHHHHHHHTSTSEEE CS
         AAA   2 llyGppGtGKTllakavakelgve....................fleisgsellsk..................yvgesekkirelfkeakekakpsil 62 
                 l++  p tGKT+l + +a++++++                    +                             +v  +e  i++  + +++  k++++
  AHX11047.1 250 LIVAQPKTGKTILLQNIAHSISSNypdihliilliderpeevtdM----------RrsvnaevvsstfdepadkHVYVAEFAIEKAKRLVEQG-KHVVI 337
                 77889***************9766444445554444444444442..........03333333334333333335555555555555555555.59*** PP

                 EEETGGGHHHHH CS
         AAA  63 fiDEidalaksr 74 
                 ++D i +la++ 
  AHX11047.1 338 LLDSITRLARAY 349
                 *******99876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   2.5e-05     0.064      11      99 ..     257     351 ..     250     378 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.5e-05
                 TCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-.....-HCHHHCCCCTS--SSS-CCHHHHCCSCCCEE.......EEEE-STT-SS-TCH CS
       NACHT  11 sGKTtLlqklalawaegklpqgafklvFflslrelsrsgna..rsladllfsqlpepaapvsevwavllelperlL.......lilDglDelvtdlgq 99 
                  GKT+Llq +a+ + +++++     l+++l   + ++ +++     a+++ s ++epa+++  v ++ +e ++rl+       ++lD++ +l++  + 
  AHX11047.1 257 TGKTILLQNIAHSISSNYPDIH---LIILLIDERPEEVTDMrrSVNAEVVSSTFDEPADKHVYVAEFAIEKAKRLVeqgkhvvILLDSITRLARAYNS 351
                 5*****************8883...3333333333333333422567888888899988888866666666666666666666*****9999886655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1         1   2.6e+03      31      84 ..      53     106 ..      39     113 .. 0.60
   2 ?   11.3   0.0   0.00012      0.32       8     103 ..     249     345 ..     244     394 .. 0.73
   3 ?   -3.5   0.0       4.5   1.2e+04      80     103 ..     459     481 ..     450     490 .. 0.61

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
      AAA_22  31 eeakaeeerpevvfvtlpsstsskdl.lrellralglelkaerlsseellealeq 84 
                 e+++++ee ++ +f++l+++ s +   l + +++l+l++ a + s+++l+ +++q
  AHX11047.1  53 EQPEQNEEADHGAFIDLSELRSKTACeLLKRAENLNLQNLA-GTSKQDLIVLIAQ 106
                 34444446777777777777755444444445555555555.6677777665555 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00012
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelkaerlsseell.ealeqalrarav...ielliiDEa 100
                  ++++++ tGKT ll++++++       ++++ +++  +++   + + +d++r +  ++ +++ +e+++++ ++ e   + +++      ++++++D +
  AHX11047.1 249 ALIVAQPKTGKTILLQNIAHSIS----SNYPDIHLIilLIDERPE-EVTDMRRSVNAEVVSSTFDEPADKHVYVaEFAIEKAKRLVEqgkHVVILLDSI 342
                 689******************84....444677777634444444.69999999999999999998888888884444444444443666788888877 PP

      AAA_22 101 qhl 103
                  +l
  AHX11047.1 343 TRL 345
                 776 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 4.5
      AAA_22  80 ealeqalraravielliiDEaqhl 103
                 +++ +++ ++++   ++iD  q+ 
  AHX11047.1 459 RRILNQMTDADA-IEFVIDKLQRT 481
                 455555555555.56677777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (497 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.37
# Mc/sec: 4072.20
//
Query:       AHX11048.1  [L=50]
Description: hypothetical protein NHE_0077 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 388.52
//
Query:       AHX11049.1  [L=275]
Description: hypothetical protein NHE_0078 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
        3.4    7.8   6.7         34    4.5   0.0    2.2  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        8.9    6.8   5.8         12    6.4   0.0    2.8  3  DUF202           Domain of unknown function (DUF202)


Domain annotation for each model (and alignments):
>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.0    0.0038        34      44      89 ..      24      69 ..       4      84 .. 0.52
   2 ?    3.7   4.1     0.007        63      46      84 ..     109     161 ..     106     165 .. 0.63

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0038
  Phage_holin_3_6 44 gvlallalllllvalalalaalwlaalivaavllvlagvlalvglk 89
                     +++a++al++ll+ +a+ + +   +  +v  + +++++ l l g +
       AHX11049.1 24 AFIAFIALATLLMYVAVRMPFTTNGKYLVPMMDFLVGISLCLCGAA 69
                     4566666666666665333212222222333333333333333333 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.007
  Phage_holin_3_6  46 lallalllllvala.............lala.alwlaalivaavllvlagvla 84 
                      +++lal+l l++l+             l+l+ ++ +a ++ ++v++ l++ +a
       AHX11049.1 109 FVFLALILSLIGLVvmgccndvfpsdsLLLGiVRHAAEIVFGVVFVCLTAYVA 161
                      44555555555553345555558888866665688888888888888777665 PP

>> DUF202  Domain of unknown function (DUF202)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.1     0.032   2.8e+02      45      60 ..      26      41 ..       8      47 .. 0.67
   2 ?    6.4   0.0    0.0014        12      17      57 ..      60     126 ..      59     128 .. 0.83
   3 ?   -0.9   0.5      0.26   2.3e+03      40      55 ..     146     161 ..     135     164 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.032
      DUF202 45 lilivlgiltllvglv 60
                +++i+l++l++ v+++
  AHX11049.1 26 IAFIALATLLMYVAVR 41
                3477777777777665 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0014
      DUF202  17 slalialglallrffl..........................tgepsalgkilglilivlgiltllv 57 
                 +++l   g+a+++f                            t++++++ + l+lil ++g++++++
  AHX11049.1  60 GISLCLCGAAIMKFCEesprayvqegrvprsgngsgarvmvtTKNETPAFVFLALILSLIGLVVMGC 126
                 7999999******977899999999999998888888888887777777788899999999988865 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.26
      DUF202  40 gkilglilivlgiltl 55 
                   ++g++++ l++ ++
  AHX11049.1 146 EIVFGVVFVCLTAYVA 161
                 3567888888877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1954.27
//
Query:       AHX11050.1  [L=201]
Description: hypothetical protein NHE_0079 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.018   14.9   0.7      0.018   14.9   0.7    1.6  2  DUF2637   Protein of unknown function (DUF2637)
        0.3   11.0   9.3       0.24   11.3   0.4    2.1  2  DUF2721   Protein of unknown function (DUF2721)
        2.4    7.8   7.5        8.6    6.0   0.6    2.2  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF2637  Protein of unknown function (DUF2637)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.7   3.1e-06     0.018       6      43 ..      33      70 ..      29      92 .. 0.83
   2 ?   -2.0   0.1      0.49   2.9e+03      71     108 ..     119     156 ..     112     163 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-06
     DUF2637  6 fvlivaviafvlSFaalrdlAqkaglsealawlfPltv 43
                +  +v v + +l +++lr ++ +agl+++law++ + +
  AHX11050.1 33 VFFAVLVLGMLLAYITLRTYGSRAGLPGYLAWIIAAAF 70
                445677899************************97765 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.49
     DUF2637  71 awllvalsswiNgieatdvtlkvvaaalslaanvafel 108
                 ++ +++ ++    + atd++lk v +   + ++++ +l
  AHX11050.1 119 FITALVCTICLDCSVATDPALKYVELPFFILGVLLAAL 156
                 45555556667777777777777777666666666555 PP

>> DUF2721  Protein of unknown function (DUF2721)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   3.1     0.011        64      65     109 ..      33      77 ..      28      81 .. 0.88
   2 ?   11.3   0.4   3.9e-05      0.24      59     115 ..     104     160 ..      83     163 .. 0.85

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.011
     DUF2721  65 railllvlsallvvlvvlllflsallsldlsllaailfvlallll 109
                   +++lvl++ll+ ++  ++  +a l   l++++a+ fv++++ll
  AHX11050.1  33 VFFAVLVLGMLLAYITLRTYGSRAGLPGYLAWIIAAAFVASMFLL 77 
                 55678899999999999999999999999*************998 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 3.9e-05
     DUF2721  59 Rarlirrailllvlsallvvlvvlllflsallsldlsllaailfvlalllllvslll 115
                 R +++ +  +l ++++++++++ ++l  s++++  l+ +   +f+l++ll ++s  +
  AHX11050.1 104 RGKCVAAFGVLSAACFITALVCTICLDCSVATDPALKYVELPFFILGVLLAALSYYV 160
                 77777777778888888888888888889999*****************99988765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   1.2     0.002        12      10      52 ..      35      80 ..      27     104 .. 0.49
   2 ?    6.0   0.6    0.0014       8.6       9      54 ..     115     167 ..     105     182 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.002
     DUF4131 10 lalllllllllllllrr...rprrrvllllllllllallgfalrap 52
                +a+l+l +ll+++ lr    r      l++++++++++++f+l+  
  AHX11050.1 35 FAVLVLGMLLAYITLRTygsRAGLPGYLAWIIAAAFVASMFLLPIV 80
                3444444444444332233422222233333344444444444433 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0014
     DUF4131   9 llalllllllllllllrr.......rprrrvllllllllllallgfalrapqp 54 
                   a ++ +l++ ++l  +       ++    +++l++ll+++++++ +  p+p
  AHX11050.1 115 SAACFITALVCTICLDCSvatdpalKYVELPFFILGVLLAALSYYVSHVRPSP 167
                 23333334444455544498888877777778888888888888777766665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1634.03
//
Query:       AHX11051.1  [L=71]
Description: hypothetical protein NHE_0080 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       223  (0.0124379); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 589.40
//
Query:       AHX11052.1  [L=90]
Description: hypothetical protein NHE_0081 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   12.8   0.2      0.056   12.8   0.2    1.1  1  ApoL      Apolipoprotein L


Domain annotation for each model (and alignments):
>> ApoL  Apolipoprotein L
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   3.1e-06     0.056     129     170 ..       3      44 ..       2      86 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.1e-06
        ApoL 129 vLsatGlgLGaaaavTsvstsiveessnssakaeasrlvsts 170
                  L ++G+  G+ +a+ + +++i e++++  a+ae++  + ++
  AHX11052.1   3 CLITAGVTAGVLSAIVDYAANIAESTQKNLATAEVRLFAISN 44 
                 5899******************************98665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (90 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       899  (0.0501422); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 705.88
//
Query:       AHX11053.1  [L=247]
Description: hypothetical protein NHE_0082 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      0.003   17.9  10.6        0.3   11.5   1.4    2.2  2  DUF3995   Protein of unknown function (DUF3995)
  ------ inclusion threshold ------
      0.047   13.6   3.3      0.071   13.0   3.3    1.3  1  DUF4386   Domain of unknown function (DUF4386)
      0.074   13.3   0.2      0.074   13.3   0.2    2.2  2  TrbC      TrbC/VIRB2 family
        3.8    7.2   5.8         27    4.4   1.7    2.3  2  DUF4131   Domain of unknown function (DUF4131)


Domain annotation for each model (and alignments):
>> DUF3995  Protein of unknown function (DUF3995)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   3.1    0.0001      0.47      34      84 ..      50     104 ..      37     124 .. 0.70
   2 !   11.5   1.4   6.6e-05       0.3      10      78 ..     123     190 ..     115     215 .. 0.67

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
     DUF3995  34 a....vPsavatlavallllaaAllvlalarllgaplssrllrlaawvvaavlll 84 
                 +    +P+++a l v +lll+aA+ v+++a +  + +  +   +  ++ aavll+
  AHX11053.1  50 KcvlcAPGVAASLSVSMLLLMAAAYVVLRAPWKDGDPIAKSYHVFPVIFAAVLLA 104
                 355568************************7775555555555555555555543 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 6.6e-05
     DUF3995  10 yWalGGtwgleslaeavvgekegsavPsavatlavallllaaAllvlalarllgaplssrllrlaawvv 78 
                 ++  GG++g e l e+v + + g  +P++ ++ + +l+l+a+ ++++ + r  g+p s   + + ++ +
  AHX11053.1 123 AYREGGRVGREVLHEEVRKATWG-VRPGFTMVCMAVLFLAAGTVFAAFRDRCSGSPTSVDQVVCSVLEL 190
                 55669****77777777766665.479999999999999999999999998876665544444433322 PP

>> DUF4386  Domain of unknown function (DUF4386)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   3.3   1.6e-05     0.071      51     156 ..      63     165 ..      55     205 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.6e-05
     DUF4386  51 ellmalllvvlavlLypllrrvnpglallaaafrlveaaviavgllrl.lallpllaeaaalaapalraalallllalhdygyllgliffglwllllgl 148
                  + m ll+++++v+L +  +  +  +a  + +f ++ aav+++gl+ l l++  +la   a+  +  r    +l+ +++  ++ + + f+   ++++++
  AHX11053.1  63 SVSMLLLMAAAYVVLRAPWKDGD-PIAKSYHVFPVIFAAVLLAGLVYLsLFIKKVLAPVRAAYREGGRVGREVLHEEVRKATWGVRPGFT---MVCMAV 157
                 44555555666666666666666.5***********88888888776626666788888999999999999****************999...667777 PP

     DUF4386 149 lllrsrll 156
                 l+l ++ +
  AHX11053.1 158 LFLAAGTV 165
                 77666655 PP

>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   1.9      0.92   4.1e+03       9       9 ..      89      89 ..      56     115 .. 0.57
   2 ?   13.3   0.2   1.7e-05     0.074       7      60 ..     144     202 ..     137     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.92
        TrbC  9 r 9 
                +
  AHX11053.1 89 K 89
                0 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.7e-05
        TrbC   7 karrlllalalalvllllaspalAqaagg.....dpvetvlqnivdfltgplakviati 60 
                 +  r+ +++++++vl+l+a +++A+  +      ++v++v+++++  + + +a+++++ 
  AHX11053.1 144 WGVRPGFTMVCMAVLFLAAGTVFAAFRDRcsgspTSVDQVVCSVLELMCASIAFLAIIG 202
                 56677889999*************8777699999****************777777765 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0    0.0078        35      33      61 ..      61      89 ..      51      93 .. 0.85
   2 ?    4.4   1.7     0.006        27       6      48 ..      95     166 ..      90     182 .. 0.71

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0078
     DUF4131 33 llllllllllallgfalrapqpnandlsq 61
                 l++++lll+a+++++lrap++  +++++
  AHX11053.1 61 SLSVSMLLLMAAAYVVLRAPWKDGDPIAK 89
                688999**************999998876 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.006
     DUF4131   6 alvllalllllllllllllrr.............................rprrrvllllllllllallgfa 48 
                 ++++ a+ll+ l++l l+ ++                               r+ + ++++++l+la++ ++
  AHX11053.1  95 PVIFAAVLLAGLVYLSLFIKKvlapvraayreggrvgrevlheevrkatwGVRPGFTMVCMAVLFLAAGTVF 166
                 555566666666666555555899999999999999999999888877776666667778877777776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      365  (0.0203581); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 1977.04
//
Query:       AHX11054.1  [L=201]
Description: hypothetical protein NHE_0083 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0056   16.4   3.8     0.0081   15.9   3.8    1.2  1  Yip1      Yip1 domain
  ------ inclusion threshold ------
      0.027   13.3   1.5       0.59    8.9   2.9    1.9  2  MscS_TM   Mechanosensitive ion channel inner membrane domain 


Domain annotation for each model (and alignments):
>> Yip1  Yip1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   3.8   9.1e-07    0.0081      11     150 ..      17     154 ..      13     162 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.1e-07
        Yip1  11 rlkkeppilrapdlallllalltlllgllaslnlgqtlasgeevqgltlssllgaiiggylglllgllllalllhl.iakllg.gkgsfkqtlsvvgya 107
                 r+++++    +   +l+  ++l ll+++++s +l+ +  +g    g++++ +l+++i+++    +gl++l++ll+   ++ +g ++ s +++  ++g++
  AHX11054.1  17 RIRQKKF---WRNCGLATCCVLWLLVLAAYS-ALRPPWKDG---KGIAKGLHLWVAILSLM---VGLWVLSWLLDAnRSRGAGeSEDSDTRAAVFAGFS 105
                 6677777...333345555555555555555.334444444...56899999999999999...999999999998655555586666678******** PP

        Yip1 108 llPlilgaliaillllllgt......llllvgllaliWslvllylglka 150
                 l+P++ +a i+i+   l+ +        ++v++  ++ sl ll+l++ +
  AHX11054.1 106 LFPFVPAAMIFIVHDALFVGaypgyyDPAAVIAEVFFLSLTLLILFIGS 154
                 ************9998888899****55555555555555555555544 PP

>> MscS_TM  Mechanosensitive ion channel inner membrane domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0    0.0065        59     183     218 ..       8      43 ..       2      47 .. 0.77
   2 ?    8.9   2.9   6.6e-05      0.59     135     240 ..      36     152 ..      19     161 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.0065
     MscS_TM 183 ankkeeeknslrlrrllylllvlaPlalavlaalGY 218
                  +kk  e++++r ++++++  ++++ +l +l+++ Y
  AHX11054.1   8 SDKKAAEEKRIRQKKFWRNCGLATCCVLWLLVLAAY 43 
                 4555555555599****************9999866 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 6.6e-05
     MscS_TM 135 plllvlilaealsdalardvlG.....rlaflllllllavflarllrpalglyankkeeeknsl.......rlrrllylllvlaPlalavlaalGYyyT 221
                  ll++++ +   +     + ++      +a+l l+++l v+++ l  ++++  a ++e+++++        ++ ++   +++++  al v a  GYy  
  AHX11054.1  36 WLLVLAAYSALRPPWKDGKGIAkglhlWVAILSLMVGLWVLSWLLD-ANRSRGAGESEDSDTRAavfagfsLFPFVPAAMIFIVHDALFVGAYPGYYDP 133
                 4444444444444444444444444434555566666655555554.44444444433444333366666666666666677777788999999***** PP

     MscS_TM 222 alqLlerlilsllllllll 240
                 a  ++e ++lsl ll+l++
  AHX11054.1 134 AAVIAEVFFLSLTLLILFI 152
                 ************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (201 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      500  (0.0278878); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1452.73
//
Query:       AHX11055.1  [L=208]
Description: hypothetical protein NHE_0084 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.045   13.7   0.5       0.52   10.3   0.2    2.1  2  DUF679    Protein of unknown function (DUF679)
        1.1    9.6   7.7      0.098   13.0   1.8    1.9  2  DUF3021   Protein of unknown function (DUF3021)
        1.4    7.2   3.5       0.93    7.7   0.3    1.8  2  DUF2070   Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> DUF679  Protein of unknown function (DUF679)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0     0.049   2.9e+02     106     126 ..      58      78 ..      48      95 .. 0.78
   2 ?   10.3   0.2   8.7e-05      0.52      38      78 ..     106     148 ..      88     152 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.049
      DUF679 106 svvvFlavalsdknvvkClfp 126
                  v++F+++al ++ + +C + 
  AHX11055.1  58 PVLMFATLALETSPILSCDIW 78 
                 6899**************554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 8.7e-05
      DUF679  38 ltaaLlall..avscvllsfTDsivgedgkvyYgvatlkglkv 78 
                 + + L++l+  a++c+l s+ D +  +d+++  g++++++l v
  AHX11055.1 106 VQVWLVTLCcfAAVCILASIIDWVPIQDNRLKIGLIVAESLCV 148
                 45566666522679**********************9998865 PP

>> DUF3021  Protein of unknown function (DUF3021)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.4      0.26   1.6e+03      74     107 ..      20      55 ..      10      68 .. 0.48
   2 ?   13.0   1.8   1.6e-05     0.098      63     115 ..     102     156 ..      98     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 0.26
     DUF3021  74 lvvlllvlllalllg..Wfplsvigilivilifiii 107
                 ++++l+vl++ + l+  W +      ++ + +f+i+
  AHX11055.1  20 IFGWLAVLVAHVTLRapWKNGESLMKAWKVSLFLIV 55 
                 333444444443333335555333334444444444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.6e-05
     DUF3021  63 lsllkqtlihflvvlllvlllalllgWfpl.....svigilivilifiiiyliiwlif 115
                 ls ++q+++  l+++++v +la ++ W+p+     +   i ++++  + + ++i+++ 
  AHX11055.1 102 LSNKVQVWLVTLCCFAAVCILASIIDWVPIqdnrlK---IGLIVAESLCVGFAICFFL 156
                 788999************************995441...4444444433333333322 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.3   0.00016      0.93      79     125 ..      15      68 ..       6      74 .. 0.90
   2 ?    0.1   0.2     0.031   1.8e+02      71     114 ..     103     156 ..      88     171 .. 0.40

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00016
     DUF2070  79 elivviisllaillsall.......qalvllalvlslalvfalrllvlvavsde 125
                  ++++i+ +la+l+++++        ++++ a+ +sl+l++ +++l++ +++ e
  AHX11055.1  15 RVFFLIFGWLAVLVAHVTlrapwknGESLMKAWKVSLFLIVPVPVLMFATLALE 68 
                 6899*******************999******************9999988755 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.031
     DUF2070  71 s..lflalltelivviisllaillsall........qalvllalvlslalvfal 114
                 s  + + l+t+  ++++ +la+++ ++           +v  +l +++a+ f+l
  AHX11055.1 103 SnkVQVWLVTLCCFAAVCILASIIDWVPiqdnrlkiGLIVAESLCVGFAICFFL 156
                 333333333333333333444444443344332233333333333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       905  (0.0504769); expected 358.6 (0.02)
Passed bias filter:                      593  (0.0330749); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1551.05
//
Query:       AHX11056.1  [L=118]
Description: hypothetical protein NHE_0085 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.065   12.3   0.1      0.072   12.1   0.1    1.0  1  PHO4          Phosphate transporter family
      0.066   12.4   2.4      0.096   11.8   2.4    1.4  1  BPD_transp_2  Branched-chain amino acid transport system / pe


Domain annotation for each model (and alignments):
>> PHO4  Phosphate transporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1     8e-06     0.072      78     144 ..      21      86 ..      13     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8e-06
        PHO4  78 llatvlglPvStthslvGaliGaalaaegg.eavkwkklvkivlswvlsPllggiiaallfllvkrli 144
                 l+at  ++Pv    + v a i   ++++   +av+    ++i+l+++ s+llg+i++ +++++  +l+
  AHX11056.1  21 LTATRKKYPVALLLCFVLAAIRCCIVTGFLeNAVDYR--TQIALALIESVLLGVIFGCIMATMCFYLN 86 
                 8899**********************74445888887..89***************999998877772 PP

>> BPD_transp_2  Branched-chain amino acid transport system / permease component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   2.4   1.1e-05     0.096      45      95 ..      44     100 ..      19     114 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.1e-05
  BPD_transp_2  45 alllalllsl......lllallvallvgaavglllgllvlrlkvdeliitllllsvl 95 
                    ++  +l++       ++lal+ ++l+g+++g+++++++ +l+ ++  + ++l+++ 
    AHX11056.1  44 CIVTGFLENAvdyrtqIALALIESVLLGVIFGCIMATMCFYLNKNQSTFITGLSVET 100
                   33333333336666889**************************99999999888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (118 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      602  (0.0335769); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 910.53
//
Query:       AHX11057.1  [L=46]
Description: hypothetical protein NHE_0086 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      224  (0.0124937); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.25s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 372.97
//
Query:       AHX11058.1  [L=260]
Description: hypothetical protein NHE_0087 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
       0.19   11.9   3.1       0.21   11.8   0.1    2.2  2  DUF4079          Protein of unknown function (DUF4079)
        5.1    7.2  11.8        2.7    8.1   0.0    2.2  2  Phage_holin_3_6  Putative Actinobacterial Holin-X, holin supe
        7.1    7.2   9.1       0.79   10.2   2.0    2.2  2  DUF3681          Protein of unknown function (DUF3681)


Domain annotation for each model (and alignments):
>> DUF4079  Protein of unknown function (DUF4079)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   3.5e-05      0.21      59     108 ..      22      71 ..       8      78 .. 0.84
   2 ?    0.1   0.4      0.14   8.1e+02       5      30 ..     146     171 ..     142     211 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.5e-05
     DUF4079  59 llvvlgaigglvllylrrgklfpssHlyaGlavvvLlalsaalvpeiqkg 108
                 +l  ++ +++ ++++l+  k     H   Gla+v+L++  +a v +i++ 
  AHX11058.1  22 FLSCTLFLAATAMTFLQHCKSGLIAHCCLGLAMVCLVLSFVAGVASISQM 71 
                 56667788899999***********************9998888888765 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.14
     DUF4079   5 HPvlmvllvfpllgavaylGwqtrqr 30 
                  +v+ ++++ + l a++ylG+ + qr
  AHX11058.1 146 SAVSCGIVISAGLCAACYLGFWVAQR 171
                 56677777777777777777655555 PP

>> Phage_holin_3_6  Putative Actinobacterial Holin-X, holin superfamily III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00045       2.7      35      91 ..      18      71 ..      10      82 .. 0.59
   2 ?   -0.4   9.1       0.2   1.2e+03      30      83 ..     134     197 ..     130     204 .. 0.63

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00045
  Phage_holin_3_6 35 sgagllgaagvlallalllllvalalalaalwlaalivaavllvlagvlalvglkkl 91
                        ++l  +++la++a+++l  +   ++   + ++l +a v+lvl  v++++ ++++
       AHX11058.1 18 LVHAFLSCTLFLAATAMTFLQHCKSGLI---AHCCLGLAMVCLVLSFVAGVASISQM 71
                     4555666666666666666666665444...34444456666666666666665555 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.2
  Phage_holin_3_6  30 akragsgagllgaagvlallalllllvalalala.a.........lwlaalivaavllvlagvl 83 
                      ++r+ +g + l+ a+ ++++  + l++a+ l++  a         +w+  ++  + llv a +l
       AHX11058.1 134 KTRFKVGWAGLVSAVSCGIVISAGLCAACYLGFWvAqrgdsstlaSWALMFVQIVTLLVTACAL 197
                      6788888899999999999999999999976662223445556544444444444444444333 PP

>> DUF3681  Protein of unknown function (DUF3681)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.7       0.1   6.1e+02       8      59 ..      21      68 ..      14      72 .. 0.59
   2 ?   10.2   2.0   0.00013      0.79      54      96 ..     156     200 ..     131     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
     DUF3681  8 aLiagGvvkaaaalllalfrspggvflrhgkallylYYgiLvavvvfGlaea 59
                a +++ ++ aa a++ + + +  g+++   ++ l l  + Lv  +v+G+a +
  AHX11058.1 21 AFLSCTLFLAATAMTFLQHCK-SGLIA---HCCLGLAMVCLVLSFVAGVASI 68
                556666666666554433333.45665...3445566677777888887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00013
     DUF3681  54 fGl.aeasvgfWvsgdperrravGktvlwvsvlplvl.vaalGGf 96 
                 +Gl a   +gfWv+++ ++   +  ++++v ++ l++ + al Gf
  AHX11058.1 156 AGLcAACYLGFWVAQRGDSSTLASWALMFVQIVTLLVtACALCGF 200
                 455134569********9*************99875516789887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       932  (0.0519828); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1967.53
//
Query:       AHX11059.1  [L=484]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
   1.5e-107  359.1   0.0   1.9e-107  358.7   0.0    1.1  1  GatB_N     GatB/GatE catalytic domain
    6.6e-42  142.9   0.1    1.1e-41  142.2   0.1    1.3  1  GatB_Yqey  GatB domain


Domain annotation for each model (and alignments):
>> GatB_N  GatB/GatE catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.7   0.0  2.2e-111  1.9e-107       1     273 []      13     294 ..      13     294 .. 0.97

  Alignments for each domain:
  == domain 1  score: 358.7 bits;  conditional E-value: 2.2e-111
                 EEEEEEEEEEB--SB-SSSSSBSSSSCESTTSS--TTTTTSTT..--EEHHHHHHHHHHHHHTTEEE-SEE-EEEEE-TCTTCTTSEEEEESSS.SEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N   1 lviGlEiHaqlktksKlFssasteeegeepnsevsevdlalPGtlPvlnkeavelaikaalalnceiaeeskfdRKnyfypdlpkgyQitqkeeplake 99 
                 +viGlE+Haq+ +k+KlFs+a+  ++++epn++v+ +d+a+PG+lPvln +++e+a+ka+l l+ +i+  s f+RK+yfypdlp+gyQitq++ pl+++
  AHX11059.1  13 VVIGLEVHAQILSKNKLFSDAPC-DHRKEPNTSVTLFDAAMPGVLPVLNFNCIEKAVKAGLGLQGKINLYSVFERKHYFYPDLPHGYQITQNTYPLITG 110
                 69********************6.5999*********************************************************************** PP

                 EEEEE...TEEEEEEEEEEEE---EEEEE.ETTEEEEETTSTT-EEEEEEE-STB-SHHHHHHHHHHHHHHHHHHTSB--SGGGTTEEEEEEEEECTSE CS
                 xxxxx...xxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 100 Gslel...ekkvrierihlEeDaaksvhe.ekeeslvdlnRaGvpLiEivtepdlrspeearavveklrellralgvsdgnmeeGslRcDvNvSvreee 194
                 G +++   ek +ri++ih+E+Da+ks+h+ + +++++dlnRaGvpL+Eiv+epd+rsp+ea+a+v+kl+ +l+++g+s++nme+G+lRcDvNvSvr+  
  AHX11059.1 111 GCVRIknpEKVIRIHHIHIEQDAGKSIHDlSPDKTYIDLNRAGVPLMEIVSEPDIRSPAEAVAYVNKLKLILQCVGASNANMEKGELRCDVNVSVRKL- 208
                 ****99988999****************87888***************************************************************55. PP

                 TTSSS..--EEEEEE-SHHHHHHHHHHHHHHHHHHH.......-EEEEEETTTTEEEEECC----...-EEE-TTS--EE--HHHHH CS
                 xxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      GatB_N 195 kgeee.gtrvEiKnlnslksiekaieyeierqiell.......qeTrkfdedkgetvslRskeeaedYryfpepdlppleiseelie 273
                  gee+ g+r+EiKnlns+ks+++aieye++rq+e+l        eT+ fd ++ +t+++Rske+  dYryfp+pdl pl+++ee+ie
  AHX11059.1 209 -GEEKmGNRCEIKNLNSTKSLAQAIEYEARRQVEILesggsieVETKLFDVNNLNTRAIRSKESVMDYRYFPDPDLLPLVLEEEYIE 294
                 .66667******************************************************************************996 PP

>> GatB_Yqey  GatB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.1   1.2e-45   1.1e-41       2     148 .]     334     480 ..     333     480 .. 0.98

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 1.2e-45
                 HHHHHHHHSS.HHHHHHHHHTCHHHHHHHHTXXTTCSSTTHHHHHHHHHHHHTTSSGHHHHHHHHHHHHHHTXXHHHHHHHCTXXXXXXSSXHHHHHHH CS
   GatB_Yqey   2 ffeevvkegadaklaanwllnellgelnkegleieelkltpeqlaellkliaegkIskkiakevleelleegkspeeiieekgLkqisdeeeleklvee 100
                 +f+ +++ g+ aklaa+wl++el g lnk+++++e++k+tpe l ell+l+ +++Is+++akevl++ l++ +sp+ei+++ gL+qi+d++ +   ve 
  AHX11059.1 334 YFDCLLEMGHAAKLAARWLTVELFGLLNKNNISFEDNKITPEILGELLTLVVDEEISERTAKEVLAKSLDGVSSPKEIVKRDGLQQITDQNIILGHVET 432
                 89999999999**************************************************************************************** PP

                 HHHTXHHHHHHHTTXXTTSTHHHHHHHHHTTSSXSXHHHHHHHHHHHS CS
   GatB_Yqey 101 viaenpkavedyksgkekalkflvGqvMkktkGkadpklvnellkekL 148
                 v++enp+++++y sg +k l+f+vGq+ k+++G a p +vn++l++++
  AHX11059.1 433 VLNENPDKLQEYLSGRDKILGFFVGQIIKRSNGNASPHVVNKILMQEI 480
                 ********************************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (484 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3707.27
//
Query:       AHX11060.1  [L=144]
Description: cytidine and deoxycytidylate deaminase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.6e-22   77.2   0.0    1.1e-21   77.1   0.0    1.1  1  MafB19-deam      MafB19-like deaminase
    1.1e-21   76.6   0.0    1.3e-21   76.3   0.0    1.1  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
  ------ inclusion threshold ------
      0.013   15.6   0.5       0.22   11.6   0.5    2.1  1  Bd3614-deam      Bd3614-like deaminase
      0.036   14.1   0.0      0.051   13.6   0.0    1.2  1  APOBEC2          APOBEC2
      0.037   14.2   0.0       0.06   13.5   0.0    1.3  1  SNAD4            Secreted Novel AID/APOBEC-like Deaminase 4
       0.17   12.0   0.0       0.26   11.4   0.0    1.4  1  APOBEC3          APOBEC3


Domain annotation for each model (and alignments):
>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.1   0.0   3.6e-25   1.1e-21      19     138 .]      11     138 ..       1     138 [. 0.93

  Alignments for each domain:
  == domain 1  score: 77.1 bits;  conditional E-value: 3.6e-25
  MafB19-deam  19 kikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepCdmCagaivqaglkklvygagnpks........ln 108
                  + ke+++gav v+d+ v+a+  n+   + ++taHaE+ +++ A kkl+s  ld+a lyvtlepC+mC  ai  +++k l ++a ++k          n
   AHX11060.1  11 SDKEVPVGAVLVQDGVVVASSGNRMFRDSDPTAHAEMIVIKVALKKLGSGFLDEAELYVTLEPCPMCMYAISLSRIKALYFAAYDEKRgaisncclGN 108
                  5589**********************************************************************************999999999778 PP

  MafB19-deam 109 kLkvkekngrvelveddckeilkgffkklr 138
                   + ++ +     l++++ + +l++ffkklr
   AHX11060.1 109 DVYFHIPQVYDGLMQEEASSLLSDFFKKLR 138
                  99999998888899**************98 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   4.5e-25   1.3e-21       8     100 ..       1      92 [.       1      93 [. 0.96

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 4.5e-25
                      HHHHHHHHHHHHTTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHH.TSSCETTEEEEEEE--BHHHHHHHHHHT-SEEEEE CS
  dCMP_cyt_deam_1   8 lelalkaakeaqkcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaakn.ggsklegatlyvtlePCsmCakaiiqsgikkvvvg 100
                      ++lal+ a+e+  +++++VGav+v++g +++   n+ ++++++t+HAE++ i  a+k+ g+  l++a lyvtlePC+mC  ai  s+ik ++++
       AHX11060.1   1 MKLALEIARES--DKEVPVGAVLVQDGVVVASSGNRMFRDSDPTAHAEMIVIKVALKKlGSGFLDEAELYVTLEPCPMCMYAISLSRIKALYFA 92 
                      8999*****99..9********************************************88768899************************9986 PP

>> Bd3614-deam  Bd3614-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.5   7.3e-05      0.22      76      92 ..      63      79 ..       6     103 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
  Bd3614-deam 76 egarllvtlqcCkmCAa 92
                 ++a l+vtl++C mC  
   AHX11060.1 63 DEAELYVTLEPCPMCMY 79
                 5799***********64 PP

>> APOBEC2  APOBEC2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   1.7e-05     0.051      41      89 ..      34      81 ..      19      88 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.7e-05
     APOBEC2 41 GvlenkekkcHaEllflskvkkkkleekkeykvtwyvswsPCaeCaeev 89
                 ++++ ++++HaE+++++   k kl +    +  +yv+  PC+ C+  +
  AHX11060.1 34 RMFRDSDPTAHAEMIVIKVALK-KLGSGFLDEAELYVTLEPCPMCMYAI 81
                5788889999*******99998.8999999999************9876 PP

>> SNAD4  Secreted Novel AID/APOBEC-like Deaminase 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     2e-05      0.06      17      60 ..      36      81 ..      25      87 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
       SNAD4 17 lkn.kke.haEllflekikseldpsqeyrvtwylswsPCaeCaeki 60
                +++ + + haE+++++   ++l +    +  +y++  PC+ C+ +i
  AHX11060.1 36 FRDsDPTaHAEMIVIKVALKKLGSGFLDEAELYVTLEPCPMCMYAI 81
                44423336**********************************9876 PP

>> APOBEC3  APOBEC3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.5e-05      0.26      23      67 ..      34      78 ..      22     131 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.5e-05
     APOBEC3 23 gyfkn.kekkHAEerfidkirslnldslkqykitcylswsPcpkCa 67
                 +f++   + HAE+  i+   + +l s    +  +y++  Pcp C 
  AHX11060.1 34 RMFRDsDPTAHAEMIVIKVALK-KLGSGFLDEAELYVTLEPCPMCM 78
                5677734578***999976666.99999999**************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (144 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1232.84
//
Query:       AHX11061.1  [L=338]
Description: glycosyltransferase family 28 domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.1e-33  113.8   0.0    1.2e-32  113.2   0.0    1.2  1  Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal dom
    1.5e-23   83.4   0.1    3.9e-22   78.8   0.0    2.3  2  Glyco_transf_28  Glycosyltransferase family 28 N-terminal dom
  ------ inclusion threshold ------
       0.27   11.0   0.2       0.69    9.8   0.1    1.6  2  NDUF_B8          NADH-ubiquinone oxidoreductase ASHI subunit 


Domain annotation for each model (and alignments):
>> Glyco_tran_28_C  Glycosyltransferase family 28 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.0   1.9e-36   1.2e-32       2     144 ..     171     312 ..     170     337 .. 0.93

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 1.9e-36
                      EEEEE-SSSHHHHHCCCTSHHHHHHHHHHHHCHHHCCT-EEC---STT-TTTTCEEEEEESSSSHHHHHHHH-EEEECS-CHHHHHHHHTT--E CS
  Glyco_tran_28_C   2 ilVtGGSqgaeaLnelvlselkllelksrelqvlhqtGkreleevkikveeltlkvevfefidkmaeaikaadLvIsRAGagtiaEllalgkpl 95 
                      ilV+GGSqg++ L  +v  +l++ ++k  +l+++hq+ + +   +++ + e +l+ ev  f++++ e i+ adLvIsR+Ga +i E+l +g p 
       AHX11061.1 171 ILVIGGSQGSSVLGLAVARILAKFAEK-TNLEITHQCKEADVIALRNFYIENKLTAEVSHFFNNIPEKIEHADLVISRSGAISISEILTIGRPG 263
                      99*************************.7*************999999777779**************************************** PP

                      EEE--TT....S-HHHHHHHHHHHHHHSSEEEE-STTCHHHHHHHHCCS CS
  Glyco_tran_28_C  96 IlvplpeaaenhqdnNakelekagaalvleqkeltpekLeeallelaae 144
                      I++p+pea +nhq  Nak + ++  +++le+k++t e+L++a +++++ 
       AHX11061.1 264 IFIPYPEAKDNHQFFNAKFVDDNHMGILLEEKNFTQESLIAAMEKVFTG 312
                      *******************************************999875 PP

>> Glyco_transf_28  Glycosyltransferase family 28 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.8   0.0   6.6e-26   3.9e-22       2     138 ..       8     135 ..       7     136 .. 0.89
   2 ?    2.4   0.0     0.024   1.5e+02       2      42 ..     171     206 ..     170     246 .. 0.71

  Alignments for each domain:
  == domain 1  score: 78.8 bits;  conditional E-value: 6.6e-26
                      EEEE-SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHHHHCCT-EEEE---GHCTT..CHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC CS
  Glyco_transf_28   2 vllggGTgGhvfPalAlakeLkkegheVrylgtkrgleerlveeaglefepiageklrrklspknlkeilkvlkavvkakkilkeakpdavvgt 95 
                      ++++gGTgGh+fPalA+a++L  eg     ++t+++ ++  +++   +   +++       s +++k + ++l +v k+ k+++ ++p+ ++++
       AHX11061.1   8 FIAAGGTGGHIFPALAVAEALGNEG----LFITDKRSRNYGNRNIIAPCSVLPIV-----SSARKFKFLISFLPSVLKTLKLIIIHRPEGILSF 92 
                      689**********************....69999999999744444445447777.....45668888888888899***************** PP

                      CCCCCHCCCCCHCCCTTHCCCCCHCTS-ECCCCCCCCC-SCCC CS
  Glyco_transf_28  96 ggyvslpaviaaplaripviihEqnaipglanktlsrtatkva 138
                      ggy  lp++ aa l r  +++hE+n +pg +n+++ r+a+k++
       AHX11061.1  93 GGYPCLPVLTAALLTRRRIFLHESNTVPGRVNRIFMRFAKKIM 135
                      *****************************************97 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.024
                      EEEE-SSHHHHHHHHHHHHHHHCTT-EEEEEEETCCCHHHH CS
  Glyco_transf_28   2 vllggGTgGhvfPalAlakeLkkegheVrylgtkrgleerl 42 
                      +l++gG+ G   + lA+a+ L+k   ++       +++++ 
       AHX11061.1 171 ILVIGGSQGSSVLGLAVARILAKFAEKTN-----LEITHQC 206
                      6899******************9996666.....3344444 PP

>> NDUF_B8  NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0      0.67     4e+03      57      69 ..      91     103 ..      86     104 .. 0.80
   2 ?    9.8   0.1   0.00011      0.69       7      32 ..     143     168 ..     139     170 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.67
     NDUF_B8  57 gaGDYPklpvvsa 69 
                   G YP lpv +a
  AHX11061.1  91 SFGGYPCLPVLTA 103
                 6899*****9885 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00011
     NDUF_B8   7 avsrilrarspltkdhkPgpyPktee 32 
                 ++sr++++  plt+d+ P pyPk+ +
  AHX11061.1 143 KISRTVETGNPLTRDVIPKPYPKNSK 168
                 7899999****************975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.19s 00:00:00.65 Elapsed: 00:00:00.45
# Mc/sec: 2250.41
//
Query:       AHX11062.1  [L=296]
Description: methionyl-tRNA formyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.7e-31  107.9   0.0    6.6e-31  107.4   0.0    1.2  1  Formyl_trans_N  Formyl transferase
    3.9e-07   30.2   0.0    7.5e-07   29.3   0.0    1.5  1  Formyl_trans_C  Formyl transferase, C-terminal domain


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0   7.4e-35   6.6e-31       1     180 [.       1     174 [.       1     175 [. 0.85

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 7.4e-35
                     -EEEEEESESSHHHHHH.HHHHHHTTSECEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-SEEEEES--S---H CS
  Formyl_trans_N   1 kkivvlisgtgsnlqal.ldalkkgsleadvvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkadlivlagymkllpk 94 
                     +ki+++  g+++++    l+ l   +l  +vv v+s+++k++g++ ++   +   ++ +++l+ +   ++ l+ee+ +   d+iv+++y+++lp+
      AHX11062.1   1 MKIIFM--GSSEFAIPTlLKLLTIPEL--EVVEVYSKPPKPKGRGLQTVITPIHSIALQHDLSVK--TPSSLKEEILQ-DCDVIVVVSYGLILPN 88 
                     567777..4444444441444444444..6****************9999998888888887776..67777777765.689************* PP

                     HHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHH CS
  Formyl_trans_N  95 elvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtkeeleqrvadaehkalvea 180
                      +++++r  ++niHpSLLPr++G ++iq +l+ Gdke+Gv+i  v++elD Gai+aq+ +  + ++t + l +r+a ++ ++l ++
      AHX11062.1  89 SVLAHPRIAAINIHPSLLPRWRGPSPIQYTLLGGDKEAGVSIIDVTQELDAGAIYAQEFIILDGTETYSALHDRLAILGASMLCDV 174
                     **********************************************************999999***********99999988877 PP

>> Formyl_trans_C  Formyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   0.0   8.3e-11   7.5e-07       9      99 ..     203     290 ..     198     291 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 8.3e-11
                     --TTSBHHHHHHHHHHT-TS--EEEEETTEEEEEEEEEEE-S--SS-.TTSEEETT..TEEEE-SBSEEEEEEEEETTS--EEHHHHHHH. CS
  Formyl_trans_C   9 idwnqsaeeihnlvrglspwPgayttlngkrvkllkaevvsesssaespGtivavdkggllvacgdgallilelqlegkkamsaedflngl 99 
                     +d+++s+e   ++ r +    +++++  + r+k+++a+  +++  +++ G + + + ++l+++ +dg +li+ +q+ +kk+m+++dflng+
      AHX11062.1 203 VDFEESVEIFFRKLRVF---GAVFAEAFDMRIKIVEASLSDAHLYTDELGLVFKKETKELFLQFRDGKVLIKIVQPVNKKKMPVRDFLNGI 290
                     56666666666666666...4556666778**********99999999******9999*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2240.68
//
Query:       AHX11063.1  [L=272]
Description: NAD+ synthetase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-75  252.7   0.2      3e-75  252.5   0.2    1.0  1  NAD_synthase    NAD synthase
    7.4e-07   29.1   0.0    8.9e-07   28.9   0.0    1.3  1  Asn_synthase    Asparagine synthase
      1e-06   28.4   0.1    2.2e-06   27.3   0.0    1.6  2  QueC            Queuosine biosynthesis protein QueC
    0.00014   21.6   0.0    0.00024   20.7   0.0    1.4  1  ThiI            Thiamine biosynthesis protein (ThiI)
    0.00035   19.5   0.0     0.0006   18.7   0.0    1.4  1  tRNA_Me_trans   tRNA methyl transferase
  ------ inclusion threshold ------
       0.01   15.4   0.2        0.7    9.4   0.0    2.3  2  DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase dom
      0.079   12.7   0.0       0.12   12.1   0.0    1.5  1  ATP_bind_3      PP-loop family


Domain annotation for each model (and alignments):
>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.5   0.2   1.2e-78     3e-75       5     240 ..       8     260 ..       4     262 .. 0.96

  Alignments for each domain:
  == domain 1  score: 252.5 bits;  conditional E-value: 1.2e-78
                   HHHHHHHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTHHHHHHHHHHHHHHTSEEEE---HHHHHHHHHHHHHHH....- CS
  NAD_synthase   5 lvdflkeyvkkagakgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsseedvedalalaenlgievktidikpivrafeqelkeak....e 97 
                   +v+ l++y++++g+++v++GlSGG+DS+lvaa+av+alg+e+v ++++Ps ++s++++eda ++a++l++e + i+i++i+++fe++l+       e
    AHX11063.1   8 IVQELQKYLRESGFSNVLIGLSGGIDSALVAAIAVDALGSERVYTVMMPSPYTSKQSIEDAEEIAKRLEVEHTIIPINHIMKSFEASLSRVVewepE 104
                   67889********************************************************************************95555444456* PP

                   HHHHHHHHHHHHHHHHHHHHHHHTEEEB---BHHHHTTT-S-TTTTT--SBETTTTS-HHHHHHHHHHTT..............--HHHHCS--B-- CS
  NAD_synthase  98 dlakgNlkaRiRmailyaianklnllvlgTgnksElvvGyfTkyGDgaadlapiaellKtevkeLakeln..............vPervlkkpPsAd 180
                   d++++Nl+aRiR +il+  +nk+n++vl+T+nksE+++GyfT++GD  ++ api +l+Kt+v+eL+++ n              +P+ + +k P+A+
    AHX11063.1 105 DITEQNLQARIRGVILMGLSNKTNKMVLATSNKSEILTGYFTLHGDTCGGYAPISSLFKTQVYELVRWRNeniveglnlqkryiIPKTISEKLPTAE 201
                   ************************************************************************************************* PP

                   SSTT-BHHHHHSS-HHHHHHHHTHSSSS...HHHHHTTT--HHHHHHHHHHHHHTGGGGS CS
  NAD_synthase 181 LkpgqtDeeeLgikYdelDeiLklvekkkspeeiikekelpaevvekieklvkksehKrk 240
                   L+ +q D + L+ +Y++lD+iL l  +k+  ++++k ++l+++vv++++++vkkse+Kr+
    AHX11063.1 202 LRYSQKDLDTLP-EYKILDQILALDLQKQGIQDVAKALQLDEQVVSRVADMVKKSEYKRR 260
                   ************.**********99999999****************************8 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.9   0.0   3.5e-10   8.9e-07      20      93 ..      24     100 ..      17     242 .. 0.72

  Alignments for each domain:
  == domain 1  score: 28.9 bits;  conditional E-value: 3.5e-10
  Asn_synthase  20 vGalLSGGlDSSliaalaarqsksplktFsigfee..kgsdeakyakevaehlgtehtelvlte..eelldalpdviy 93 
                   v + LSGG+DS+l+aa+a   +  + + +++ + +   + + ++ a+e+a++l++eht + ++   + +++ l +v++
    AHX11063.1  24 VLIGLSGGIDSALVAAIAVDALG-SERVYTVMMPSpyTSKQSIEDAEEIAKRLEVEHTIIPINHimKSFEASLSRVVE 100
                   6677****************997.899*****933578889999*************998887532455555666666 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   8.5e-10   2.2e-06       2      74 ..      24      97 ..      23     126 .. 0.84
   2 ?   -2.6   0.0       1.3   3.2e+03      53      71 ..     226     244 ..     194     264 .. 0.51

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 8.5e-10
                EEEE--SSHHHHHHHHHHHHH-..SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-GGGGGGSCGGG-- CS
        QueC  2 avvllSGGlDSttvlalakkeg..kevealtfdYgqrhkkeleaakkiakelgveehkildldllkelggsaLtd 74
                +++ lSGG+DS+ v+a+a ++   ++v+++ +      k+ +e a++iak+l+v eh+i+ ++++ +  + +L +
  AHX11063.1 24 VLIGLSGGIDSALVAAIAVDALgsERVYTVMMPSPYTSKQSIEDAEEIAKRLEV-EHTIIPINHIMKSFEASLSR 97
                57789*************99865689**9999888888889999**********.********998888887765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.3
                 -.-EEEEE-GGGGGGSCGG CS
        QueC  53 veehkildldllkelggsa 71 
                 ++++ i d+    +l ++ 
  AHX11063.1 226 LQKQGIQDVAKALQLDEQV 244
                 3333333333333333333 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   9.4e-08   0.00024       5      87 ..      23     106 ..      20     129 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 9.4e-08
        ThiI   5 kvlaLlSgGiDSp.VaaylllkRGcrvvlvhlknepgtseeaiekveklaellaeyqtslevklvvvdfkevlkeilekvkekl 87 
                 +vl  lSgGiDS  Vaa  +   G + v+  +  +p+ts++ ie  e++a+ l   +t + ++ ++ +f+  l+ ++e  +e+ 
  AHX11063.1  23 NVLIGLSGGIDSAlVAAIAVDALGSERVYTVMMPSPYTSKQSIEDAEEIAKRLEVEHTIIPINHIMKSFEASLSRVVEWEPEDI 106
                 68889*******85777888889**999999999************************************99999998777665 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.3e-07    0.0006       2      70 ..      23      84 ..      22      97 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.3e-07
  tRNA_Me_trans  2 kvvvalSgGVDSsvaaallkeq.gyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdf 70
                   +v+++lSgG+DS+++aa+  ++ g e  +v+  ++ +        ++++ ++dae++a++l+++++++ +
     AHX11063.1 23 NVLIGLSGGIDSALVAAIAVDAlGSE--RVYTVMMPS------PYTSKQSIEDAEEIAKRLEVEHTIIPI 84
                   79***********8877766551444..444444444......3467789**************998765 PP

>> DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.014        35     119     168 ..      40      94 ..      33     148 .. 0.62
   2 ?    9.4   0.0   0.00027       0.7     140     168 ..     227     255 ..     222     267 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.014
                     HHHHHH-TTTEEEEEEEEE--HHHHHHHH...HHHH-GGHHH..HHHHHHTS--- CS
  DNA_pol3_alpha 119 yvkekyGkenvaqiitfgtlaakaairdv...gralglplke..vdklaklipke 168
                     ++++  G+e+v+++++ + +++k+ i d+   ++ l+++ ++  +++++k+++ +
      AHX11063.1  40 IAVDALGSERVYTVMMPSPYTSKQSIEDAeeiAKRLEVEHTIipINHIMKSFEAS 94 
                     5667779999999999999999999998611144555543331123344433333 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00027
                     HHHHHHHHHHHH-GGHHHHHHHHHTS--- CS
  DNA_pol3_alpha 140 akaairdvgralglplkevdklaklipke 168
                     +k+ i+dv++al+l++++v+++a++++k+
      AHX11063.1 227 QKQGIQDVAKALQLDEQVVSRVADMVKKS 255
                     6999*********************9986 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.8e-05      0.12       2      60 ..      24      82 ..      23     171 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.8e-05
                EEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-E CS
  ATP_bind_3  2 vlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnik 60
                vl+++SgG+DS +   ++++   ++ +  v++   +  +++ ++ +e+ k+l  ++ i 
  AHX11063.1 24 VLIGLSGGIDSALVAAIAVDALGSERVYTVMMPSPYTSKQSIEDAEEIAKRLEVEHTII 82
                89**********99999999988888888888888888888888888888877776642 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2341.80
//
Query:       AHX11064.1  [L=210]
Description: lipoyl(octanoyl) transferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.7e-10   38.5   0.0    1.4e-09   37.9   0.0    1.2  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.9   0.0   7.9e-14   1.4e-09      21     128 ..      56     159 ..      47     162 .. 0.84

  Alignments for each domain:
  == domain 1  score: 37.9 bits;  conditional E-value: 7.9e-14
                    --TT-EEEEEEESS-B-B--B-TTSEEEEEEEEESS...-CCGTHHHHHHHHHHHHHHH............HHTT-TTEEEETTTEEEETTEEEEE CS
  BPL_LplA_LipB  21 lesgglvvvrrqtgGrnvwhspkgeltyslllspeqktfqnrvlelyvsllvlavlealgyrd......skpgiegipvfikwpnDlyvngrKlaG 110
                    l++ +  v+   +gGr ++h+p++ + y +l++   k+++  +l++y+sll+  v++al   +       k ++ g++v+     D +  ++K+a+
     AHX11064.1  56 LNQSTFPVFHVGRGGRYTYHGPGQRVVYLMLDL---KKRDLCDLRRYISLLEEVVIRALS--KfgvmgiRKEKYIGVWVE---TKDGL--QKKIAA 141
                    566667788899*********************...5569999****************6..334444589999999999...44554..89**** PP

                    EEEEEEETTS-EEEEEEE CS
  BPL_LplA_LipB 111 iavtstrgktlhhivigv 128
                    i+v+  +++  h+i+i++
     AHX11064.1 142 IGVRISKWVSYHGIAINL 159
                    ****************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 1825.30
//
Query:       AHX11065.1  [L=232]
Description: tRNA pseudouridine(55) synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-49  167.4   0.0    3.3e-49  167.1   0.0    1.1  1  TruB_N    TruB family pseudouridylate synthase (N terminal do
    3.3e-05   23.9   0.0    5.5e-05   23.2   0.0    1.3  1  TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain


Domain annotation for each model (and alignments):
>> TruB_N  TruB family pseudouridylate synthase (N terminal domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.1   0.0   3.7e-53   3.3e-49       1     149 []      29     176 ..      29     176 .. 0.98

  Alignments for each domain:
  == domain 1  score: 167.1 bits;  conditional E-value: 3.7e-53
                 HHHTT-S-EEESS---TT-EEEEEEEEGGGGGGHHHCTTS-EEEEEEEEETEEETTSBTTS-EEE-.--TT--HHHHHHHHHHC-EEE----------- CS
      TruB_N   1 krllkakkvGhtGtLDplatGvLvvavgeaTklleylleadKeYeatirlgaetdteDaegeileeekveklteekleevlkkftGeieqvppmySAvk 99 
                 kr+l++kk+G+ GtLDplatGvLv+avg+aTkl+  + +++K+Y++t+++gaetdt D+eg+i+++ + +   +e++ evl  f Ge++q+pp +SAv+
  AHX11065.1  29 KRKLGIKKAGYLGTLDPLATGVLVIAVGKATKLIPKIDDSEKAYDFTVEWGAETDTLDSEGQIIRS-SDNIPGRESILEVLPLFIGEVTQIPPRFSAVH 126
                 899*************************************************************98.4677799************************* PP

                 ----------------------EEEEEEEEEEEEEEEEEEEEEESTTTTH CS
      TruB_N 100 vnGkrlyelaregeeverkkrkvtiyelelleveepevelevecskGtYi 149
                 +nG+r+y+lar+g+e+++++++v i++lel+e   ++  ++v c +GtY+
  AHX11065.1 127 INGRRAYSLARAGIEFDINPKTVVIHALELIEHVYKRSIFRVLCGRGTYV 176
                 *************************************************8 PP

>> TruB_C_2  tRNA pseudouridylate synthase B C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   6.1e-09   5.5e-05       1      40 [.     177     216 ..     177     230 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.1e-09
                 HHHHHHHHHHTTS-EEEEEEEEEEETTEGG-..B-HHHHH CS
    TruB_C_2   1 RtLcdDiGeaLgcgAhveeLRRtrvgpfdeedmvtledLe 40 
                 R +++Di+ +L   A v+  RRt++g f  +d +tl++++
  AHX11065.1 177 RAIARDIAHKLDSLAFVSGIRRTKSGIFGLADSHTLSEIT 216
                 99**************************99999****987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.27s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1671.89
//
Query:       AHX11066.1  [L=68]
Description: hypothetical protein NHE_0096 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.076   12.9   0.0       0.08   12.8   0.0    1.2  1  Mid2          Mid2 like cell wall stress sensor
       0.14   12.4   0.0       0.15   12.3   0.0    1.0  1  AJAP1_PANP_C  AJAP1/PANP C-terminus
       0.22   11.0   1.3       0.37   10.3   1.3    1.3  1  DUF4244       Protein of unknown function (DUF4244)


Domain annotation for each model (and alignments):
>> Mid2  Mid2 like cell wall stress sensor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.3e-05      0.08      47      79 ..       6      38 ..       3      57 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.3e-05
        Mid2 47 niviGcvvGigvPlllvillllyifCikskrtd 79
                +++iGc +G+    + +il l+ + C ++kr +
  AHX11066.1  6 KVLIGCALGLLAVTFAAILYLVLHQCCEDKRSN 38
                789*******9999***************9987 PP

>> AJAP1_PANP_C  AJAP1/PANP C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   2.5e-05      0.15      91     131 ..       9      50 ..       4      64 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.5e-05
  AJAP1_PANP_C  91 ititvslimviaalittlvlknccaq.sgngrrnshqrkinq 131
                   i  ++ l+ v  a i  lvl  cc    +n  +  h   ++ 
    AHX11066.1   9 IGCALGLLAVTFAAILYLVLHQCCEDkRSNDEKRKHSEHLHS 50 
                   667788999999************751344444444444433 PP

>> DUF4244  Protein of unknown function (DUF4244)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   1.3   6.1e-05      0.37      20      36 ..      13      28 ..       9      30 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 6.1e-05
     DUF4244 20 vgtlAAvafAavLykvv 36
                +g+l Av+fAa+Ly v+
  AHX11066.1 13 LGLL-AVTFAAILYLVL 28
                5555.799********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (68 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      564  (0.0314574); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 538.64
//
Query:       AHX11067.1  [L=277]
Description: hypothetical protein NHE_0097 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (277 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       636  (0.0354733); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2193.06
//
Query:       AHX11068.1  [L=257]
Description: hypothetical protein NHE_0098 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
      0.018   15.8   0.0      0.033   14.9   0.0    1.5  1  Cadherin_C_2  Cadherin cytoplasmic C-terminal


Domain annotation for each model (and alignments):
>> Cadherin_C_2  Cadherin cytoplasmic C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.8e-06     0.033       3      40 ..       4      42 ..       2      75 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.8e-06
  Cadherin_C_2  3 tlYLviaLasvSflFLltvivlva.vrlrkerksaalqk 40
                  t+ L iaLa+v  l Ll ++ l+a +r+++ + + ++ +
    AHX11068.1  4 TIKLCIALAVVCALLLLLILALLAcLRCHRGQIQVEVPS 42
                  888**********99998887654267777666555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      599  (0.0334096); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.18s 00:00:00.64 Elapsed: 00:00:00.35
# Mc/sec: 2194.44
//
Query:       AHX11069.1  [L=286]
Description: hypothetical protein NHE_0099 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       401  (0.022366); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.34
# Mc/sec: 2515.97
//
Query:       AHX11070.1  [L=41]
Description: hypothetical protein NHE_0100 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      161  (0.00897987); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.21s 00:00:00.49 Elapsed: 00:00:00.33
# Mc/sec: 374.38
//
Query:       AHX11071.1  [L=43]
Description: hypothetical protein NHE_0101 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      223  (0.0124379); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.20s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 385.98
//
Query:       AHX11072.1  [L=69]
Description: hypothetical protein NHE_0102 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (69 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       195  (0.0108762); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.20s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 622.36
//
Query:       AHX11073.1  [L=163]
Description: hypothetical protein NHE_0103 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.20s 00:00:00.59 Elapsed: 00:00:00.34
# Mc/sec: 1420.32
//
Query:       AHX11074.1  [L=152]
Description: hypothetical protein NHE_0104 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1175.87
//
Query:       AHX11075.1  [L=39]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       791  (0.0441185); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 325.97
//
Query:       AHX11076.1  [L=854]
Description: ATP-dependent chaperone protein ClpB [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-56  191.5   0.1    3.1e-55  186.9   0.0    3.0  2  AAA_2            AAA domain (Cdc48 subfamily)
    1.5e-35  121.2   4.5    1.5e-35  121.2   4.5    2.9  2  AAA_lid_9        AAA lid domain
      1e-25   89.6   1.2    3.6e-25   87.8   0.0    2.7  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
      4e-23   82.3   0.0    7.4e-13   49.1   0.0    3.2  2  AAA              ATPase family associated with various cellul
    8.5e-22   77.0   1.0    4.9e-10   39.4   0.0    3.0  2  Clp_N            Clp amino terminal domain, pathogenicity isl
    5.7e-18   65.2   0.8    4.8e-13   49.3   0.0    3.9  4  AAA_5            AAA domain (dynein-related subfamily)
    1.1e-10   42.2   8.3    6.6e-06   26.6   0.0    5.1  4  AAA_16           AAA ATPase domain
    1.6e-07   31.2   0.4    0.00023   20.9   0.1    2.8  2  Sigma54_activat  Sigma-54 interaction domain
    2.7e-07   30.5   0.0        0.1   12.3   0.0    3.6  3  IstB_IS21        IstB-like ATP binding protein
    2.7e-06   26.9   0.0     0.0015   18.0   0.0    3.4  2  TniB             Bacterial TniB protein
    1.6e-05   24.5   0.0      0.098   12.2   0.0    2.7  2  AAA_7            P-loop containing dynein motor region
      3e-05   24.3   3.7       0.21   11.8   0.0    4.3  3  AAA_22           AAA domain
      9e-05   22.0   0.5        2.4    7.5   0.0    3.5  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00016   21.6   0.0        0.9    9.4   0.0    2.9  2  RsgA_GTPase      RsgA GTPase
    0.00019   21.7   0.0       0.67   10.2   0.0    2.7  2  Roc              Ras of Complex, Roc, domain of DAPkinase
    0.00022   21.8  18.8     0.0062   17.1   9.5    4.0  3  AAA_23           AAA domain
    0.00025   21.6   1.7       0.99   10.0   0.0    3.7  2  AAA_18           AAA domain
    0.00043   20.3   0.0       0.83    9.7   0.0    2.8  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00048   20.1   6.4        0.4   10.6   0.0    5.0  5  ATPase_2         ATPase domain predominantly from Archaea
    0.00056   19.7   3.5       0.81    9.4   0.0    3.9  3  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00077   19.8  12.5       0.15   12.3  12.0    2.5  2  zf-C4H2          Zinc finger-containing protein
    0.00079   19.2   0.8        5.1    6.9   0.0    3.7  3  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.002   17.9   0.0        0.5   10.1   0.0    2.9  2  AAA_24           AAA domain
     0.0029   17.5   0.1        1.3    8.9   0.0    3.2  2  AAA_3            ATPase family associated with various cellul
     0.0072   16.2   0.0       0.42   10.5   0.0    3.0  2  NACHT            NACHT domain
      0.008   15.9   0.1       0.57   10.0   0.0    2.5  2  AAA_29           P-loop containing region of AAA domain
     0.0083   16.5   0.0          6    7.3   0.0    2.7  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.018   15.2   0.0      0.051   13.7   0.0    1.8  1  Torsin           Torsin
      0.018   15.3   0.0         11    6.2   0.0    3.2  3  AAA_28           AAA domain
      0.027   14.5   0.7        1.7    8.6   0.0    3.7  4  ResIII           Type III restriction enzyme, res subunit
      0.033   14.4   0.0          7    6.8   0.0    2.9  2  AAA_33           AAA domain
      0.044   13.1   0.1        4.4    6.5   0.0    3.1  2  Zeta_toxin       Zeta toxin
      0.045   14.0   0.1        2.1    8.7   0.1    3.0  2  DUF3870          Domain of unknown function (DUF3870)
       0.06   13.7   0.1       0.99    9.7   0.0    2.8  2  AAA_19           AAA domain
       0.13   12.8   2.0        6.8    7.2   0.0    3.6  3  ABC_tran         ABC transporter
       0.18   11.3   1.0       0.52    9.8   1.0    1.8  1  Z1               Z1 domain
        2.9    7.6  13.4       0.32   10.7   5.2    3.0  2  HAUS2            HAUS augmin-like complex subunit 2
          3    6.3  15.4        0.3    9.6   9.9    2.0  2  FapA             Flagellar Assembly Protein A
        8.2    5.2   5.7         15    4.3   5.7    1.3  1  5_nucleotid      5' nucleotidase family


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.92   4.2e+02       7      36 ..     204     232 ..     198     297 .. 0.60
   2 !  186.9   0.0   6.6e-58   3.1e-55       1     171 []     595     757 ..     595     757 .. 0.98

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.92
                 EEE--TTSSHHHHHHHHHHHTT-....-EE CS
       AAA_2   7 lllgptgvGktelakalaellfvkkekkli 36 
                  l+g  gvGkt + + la  + + k+ +  
  AHX11076.1 204 VLIGDPGVGKTAIVEGLAMRMVA-KDVPQN 232
                 67899999999998888877753.333333 PP

  == domain 2  score: 186.9 bits;  conditional E-value: 6.6e-58
                 -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS............EEEEETGGG-------- CS
       AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG............ivllDEidKihpkessg 87 
                 rp++s+++lg+tgvGktel+kala++lf ++e++l r+d+se++e    +h+v+rligappgyvg+eegG            ++l+DEi+K+h+     
  AHX11076.1 595 RPLGSFMFLGSTGVGKTELSKALAKFLF-DDESALLRVDMSEYME----KHSVARLIGAPPGYVGYEEGGvlteavrrrpyqVILFDEIEKAHH----- 683
                 6899************************.****************....*********************************************..... PP

                 -----HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS-STTTTSGGG--HHHHHHTT--HHHHTT--EE CS
       AAA_2  88 advSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrskeeeeekkkeeveeelkkglipEllgRlpei 171
                       +V+++LLq+l++g+ltd+qg+ vd+kn+++I+t+++g++  s+++r+    ++++k++++e ++k+++pE+l+Rl+ei
  AHX11076.1 684 ------DVFNILLQVLDEGRLTDSQGHVVDFKNTILILTSNLGAEVLSETERI----TDTEKTQIMEIVRKFFRPEFLNRLDEI 757
                 ......*******************************************7665....99999********************86 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.2   4.5   3.3e-38   1.5e-35       1     103 [.     343     445 ..     343     446 .. 0.98
   2 ?    0.6   2.3       1.2   5.4e+02      63      91 ..     465     493 ..     442     503 .. 0.57

  Alignments for each domain:
  == domain 1  score: 121.2 bits;  conditional E-value: 3.3e-38
   AAA_lid_9   1 seeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpeeleklekelaklekekealekeeekekaer 99 
                 +ee+ti+iLrg+kekye hHg++i d+a+++a++lS+rYi+drflPdkAIDl+Deaa+++r++++skpe +++l++++ +l+ e eal+ke++ ++ +r
  AHX11076.1 343 TEEDTISILRGIKEKYEVHHGIRIADSAVVSAATLSNRYITDRFLPDKAIDLMDEAASKIRIESDSKPEVIDELDRKIIQLKIEAEALKKEKDANSVSR 441
                 689********************************************************************************************9999 PP

   AAA_lid_9 100 lkel 103
                 l+++
  AHX11076.1 442 LEKI 445
                 9876 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
   AAA_lid_9  63 kkeskpeeleklekelaklekekealeke 91 
                 +++sk +e++k+++el++ +++ e ++++
  AHX11076.1 465 SEKSKLKEIQKIKEELNEARQSLEVAQRN 493
                 23344445555555555555555554444 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   7.8e-28   3.6e-25       1      79 [.     763     841 ..     763     843 .. 0.95

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 7.8e-28
                    SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSSTTSEE CS
  ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelkegdtv 79 
                    L++e++ kI++++l kl++ lk++++e+e+t+ a+d+++e+gy p yGARpL+r+iq+++++pla+ ilsg+++  +++
     AHX11076.1 763 LSNEDIGKIAEIQLCKLQNLLKSKNLEIEFTQRAKDWICEQGYHPIYGARPLKRVIQQHVQNPLAQIILSGKVAVDGKI 841
                    899*********************************************************************9965554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.1   0.0   1.6e-15   7.4e-13       2     125 ..     204     335 ..     203     340 .. 0.83
   2 !   29.6   0.0   1.7e-09   7.9e-07       2     111 ..     601     719 ..     600     737 .. 0.85

  Alignments for each domain:
  == domain 1  score: 49.1 bits;  conditional E-value: 1.6e-15
                 EEESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHH CS
         AAA   2 llyGppGtGKTllakavakel..........gvefleisgsell..skyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnq 88 
                 +l+G pG+GKT++++ +a  +          g+++l++++  l+  sky ge e++++ +++e+  +a+  ilfiDE++ l+++    +++ ++++ n 
  AHX11076.1 204 VLIGDPGVGKTAIVEGLAMRMvakdvpqnlaGASLLSLDLGALIagSKYRGEFEERLKSVINELTDSAGGIILFIDELHTLVGAG---ATDGAMDASNL 299
                 599*****************76665555555799********998899****************999966***************...99999999999 PP

                 HHHHHHHTTTSSSTEEEEEEESS...GGGSTHHHHS.TTSS CS
         AAA  89 Llteldgvkkkeskvivigatnr...pdkldpallr.gRfd 125
                 L ++l + +       ++gat+     +++++   + +Rf+
  AHX11076.1 300 LKPALARGEI-----HCVGATTLdeyKKHIEKDAALaRRFQ 335
                 9999999877.....58888877565555555555446666 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 1.7e-09
                 EEESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS............STTHHHHHHHHHHHHHHHTSTS.EEEEEETGGGHHHHHTTCCCHHHHH CS
         AAA   2 llyGppGtGKTllakavakel...gvefleisgsellsk............yvgesekkirelfkeakekakp.silfiDEidalaksrsgseseeeer 84 
                 ++ G  G+GKT l ka+ak l   ++ +l++++se ++k            yvg  e  +   ++ea + + p  ++++DEi++ + +           
  AHX11076.1 601 MFLGSTGVGKTELSKALAKFLfddESALLRVDMSEYMEKhsvarligappgYVGYEEGGV---LTEAVRRR-PyQVILFDEIEKAHHDV---------- 685
                 689*****************9776699**********999********999999999865...55555555.779**********8777.......... PP

                 HHHHHHHHHHHTTTS........SSTEEEEEEESS CS
         AAA  85 vvnqLlteldgvkkk........eskvivigatnr 111
                   n Ll++ld+ +           +++i+i+++n 
  AHX11076.1 686 -FNILLQVLDEGRLTdsqghvvdFKNTILILTSNL 719
                 .*********9999889999999555999999997 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.1e-12   4.9e-10       5      51 ..      21      67 ..      17      69 .. 0.93
   2 !   35.3   0.1     2e-11   9.3e-09       4      53 .]      98     146 ..      95     146 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.1e-12
                HHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHH CS
       Clp_N  5 AkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekl 51
                A s+ghq+++t H+L++L+++ dGl+ +lL++++++++ + k i  +
  AHX11076.1 21 AVSMGHQMLTTLHILKSLINNTDGLIPQLLEQCNANPEIILKKISTA 67
                899***********************************999998766 PP

  == domain 2  score: 35.3 bits;  conditional E-value: 2e-11
                 HHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHHC CS
       Clp_N   4 lAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekllg 53 
                 +A++++++++++E LL ++++e+ + a+++Lk++Gv+  +l++ i++ +g
  AHX11076.1  98 IAQRAQDSFVTVERLLQGIAAEK-SEASEILKDQGVSAPKLQQIIDATRG 146
                 8*****************99977.*********************99876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       6.5     3e+03      80     108 ..      30      58 ..      17      69 .. 0.78
   2 !   11.4   0.0   0.00051      0.24       3      24 ..     204     227 ..     202     334 .. 0.85
   3 ?   -2.0   0.0       7.2   3.3e+03      23      72 ..     330     396 ..     323     435 .. 0.64
   4 !   49.3   0.0   1.1e-15   4.8e-13       2     123 ..     600     720 ..     599     732 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 6.5
                 HHHHHHHHHHHSSEEE..-SSSEEE---. CS
       AAA_5  80 evlnsLlslleerrllleeggelvkaknd 108
                  +l +L sl+++   l++++ e+++a+++
  AHX11076.1  30 TTLHILKSLINNTDGLIPQLLEQCNANPE 58 
                 68899*******99999999999999885 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00051
                 EEE--SSSSHHHHHHHGGGGB..S CS
       AAA_5   3 lLvGppGtgKselaerlaaal..n 24 
                 +L+G+pG+gK+ ++e la ++  +
  AHX11076.1 204 VLIGDPGVGKTAIVEGLAMRMvaK 227
                 79**************99887542 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.2
                 BS--EEEEE--TT--HHHHH--B--..............--------............G-SEEEEE CS
       AAA_5  23 lnreveyvqltrdtteedlkgrreik.....ngttslvdsplvraar............egeilvlD 72 
                 l r+++ v   + t+e+++   r ik       + +  ds++v aa+             ++i ++D
  AHX11076.1 330 LARRFQPVFVGQPTEEDTISILRGIKekyevHHGIRIADSAVVSAATlsnryitdrflpDKAIDLMD 396
                 5556666666666666666666665555555777788888888888866666666666544444444 PP

  == domain 4  score: 49.3 bits;  conditional E-value: 1.1e-15
                 EEEE--SSSSHHHHHHHGGGGB...S--EEEEE--TT--HHHHH--B--..........--------..G-SEEEEESGGG--HHHHHHHHHHHHSSEE CS
       AAA_5   2 vlLvGppGtgKselaerlaaal...nreveyvqltrdtteedlkgrreikngttslvd.splvraar..egeilvlDEveraesevlnsLlslleerrl 94 
                 ++ +G +G+gK+el++ la++l   ++ ++ v +++++++  +   +   +g   +++ ++l++a+r    +++++DE+e+a+ +v+n+Ll++l+e rl
  AHX11076.1 600 FMFLGSTGVGKTELSKALAKFLfddESALLRVDMSEYMEKHSVARLIGAPPGYVGYEEgGVLTEAVRrrPYQVILFDEIEKAHHDVFNILLQVLDEGRL 698
                 6899********************999999*************9999977666655551788888889889**************************** PP

                 E..-SSSEEE---......-EEEEEESS- CS
       AAA_5  95 lleeggelvkaknddllerfrviatanpl 123
                   ++ g++v++kn      + +i t+n  
  AHX11076.1 699 T-DSQGHVVDFKN------TILILTSNLG 720
                 9.99999999999......7888888865 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.2       2.2     1e+03     121     137 ..      90     106 ..      26     174 .. 0.52
   2 !   26.6   0.0   1.4e-08   6.6e-06       2      50 ..     181     226 ..     180     310 .. 0.82
   3 ?   -2.0   0.4       9.1   4.2e+03      91     107 ..     467     488 ..     412     521 .. 0.43
   4 !   12.6   0.0   0.00029      0.13       2      60 ..     569     633 ..     568     651 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 2.2
      AAA_16 121 ellkrllallsrderpl 137
                 ++++ ++  ++r ++ +
  AHX11076.1  90 QAIQGAMGIAQRAQDSF 106
                 33333333333322222 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 1.4e-08
      AAA_16   2 lvGReeeleqLlsalervrsgrpelvllsGesGvGKsslvrellralek 50 
                 ++GR+ee++++ ++l+r  ++ p   +l+G++GvGK+++v+ l+ ++ +
  AHX11076.1 181 VIGRDEEIRRVMQVLSRRTKNNP---VLIGDPGVGKTAIVEGLAMRMVA 226
                 78**************8888766...899***********887755444 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 9.1
      AAA_16  91 saeleawrekleeala................a 107
                 +++l           +                +
  AHX11076.1 467 KSKL-----------KeiqkikeelnearqslE 488
                 1122...........122222222223333332 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 0.00029
      AAA_16   2 lvGReeeleqLlsalervrsgrp......elvllsGesGvGKsslvrellralekdggiflrgkc 60 
                 ++G  e +e++ +a++r+r+g        ++ ++ G  GvGK+ l ++l++ l +d+  +lr + 
  AHX11076.1 569 VIGQNEAVEAVSNAVKRARAGIQdanrplGSFMFLGSTGVGKTELSKALAKFLFDDESALLRVDM 633
                 6788899999******999998888888**********************999988766666555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0055       2.5       2     105 ..     182     284 ..     181     321 .. 0.70
   2 !   20.9   0.1     5e-07   0.00023       5     124 ..     580     700 ..     548     755 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0055
                      ---SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBS.SSSSTTTSS-BEHHHHHTTT CS
  Sigma54_activat   2 igesealkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhe.kGaFtGAekekkGlfekadg 94 
                      ig++e+++++++ +++ +k + +vl  G+ G+GK+ + + +  +   k+ p      a++ +  l + + G + +G F    k+    +  + g
       AHX11076.1 182 IGRDEEIRRVMQVLSRRTK-NNPVL-IGDPGVGKTAIVEGLAMRMVAKDVPQNLAG-ASLLSLDLGALIAGSKyRGEFEERLKSVINELTDSAG 272
                      7788888888888877544.34555.6**********9999887776665543332.2333333445555544378888888888866666666 PP

                      S.EEEEETGGGS CS
  Sigma54_activat  95 G.tlfLDeigel 105
                      G +lf+De+++l
       AHX11076.1 273 GiILFIDELHTL 284
                      626899999987 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 5e-07
                      SHHHHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHT....TT CS
  Sigma54_activat   5 sealkelleqikkvaktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfeka....dg 94 
                      s+a+k++++ i+ + +   s + +G +G+GK+ l++a+ +    +e+ +++v+++++ e+   ++L G   G + G e+   G + +a      
       AHX11076.1 580 SNAVKRARAGIQDANRPLGSFMFLGSTGVGKTELSKALAKFLFDDESALLRVDMSEYMEKHSVARLIGAPPG-YVGYEEG--GVLTEAvrrrPY 670
                      3344444444444444448899**********************************************9998.8887665..555555111156 PP

                      SEEEEETGGGS-HHHHHHHHHHHHHSEEES CS
  Sigma54_activat  95 GtlfLDeigelplelQekLlrvlqegever 124
                       ++++Dei++   ++ + Ll+vl+eg+++ 
       AHX11076.1 671 QVILFDEIEKAHHDVFNILLQVLDEGRLTD 700
                      79999********************98764 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.0     0.066        30      57     139 ..      78     166 ..      69     177 .. 0.75
   2 !   12.3   0.0   0.00022       0.1      45      76 ..     198     229 ..     183     281 .. 0.80
   3 !    9.3   0.0    0.0019      0.87      50      94 ..     600     644 ..     594     650 .. 0.82

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.066
   IstB_IS21  57 GvGKshl....aial.gveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdl.lilDdl.gllpldqaeaellfeviekrye 139
                 G+G  hl    a a+ g  ++++  + +fv+ve+L++ +++++++ +   + + + +++l  i+D   g  + d+a+ae  f+ ++ ry 
  AHX11076.1  78 GAGHIHLtpdaAQAIqGAMGIAQRAQDSFVTVERLLQGIAAEKSEASEILKDQGVSAPKLqQIIDATrGNRKADSANAESTFNALK-RYT 166
                 777777733323444356678899999****************9999888877777777633667543889999999999988874.555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00022
   IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavragl 76 
                 ++k+n vl+G +GvGK+ +   l+++ v++++
  AHX11076.1 198 RTKNNPVLIGDPGVGKTAIVEGLAMRMVAKDV 229
                 67899*******************99998775 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.0019
   IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrar 94 
                 +++lG +GvGK+ l+ al++    ++ + l v +++ +e+ ++ar
  AHX11076.1 600 FMFLGSTGVGKTELSKALAKFLFDDESALLRVDMSEYMEKHSVAR 644
                 789****************99888888887777777776666665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.3e-06    0.0015      23     183 ..     188     338 ..     184     342 .. 0.80
   2 ?   -0.4   0.0       1.4   6.5e+02      36      55 ..     598     617 ..     565     627 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.3e-06
        TniB  23 LeeLleypkrkrmpnlllvGdsnnGKtmivekFarlhppekdedaekvpvlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrll.relkv 120
                 +++++++ +r   +n +l+Gd+ +GKt+ive  a              ++++ ++p++   + l +  L al a  k r + ++  + v++ l ++ + 
  AHX11076.1 188 IRRVMQVLSRRTKNNPVLIGDPGVGKTAIVEGLAM-------------RMVAKDVPQNLAGASLLSLDLGALIAGSKYRGEFEERLKSVINELtDSAGG 273
                 56667777777778889999999999999987764.............455566888888899999999999999999999886666666555156677 PP

        TniB 121 rvLiiDEihnll.agsarkqreflnalksLgnelkipivlvGteeal.ralrtDpqlasRFepia 183
                  +L iDE+h l+ ag  +    + n+lk    + +i  v++ t + + +++++D+ la+RF+p+ 
  AHX11076.1 274 IILFIDELHTLVgAGATDGAMDASNLLKPALARGEIHCVGATTLDEYkKHIEKDAALARRFQPVF 338
                 7899******984677777889******************9996555279************985 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.4
        TniB  36 pnlllvGdsnnGKtmivekF 55 
                  + +++G + +GKt + +  
  AHX11076.1 598 GSFMFLGSTGVGKTELSKAL 617
                 578999********998755 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.0    0.0017       0.8      32      58 ..     199     226 ..     185     236 .. 0.70
   2 !   12.2   0.0   0.00021     0.098      36      82 ..     600     646 ..     590     649 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0017
       AAA_7  32 nkkpvllvGptGtGKtviikd.llkkld 58 
                  k++ +l+G+ G+GKt+i++   ++ + 
  AHX11076.1 199 TKNNPVLIGDPGVGKTAIVEGlAMRMVA 226
                 45567899************95555444 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00021
       AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                 +++ G+tG+GKt + k l k l +++   l + +s +++ +++ ++i
  AHX11076.1 600 FMFLGSTGVGKTELSKALAKFLFDDESALLRVDMSEYMEKHSVARLI 646
                 79************************************999998887 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00046      0.21       4     103 ..     199     284 ..     196     310 .. 0.64
   2 ?   -2.2   0.1       9.9   4.5e+03      95     102 ..     411     418 ..     314     454 .. 0.54
   3 !    9.2   0.2     0.003       1.4       8     117 ..     600     694 ..     595     706 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00046
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqh 102
                 t++  v++G +G+GKT  ++ l+++ +         ++ v  +l+   + + l  +l   +  ++ + +  +e+l + +++  ++++   +l iDE + 
  AHX11076.1 199 TKNNPVLIGDPGVGKTAIVEGLAMRMV---------AKDVPQNLA---GASLLSLDLGALIAGSKYR-GEFEERLKSVINELTDSAGG-IILFIDELHT 283
                 778889****************99973.........333333333...3333333444444433333.34466666666666666666.7777777777 PP

      AAA_22 103 l 103
                 l
  AHX11076.1 284 L 284
                 6 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.9
      AAA_22  95 liiDEaqh 102
                  +iDE ++
  AHX11076.1 411 EVIDELDR 418
                 34555554 PP

  == domain 3  score: 9.2 bits;  conditional E-value: 0.003
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlrse 106
                  +  G +G+GKT l + l++ l  +      ++ +++v++++ ++  ++    +r +g +  +      e    l++a+r+r   ++++ DE+++  ++
  AHX11076.1 600 FMFLGSTGVGKTELSKALAKFLFDD------ESALLRVDMSEYMEKHSV----ARLIGAPPGY---VGYEEGGVLTEAVRRRPY-QVILFDEIEKA-HH 683
                 566799**************99532......455558888888866555....6666666666...444455667777777777.89999999988.88 PP

      AAA_22 107 ealeeLrslln 117
                 ++++ L + l+
  AHX11076.1 684 DVFNILLQVLD 694
                 88888877666 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0     0.014       6.6       9      46 ..     186     224 ..     177     249 .. 0.71
   2 !    7.5   0.0    0.0052       2.4      23      64 ..     598     643 ..     567     652 .. 0.65
   3 ?    4.7   0.0     0.038        18     109     204 ..     672     765 ..     653     768 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.014
  Mg_chelatase   9 eeakralei.aaaGgHnlllvGppGsGKtmlakrlpsll 46 
                   ee +r++++ +   + n +l+G pG GKt + + l+  +
    AHX11076.1 186 EEIRRVMQVlSRRTKNNPVLIGDPGVGKTAIVEGLAMRM 224
                   4556677662445677889***********999887655 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0052
  Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllpp....lseeealevakiasva 64 
                    +++++G+ G GKt l k+l++ l +    l + ++ e  + +sva
    AHX11076.1 598 GSFMFLGSTGVGKTELSKALAKFLFDdesaLLRVDMSEYMEKHSVA 643
                   4689*****************9996511113344555555555555 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.038
  Mg_chelatase 109 vLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpcgklkdkekectcsekeierYlsklsgp.lldRidlqvevkklea 204
                   v+++DE+ + +++v+++L + l++g++t s+  + v+f  ++ l+++ N+     l+++e+ + +++++i + ++k  +p +l+R+d  +  ++l++
    AHX11076.1 672 VILFDEIEKAHHDVFNILLQVLDEGRLTDSQG-HVVDFK-NTILILTSNLGAE-VLSETERITDTEKTQIMEIVRKFFRPeFLNRLDEILFFNRLSN 765
                   8899*********************9986654.567886.6779999999765.5677777888889999999999988878999997777666665 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0    0.0029       1.3      77     122 ..     178     223 ..     148     232 .. 0.64
   2 !    9.4   0.0     0.002       0.9      67     120 ..     564     618 ..     540     636 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.0029
                  SEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
  RsgA_GTPase  77 yevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe 122
                  +++++ + ++ + + ++ ++ +++  vl+G  GvGK+++++ l+ +
   AHX11076.1 178 LDPVIGRDEEIRRVMQVLSRRTKNNPVLIGDPGVGKTAIVEGLAMR 223
                  44444444444444455555555678**************998766 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.002
                  HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
  RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinall 120
                  +lk+++   + +v +vs+  k++ + ++++ +     +++G++GvGK+ L +al+
   AHX11076.1 564 ALKKQVIGQNEAVEAVSNAVKRARAGIQDANRPlGSFMFLGSTGVGKTELSKALA 618
                  55666666777788888888888888888888888899************99987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.2   0.0    0.0015      0.67       3      27 ..     204     228 ..     203     250 .. 0.80
   2 !    8.5   0.0    0.0049       2.2       3      35 ..     601     632 ..     599     644 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.0015
                 EEESSTTSSHHHHHHCHCT-CCC-E CS
         Roc   3 vlvGdsgvGKtsllkrfvedkfsek 27 
                 vl+Gd gvGKt +++ +  + + ++
  AHX11076.1 204 VLIGDPGVGKTAIVEGLAMRMVAKD 228
                 79************99887776655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0049
                 EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEE CS
         Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvd 35 
                 +++G +gvGKt l k + +  f+++ ++ + vd
  AHX11076.1 601 MFLGSTGVGKTELSKALAKFLFDDE-SALLRVD 632
                 89***************99888765.4445555 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0       0.5   2.3e+02      23      40 ..     204     221 ..     199     265 .. 0.92
   2 !   17.1   9.5   1.4e-05    0.0062     122     200 .]     413     488 ..     319     488 .. 0.74
   3 ?    6.6   0.1     0.022        10      20      69 ..     598     658 ..     596     803 .. 0.52

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.5
      AAA_23  23 lItGpNGaGKTTildAik 40 
                 +++G+ G GKT+i++ + 
  AHX11076.1 204 VLIGDPGVGKTAIVEGLA 221
                 678999********9986 PP

  == domain 2  score: 17.1 bits;  conditional E-value: 1.4e-05
      AAA_23 122 sellgskkiilnlilflgqerfeefelkdkkerleelekeleeledekkllekl.eqekekekeleeleeeleeilkele 200
                  ++l++k i+l+    + +e  +++++++  +rle+++++le le+++  le + + ek+k ke+++++eel+e+ + le
  AHX11076.1 413 IDELDRKIIQLK----IEAEALKKEKDANSVSRLEKIRQDLESLEKKQADLESVwQSEKSKLKEIQKIKEELNEARQSLE 488
                 333333333333....3445577788889999***********9998888888889*******************99886 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.022
      AAA_23  20 gltlItGpNGaGKTTildAiklaLygetprlsrks.grgfeksdveiese..........g 69 
                 g + + G +G GKT +  A+   L+ + + l r + ++ +ek++v+   +          g
  AHX11076.1 598 GSFMFLGSTGVGKTELSKALAKFLFDDESALLRVDmSEYMEKHSVARLIGappgyvgyeeG 658
                 67899********************999998888866688888887433334444444442 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.7   0.0    0.0051       2.3       3      22 ..     205     224 ..     204     282 .. 0.74
   2 !   10.0   0.0    0.0022      0.99       4      36 ..     603     633 ..     601     696 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0051
      AAA_18   3 ltGtpGvGKttlakeLskrl 22 
                 l G pGvGKt + + L+ r+
  AHX11076.1 205 LIGDPGVGKTAIVEGLAMRM 224
                 89**************8775 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0022
      AAA_18   4 tGtpGvGKttlakeLskrlgfgvnlrdvakeng 36 
                  G  GvGKt+l+k+L+k l   +  + +++ ++
  AHX11076.1 603 LGSTGVGKTELSKALAKFL--FDDESALLRVDM 633
                 6899***********9976..444444444444 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.7   0.0    0.0018      0.83       5      45 ..     186     226 ..     182     231 .. 0.82
   2 !    7.5   0.0    0.0084       3.9      21      43 ..     593     621 ..     570     628 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0018
                 HHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHTT- CS
        TsaE   5 eetealgkklakalgdvilLeGdLGaGKTtlvrglakalgv 45 
                 ee++++ + l + +++  +L Gd G+GKT++v gla  +  
  AHX11076.1 186 EEIRRVMQVLSRRTKNNPVLIGDPGVGKTAIVEGLAMRMVA 226
                 6777888888887788899****************988755 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0084
                 E......EEEEESTTSSHHHHHHHHHHHT CS
        TsaE  21 v......ilLeGdLGaGKTtlvrglakal 43 
                 +      +++ G  G+GKT l+++lak l
  AHX11076.1 593 AnrplgsFMFLGSTGVGKTELSKALAKFL 621
                 24445558899**************9876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00086       0.4       4      41 ..     184     221 ..     181     231 .. 0.89
   2 !    7.5   0.0    0.0076       3.5     102     137 ..     256     301 ..     243     417 .. 0.67
   3 ?   -2.1   1.7       6.3   2.9e+03      75     115 ..     439     472 ..     403     490 .. 0.45
   4 ?   -0.2   0.0       1.7   7.9e+02      27      46 ..     604     623 ..     599     647 .. 0.74
   5 ?   -1.5   0.0       4.3     2e+03     113     132 ..     665     683 ..     629     717 .. 0.81

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00086
    ATPase_2   4 RekelkeleeilerepneiyfiYGpegsGKtaLlkeii 41 
                 R++e++++ ++l+r +++  ++ G  g+GKta++  ++
  AHX11076.1 184 RDEEIRRVMQVLSRRTKNNPVLIGDPGVGKTAIVEGLA 221
                 9*******************************987665 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0076
    ATPase_2 102 vfkaielllekikkkgkkiiiiiDelqklidlgln..........g 137
                  ++ ++++++++++++  ii++iDel  l+  g            +
  AHX11076.1 256 FEERLKSVINELTDSAGGIILFIDELHTLVGAGATdgamdasnllK 301
                 578899**********************996665555555444440 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 6.3
    ATPase_2  75 kkklekal..giavpkaeleeilkeksklvfkaielllekikk 115
                 +++lek    ++          l++k++++++ +++ + k+k+
  AHX11076.1 439 VSRLEKIRqdLES---------LEKKQADLESVWQSEKSKLKE 472
                 2222222233122.........223333333333333333332 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.7
    ATPase_2  27 GpegsGKtaLlkeiienled 46 
                 G+ g+GKt L k +++ l d
  AHX11076.1 604 GSTGVGKTELSKALAKFLFD 623
                 999*******9998877644 PP

  == domain 5  score: -1.5 bits;  conditional E-value: 4.3
    ATPase_2 113 ikkkgkkiiiiiDelqklid 132
                 ++++    +i++De+ k+ +
  AHX11076.1 665 VRRR-PYQVILFDEIEKAHH 683
                 3333.3368899**999983 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.4     0.016       7.5      36      59 ..     203     226 ..     174     290 .. 0.64
   2 !    9.4   0.0    0.0018      0.81       7      55 ..     567     619 ..     562     633 .. 0.84
   3 ?   -2.0   0.1       5.6   2.6e+03      84     110 ..     669     695 ..     659     700 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.016
      RuvB_N  36 vllyGpPGlGkttlakiiakelgv 59 
                  +l+G PG+Gkt++ + +a  + +
  AHX11076.1 203 PVLIGDPGVGKTAIVEGLAMRMVA 226
                 467899999999987766655543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0018
      RuvB_N   7 eeyigqekvkeklkifieaakk....reealdhvllyGpPGlGkttlakiiak 55 
                 ++ igq++  e ++ +++ a++     +++l   ++ G+ G+Gkt l+k +ak
  AHX11076.1 567 KQVIGQNEAVEAVSNAVKRARAgiqdANRPLGSFMFLGSTGVGKTELSKALAK 619
                 57899*999999999999887522225788999****************9997 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 5.6
      RuvB_N  84 ekdvlfideihrlsraveevlysamed 110
                 + +v++ dei + ++ v ++l + +++
  AHX11076.1 669 PYQVILFDEIEKAHHDVFNILLQVLDE 695
                 5689999*******9999999888776 PP

>> zf-C4H2  Zinc finger-containing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.047        22      17     113 ..      90     186 ..      82     239 .. 0.85
   2 !   12.3  12.0   0.00033      0.15      20     107 ..     407     491 ..     390     532 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.047
     zf-C4H2  17 nklakevealekeekcleeykkelelLeqEkmaHveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselglekledlee 113
                 + ++ +++  ++ +    ++++ l+ +  Ek + +e L+       +l ++i  ++ +++   ++a+++ + +k+  +++ e+ ++  l+++   +e
  AHX11076.1  90 QAIQGAMGIAQRAQDSFVTVERLLQGIAAEKSEASEILKDQGVSAPKLQQIIDATRGNRKADSANAESTFNALKRYTKDLTEVARSGKLDPVIGRDE 186
                 6677788888888888999999999*************************************************99999999988888876665444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00033
     zf-C4H2  20 akevealekeekcleeykkelelLeqEkma.HveeLrlIhaDinalEsvikeaeeekekslekakklyeeykklkeevnelrselglek 107
                  ++ e++++ ++ + + k e e L++Ek a  v  L +I++D+++lE+  k+a  + e  +++ k++++e++k+kee+ne r++l + +
  AHX11076.1 407 DSKPEVIDELDRKIIQLKIEAEALKKEKDAnSVSRLEKIRQDLESLEK--KQA--DLESVWQSEKSKLKEIQKIKEELNEARQSLEVAQ 491
                 44557899999*****************862689*************8..444..55567777889999*************9987664 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.4      0.75   3.5e+02       3      97 ..     345     454 ..     343     487 .. 0.71
   2 ?    6.8   0.0     0.012       5.3      12      48 ..     590     626 ..     578     639 .. 0.86
   3 ?    6.9   0.0     0.011       5.1     101     129 ..     667     695 ..     660     718 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.75
  DNA_pol3_delta2   3 eealkilskalksgrlahayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivi................eteeke 80 
                      e++++il+++ ++ +++h + ++ ++ +   +l +++++  +  +k  +   +e  s  +ie+ + p+vi                  ++++++
       AHX11076.1 345 EDTISILRGIKEKYEVHHGIRIADSAVVSAATLSNRYITDRFLPDKAID-LMDEAASKIRIESDSKPEVIDEldrkiiqlkieaealkKEKDAN 437
                      6678899999999999999999999999999999999888888888777.67888888889999999887555555556666555554223333 PP

  DNA_pol3_delta2  81 rsikldqirelieelsr 97 
                      ++ +l++ir+  e+l++
       AHX11076.1 438 SVSRLEKIRQDLESLEK 454
                      34455555554444444 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.012
  DNA_pol3_delta2  12 alksgrlahayLfeGdegigkkelalnlakallceek 48 
                      +   +r   +++f G++g+gk el ++lak l+ +e 
       AHX11076.1 590 IQDANRPLGSFMFLGSTGVGKTELSKALAKFLFDDES 626
                      55677888899*********************98775 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.011
  DNA_pol3_delta2 101 eskkkiiiiedaekmtksAaNalLktlEE 129
                         +++i+ +++ek ++   N+lL++l E
       AHX11076.1 667 RRPYQVILFDEIEKAHHDVFNILLQVLDE 695
                      56789**********************99 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   0.0     0.048        22       3      22 ..     201     220 ..     199     284 .. 0.88
   2 !   10.1   0.0    0.0011       0.5       6      85 ..     601     689 ..     599     761 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.048
      AAA_24   3 lkiliyGpsgiGKTtlakel 22 
                 ++ +++G++g+GKT ++  l
  AHX11076.1 201 NNPVLIGDPGVGKTAIVEGL 220
                 56689*********988765 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0011
      AAA_24   6 liyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdieswedfldevvel...........aaeladyktlviDtideleelclaev 85 
                 +  G+ g+GKT l k l  k+l +d e  l ++d  ++ + +s++ ++ +               a   ++y+++ +D i+++   +++ +
  AHX11076.1 601 MFLGSTGVGKTELSKAL-AKFL-FDDESALLRVDMSEYMEKHSVARLIGAPPGYvgyeeggvlteAVRRRPYQVILFDEIEKAHHDVFNIL 689
                 6689*************.6666.577888********9977777777766555588899999999999999*********99988777665 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.09        41       4      24 ..     205     225 ..     203     267 .. 0.81
   2 !    8.9   0.0    0.0028       1.3      63     107 ..     670     715 ..     600     724 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.09
       AAA_3   4 legvPGlaktllvkalakald 24 
                 l g PG++kt +v+ la  + 
  AHX11076.1 205 LIGDPGVGKTAIVEGLAMRMV 225
                 5688************97664 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0028
       AAA_3  63 anllladeinrappktqsalleameerqvtv.egethklpepflvl 107
                  +++l dei++a   +   ll++++e ++t  +g+  +++++ l+l
  AHX11076.1 670 YQVILFDEIEKAHHDVFNILLQVLDEGRLTDsQGHVVDFKNTILIL 715
                 4799************************995145566666666655 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.5   0.0   0.00092      0.42       4      32 ..     204     232 ..     203     243 .. 0.88
   2 ?    2.1   0.0      0.35   1.6e+02       5      24 ..     602     621 ..     599     684 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00092
                 EEEC-TTTCHHHHHHHHHHHHCTS-SCCC CS
       NACHT   4 ilqGeaGsGKTtLlqklalawaegklpqg 32 
                 +l G++G+GKT+ +++la+ + +++ pq+
  AHX11076.1 204 VLIGDPGVGKTAIVEGLAMRMVAKDVPQN 232
                 689****************9988888874 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.35
                 EEC-TTTCHHHHHHHHHHHH CS
       NACHT   5 lqGeaGsGKTtLlqklalaw 24 
                   G  G+GKT L + la  +
  AHX11076.1 602 FLGSTGVGKTELSKALAKFL 621
                 579*********99998755 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0    0.0012      0.57      20      57 ..     198     234 ..     190     237 .. 0.82
   2 ?    2.9   0.0       0.2        91      23      43 ..     598     618 ..     590     626 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0012
      AAA_29  20 dlkgatlltGpsGsGKSTllDAiqalLvpakkvrfNka 57 
                 ++k++ +l+G+ G+GK++++  +++ +v++  v  N a
  AHX11076.1 198 RTKNNPVLIGDPGVGKTAIVEGLAMRMVAKD-VPQNLA 234
                 4556789*****************9999998.777776 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.2
      AAA_29  23 gatlltGpsGsGKSTllDAiq 43 
                 g++++ G +G+GK+ l  A++
  AHX11076.1 598 GSFMFLGSTGVGKTELSKALA 618
                 5789*********98876665 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.0     0.029        13       3      23 ..     205     225 ..     204     236 .. 0.85
   2 ?    7.3   0.0     0.013         6       2      23 ..     601     622 ..     600     642 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.029
  RNA_helicase   3 lyGpsgeGKStlakeLakall 23 
                   l G++g+GK+ +++ La ++ 
    AHX11076.1 205 LIGDPGVGKTAIVEGLAMRMV 225
                   78*************999886 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.013
  RNA_helicase   2 wlyGpsgeGKStlakeLakall 23 
                   ++ G++g+GK+ l+k Lak l 
    AHX11076.1 601 MFLGSTGVGKTELSKALAKFLF 622
                   689*************998765 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   0.00011     0.051      15      80 ..     557     624 ..     549     640 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 0.00011
                 -HHHHHHHHHHH--S-HHHHHHHHHHHHHH.HT-SS-SS-E.EEEEEE-TTSSHHHHHHHHHHHHSTT CS
      Torsin  15 nleeLekdlekklfGqhlvkklvvksvkay.lenekpkkpL.vlsfhGwtGtGknfvaeiiaenlyrd 80 
                 +l ++e+ l+k+++Gq  + + v ++vk      +++++pL  + f G tG Gk  +++ +a+ l+ d
  AHX11076.1 557 KLLNIENALKKQVIGQNEAVEAVSNAVKRArAGIQDANRPLgSFMFLGSTGVGKTELSKALAKFLFDD 624
                 56788999*******************965155678999*9558899****************99987 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0     0.048        22       3      22 ..     204     223 ..     202     235 .. 0.86
   2 ?   -2.2   0.1       9.4   4.3e+03      46      70 ..     413     436 ..     377     457 .. 0.60
   3 ?    6.2   0.0     0.025        11       3      21 ..     601     619 ..     599     642 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.048
      AAA_28   3 vitGgestGKTtlleaLaar 22 
                 v++G ++ GKT ++e La r
  AHX11076.1 204 VLIGDPGVGKTAIVEGLAMR 223
                 89***************965 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 9.4
      AAA_28  46 lpwvedllafaervleeqleeeaaa 70 
                 +++  d+  ++ ++++e+l++e++a
  AHX11076.1 413 IDEL-DRKIIQLKIEAEALKKEKDA 436
                 2222.33334444444444444444 PP

  == domain 3  score: 6.2 bits;  conditional E-value: 0.025
      AAA_28   3 vitGgestGKTtlleaLaa 21 
                 +++G  + GKT l++aLa+
  AHX11076.1 601 MFLGSTGVGKTELSKALAK 619
                 799**************95 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0      0.96   4.4e+02      11      47 ..     187     223 ..     161     233 .. 0.79
   2 ?   -1.0   0.0       3.2   1.5e+03     129     146 ..     269     286 ..     249     303 .. 0.71
   3 ?   -2.2   0.5       7.9   3.7e+03      89     121 ..     449     483 ..     415     503 .. 0.56
   4 ?    8.6   0.0    0.0038       1.7       7      51 ..     571     624 ..     555     639 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.96
                 HHHHHT......TTSEEEEEESTTSTHHHHHHHHHHH CS
      ResIII  11 aienlleklkskrdkrglikmaTGtGKTlvaaklier 47 
                  i+++++ l+ + +++ ++    G+GKT +   l+ r
  AHX11076.1 187 EIRRVMQVLSRRTKNNPVLIGDPGVGKTAIVEGLAMR 223
                 56777777776667778899999*****998555444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 3.2
                 HTTT-SEEEEETGGGTTS CS
      ResIII 129 lrdrfdviiiDEaHrlga 146
                 ++    +++iDE H l +
  AHX11076.1 269 DSAGGIILFIDELHTLVG 286
                 333444899*****9877 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 7.9
                 ESSS-B--.........-SEEEEEHHHHHHTH... CS
      ResIII  89 vsgdkkka..kekdstnkkilvttiqsldadseee 121
                 +++ +kk+   e+  ++ k  + +iq+++++++e+
  AHX11076.1 449 LESLEKKQadLESVWQSEKSKLKEIQKIKEELNEA 483
                 33333333444455566666667777777777443 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.0038
                 HHHHHHHHHT..............TTS...EEEEEESTTSTHHHHHHHHHHHH-S. CS
      ResIII   7 yQeeaienlleklks........krdk...rglikmaTGtGKTlvaaklierllkk 51 
                  Q ea+e++ +++k         +  +    +++   TG+GKT ++ +l++ l+  
  AHX11076.1 571 GQNEAVEAVSNAVKRaragiqdaN--RplgSFMFLGSTGVGKTELSKALAKFLFDD 624
                 589999999999888888886543..2457899*************9999888764 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0       0.1        46       4      20 ..     205     221 ..     204     271 .. 0.86
   2 ?    6.8   0.0     0.015         7       3      24 ..     601     622 ..     600     681 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.1
      AAA_33   4 lvGlpGsGKstlaerll 20 
                 l+G pG+GK+  +e+l+
  AHX11076.1 205 LIGDPGVGKTAIVEGLA 221
                 79************997 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.015
      AAA_33   3 llvGlpGsGKstlaerllkklg 24 
                 ++ G  G+GK+ l++ l+k l 
  AHX11076.1 601 MFLGSTGVGKTELSKALAKFLF 622
                 899**************98665 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.13        61      13      40 ..     197     224 ..     184     230 .. 0.75
   2 ?    6.5   0.0    0.0096       4.4      14      58 ..     594     640 ..     581     651 .. 0.76

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.13
  Zeta_toxin  13 qerPklillgGqpGAGKselaellkdel 40 
                 ++++   +l G pG GK+++ e l+ ++
  AHX11076.1 197 RRTKNNPVLIGDPGVGKTAIVEGLAMRM 224
                 4555555677***********9998877 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0096
  Zeta_toxin  14 erPklill.gGqpGAGKselaellkdele.rqgnvvrldpDdlRelh 58 
                 +rP   ++  G++G GK+el+++l++ l   ++  +r+d  ++ e h
  AHX11076.1 594 NRPLGSFMfLGSTGVGKTELSKALAKFLFdDESALLRVDMSEYMEKH 640
                 55555444259***************998666777888888887777 PP

>> DUF3870  Domain of unknown function (DUF3870)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.81   3.7e+02      50      74 ..     334     358 ..     326     374 .. 0.91
   2 ?    8.7   0.1    0.0045       2.1      23      52 ..     719     748 ..     711     755 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.81
     DUF3870  50 vrsllvgkslledieeieeeikerY 74 
                 ++ ++vg+ ++ed+ +i + ike+Y
  AHX11076.1 334 FQPVFVGQPTEEDTISILRGIKEKY 358
                 57899*******************9 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0045
     DUF3870  23 islvvdkktgeivdadctltlelteeFvrs 52 
                 ++++v ++t++i d+++t ++e+ ++F+r 
  AHX11076.1 719 LGAEVLSETERITDTEKTQIMEIVRKFFRP 748
                 578999**********************96 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0021      0.99      10      38 ..     200     228 ..     192     336 .. 0.68
   2 ?   -0.1   0.0       2.3   1.1e+03      13      34 ..     600     621 ..     590     631 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0021
      AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelg 38 
                 +++ ++++ pG GKT ++++    +v+  
  AHX11076.1 200 KNNPVLIGDPGVGKTAIVEGLAMRMVAKD 228
                 5667899***********99888877665 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 2.3
      AAA_19  13 llvtaGpGtGKTrvlkhivall 34 
                 ++ ++  G GKT++ k+  + l
  AHX11076.1 600 FMFLGSTGVGKTELSKALAKFL 621
                 567899******9988777766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0      0.55   2.5e+02      15      32 ..     204     221 ..     195     228 .. 0.84
   2 ?   -1.1   1.2       5.6   2.6e+03      52      87 ..     464     482 ..     395     570 .. 0.60
   3 ?    7.2   0.0     0.015       6.8      15      41 ..     601     627 ..     597     653 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.55
                 EEEESTTSSHHHHHHHHT CS
                 xxxxxxxxxxxxxxxxxx RF
    ABC_tran  15 aivGenGaGKStLlklla 32 
                 +++G+ G GK+ +++ la
  AHX11076.1 204 VLIGDPGVGKTAIVEGLA 221
                 79**********998776 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 5.6
                 B-HHHCCHCEEEE-SS--S-TTSBHHHHHHHTCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  52 qeleslrkeigvlpqepqlfpeltvrenesdeeiek 87 
                 q+++s  kei+ +++e                 +++
  AHX11076.1 464 QSEKSKLKEIQKIKEE-----------------LNE 482
                 2222222222222222.................222 PP

  == domain 3  score: 7.2 bits;  conditional E-value: 0.015
                 EEEESTTSSHHHHHHHHTTSS--SEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  15 aivGenGaGKStLlkllagllkpteGe 41 
                  ++G++G GK+ L k+la+ l ++e  
  AHX11076.1 601 MFLGSTGVGKTELSKALAKFLFDDESA 627
                 589***************987665554 PP

>> Z1  Z1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   1.0    0.0011      0.52      56     122 ..     444     504 ..     402     513 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0011
          Z1  56 elkesaeekkeellkeleklwekektstkseeeelsfeevkeelkealekievvvvNsskkk.erldY 122
                 +++++  e+ e++ ++le++w++e      +++  +++++keel+ea +++ev+  N++  +  rl Y
  AHX11076.1 444 KIRQD-LESLEKKQADLESVWQSE------KSKLKEIQKIKEELNEARQSLEVAQRNGDLATaGRLLY 504
                 12222.333445555555555555......566678999******************98765456655 PP

>> HAUS2  HAUS augmin-like complex subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   5.2   0.00069      0.32       8     102 ..     373     469 ..     367     478 .. 0.74
   2 ?    1.0   0.1      0.68   3.1e+02      46      69 ..     775     798 ..     767     801 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00069
       HAUS2   8 alaeelgffvasgsvedevlklakkka....ekndalisvLrelsavqrelaklnlElqlrkddkdvadlthvselekkcealqrvtthLkavik.eKd 101
                 ++a++ ++ + +    d+ ++l  + a      +d   +v   + ++ r++ +l++E + +k++kd+  +   +++ +  e+l++ ++ L+ v + eK 
  AHX11076.1 373 SAATLSNRYITDRFLPDKAIDLMDEAAskirIESDSKPEV---IDELDRKIIQLKIEAEALKKEKDANSVSRLEKIRQDLESLEKKQADLESVWQsEKS 468
                 6666667777666666666666666652222233333333...44589*********************************************983444 PP

       HAUS2 102 r 102
                 +
  AHX11076.1 469 K 469
                 4 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.68
       HAUS2  46 elsavqrelaklnlElqlrkddkd 69 
                 +l ++q+ l+ +nlE++  ++ kd
  AHX11076.1 775 QLCKLQNLLKSKNLEIEFTQRAKD 798
                 68899************9999887 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.2       2.2   9.9e+02     330     360 ..      98     137 ..      14     177 .. 0.52
   2 ?    9.6   9.9   0.00066       0.3     319     431 ..     397     510 ..     363     532 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.2
        FapA 330 ldepelkeklkeleeeleel...eeeleklkkk.......i 360
                 +  + +++++  +e++l+ +   ++e  ++ k+       +
  AHX11076.1  98 IA-QRAQDSFVTVERLLQGIaaeKSEASEILKDqgvsapkL 137
                 44.44444443333333333211222222222233332221 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00066
        FapA 319 elgtkteievgldepelkeklkeleeeleeleeeleklkkk.....ikklpklkaekqlesekkeqlkklletkeklkeeleeleeelkelkeeleskk 412
                 e+ +k++ie   + pe++   +el++++ +l+ e e lkk+     +++l+k++++ +  ++k+ +l+++ ++ ++  +e+++++eel+e  ++le  +
  AHX11076.1 397 EAASKIRIESDSK-PEVI---DELDRKIIQLKIEAEALKKEkdansVSRLEKIRQDLESLEKKQADLESVWQSEKSKLKEIQKIKEELNEARQSLEVAQ 491
                 5566666666555.5554...5577777777666666666666689899999999999999999**********************************8 PP

        FapA 413 eeakikvnkeiypgvkiki 431
                 +++ +++  ++ +g+   +
  AHX11076.1 492 RNGDLATAGRLLYGTIRDL 510
                 8889999999999954443 PP

>> 5_nucleotid  5' nucleotidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   5.7     0.033        15     332     399 ..     422     488 ..     419     501 .. 0.69

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.033
                  THHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHHHHHT.T.THHHHHHHHHHHHHHHHHHHHHHHHHH CS
  5_nucleotid 332 ELeeElevleekkekeeleelekleelledelkklksseee.skekleeleedleelkkeirelreelk 399
                   L+ E e+l+++k+ +++++lek+++ le+ l+k +   e+  ++++++l+ +++++k+e++e+r++l+
   AHX11076.1 422 QLKIEAEALKKEKDANSVSRLEKIRQDLES-LEKKQADLESvWQSEKSKLK-EIQKIKEELNEARQSLE 488
                  6888999******99999999999999998.44444433333333334444.67777777777776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (854 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1838  (0.102515); expected 358.6 (0.02)
Passed bias filter:                      867  (0.0483574); expected 358.6 (0.02)
Passed Vit filter:                       145  (0.00808746); expected 17.9 (0.001)
Passed Fwd filter:                        46  (0.00256568); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              39  [number of targets reported over threshold]
# CPU time: 1.00u 0.29s 00:00:01.29 Elapsed: 00:00:00.45
# Mc/sec: 5657.79
//
Query:       AHX11077.1  [L=555]
Description: ribonuclease, Rne/Rng family domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-79  265.1   3.6    9.1e-79  264.7   3.6    1.2  1  RNase_E_G      Ribonuclease E/G family
    4.2e-09   36.6   0.2    7.8e-08   32.6   0.1    2.8  2  S1             S1 RNA binding domain
  ------ inclusion threshold ------
      0.043   12.7   0.0      0.089   11.6   0.0    1.4  1  FBPase_glpX    Bacterial fructose-1,6-bisphosphatase, glpX-en
       0.13   12.7   0.1       0.23   11.9   0.1    1.4  1  DnaJ_CXXCXGXG  DnaJ central domain


Domain annotation for each model (and alignments):
>> RNase_E_G  Ribonuclease E/G family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  264.7   3.6     2e-82   9.1e-79       2     270 .]     134     403 ..     133     403 .. 0.97

  Alignments for each domain:
  == domain 1  score: 264.7 bits;  conditional E-value: 2e-82
   RNase_E_G   2 laGrylVllpegkkvgvSkkiedeeererlkell.eelkpeevGlIvRtaaegaseeelekdleelkkkweeilekakkrkapsllyeeedlllrvlrd 99 
                 l+ ry+Vl+p++k   +Sk+i+de+  +rl +l+ e++ ++++G+I+++ +e+a+e+++ +d++ l+++w+ i ++ ++ kap+l+++e++l++++lrd
  AHX11077.1 134 LPNRYCVLMPFSKDFVLSKQISDEKAVNRLTQLVeEKIGDRKYGVIFKSYCENADEKNIINDYNLLVSQWDAIASRKEEGKAPRLIFREANLVKKILRD 232
                 799*******99999*******************6666689*************************************9******************** PP

   RNase_E_G 100 llnedieeivvddkelyeeikeyleevapeleekvelyeeeeplfelysiekqiekalsrkvwlksGgylvIeqTEAltvIDVNsGkftgkknleetvl 198
                  +++++  i+++dk++y+e+ +y+++     +++v+lyee+ plf++y++e+qi+++++++v l++Ggy+vI++TEAlt+IDVNsG++++++n+eet++
  AHX11077.1 233 SYDSSVGAIIINDKHVYQETVDYVQSALYFDNHHVTLYEERLPLFDKYKVEAQIDSLYEENVPLRNGGYIVINTTEALTAIDVNSGRMKKETNIEETAY 331
                 ************************8888888889****7777********************************************************* PP

   RNase_E_G 199 ktNleAaeeiarqlrLRnlgGiIviDFIdmkeeenreevleelkealkkDraktqvleitklgLveitRkrv 270
                 k+N+ A+ ei+rql LR ++GiIviD Idm++++   +v ++l + +k+ +a++q+++i k+gLv i+++r+
  AHX11077.1 332 KVNMDAVVEIVRQLELRGIAGIIVIDLIDMSNSKYIANVEKALLDGFKRYKARVQITSINKFGLVTISKQRT 403
                 **********************************************************************96 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   1.7e-11   7.8e-08       2      72 ..      35     128 ..      34     130 .. 0.96
   2 ?    0.4   0.0      0.19   8.4e+02      18      40 ..     381     404 ..     378     412 .. 0.68

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 1.7e-11
                 STTTCEEEEEEEEEET..TEEEEEETTTEEEEEEGGGSSSS.....................CEESCHHHCEETTEEEEEEEEEEETTTTEEEE CS
          S1   2 pekgevveGeVtsvtk..gGafVelgngvegfvpaselsrd.....................arvedpdevlkvGdevkvkvlkvdkdrrriil 72 
                 p+kg+++ G+V++v++   +afVe++ g  gf+p se++                       +++++ +ev+k+G  + v+v+k ++ ++ + l
  AHX11077.1  35 PQKGNIYLGVVFRVDDslQAAFVEYLPGEYGFLPFSEIPVTyfdlledvkvnaiaedkhvylYKNFNATEVIKKGLVIFVQVTKEKRRNKDVTL 128
                 89*************************************99*********************************************99997765 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.19
                 TEEEEEET.TTEEEEEEGGGSSSS CS
          S1  18 gGafVelg.ngvegfvpaselsrd 40 
                 + a+V++   +  g+v++s +  +
  AHX11077.1 381 YKARVQITsINKFGLVTISKQRTR 404
                 567777777777777777776665 PP

>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0     2e-05     0.089      64     108 ..     468     512 ..     462     516 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2e-05
  FBPase_glpX  64 LyiGekvGsgegpevdiavdpleGttlvAkglpnaisviAvaekg 108
                  +   e++G + + +vd+ +dpl G ++  +g++  +s+ A+ ek+
   AHX11077.1 468 IRAEEEIGVKISIKVDVHMDPLKGFEISVQGKDKGVSISAIQEKN 512
                  56789****999****************************99987 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1     5e-05      0.23      14      55 ..     412     426 ..     394     448 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 5e-05
  DnaJ_CXXCXGXG  14 kktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvik 55 
                    + +C++C+G+G                           k++k
     AHX11077.1 412 MAKCPQCGGKG---------------------------KTLK 426
                    34555555555...........................4442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (555 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 4145.23
//
Query:       AHX11078.1  [L=404]
Description: cytochrome C and Quinol oxidase polypeptide I family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        8.2    6.3  10.2        1.4    8.8   3.5    2.6  2  60KD_IMP  60Kd inner membrane protein


Domain annotation for each model (and alignments):
>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   3.5   7.9e-05       1.4      68     149 ..      19     165 ..      14     174 .. 0.60
   2 ?    0.9   0.5     0.021   3.7e+02      91     103 ..     263     302 ..     182     398 .. 0.55

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 7.9e-05
    60KD_IMP  68 aGclplLiqlpifialyrvlrsla.........sfwikdLsapd............................................lpillavttfl 113
                  +c++lL+ lp+f++l   +  ++         ++w+  ++ ++                                            lp +++v+ + 
  AHX11078.1  19 FSCFVLLLRLPFFVGLIPNIFDVSliihvtlgiNVWMLAITVSTwdrqglvqrfsynlcfiaviliflsgfipgtdviksnyipfldnLPYITGVALL- 116
                 68***************999998888888777733433333322336666667777744444444444444444444444444444443333333333. PP

    60KD_IMP 114 qqklsksk....................kmqkmmlyvmplmilffslsfpaglvlY 149
                                             +++ ++ ++  + + +  +++p++l+l 
  AHX11078.1 117 -------LfgilinsldtiirsnsercdRITATIFLISQVCMCLAYARMPSALTLH 165
                 .......0333333333444444555654456777899999999999999999986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.021
    60KD_IMP  91 a..sfwikdLsapd.........................l 103
                 +   fw+  Lsa+                          +
  AHX11078.1 263 PhsYFWAFALSASLfvyggllgfliresniiipahyhgsI 302
                 2323344445552244444444444444444444444441 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      306  (0.0170673); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 2928.58
//
Query:       AHX11079.1  [L=315]
Description: nicotinate-nucleotide diphosphorylase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.7e-52  177.6   0.5    2.5e-52  177.0   0.5    1.3  1  QRPTase_C       Quinolinate phosphoribosyl transferase, C-ter
    1.4e-15   57.1   0.0    2.7e-15   56.2   0.0    1.4  1  QRPTase_N       Quinolinate phosphoribosyl transferase, N-ter
  ------ inclusion threshold ------
      0.041   13.2   0.2       0.19   11.0   0.1    2.1  2  TMP-TENI        Thiamine monophosphate synthase
      0.082   12.3   0.1       0.26   10.6   0.1    1.9  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family


Domain annotation for each model (and alignments):
>> QRPTase_C  Quinolinate phosphoribosyl transferase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.0   0.5   5.6e-56   2.5e-52       1     168 [.     140     306 ..     140     307 .. 0.99

  Alignments for each domain:
  == domain 1  score: 177.0 bits;  conditional E-value: 5.6e-56
                 HHHHHHHHHHHHHCTSSEEEE-S---TTTHHHHHHHHHHTTSB--TSSTTTSEEE-HHHHHHHSSHHHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHH CS
   QRPTase_C   1 iAtltarmveaaksakvrildTRkttPglrllekyAvliGGgdnhrlgLsdmvlikdnhiaaagsiveavksvreavdkevkievevesleeleevlea 99 
                 iA+ t+++v+++++++++i +TRkttPg+r +e yA+++GGg+n r +Lsd vl+kdnhia+ g++++av+s+r+ +++   i+ve+++ ++++e+++ 
  AHX11079.1 140 IASITRKFVDKVAHTNAKIRGTRKTTPGMRCMELYAIKVGGGENYRDSLSDKVLLKDNHIAISGGVKSAVNSLRSSLGEVY-ITVECDTFQQVREAASL 237
                 8****************************************************************************9986.***************** PP

                 T-SEEEEES--HHHHHHHHHHHHHHSTTSEEEEESS--TTTHHHHHCTT-SEEEECHHCHTB----EEE CS
   QRPTase_C 100 eadiimLDnfsveelkkaveelkeknkrvlievSGgvtlenveeyaksgvdvisvgalthsvkalDisl 168
                 ++  i+LDn+svee+k++v +++   ++++i +SGg+tle+v  +a++gvd+isvg+lths +  Di +
  AHX11079.1 238 NVGTILLDNMSVEEIKNCVGYVRGVRPSIAIDASGGITLETVVRIAETGVDYISVGMLTHSINGTDIGI 306
                 ******************************************************************986 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0     6e-19   2.7e-15       4      89 .]      54     138 ..      52     138 .. 0.98

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 6e-19
                 --HHHHHHGCTTSEEEEEEEESSSEEE-SHHHHHHHHHHHTTTEEEESS-TT-EEETTEEEEEEEEEHHHHHHHHHHHHHHHHHHH CS
   QRPTase_N   4 gDlttealipeekkakaeiiakeegvvaGlevaeevfellpglevellvkDGervekgdvlleieGnarallsaERvaLnllqrlS 89 
                  D+t++++i+++ k+ +e+ ++++ vv+  +v e ++ +  g+e  l+++DGe v+++++++   +n+ all++ERv Ln++qr +
  AHX11079.1  54 YDITSDNVIDPDLKVPFEVNTRDATVVCVRPVTELLLGQT-GIEYILHKSDGEMVQENETIISGYANSLALLKVERVFLNFIQRSC 138
                 6***************************************.******************************************976 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       0.4   1.8e+03     153     173 ..     137     157 ..     123     158 .. 0.85
   2 ?   11.0   0.1   4.3e-05      0.19     139     177 ..     249     292 ..     203     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.4
    TMP-TENI 153 vvaiGGitlenvaevleagad 173
                  +ai+ it + v++v++++a+
  AHX11079.1 137 SCAIASITRKFVDKVAHTNAK 157
                 689999999999999999885 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 4.3e-05
    TMP-TENI 139 leglkelaeale.....iPvvaiGGitlenvaevleagadgvav 177
                 +e +k+++  ++     i + a GGitle+v +++e+g+d ++v
  AHX11079.1 249 VEEIKNCVGYVRgvrpsIAIDASGGITLETVVRIAETGVDYISV 292
                 45555555555566566777788*****************9998 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   5.8e-05      0.26     152     194 ..     251     293 ..     240     296 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 5.8e-05
                     HHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--EEEES CS
  Ribul_P_3_epim 152 kikkvrklidekeldlkievDGGvkldnieqiaeagadvlVag 194
                     +ik+   ++     ++ i + GG++l+++ +iae g+d + +g
      AHX11079.1 251 EIKNCVGYVRGVRPSIAIDASGGITLETVVRIAETGVDYISVG 293
                     445544555555567888888*****************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2469.96
//
Query:       AHX11080.1  [L=47]
Description: hypothetical protein NHE_0110 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       208  (0.0116013); expected 358.6 (0.02)
Passed bias filter:                      171  (0.00953762); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 392.74
//
Query:       AHX11081.1  [L=81]
Description: ribosomal protein S16 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-26   90.7   0.0    5.3e-26   90.5   0.0    1.1  1  Ribosomal_S16  Ribosomal protein S16


Domain annotation for each model (and alignments):
>> Ribosomal_S16  Ribosomal protein S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.5   0.0     3e-30   5.3e-26       1      62 []       8      69 ..       8      69 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.5 bits;  conditional E-value: 3e-30
                   EESCTTCEEEEEEEEETTSSTTSSESEEEEEEETTTTSSTS.SEEE-HHHHHHHHHTTEEEE CS
  Ribosomal_S16  1 RfGrknrPfYrivvadsrkprdgrpiEklGtYdPlakkkekkevelneerikyWlgvGAqpt 62
                   RfGrknrP+Y+ivva+s++prdg+++E++G+YdPl +k+++ +v ln+eri+yW +vGA+pt
     AHX11081.1  8 RFGRKNRPYYKIVVANSSAPRDGKFLEQVGSYDPLLSKDNPLRVLLNKERIQYWTSVGAKPT 69
                   9*********************************999999999******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       315  (0.0175693); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 677.42
//
Query:       AHX11082.1  [L=160]
Description: 16S rRNA processing protein RimM [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-10   39.6   0.1    2.3e-09   37.3   0.1    2.0  1  RimM      RimM N-terminal domain
    0.00012   22.1   0.0    0.00027   20.9   0.0    1.7  2  PRC       PRC-barrel domain


Domain annotation for each model (and alignments):
>> RimM  RimM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.1   2.6e-13   2.3e-09       2      82 ..       4      79 ..       3      81 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 2.6e-13
                EEEEEEEETTTTEEEEEE-SSSGGGGGGSSSEEEE.ETTEEEEE-EEEEE.EETTEEEEEETT--SHHHHHTTTT-EEEEET CS
        RimM  2 vGkIvgahGlkGevkVkpftdfpealfkygrvlleakkgetreltvesvr.vhkkgvivklegvddrdaAealkgaelfvpr 82
                 G+++++hG++G ++V+++  +   +    +v +      + ++tv++    + + v+++l gvd+ ++Ae+l+g+++fv++
  AHX11082.1  4 AGRVASTHGVRGCIRVQSYMCSTFGFV-GAEVSIG----GI-SYTVRTSFnRKPSLVVLSLLGVDSASEAESLVGCDVFVAE 79
                59*****************77665444.4444444....23.4999987735588*************************87 PP

>> PRC  PRC-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.0      0.85   7.6e+03       6      15 ..      67      76 ..      64      76 .. 0.80
   2 !   20.9   0.0   3.1e-08   0.00027       1      72 [.      87     154 ..      87     160 .] 0.78

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.85
                S---TT-EEE CS
         PRC  6 asdliGkeVy 15
                a +l+G++V+
  AHX11082.1 67 AESLVGCDVF 76
                67899**996 PP

  == domain 2  score: 20.9 bits;  conditional E-value: 3.1e-08
                 XEECCS---TT-EEEETTSSEEEEEEEEEEETT.TTEEEEEEEEETTT.....-EEEEEGG.....CEECCCTEEEE CS
         PRC   1 edefrasdliGkeVytedGeklGkVkDvvidek.egrvralvvsvggflgigekevliPfd....lavkigkdriiv 72 
                 ede+++ dliG+ V +  Ge++G V  +  d++ + +v+++  + g       k++ iPf+      v++ +++i v
  AHX11082.1  87 EDEYYYKDLIGMAVCSK-GEHVGSVLML-YDFGaAAQVLEITSRSG-------KKIMIPFTkefiVKVDLCAKMIEV 154
                 689************99.8******998.88844666666666665.......********8766666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (160 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1222.05
//
Query:       AHX11083.1  [L=408]
Description: rmuC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.5e-85  285.7   3.0    3.5e-85  285.7   3.0    1.8  2  RmuC            RmuC family
  ------ inclusion threshold ------
      0.061   13.6   0.3      0.061   13.6   0.3    2.4  2  Abi_2           Abi-like protein
        0.1   11.5   1.2       0.12   11.3   1.2    1.2  1  LMBR1           LMBR1-like membrane protein
       0.11   12.4   2.2       0.14   12.1   0.1    2.2  3  TPD             Protein of unknown function TPD sequence-moti
        1.7    9.1   7.3         10    6.5   0.3    2.8  2  CENP-H          Centromere protein H (CENP-H)
        3.9    7.5  14.3        4.5    7.3   8.7    3.2  2  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C


Domain annotation for each model (and alignments):
>> RmuC  RmuC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.9      0.32   9.6e+02      22      57 ..      55      90 ..      30     101 .. 0.53
   2 !  285.7   3.0   1.2e-88   3.5e-85       3     290 ..     109     396 ..     107     397 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.32
        RmuC 22 eeeskeeaeeleslkeqlkelqelneqlgdeaenLt 57
                 ++++e +++  +l+++ k+++  ++ +  e enL+
  AHX11083.1 55 GASNDELTKRVVQLEAEKKSFEYSQKAMYMEFENLA 90
                333345555555555555555555555555555553 PP

  == domain 2  score: 285.7 bits;  conditional E-value: 1.2e-88
        RmuC   3 leellkplkeklekfeekveeeskeeaeeleslkeqlkelqelneqlgdeaenLtkaLk.nsktrGnwGEvqLerilessgleegeeyetqvslkdeeg 100
                 l++ll+plk k+++fe+++e++ + + +e+ sl++++ ++++++e++ dea++L+k L+ ++k++G wGE++L++ile+sgl+++++y+ q++l ++  
  AHX11083.1 109 LSTLLDPLKVKIAEFEKRIEDSFSVDIKERYSLSREIARMASQTEKMIDEASKLSKSLRgDNKAQGLWGELVLSKILEHSGLQKDRDYTLQQKLGNS-- 205
                 899******************************************************************************************9444.. PP

        RmuC 101 elrpDvvvklpggkklviDsKvpleaYerlveaeddeereealkahaksvkkhikeLseKdYeele...sldyvlmFiPiEsayaealeadpeLleeal 196
                    pDv+++lp++k+lviD+K++l++Y+ +v++++    +e+l+ ++ks+++hik+L+ K+Y++++   ++++v+mF+PiEsay++al++d+eL e al
  AHX11083.1 206 -SIPDVIINLPDEKHLVIDAKTSLKHYDLYVQTNE----KEHLELFLKSIRSHIKNLAGKEYHAAHelfTPGFVFMFVPIESAYMLALSSDSELKELAL 299
                 .59*****************************888....789***********************6689****************************** PP

        RmuC 197 rkkVvlasPttLlalLrtvamlwrqeaqeknaeeiaellgelydkfekfgedleklgkklekaqksydkavkkle...gnilrkaeklkelgvkekk 290
                 r++V+l+sP++L+a+L++v+ +w+  +q+kna+eia+++g++ydkf+ f+e+l k+g+++ ++ + y++a++kl    g+++++ae+lk +g++++k
  AHX11083.1 300 RNRVMLVSPNSLIAMLQAVSSVWKIVDQNKNANEIAKKAGAMYDKFVLFVEELVKVGNAIAHSDRLYKSAINKLRdgrGSLFKRAEDLKMMGISANK 396
                 *********************************************************************************************9998 PP

>> Abi_2  Abi-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.5      0.86   2.6e+03      29      29 ..     104     104 ..      59     171 .. 0.55
   2 ?   13.6   0.3     2e-05     0.061     132     178 ..     315     366 ..     217     367 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.86
       Abi_2  29 t 29 
                  
  AHX11083.1 104 R 104
                 1 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2e-05
       Abi_2 132 fGtlsklykllkk.kdkkeiakefgl....leswlkslkklRNicAHhsrlw 178
                 +  +s++ k++++ k+ +eiak+ g+    +  +++ l k+ N++AH +rl+
  AHX11083.1 315 LQAVSSVWKIVDQnKNANEIAKKAGAmydkFVLFVEELVKVGNAIAHSDRLY 366
                 33455556666666888*******999************************9 PP

>> LMBR1  LMBR1-like membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.2   3.9e-05      0.12     172     292 ..      10     174 ..       2     323 .. 0.64

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.9e-05
       LMBR1 172 lvllilllGyGlvelPrslwreiksdldeelkklyfeaaklntekeeaereledllkevkklrksisesdplrkyleeilkkvPeeiaeklks...... 264
                 +vl+++ +  G+ ++  +l+ e ++++ e+l++  +e+  l++++  +++el + + ++++ +ks+++s++   +  e  +  ++ +++++++      
  AHX11083.1  10 VVLVLIVGYLGYLRVRAGLILEREREKIERLSAELLEIRALYEKEGASNDELTKRVVQLEAEKKSFEYSQK--AMYMEFENLANKILESNTNKfrersl 106
                 45555555567788877888866666667777777788888878888888888777777777777777773..33333333333333344444222444 PP

       LMBR1 265 ........................................nenkteeslaklekqlikalqkrertek 292
                                                            +++e+++++ ++l k+l+  ++ + 
  AHX11083.1 107 sdlstlldplkvkiaefekriedsfsvdikeryslsreiaRMASQTEKMIDEASKLSKSLRGDNKAQG 174
                 45555555555433333333333333333333333333322222333444444444444444444444 PP

>> TPD  Protein of unknown function TPD sequence-motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.3   3.9e+03      14      50 ..      66     102 ..      55     106 .. 0.66
   2 ?   12.1   0.1   4.5e-05      0.14       4      71 ..     147     215 ..     144     241 .. 0.89
   3 ?   -3.3   0.0       2.6   7.9e+03      14      33 ..     361     380 ..     349     397 .. 0.68

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.3
         TPD  14 eedsvyspladairssvGeeyEellekllkekgiafk 50 
                  + ++ +++ +  ++++  e+E+l +k+l+++  +f+
  AHX11083.1  66 VQLEAEKKSFEYSQKAMYMEFENLANKILESNTNKFR 102
                 4445555666667777778888888888887766665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 4.5e-05
         TPD   4 rlakevkeaieedsvyspladairssvGeeyEellekllkekgiafkteedlrek.gldktPDvkLevp 71 
                 r+a + +++i e s  s++   ++++ G ++E +l+k+l++ g++   + +l++k g +  PDv ++ p
  AHX11083.1 147 RMASQTEKMIDEASKLSKSLRGDNKAQGLWGELVLSKILEHSGLQKDRDYTLQQKlGNSSIPDVIINLP 215
                 56778899999999999999999**************************999866378889***99988 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.6
         TPD  14 eedsvyspladairssvGee 33 
                 ++d+ y+ ++++ r+ +G+ 
  AHX11083.1 361 HSDRLYKSAINKLRDGRGSL 380
                 56777777777777777654 PP

>> CENP-H  Centromere protein H (CENP-H)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.7   2.0     0.013        40      16      62 ..      31      84 ..      23     126 .. 0.68
   2 ?    6.5   0.3    0.0035        10       5      51 ..     135     181 ..     132     206 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.7 bits;  conditional E-value: 0.013
      CENP-H 16 lklsqelrelqeeltevekenlrlkrknrelaaellelakekesek.......e 62
                ++  ++++ l +el e+++   +  + n el++++ +l+ ek+s +       +
  AHX11083.1 31 EREREKIERLSAELLEIRALYEKEGASNDELTKRVVQLEAEKKSFEysqkamyM 84
                555667777777777777777777888888888887777777666654433331 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0035
      CENP-H   5 ieqrdelssellklsqelrelqeeltevekenlrlkrknrelaael.l 51 
                 i++r  ls e+++++++++++ +e +++ k +lr  +k + l+ el l
  AHX11083.1 135 IKERYSLSREIARMASQTEKMIDEASKLSK-SLRGDNKAQGLWGELvL 181
                 7999**********************9986.56666666677766644 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   8.7    0.0015       4.5      17      92 ..      56     130 ..      42     171 .. 0.76
   2 ?    1.0   0.1      0.13   3.8e+02      73     100 ..     231     258 ..     215     267 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0015
  CENP-F_leu_zip  17 rkadsLkdkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalrsekeeLekelqkk 92 
                      ++d L  +v +Le+e++  e +q ++ +e E+  +++ + ++++ + +++l++l++ L+ l+    e ek ++++
      AHX11083.1  56 ASNDELTKRVVQLEAEKKSFEYSQKAMYMEFENLANKILESNTNKFR-ERSLSDLSTLLDPLKVKIAEFEKRIEDS 130
                     579******************************88877665555555.5789999999988887777777766654 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.13
  CENP-F_leu_zip  73 ldLvalrsekeeLekelqkkqervseLe 100
                      dL   ++eke+Le  l+  ++ +++L 
      AHX11083.1 231 YDLYVQTNEKEHLELFLKSIRSHIKNLA 258
                     4666667788888777777777777774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1429  (0.0797033); expected 358.6 (0.02)
Passed bias filter:                      696  (0.0388198); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.29s 00:00:00.87 Elapsed: 00:00:00.42
# Mc/sec: 2923.62
//
Query:       AHX11084.1  [L=270]
Description: hypothetical protein NHE_0114 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-06   26.3   0.0    1.5e-05   25.2   0.0    1.5  1  PAS_9     PAS domain
  ------ inclusion threshold ------
      0.076   13.0   0.2       0.18   11.8   0.2    1.6  1  Sigma_1s  Sigma 1s protein
       0.12   12.7   0.0       0.21   11.8   0.0    1.3  1  PAS_4     PAS fold


Domain annotation for each model (and alignments):
>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   2.5e-09   1.5e-05       4      88 ..      16     107 ..      12     119 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 2.5e-09
       PAS_9   4 ilidnpdg..rilyaNeaalrllGyspeevlgksitdlfvtdpeanerlraaleqgrk.......kerevevvlirkngetfwvlltaspvkdd 88 
                 i+ dn+d   +i +aNea+l ll y++ e+ g++++d++  ++++++r+ + le  +          r +e+ l  k g  ++v+++++p  ++
  AHX11084.1  16 IVQDNNDKtvMISDANEALLSLLFYTSSELKGRPFFDIL--EQKDRDRILEHLEYEEYgidiesiLTRLRELSLKSKHGANIPVKIKIFPSSSA 107
                 4555555555666**************************..33333333333333333569999999999******************997666 PP

>> Sigma_1s  Sigma 1s protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.2     3e-05      0.18      22      66 ..     142     186 ..     130     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3e-05
    Sigma_1s  22 lSsgsvrdsiqqkdesvllskvgqpllrelVrtnlelidskalse 66 
                   ++ + ds + + e+vlls  ++ + ++ V   ++l ds+  s 
  AHX11084.1 142 NDTLRIMDSQSTEAEIVLLSRFCKQYRQNCVVGFIQLSDSSRTSM 186
                 5688999********************************987764 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.6e-05      0.21      17      56 ..      27      66 ..      10      68 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.6e-05
       PAS_4 17 vlyaNaaaaelfgappeellGktlaellpeedaarleral 56
                + +aN+a  +l+ ++  el G++++++l + d++r+ ++l
  AHX11084.1 27 ISDANEALLSLLFYTSSELKGRPFFDILEQKDRDRILEHL 66
                679*******************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2157.97
//
Query:       AHX11085.1  [L=259]
Description: twin arginine-targeting protein translocase TatC [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.7e-64  215.3  16.2      9e-64  215.1  16.2    1.0  1  TatC      Sec-independent protein translocase protein (TatC)


Domain annotation for each model (and alignments):
>> TatC  Sec-independent protein translocase protein (TatC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  215.1  16.2     5e-68     9e-64       2     207 .]       6     231 ..       5     231 .. 0.93

  Alignments for each domain:
  == domain 1  score: 215.1 bits;  conditional E-value: 5e-68
                 HHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHCCHHHHC..CTT..........S-EE--SSS-HHHHHHHHHHHHHHHHSHHHHHHHHHCCCTTTTS CS
        TatC   2 hLeeLrkrlirallavaiafiitfvfaeeliafllepleea.eee..........velivlspleafllklkvslvaglvlasPvilyqlwafvapgLy 89 
                 hL eLr rl++++l+++ af+++++f+ee+++fll+pl+e  + +           +li++ ++e f+++lkv+++++++l++P++++q++ fvapgLy
  AHX11085.1   6 HLSELRYRLVISVLFFLGAFCLCYYFSEEIYKFLLRPLAEIaN-QrdgvtgkncsFTLIYTGLTETFVVYLKVAFLGAILLSAPFFIWQIYMFVAPGLY 103
                 **************************************88643.1345555556689****************************************** PP

                 ---STTTHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHT..........TTTSSTTEEHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHTTSS-HHHHHTT CS
        TatC  90 kherrlvlvfliaslllfllGaafayfvvlplvlkfll..........seevepllslseylsfvlllllafgiaFelPlvlvllarlglvsaetlrkk 178
                 ++e+r+++++++++ +lf+lG+ + y++v+pl+++f++          +  +e+++s+seyl++v+++++afgiaF+lP +l+ll  +gl++++ l +k
  AHX11085.1 104 PTEKRAFIPYIVSAPILFVLGCSVVYYYVFPLAWQFFVsfeydgskpgTLPIEFMPSVSEYLDLVVQFMFAFGIAFQLPGILTLLCHIGLLDHNALVRK 202
                 **************************************88888776554445889******************************************** PP

                 HHHHHHHHHHHHHHH-S.SHHHHHHHHHH CS
        TatC 179 rryaivvilvvaavltPpdvisqlllavP 207
                 r++ iv+i++vaa+ltPpdv+sq+ la+P
  AHX11085.1 203 RKFSIVLIFIVAAILTPPDVLSQIGLAIP 231
                 ****************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       672  (0.0374812); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2225.04
//
Query:       AHX11086.1  [L=291]
Description: protein-(glutamine-N5) methyltransferase, release factor-specific [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.3e-10   39.8   0.0    1.2e-09   38.6   0.1    1.6  2  PrmC_N           PrmC N-terminal domain
    6.5e-09   35.6   0.0    7.4e-08   32.1   0.0    2.0  2  MTS              Methyltransferase small domain
    2.2e-08   34.1   0.0    3.5e-08   33.4   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.3e-05   24.7   0.0    1.8e-05   24.2   0.0    1.1  1  N6_Mtase         N-6 DNA Methylase
      2e-05   24.4   0.0      3e-05   23.8   0.0    1.3  1  UPF0020          Putative RNA methylase family UPF0020
    3.5e-05   24.4   0.0    8.5e-05   23.2   0.0    1.6  2  Methyltransf_25  Methyltransferase domain
    0.00028   20.6   0.0    0.00047   19.9   0.0    1.3  1  Cons_hypoth95    Conserved hypothetical protein 95
     0.0019   18.1   0.0      0.009   15.9   0.0    1.9  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.035   13.5   0.0      0.051   13.0   0.0    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
       0.21   12.1   0.0       0.38   11.3   0.0    1.5  1  Eco57I           Eco57I restriction-modification methylase


Domain annotation for each model (and alignments):
>> PrmC_N  PrmC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.6   0.1   6.8e-13   1.2e-09       3      62 ..      13      71 ..      11      79 .. 0.91
   2 ?   -3.3   0.0       8.2   1.5e+04      17      31 ..      96     110 ..      90     120 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.6 bits;  conditional E-value: 6.8e-13
      PrmC_N  3 LreaearLkaagieeaeldAelLlahvlglsrsdlllrgerelteeqlerfeelierRaa 62
                L+ a+ +L+   ++++ ldAelLl+hvlg +r  lll++++ l+ee+ ++f  lie R++
  AHX11086.1 13 LKFASVQLRVC-SQTPNLDAELLLTHVLGSTREKLLLNSNDGLSEEKISEFHTLIELRKK 71
                56677888888.89******************************************9976 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 8.2
      PrmC_N  17 eaeldAelLlahvlg 31 
                  ++ d e ++a+vl+
  AHX11086.1  96 IPRPDTETIVAAVLS 110
                 577788888888885 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   4.1e-11   7.4e-08      29     110 ..     115     200 ..     102     212 .. 0.86
   2 ?    0.9   0.0      0.16   2.8e+02     120     137 ..     230     247 ..     227     252 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.1e-11
                 CCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC..EEEEE-STTT..TSTTS-EEEEEE---STTT CS
         MTS  29 kelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle..vevvasdvle..eveekkfdlivsNPPfhag 110
                 +++s ++l lG+G G + ++l++e+ +a    ++++ +A ++++ n+++++l+  +++++sd     ++  +k+d+ivsNPP+ + 
  AHX11086.1 115 HRRSLRILELGTGSGCIIISLLNEYRNAIGFGFEKSNAAFRLTRINCHRHGLQsrLRLYHSDFNRvpAILRGKVDIIVSNPPYIKR 200
                 446778*********************99999*********************99999***9876224558***********8665 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.16
                 HHHHHHHHHEEEEEEEEE CS
         MTS 120 eliaeAkeaLkegGeLli 137
                 ++++ Ak++L++gGe ++
  AHX11086.1 230 AILKLAKKILNPGGEVFL 247
                 58899*********9875 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.0     2e-11   3.5e-08       3     114 ..     117     252 ..     115     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 2e-11
  Methyltransf_31   3 kglrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgld.nveFeqgdieeleklledekfDlilsn.............. 81 
                      + lr+l+lG+G+G +++ l  + + +a  +G++ s  a +l r n+ ++gl+ ++++ ++d++  +  l   k+D+i+sn              
       AHX11086.1 117 RSLRILELGTGSGCIIISLL-NEYRNAIGFGFEKSNAAFRLTRINCHRHGLQsRLRLYHSDFNRVPAILR-GKVDIIVSNppyikradlptlqt 208
                      6789****************.77889999*************************************5355.9********88888888877777 PP

  Methyltransf_31  82 .......evl....naladpdkileeiervlkpggilliedprl 114
                              +l    n +    +il+ +++ l+pgg++ +e  + 
       AHX11086.1 209 evrseprLALdggfNGILPYFAILKLAKKILNPGGEVFLEVGDY 252
                      77776653336666888888888889999999999999887774 PP

>> N6_Mtase  N-6 DNA Methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   9.9e-09   1.8e-05      48     138 ..     119     200 ..      96     221 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.9e-09
    N6_Mtase  48 esvyDpacGsggllvqaekvlkeedgktkelsiyGqeknettyrLakmNlllhgieykkvkirlgdtlekpkfekdkkfdvvvaNppfnqk 138
                   ++    Gsg ++++  +       + ++   +G ek + ++rL+++N+  hg +   ++  ++d    p      k+d++v+Npp+ ++
  AHX11086.1 119 LRILELGTGSGCIIISLLN-------EYRNAIGFGFEKSNAAFRLTRINCHRHGLQSR-LRLYHSDFNRVPAIL-RGKVDIIVSNPPYIKR 200
                 4566667777777776655.......34556679**********************99.99*****99999888.*************765 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.0   1.7e-08     3e-05      79     136 ..     144     202 ..     110     209 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.7e-08
                 EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--.STTS---EEEE--------- CS
     UPF0020  79 lygsDldrrvvqgareNaekagvgdliefsqadaakLr.lkegevdvivtnpPYGerlg 136
                  +g+++ +++ + +r N ++ g++ +  ++  d+  ++   +g+vd+iv+npPY +r +
  AHX11086.1 144 GFGFEKSNAAFRLTRINCHRHGLQSRLRLYHSDFNRVPaILRGKVDIIVSNPPYIKRAD 202
                 5899999*******************************98999***********99975 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   4.7e-08   8.5e-05       1      88 [.     121     209 ..     121     213 .. 0.88
   2 ?   -3.2   0.0         8   1.4e+04      85      97 .]     231     243 ..     230     243 .. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 4.7e-08
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT..TEEEEESBCCGBSS.STTTEEEEEEESTGGGSSHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl..nvefvqgdaedlpf.edgsfDlvvssgalhhlsdedlekalke 88 
                      +L+lG+G+G +++ l++++ +a   g++ s ++ + +r +++++gl  ++++++ d++++p    g++D++vs+    +++++dl+++  e
       AHX11086.1 121 ILELGTGSGCIIISLLNEYRNAIGFGFEKSNAAFRLTRINCHRHGLqsRLRLYHSDFNRVPAiLRGKVDIIVSN--PPYIKRADLPTLQTE 209
                      8*****************97788899*****************99999************954889*******5..467777777766655 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 8
                      HHHHHHHHEEEEE CS
  Methyltransf_25  85 alkeiarvLkpgG 97 
                      +lk ++++L+pgG
       AHX11086.1 231 ILKLAKKILNPGG 243
                      67888999***99 PP

>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   2.6e-07   0.00047      13     141 ..      89     215 ..      80     221 .. 0.80

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 2.6e-07
                    EEXTTXXXXXSSSHHHHHHHHHHHCCCHCC-EEEETT-TTSHHHHHHHHTT-SEEEE.EES-HHHHHHHHHHHCCCT--TTTEEEEES-HHHHCTS CS
  Cons_hypoth95  13 LkvlegkstRPttdrvrealFnilaaeiegarvLDlfaGsGalglEAlSRgakkavl.vekdkeavkilkenleelkleeetaelkedaleallkl 107
                    +  +++   RP t+ +  a+ +  +++ +  r+L+l  GsG + +  l  + + + + +ek+++a+++ + n+++ +l+++ + +  d  +    l
     AHX11086.1  89 VVSKNILIPRPDTETIVAAVLSRYGKHRRSLRILELGTGSGCIIISLLNEYRNAIGFgFEKSNAAFRLTRINCHRHGLQSRLRLYHSDFNRVPAIL 184
                    5555666679***********************************99987766655449********************97777766665555444 PP

                    --SS-EEEEEEE--SSSTTCH.HHHHHHHHHTT- CS
  Cons_hypoth95 108 akkkeefdivflDPPyakellieevlelleekkl 141
                        +++di+  +PPy k + + ++ ++++++  
     AHX11086.1 185 ---RGKVDIIVSNPPYIKRADLPTLQTEVRSEPR 215
                    ...5678*********999887777777776655 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06     0.009      15     140 ..     111     269 ..     100     286 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
  Methyltransf_23  15 rllpklraggrvLdiGcGtG.illevlrengf.svtgvDlspeaveiae............kakkaqkdqfdeqeaaepqgkfdlIvlrevleh 94 
                      r + k r++ r+L++G+G+G i  ++l e++     g++ s +a  + +              + + +        a   gk d+Iv++     
       AHX11086.1 111 RYG-KHRRSLRILELGTGSGcIIISLLNEYRNaIGFGFEKSNAAFRLTRinchrhglqsrlRLYHSDFNR----VPAILRGKVDIIVSNPPYIK 199
                      443.589999**********88888886664416669999876666654555554444322222222222....2334677********98888 PP

  Methyltransf_23  95 vpdpp.........................ellrqiatllkpgGylllseplaslkedrllldwlylvpag 140
                        d+p                         + l+ ++++l+pgG ++l++ + ++k  +l l++ + ++ g
       AHX11086.1 200 RADLPtlqtevrseprlaldggfngilpyfAILKLAKKILNPGGEVFLEVGD-YWKDSMLSLHNSAFRISG 269
                      888777****************************************998864.566666666666666554 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.9e-05     0.051     155     233 ..     109     194 ..     100     195 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.9e-05
        PrmA 155 leklvkege..evlDvGtGSGiLaiaaakLgakkv.vavDiDevAvkvakeNaelNkveaklevals..eellk..eekadvivaN 233
                 l ++ k+++  ++l +GtGSG + i  +    + + ++    + A + ++ N ++ +++++l+++ s  +++++  ++k+d+iv+N
  AHX11086.1 109 LSRYGKHRRslRILELGTGSGCIIISLLNEYRNAIgFGFEKSNAAFRLTRINCHRHGLQSRLRLYHSdfNRVPAilRGKVDIIVSN 194
                 5556555544489********98776654433333367888999******************996431244443668*******99 PP

>> Eco57I  Eco57I restriction-modification methylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.38       2      21 ..     187     206 ..     186     238 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
      Eco57I   2 kfdviiGNPPYqeseakkel 21 
                 k+d+i+ NPPY++  +  +l
  AHX11086.1 187 KVDIIVSNPPYIKRADLPTL 206
                 89**********98855444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       284  (0.0158403); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2273.16
//
Query:       AHX11087.1  [L=300]
Description: hypothetical protein NHE_0117 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
        1.5    8.7   4.5        3.2    7.6   0.2    3.1  3  Synaptobrevin  Synaptobrevin


Domain annotation for each model (and alignments):
>> Synaptobrevin  Synaptobrevin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.2   0.00018       3.2      55      87 ..     107     139 ..      84     141 .. 0.82
   2 ?   -0.2   0.0      0.05   8.9e+02      53      87 ..     186     220 ..     184     222 .. 0.87
   3 ?   -0.4   0.9     0.055   9.8e+02      69      88 ..     245     264 ..     241     265 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00018
                    HHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXXX CS
  Synaptobrevin  55 rklkrkmwwknmkliiililvvlililiiiivi 87 
                    + +  km w ++ l+++l+l+++  i ++i+ i
     AHX11087.1 107 HSILGKMRWARVILRVLLGLIIIGTITLLIVRI 139
                    556679****************99999988765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.05
                    HHHHHHHHHHHHTXXXXXXXXXXXXXXXXXXXXXX CS
  Synaptobrevin  53 qarklkrkmwwknmkliiililvvlililiiiivi 87 
                    +a +++ +++++++  +++ + ++l+ +++ ++++
     AHX11087.1 186 KAEEINAEQLLNKFTPTVMHGTAILCTLYLSMLAF 220
                    68899999999999999999999999999999876 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.055
                    XXXXXXXXXXXXXXXXXXXX CS
  Synaptobrevin  69 iiililvvlililiiiivic 88 
                    +++l++++li ++i ++++c
     AHX11087.1 245 VLTLGILALISLIITVASYC 264
                    56777777777777777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (300 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2356.99
//
Query:       AHX11088.1  [L=42]
Description: hypothetical protein NHE_0118 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      166  (0.00925874); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 359.31
//
Query:       AHX11089.1  [L=508]
Description: ATP synthase F1, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-74  249.9   0.1      6e-74  248.3   0.0    1.7  2  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
      1e-43  148.6   1.9    1.9e-43  147.8   1.9    1.4  1  ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal doma
    2.3e-08   34.4   2.8    6.8e-08   32.9   2.8    1.8  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
  ------ inclusion threshold ------
      0.042   13.2   0.2       0.14   11.5   0.2    2.0  2  ATPase         KaiC


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  248.3   0.0   1.3e-77     6e-74       1     213 []     151     374 ..     151     374 .. 0.97
   2 ?   -1.5   0.0      0.36   1.6e+03      52      90 ..     422     461 ..     419     467 .. 0.81

  Alignments for each domain:
  == domain 1  score: 248.3 bits;  conditional E-value: 1.3e-77
                  SSHHHHHHS-EBTT-EEEEEESTTSSHHHHH.HHHHHHSSTS.......S.EEEEEEESEEHHHHHHHHHHCHHSSGGGGEEEEEEETTS-HHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx.......x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvis.qslskqsnsd.......d.aiiyvgiGergnevaevleefpegtimkrtvlvantsnepvaareas 89 
                  Gi+++D+l+pi++Gqr+li+g++++Gkt+i+ +++++q + +       + ++iyv+iG++ ++va++ ++++e+++m++t++v++ +++++  ++++
   AHX11089.1 151 GIKAIDLLIPIGRGQRELIIGDRQTGKTTIAlDTIIHQREINknlpdnkKlYCIYVAIGQKCSTVARITRTLQEHGAMDYTTIVLAGASDSAQSQFLA 248
                  99*****************************99999998766889999768*********************************************** PP

                  HHHHHHHHHHHHHTTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETSS..EEEEEEEEEEE-GGCSTTSHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  90 iytgitlAEyfrdqgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapdr..tGsvtivaavspaggDfsdpvttatlg 185
                  +y+g++++Eyfrd+g+++l+++d+ls++a A+re+sl+l+++p++++yp+++++ +++l+ERa+k++d+   Gs+t+++++++++gD+s++++t++++
   AHX11089.1 249 PYAGCAIGEYFRDNGMHCLIVYDDLSKHAVAYREMSLLLRRPPGREAYPGDVFYIHSRLLERAAKMSDKkgAGSLTALPIIETQAGDVSAYIPTNVIS 346
                  ******************************************************************5554489************************* PP

                  HSSEEEEB-HHHHHTTBSSSBCTTTEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 186 itdgfivLdkklaqrkhfPainvlvSvS 213
                  itdg+i+L+++l+++++ Pa+nv+ SvS
   AHX11089.1 347 ITDGQIFLESELFNKGIKPAVNVGLSVS 374
                  **************************99 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.36
                  EHHHHHHHHHHCHHSS.GGGGEEEEEEETTS-HHHHHHHH CS
                  xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  52 rgnevaevleefpegt.imkrtvlvantsnepvaareasi 90 
                  +g+ ++e+l++ +++t  m++ v+++  +ne  + ++a+ 
   AHX11089.1 422 KGKRLTELLKQNQHQTlTMEEQVVLMFAANEGHLDKVAVS 461
                  6788899999999999899999999999998877777665 PP

>> ATP-synt_ab_C  ATP synthase alpha/beta chain, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.8   1.9   4.3e-47   1.9e-43       1     114 [.     381     494 ..     381     504 .. 0.96

  Alignments for each domain:
  == domain 1  score: 147.8 bits;  conditional E-value: 4.3e-47
  ATP-synt_ab_C   1 QtkamkkvagsLklelaqYrEleaFaqFgsdLDeatkkqLerGerlvelLkQkqysplsveeqviilyaatngllddipvekvkefekelleylee 96 
                    Q+ka+k+vags+kl+laqYrE+eaFaqFgsd+De+t++ L++G+rl+elLkQ+q+++l++eeqv++++aa++g+ld++ v++v +f k+lle+++ 
     AHX11089.1 381 QVKAIKQVAGSVKLTLAQYREMEAFAQFGSDIDETTQALLAKGKRLTELLKQNQHQTLTMEEQVVLMFAANEGHLDKVAVSEVGDFAKKLLEFFHL 476
                    9*********************************************************************************************** PP

  ATP-synt_ab_C  97 ekkeileeieekkklsde 114
                    +++++l++i+e++ ++++
     AHX11089.1 477 HHPDLLKSIRETGMIEES 494
                    ************998875 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   2.8   1.5e-11   6.8e-08       2      67 ..      27      92 ..      26      93 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.5e-11
                   EEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEE CS
  ATP-synt_ab_N  2 vqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkr 67
                   ++++G v++v++g   ++g+  +   e+v f+++++g ++ ++ d ++++v+g+t+ +++G+ Vkr
     AHX11089.1 27 SEEVGEVISVKDGVVIACGLESVEFNEKVFFPDGTVGLVQSIEYDHIGIVVLGNTQEIKEGDIVKR 92
                   6899***********999999999999888**********************************97 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.2   3.2e-05      0.14       1      44 [.     148     189 ..     148     224 .. 0.85
   2 ?   -2.5   0.0      0.57   2.5e+03      13      39 ..     224     250 ..     213     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 3.2e-05
      ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikga 44 
                 v+tgI+ +D ++   i +g+  li G+  tGKt++al  +i++ 
  AHX11089.1 148 VQTGIKAIDLLI--PIGRGQRELIIGDRQTGKTTIALDTIIHQR 189
                 79*********9..67799999**************99998883 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.57
      ATPase  13 kgGipegrvvlitGepGtGKtifalqF 39 
                 + G ++++++ ++G ++++ + f + +
  AHX11089.1 224 EHGAMDYTTIVLAGASDSAQSQFLAPY 250
                 578889999999999999998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (508 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      562  (0.0313459); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.38
# Mc/sec: 3996.90
//
Query:       AHX11090.1  [L=173]
Description: ATP synthase F1, delta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-24   87.4   0.3    1.5e-24   87.0   0.3    1.1  1  OSCP      ATP synthase delta (OSCP) subunit
  ------ inclusion threshold ------
       0.13   12.4   0.6        2.5    8.2   0.1    2.2  2  HTH_9     RNA polymerase III subunit RPC82 helix-turn-helix d


Domain annotation for each model (and alignments):
>> OSCP  ATP synthase delta (OSCP) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.0   0.3   1.7e-28   1.5e-24       1     169 [.       5     162 ..       5     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 87.0 bits;  conditional E-value: 1.7e-28
        OSCP   1 iarrYAkAlfelAkekgaleeveeelealeavlaedkklaellsnpavsaeekkdlleelfkeklseavknflkllaenkRlalLpeiaeefeellaea 99 
                 ia+rYA++l+e++ +  +le+v++e+ al   l+e+    ++ls+ ++ ++ k++++e++    + +a++n++k+l+ n+R al +++++e+ ++++++
  AHX11090.1   5 IANRYARSLYEVCAD--ELEKVAHEFIAL---LREN----DFLSSTRIASAMKVHVVENIG---VPVALRNLCKILLTNHRGALCSKVLTEYLKIVKKN 91 
                 89***********74..699999998777...5554....799****************95...89********************************* PP

        OSCP 100 rgiveaeVtsavpLtdeqlekleaalakkl.gkkkvkleekvdpsliGGvvvkvgdkviDgSvkgkLeklk 169
                 rg++++ V s + L+ + ++ + aal   + + kkv++ +k+++ l+GG+++k+++ +iD S+ g+Lek +
  AHX11090.1  92 RGEIDVLVESYTDLNTKAEKSIIAALVGIFpEFKKVNIVQKINSGLLGGFTIKMNSIMIDLSIIGRLEKYR 162
                 **************************888744468*********************************987 PP

>> HTH_9  RNA polymerase III subunit RPC82 helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.019   1.7e+02       2      38 ..      13      48 ..      12      53 .. 0.89
   2 ?    8.2   0.1   0.00028       2.5       1      51 [.      63     117 ..      63     119 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.019
                HHHHHHHHCSTTHHHHHHHHHHHHSSBEHHHHHHHHS CS
       HTH_9  2 lcteiieehFGevvakVvetLlrkgrltlrelvkktk 38
                l++ +++e + +v+   + +L ++ +l+++ ++++ k
  AHX11090.1 13 LYEVCADE-LEKVAHEFIALLRENDFLSSTRIASAMK 48
                88889999.99999999***************99987 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00028
                 HHHHHHHHHCSTTHHHHHHH...HHHHHSSBEHHHHHHHHS.STHHHHHHHHHHH CS
       HTH_9   1 elcteiieehFGevvakVve...tLlrkgrltlrelvkktk.LsldqVkksLvvL 51 
                 +lc+++++ h G +++kV +    +++k+r  ++ lv++   L+ +  k++ ++L
  AHX11090.1  63 NLCKILLTNHRGALCSKVLTeylKIVKKNRGEIDVLVESYTdLNTKAEKSIIAAL 117
                 59****************7522246788888888888876667777766666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1340.28
//
Query:       AHX11091.1  [L=39]
Description: hypothetical protein NHE_0121 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      169  (0.00942607); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 327.12
//
Query:       AHX11092.1  [L=183]
Description: 5-formyltetrahydrofolate cyclo-ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-25   90.3   0.0    1.5e-25   90.1   0.0    1.0  1  5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family


Domain annotation for each model (and alignments):
>> 5-FTHF_cyc-lig  5-formyltetrahydrofolate cyclo-ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   8.6e-30   1.5e-25       1     186 [.       3     175 ..       3     176 .. 0.87

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 8.6e-30
                     HHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHTSHHHHH-SEEEE----TTS---HHHHHHHHHTTEEEEEEEECSSCTEECEEEEEECCCCCCC CS
  5-FTHF_cyc-lig   1 KqelRkqllaalralseeevaaesealsqrieslkesqeakrvalyvsvkgeidtkelikklleegkevllPrvrlesgslkvvrlttlkeedsl 95 
                     K+ lRk+ ++++++l ++       ++++++ +    ++   + ly++++ge+d   l+++l    k ++lP+++ +      + + t+k+ d+l
      AHX11092.1   3 KAPLRKKYRQIRKELPNKPLLDT--SIMENFLREFRLRQYASIGLYIPLDGEVDPMLLLNNLTD--KILCLPCTSGSR----EMLFRTWKNGDEL 89 
                     6779***9999999995554444..47888888888888899*******************976..56****999999....4556666666666 PP

                     CC.HCTSSCE--TTECCBCGGGG-SEEEE--SEEETTS-EE-SSTTHHHHHHHHHTST-SS--EEEEE--GGGEES-----ST----SEEE- CS
  5-FTHF_cyc-lig  96 es.gkyglkePeeeeerelalekldlvlvPgvAfdkeGaRlGkGkGyyDrflarlkggagdkpltvglaldeqlverlPleehDvpvdevvt 186
                     ++ +++++ +P++  ++     ++d+vlvP +Af+++  RlG+GkG++Drf+   +  +g ++  +gl +deql+++l +e+hD+p+d ++t
      AHX11092.1  90 IQlKNSQIRQPKNGVRI-----TPDVVLVPLIAFNEDCHRLGFGKGFFDRFIDSSRS-NGFHTRYIGLGYDEQLCAELKIEKHDQPLDSIIT 175
                     65145779999999997.....78********************************9.9*******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1499.93
//
Query:       AHX11093.1  [L=45]
Description: hypothetical protein NHE_0123 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       271  (0.0151152); expected 358.6 (0.02)
Passed bias filter:                      184  (0.0102627); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 343.74
//
Query:       AHX11094.1  [L=170]
Description: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-54  184.2   0.0    2.1e-54  184.0   0.0    1.0  1  YgbB      YgbB family


Domain annotation for each model (and alignments):
>> YgbB  YgbB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.0   0.0   1.1e-58   2.1e-54       1     154 [.       2     163 ..       2     164 .. 0.95

  Alignments for each domain:
  == domain 1  score: 184.0 bits;  conditional E-value: 1.1e-58
                 EEEEEEEEEEEEE.....EECEEEETTEEEEESEEEESSSTCHHHHHHHHHHHHHHT...T--SHHHHSTTTCGGCTTTCHHHHHHHHHHHHHHTTEEE CS
        YgbB   1 iriGlGyDvHrla.....egrklvlgGveieaekgllahSDgDvllhAlvDAllGal...algdigelfpdtdpkykgadSaelLeevlellkekgyki 91 
                 +riG+GyDvHr++     ++   +l+ ++i+++  + ahSDgDv+lhAlvDAllGa+    ++dig+lfp+tdp++kg  S+ l++ev++ll+++gy++
  AHX11094.1   2 FRIGFGYDVHRIErvqseDDGFTMLCSIQIPCSYRVIAHSDGDVALHALVDALLGAAnieYANDIGTLFPNTDPQWKGKASSYLVREVISLLSREGYQV 100
                 69**********96544223579**********************************777789************************************ PP

                 EEEEEEEECSSSTCGGGHHHHHHHHHHHHTS-GGGEEEEEEETTTSHHHHTTSEEEEEEEEEE CS
        YgbB  92 vnvdvtiiaekpklapykeamrenlakllgleeeqvsvkattteklgfvGrgegiaalavvll 154
                 +n+d+ti++e+pk+++yk+ mr ++a llg+ ++qvs+kattteklgf Gr+egi+++avv l
  AHX11094.1 101 NNADLTIVCEAPKIQSYKDVMRGKVAVLLGVAKSQVSIKATTTEKLGFEGRKEGISTYAVVSL 163
                 ************************************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (170 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       330  (0.0184059); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.20s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1364.17
//
Query:       AHX11095.1  [L=58]
Description: hypothetical protein NHE_0125 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       244  (0.0136092); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 507.78
//
Query:       AHX11096.1  [L=405]
Description: liporeleasing system, transmembrane, LolC/E family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-16   59.4   2.8    1.3e-15   58.3   2.8    1.6  1  MacB_PCD      MacB-like periplasmic core domain
      1e-08   35.5   4.3      1e-08   35.5   4.3    3.4  3  FtsX          FtsX-like permease family
  ------ inclusion threshold ------
      0.021   14.9   0.4      0.055   13.5   0.4    1.7  1  NPCC          Nuclear pore complex component
      0.028   13.4   2.0       0.05   12.5   2.0    1.3  1  TMEM117       TMEM117 protein family
       0.12   12.1   0.5       0.45   10.3   0.0    1.9  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr


Domain annotation for each model (and alignments):
>> MacB_PCD  MacB-like periplasmic core domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.3   2.8   3.7e-19   1.3e-15       1     171 [.      25     208 ..      25     236 .. 0.64

  Alignments for each domain:
  == domain 1  score: 58.3 bits;  conditional E-value: 3.7e-19
    MacB_PCD   1 slltvLGiaiGvaaviaivslgeglqasvlsqisdlgnlvtvtpgkgsgeslsdpdvealrr...evp.veavapvv....tvrgggsg.eeevtvvgv 90 
                 s+l++LGiaiGva++i+++s+++g+++ + s++ + g  v++++      + +++d+ +l +   e++ ++ v+p +    +v++g++  +  v v ++
  AHX11096.1  25 SILSLLGIAIGVASLIVVTSVMDGFRNELFSSLIGIGGHVNIRVR-----HYTYDDFATLNAslsEIEhISTVVPALemqsIVSNGNEVtG--VLVKAM 116
                 79********************************99764556665.....36788886563323345567778887687654455553223..555554 PP

    MacB_PCD  91 d.pdyfk....vfglklaeGrffteadlrggpnvvvigeelaerlf.pvGdtirl................kpftVvGvledppgsgsalgddavylpl 167
                 + +d+ +    + +        + + ++ g +++v+ig+++a+ l   vGd+i++                k+ ++++++ ++ g+   ++   +y+p+
  AHX11096.1 117 SlQDFSDdhfvMDK--------IVAGEVSGFQDGVIIGKRIADSLGvGVGDEITFlsasysntilgpiprmKRIKIAAIF-SF-GMV-EYDSALIYMPF 204
                 42244442111333........455577777889**********99*************555555555555555555555.22.322.334667****6 PP

    MacB_PCD 168 ttlq 171
                   ++
  AHX11096.1 205 DIAS 208
                 5542 PP

>> FtsX  FtsX-like permease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.3     0.046   1.7e+02      27      56 ..      26      54 ..      12      73 .. 0.63
   2 ?    1.9   0.1     0.087   3.1e+02      18      84 ..     265     279 ..     230     288 .. 0.64
   3 !   35.5   4.3   2.8e-12     1e-08       1      96 []     292     400 ..     292     400 .. 0.80

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.046
        FtsX 27 litlvalviGlglgllaaqllsdvllssvf 56
                +++l++++iG++ +l++   ++d++ +++f
  AHX11096.1 26 ILSLLGIAIGVA-SLIVVTSVMDGFRNELF 54
                556666666633.33333334555555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.087
        FtsX  18 lllllteillitlvalviGlglgllaaqllsdvllssvfsselkisidlitvliiivlllllallag 84 
                 +                                                     ii+++++l+ ++ 
  AHX11096.1 265 M----------------------------------------------------SIILMMIVLVAAFN 279
                 2....................................................22222222222222 PP

  == domain 3  score: 35.5 bits;  conditional E-value: 2.8e-12
        FtsX   1 kreigilralGmkkkqvlllllteillitlvalviGlglgllaaqllsdvllss.............vfsselkisidlitvliiivlllllallagll 86 
                 k+ i+ilr++Gm+k+++++++++ + +i++ ++++G  lg+l++  ++ v + +             +f + +++s+++  v +i + ++l+a la++ 
  AHX11096.1 292 KQSIAILRTMGMTKASIIRIFISCGSIIGVAGTALGAFLGVLLSLNINGVRSMIeklteeplfdpsvYFVDKIPVSLSFTGVTVISLSAMLIAFLATIP 390
                 689*********************************77777776654433332244455565555543349999999999999999999999999999* PP

        FtsX  87 siskilkkep 96 
                 +++k++ ++p
  AHX11096.1 391 PAYKASIQNP 400
                 ***9998876 PP

>> NPCC  Nuclear pore complex component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.4   1.5e-05     0.055      26      92 ..     215     291 ..     207     297 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.5e-05
        NPCC  26 iaNvllll.....vfnlikklvklll..klyelkkkss...eeslasalyaelveklirllfllniviallkLlrkq 92 
                 ++Nv ++l     ++ + kk++++l+   +++++++++        ++  ++++  +i l+ ++ni+ +l++L+ ++
  AHX11096.1 215 LNNVSIYLddpgiAHDVSKKIMSKLPemDISSWQDEKNpyfRAIKIEKSIMSIILMMIVLVAAFNIISSLFMLVDEK 291
                 567777777777788889999999997777778877777753334556678899999*****************884 PP

>> TMEM117  TMEM117 protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.0   1.4e-05      0.05     101     160 ..     261     321 ..     254     349 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
     TMEM117 101 kgswlvmflstllflfvfsliynlllllegeleaykisdllGirnesfmkv.aavGtwlGd 160
                 ++s + ++l++++++  f  i +l++l+++++++  i  ++G++ +s +++  ++G+ +G 
  AHX11096.1 261 EKSIMSIILMMIVLVAAFNIISSLFMLVDEKKQSIAILRTMGMTKASIIRIfISCGSIIGV 321
                 568899*****************************************99862567766664 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.1      0.32   1.2e+03      67      91 ..      21      44 ..      13      57 .. 0.61
   2 ?   10.3   0.0   0.00012      0.45      69     146 ..     267     344 ..     257     351 .. 0.84

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.32
  Trp_oprn_chp 67 rrvvgvllalagagaavaalslltd 91
                  r +v++l  l+g++++va+l ++t+
    AHX11096.1 21 RGLVSILS-LLGIAIGVASLIVVTS 44
                  44444443.4466666666655554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00012
  Trp_oprn_chp  69 vvgvllalagagaavaalslltdpadaaraaaaaatgvasaaaaveltawpvlalaggvllllagvllllrarswpam 146
                   ++ + ++l++a  ++++l +l+d++++  a  ++++ ++++  ++ ++ + ++ +ag++l ++ gvll l+ +  ++m
    AHX11096.1 267 IILMMIVLVAAFNIISSLFMLVDEKKQSIAILRTMGMTKASIIRIFISCGSIIGVAGTALGAFLGVLLSLNINGVRSM 344
                   4556788999999999999999999888888899899988888888**********************9887666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (405 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       980  (0.05466); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3108.90
//
Query:       AHX11097.1  [L=320]
Description: pseudouridine synthase, RluA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-34  118.4   0.7    4.3e-34  117.9   0.7    1.2  1  PseudoU_synth_2  RNA pseudouridylate synthase
    3.2e-06   26.8   0.1    6.5e-06   25.8   0.1    1.6  1  S4               S4 domain


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  117.9   0.7   4.8e-38   4.3e-34       2     159 ..      89     242 ..      88     243 .. 0.96

  Alignments for each domain:
  == domain 1  score: 117.9 bits;  conditional E-value: 4.8e-38
  PseudoU_synth_2   2 lvvvnKPagvpvqpeak....dgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkYlalvfgapeee 91 
                      lvv++KPag++v+p+      + +++  +   +++ ++  + ++++vhRLDk+t+G l++Ak+   ++ l +++++r+vr+kYla+++  p  +
       AHX11097.1  89 LVVLYKPAGLVVHPGIGnkdrTLVNALLHHYTQEQLSNAGSIRPGIVHRLDKDTEGFLIVAKTDHVHALLCEMIKNREVRRKYLAITHAVPGLT 182
                      79************988888899999999999999999******************************************************** PP

  PseudoU_synth_2  92 egaikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhla 159
                      +gai++ i++     +++++ + + +gk+a+ty++v+++    ++ k+s++e++letGr+hQiRvh++
       AHX11097.1 183 SGAIRTLIKR-----DRKKMVVSQHTGKSAITYYNVIAQS---SDRKYSVIECTLETGRTHQIRVHMK 242
                      **********.....899999*******************...***********************97 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.1   7.3e-10   6.5e-06       1      40 [.      14      53 ..      14      55 .. 0.96

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 7.3e-10
                EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT- CS
          S4  1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsy 40
                +RLd +l r++ + sr++++qlI+ G V++ Gk v +ps+
  AHX11097.1 14 VRLDLFLLRALAVLSRSKVQQLIRWGMVTLAGKSVLKPSQ 53
                6************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (320 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       620  (0.0345808); expected 358.6 (0.02)
Passed bias filter:                      568  (0.0316805); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2425.44
//
Query:       AHX11098.1  [L=376]
Description: hypothetical protein NHE_0129 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2903.18
//
Query:       AHX11099.1  [L=285]
Description: phage integrase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.5e-43  147.3   0.1    4.9e-43  146.9   0.1    1.2  1  Phage_integrase  Phage integrase family
    2.3e-14   53.5   0.9    1.4e-13   51.0   0.5    2.4  2  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
    2.1e-07   31.3   1.4    6.4e-07   29.8   0.8    2.0  2  Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
     0.0016   18.7   0.8     0.0041   17.4   0.8    1.6  1  Phage_int_SAM_5  Phage integrase SAM-like domain
     0.0095   15.9   0.0       0.12   12.3   0.0    2.3  2  Phage_integr_3   Archaeal phage integrase
  ------ inclusion threshold ------
      0.036   14.3   0.0       0.29   11.4   0.0    2.4  2  HTH_52           Helix-turn-helix domain
      0.066   13.7   0.2       0.51   10.8   0.1    2.4  2  Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; D


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  146.9   0.1   1.9e-46   4.9e-43       2     171 ..      96     267 ..      95     268 .. 0.95

  Alignments for each domain:
  == domain 1  score: 146.9 bits;  conditional E-value: 1.9e-46
                      HHHHHHHHHHHHCCGC..HHHHHHHHHHHHHHHHT--HHHHTT-BGGGEE..CTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHCC CS
  Phage_integrase   2 vltedeverllaalee..slkirdklllellyetGlRisEllsLrvkdld..lengvilvheregKgskeravplseealellkellskaleea 91 
                      +l ++e++ ll++l +  ++ +r  ++le+ly++G+R+sEl++L++ d+   l+ + +++   +gKg+ker++p+s+   e+l ++l  +   +
       AHX11099.1  96 YLIKEEIKGLLTFLGQgyPDTLRLHTMLEMLYASGMRVSELIRLKIADIGplLKGQQHII--IQGKGRKERILPFSKRSIEVLIRYLHSH---Q 184
                      7889********************************************743356666666..8***************************...9 PP

                      TTTSBSSBET..TSSB--HHHHHHHHHHHHHHCT-S.SC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHCCCH CS
  Phage_integrase  92 eksellfask..rgkplsrqtvrkafkraveeagie.kpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYthvak 171
                      + se+lf+ +  +++++srq + + +k+++ + +i  ++++pH +Rhsfat+Ll +g+d++ vq+llGHs+i ttqiYthv++
       AHX11099.1 185 STSEWLFPGTggKNRHISRQRLGQLLKELAIKCNIApERISPHVIRHSFATHLLDRGMDIKLVQDLLGHSQITTTQIYTHVSQ 267
                      ********************************************************************************986 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.0   0.5   5.3e-17   1.4e-13      10      83 ..       3      73 ..       1      74 [. 0.96
   2 ?   -0.7   0.0      0.72   1.8e+03      26      60 ..     206     241 ..     203     248 .. 0.72

  Alignments for each domain:
  == domain 1  score: 51.0 bits;  conditional E-value: 5.3e-17
                     HTT-S-HHHHHHHHHHHHHHHHHHHH.TS--TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHHHHT CS
  Phage_int_SAM_1 10 kerglspnTlraYrrdLrrflkflaergkesleqlttedvraflaeleeeglsatslarrlsalrsFfqflvre 83
                     +er++s nT+++Y+ dL  ++kfl+e     + q++ ed+ +++  l+e+g+s+++++r++++lr+F+ fl+ e
       AHX11099.1  3 VERNASFNTIASYKTDLVLLQKFLEE---TEFIQASKEDLCSYITGLKERGYSSATIRRKIATLRQFYTFLYFE 73
                     69************************...******************************************866 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.72
                      HHHHHHHHHH.TS--TTT--HHHHH.HHHHS----- CS
  Phage_int_SAM_1  26 Lrrflkflaergkesleqlttedvr.aflaeleeeg 60 
                      L  +lk la +   + e+++++ +r +f  +l+++g
       AHX11099.1 206 LGQLLKELAIKCNIAPERISPHVIRhSFATHLLDRG 241
                      555566666666677889999999768988888776 PP

>> Phage_int_SAM_4  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.8   0.8   2.5e-10   6.4e-07      13      78 ..       6      70 ..       2      75 .. 0.93
   2 ?   -0.8   0.0      0.89   2.3e+03      36      56 ..     219     239 ..     172     271 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.8 bits;  conditional E-value: 2.5e-10
  Phage_int_SAM_4 13 glserTiksYlsaikrflrflkkkapeeltkedieaYlnyLanerklsastqknalnalsffykkv 78
                     + s +Ti sY++ +  + +fl++ ++ + +ked+ +Y++ L  er +s +t++++++ l++fy+ +
       AHX11099.1  6 NASFNTIASYKTDLVLLQKFLEETEFIQASKEDLCSYITGLK-ERGYSSATIRRKIATLRQFYTFL 70
                     56679*************************************.********************875 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.89
  Phage_int_SAM_4  36 kapeeltkedie.aYlnyLane 56 
                       ape ++++ i+ ++ ++L+ +
       AHX11099.1 219 IAPERISPHVIRhSFATHLL-D 239
                      34444444444323444444.3 PP

>> Phage_int_SAM_5  Phage integrase SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.8   1.6e-06    0.0041      15      95 ..       5      82 ..       3      89 .. 0.93

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.6e-06
                     TTS-HHHHHHHHHHHHHTTTS-..S---TTT--HHHHHHHHHHHHHTS---HHHHHHHHHHHHHHHHHHHHTTS--S-HHH CS
  Phage_int_SAM_5 15 kkgskgtlrnykstlkhlkkFlkkkditfeeidkefleeFedYLkkkkglsentiskyfkklkavlnkAikegilkknpyp 95
                     ++ s +t+ +yk+ l  l+kFl  ++ +f +  ke l ++++ L k++g+s +ti++ + +l++++   + e+++  np++
       AHX11099.1  5 RNASFNTIASYKTDLVLLQKFL--EETEFIQASKEDLCSYITGL-KERGYSSATIRRKIATLRQFYTFLYFEKLIYINPMK 82
                     567899****************..9*******************.9****************************9999954 PP

>> Phage_integr_3  Archaeal phage integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0       0.2   5.1e+02      22      43 ..     118     139 ..      99     147 .. 0.84
   2 !   12.3   0.0   4.6e-05      0.12      89     137 ..     209     257 ..     198     270 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.2
                     HHHHHHHHHHHH---HHHHHHH CS
  Phage_integr_3  22 evelvykllvfsGiRLkevlkl 43 
                     +++++  +l  sG+R +e ++l
      AHX11099.1 118 RLHTMLEMLYASGMRVSELIRL 139
                     56788899999****9999875 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.6e-05
                     B--HHHHHHHHHT-T--GHHHHHHHHHHHHHTT--HHHHHHHTTSS-CC CS
  Phage_integr_3  89 elseeavkefeakkkvkakyiRkwvatklaelgvpeevidFiqGrkpss 137
                      l+e a+k + a + ++ ++iR+ +at l+++g++ ++++ + G+ + +
      AHX11099.1 209 LLKELAIKCNIAPERISPHVIRHSFATHLLDRGMDIKLVQDLLGHSQIT 257
                     478999*******99*************************999998755 PP

>> HTH_52  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00011      0.29      23      50 ..      10      37 ..       7      52 .. 0.88
   2 ?   -0.7   0.0      0.68   1.7e+03      32      41 ..     173     182 ..     164     187 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00011
      HTH_52 23 peledYsvDLevlleyLveKgiievvkv 50
                + +  Y++DL +l ++L e ++i++ k+
  AHX11099.1 10 NTIASYKTDLVLLQKFLEETEFIQASKE 37
                57899*******************9876 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.68
      HTH_52  32 LevlleyLve 41 
                 +evl++yL  
  AHX11099.1 173 IEVLIRYLHS 182
                 6899999976 PP

>> Acetyltransf_11  Udp N-acetylglucosamine O-acyltransferase; Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.1    0.0002      0.51      21      58 ..      44      93 ..      42     118 .. 0.73
   2 ?   -0.3   0.0      0.59   1.5e+03      35      54 ..     118     137 ..     110     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0002
                     HHHHHTT--HHH....HHHHHHHHHHHHSSSS-HHHHHHHH........H CS
  Acetyltransf_11 21 vgLkRrgfseee....ikalkkayrllyrsglsleealeel........e 58
                      gLk rg+s+++    i+ l+++y  ly ++l   + ++ +         
       AHX11099.1 44 TGLKERGYSSATirrkIATLRQFYTFLYFEKLIYINPMKDIelpkkaliL 93
                     79*******9887777999**********999888887777555555551 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.59
                      HHHHHHHHHHSSSS-HHHHH CS
  Acetyltransf_11  35 alkkayrllyrsglsleeal 54 
                      +l+++ ++ly sg++++e +
       AHX11099.1 118 RLHTMLEMLYASGMRVSELI 137
                      68889999999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.42u 0.19s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2464.76
//
Query:       AHX11100.1  [L=37]
Description: hypothetical protein NHE_0131 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       364  (0.0203023); expected 358.6 (0.02)
Passed bias filter:                      230  (0.0128284); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.20s 00:00:00.50 Elapsed: 00:00:00.34
# Mc/sec: 330.11
//
Query:       AHX11101.1  [L=49]
Description: hypothetical protein NHE_0132 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       907  (0.0505884); expected 358.6 (0.02)
Passed bias filter:                      600  (0.0334653); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 434.47
//
Query:       AHX11102.1  [L=298]
Description: deoC/LacD aldolase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-28   98.3   0.0    6.1e-28   98.0   0.0    1.1  1  DeoC      DeoC/LacD family aldolase


Domain annotation for each model (and alignments):
>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.0   0.0   3.4e-32   6.1e-28       2     235 .]      38     280 ..      37     280 .. 0.85

  Alignments for each domain:
  == domain 1  score: 98.0 bits;  conditional E-value: 3.4e-32
                 EEEEECCSHHHHHHHHCTSSHHHHHHHHHHHHHHGGGSSEEEEETTTHHHHHHCSCTTSEEEEETECSSCCTTSTTEEEE..TTCHHHHHHHTT-SEEE CS
        DeoC   2 vilavDqrvankddtasaqneqledlkalvkealtpgasavlldpgviasaskeyakdiallvkldkgtyllkskqrdvd..evasveeakalGAdavk 98 
                 +il+vDq+ ++++d++++ n    d++  ++ a+++g sa +  + ++a+++ +y ++++l++kl++  +l +++  ++d     + e a++lG + ++
  AHX11102.1  38 LILPVDQGFEHGPDESFHGNLPSYDPEYHIQLAIEAGLSAYAAPLSMLADVAHKYPNRVPLILKLNSASKLFPKS-CPPDqaYIGTPEDALKLGCVGIG 135
                 69******************8899******************************************777776666.888876666789*********** PP

                 EEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEEEEE-CTTBSSTT.CHHHHHHHHHHHHTCCT-SEEEE--SSCC.B.HHHHHHHHHHHHHCHSS CS
        DeoC  99 vvvyyradgseeeqqklaeikrvkeacheeglplilelylrdeaikdek.vdpdlvaeAarvsaelGaDiiKvevpkevvnateedaevfkdvikaapv 196
                 +++y    gse+ + +l e ++v ++++++gl++++++y+r+ +   +   + d v  Aa+++  +GaDi+Kv++p +       +  v +d+ ++++v
  AHX11102.1 136 LTIYP---GSENYRLMLGESAKVIAKAKSLGLLVVIWAYPRGGDLPSKDeIALDIVSYAAHMACLAGADIVKVKLPSADLANAHSKLGVVEDLSDRVKV 231
                 *****...**********************************99877766899***********************66666666777777777777776 PP

                 T...E......EEEETTSSHHHHHHHHHHHHH...HHTHCEEEESHHHHTT CS
        DeoC 197 p...g......vvlsGGvseedfletvedAvk...eagasGvlsGRaifqk 235
                     +      v+ sGG   + ++ t+ + +k   + g++G ++GR++fq+
  AHX11102.1 232 IvrsCfagkrlVLFSGGQ-SKGLP-TLYEEIKairNGGGAGSIMGRNAFQR 280
                 6555245567799****6.44444.44444443535566**********95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (298 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       263  (0.014669); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2149.58
//
Query:       AHX11103.1  [L=224]
Description: hypothetical protein NHE_0134 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0088   16.3   1.1        5.3    7.4   0.0    2.5  2  Orf78          Orf78 (ac78)
  ------ inclusion threshold ------
       0.19   11.9   0.4       0.28   11.3   0.4    1.4  1  TMEM190        Transmembrane protein 190


Domain annotation for each model (and alignments):
>> Orf78  Orf78 (ac78)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.3   0.00068       6.1      49      83 ..      24      58 ..       5      64 .. 0.62
   2 !    7.4   0.0    0.0006       5.3      69      94 ..      75     100 ..      66     108 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00068
       Orf78 49 itekesnaaekaqalnillisllavvcvlvllyvi 83
                ++ + ++++ ++    ++ i+l  +++v vl+y +
  AHX11103.1 24 SSRSCTKSQATKLLHRNICIALALIFIVAVLVYNL 58
                22222223455667789999999999999999965 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0006
       Orf78  69 sllavvcvlvllyviyYfvilrerqk 94 
                  +l ++++l+l++   Y+++++ r++
  AHX11103.1  75 LALNIIALLILIFSFCYYLLVKAREY 100
                 56899***************999876 PP

>> TMEM190  Transmembrane protein 190
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.4   3.1e-05      0.28      62      89 ..      73     100 ..      25     133 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.1e-05
     TMEM190  62 walsltcigllllisliclfwwakrrdl 89 
                  +l+l  i ll+li++ c++   k r+ 
  AHX11103.1  73 TTLALNIIALLILIFSFCYYLLVKAREY 100
                 58999*******************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       834  (0.0465168); expected 358.6 (0.02)
Passed bias filter:                      543  (0.0302861); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1667.57
//
Query:       AHX11104.1  [L=49]
Description: hypothetical protein NHE_0135 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (49 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 371.70
//
Query:       AHX11105.1  [L=48]
Description: hypothetical protein NHE_0136 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       281  (0.0156729); expected 358.6 (0.02)
Passed bias filter:                      225  (0.0125495); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 384.00
//
Query:       AHX11106.1  [L=342]
Description: efflux transporter, RND family, MFP subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-17   62.8   0.2      9e-15   55.3   0.0    2.4  2  HlyD_3           HlyD family secretion protein
      1e-12   47.7   0.0      2e-12   46.8   0.0    1.4  1  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    5.9e-08   32.4   5.3     0.0021   17.9   0.8    3.1  3  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0002   21.3   0.1     0.0053   16.8   0.0    2.8  3  QRPTase_N        Quinolinate phosphoribosyl transferase, N-te
  ------ inclusion threshold ------
      0.018   14.8   5.8       0.26   11.2   0.1    3.2  3  Biotin_lipoyl    Biotin-requiring enzyme
       0.14   11.9   0.0       0.21   11.3   0.0    1.2  1  DUF2931          Protein of unknown function (DUF2931)


Domain annotation for each model (and alignments):
>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.1     0.013        39       6      30 ..      68      92 ..      64     101 .. 0.82
   2 !   55.3   0.0     3e-18     9e-15       2      96 ..     158     250 ..     157     259 .. 0.93

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.013
      HlyD_3  6 vdGvvvelnveegevvqagdellei 30
                v+ +vv++  + gevvq+gde+l++
  AHX11106.1 68 VQAEVVQKVSKDGEVVQQGDEILRL 92
                566777777799**********975 PP

  == domain 2  score: 55.3 bits;  conditional E-value: 3e-18
      HlyD_3   2 lrApvdGvvvelnveegevvqagde.lleiippdtllveakvpaadlgsikkkgqkvtlkldqgsdytlkgkierisptvdaktgaykvevslenp 96 
                 +rApv+Gv++++nv++g+ v++g + l eiip  ++lv++kv+++++ ++k +g  ++++l+ g     +gk++ +s  +d+ t++++ve+++++ 
  AHX11106.1 158 IRAPVSGVLSKINVSHGDLVSPGVTlLGEIIPFGDYLVRIKVSERNILTLK-EGLDAEIELS-GL-GDCRGKVKFVSLVPDTATRTFPVEIKINQG 250
                 8**********************88699**********************5.*********8.43.389************************986 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   6.6e-16     2e-12      30     201 ..      73     247 ..      50     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 6.6e-16
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23  30 veklyvnatgdkVkkGqpLaelyspelvaaqeeyllalkakkklkkke........lleaarerLrllgvseeqiaelektgkvqktvtvkapisGvVt 120
                 v+k+     g+ V++G+++++l+s+     + + l al+++++++ +          l aa+    l g+++++ a+l++ ++  ++  ++ap+sGv  
  AHX11106.1  73 VQKVSK--DGEVVQQGDEILRLDSSVQE-IHLQSLRALAEERRMEYQAakdlhesgYLPAAKFSGALAGLKKAE-ADLKALENQIEKHIIRAPVSGVLS 167
                 344444..6*************996432.222223333322222222245678888666666655556665555.333433444455679********* PP

                 XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 121 eknvreGqyvqpgdtlf.tiadlstVWveaevyeqqlalvkvgqkvevtvealpgktfeGkvdyiyptvdpetRtvkvRiel 201
                 + nv +G+ v+pg tl+ +i    +  v ++v e+++ ++k+g ++e++++ l +   +Gkv++++ + d++tRt+ v i++
  AHX11106.1 168 KINVSHGDLVSPGVTLLgEIIPFGDYLVRIKVSERNILTLKEGLDAEIELSGLGD--CRGKVKFVSLVPDTATRTFPVEIKI 247
                 *************997659**********************************98..9******************998876 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.8     7e-07    0.0021       7      47 ..      66     106 ..      64     119 .. 0.91
   2 !   15.4   0.0   4.1e-06     0.012       5      27 ..     158     180 ..     154     184 .. 0.91
   3 ?   -2.5   0.0       1.6   4.8e+03       5      19 ..     290     306 ..     289     306 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 7e-07
  Biotin_lipoyl_2   7 apvsGrVaqlnVkdGqrVkaGdvLaelDsralqlalaqaea 47 
                      ++v + V+q   kdG +V++Gd +++lDs+  +  l+ + a
       AHX11106.1  66 PQVQAEVVQKVSKDGEVVQQGDEILRLDSSVQEIHLQSLRA 106
                      789999999999******************99999998776 PP

  == domain 2  score: 15.4 bits;  conditional E-value: 4.1e-06
  Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaG 27 
                      I apvsG+++++nV +G+ V  G
       AHX11106.1 158 IRAPVSGVLSKINVSHGDLVSPG 180
                      99******************998 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.6
  Biotin_lipoyl_2   5 Iaapv..sGrVaqlnVk 19 
                      I+++v   G V++++V+
       AHX11106.1 290 ITMKVisEGAVKSVHVE 306
                      6777777899**99995 PP

>> QRPTase_N  Quinolinate phosphoribosyl transferase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.8e-06    0.0053      27      75 ..      47     100 ..      27     102 .. 0.87
   2 ?    1.0   0.0      0.15   4.4e+02      23      44 ..     129     156 ..     121     187 .. 0.67
   3 ?   -2.8   0.0       2.3   6.8e+03      55      76 ..     185     206 ..     181     207 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.8e-06
                 SEEE-SHHHHHHHHHHH..TTTEEE...ESS-TT-EEETTEEEEEEEEEHHHHH CS
   QRPTase_N  27 egvvaGlevaeevfell..pgleve...llvkDGervekgdvlleieGnarall 75 
                 + v++G  +++ v +++  p++++e      kDGe v++gd +l++  ++++++
  AHX11106.1  47 PVVISGYGFVDTVQRYFlyPQVQAEvvqKVSKDGEVVQQGDEILRLDSSVQEIH 100
                 5799***********999*8887774446779*****************99997 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.15
                 EESSSEEE-SHHHHHHHHHHH......T CS
   QRPTase_N  23 iakeegvvaGlevaeevfell......p 44 
                  ak +g +aGl+ ae+ ++ l      +
  AHX11106.1 129 AAKFSGALAGLKKAEADLKALenqiekH 156
                 5788899999999999888885433330 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.3
                 T-EEETTEEEEEEEEEHHHHHH CS
   QRPTase_N  55 GervekgdvlleieGnaralls 76 
                 Ge +  gd l++i+ + r++l+
  AHX11106.1 185 GEIIPFGDYLVRIKVSERNILT 206
                 6777778999999999998886 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   0.2     0.007        21      16      36 ..      72      92 ..      66     103 .. 0.67
   2 ?   11.2   0.1   8.5e-05      0.26      44      70 ..     157     183 ..     150     187 .. 0.90
   3 ?   -1.6   0.2      0.85   2.5e+03      48      59 ..     295     306 ..     288     310 .. 0.71

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.007
                   ECSESSSTTCEE-TTSEEEEE CS
  Biotin_lipoyl 16 vvevlvkvGdkVkagqvlaev 36
                   vv+   k+G+ V++g+ ++ +
     AHX11106.1 72 VVQKVSKDGEVVQQGDEILRL 92
                   555556666666666666554 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 8.5e-05
                    EEEBSSSEEEEEESSTTTEEE-TTCEE CS
  Biotin_lipoyl  44 eieapkaGvvkeilvkeGdtvevgdll 70 
                     i ap++Gv+++i v+ Gd v+ g  l
     AHX11106.1 157 IIRAPVSGVLSKINVSHGDLVSPGVTL 183
                    699******************999665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.85
                    SSSEEEEEESST CS
  Biotin_lipoyl  48 pkaGvvkeilvk 59 
                     ++G vk+++v+
     AHX11106.1 295 ISEGAVKSVHVE 306
                    457888888886 PP

>> DUF2931  Protein of unknown function (DUF2931)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   6.9e-05      0.21       2      75 ..       6      81 ..       5     121 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 6.9e-05
     DUF2931  2 iillllllllaaCstkkkkkpqek..pkfeWsvsvvaPkaypveVtqvkildedgkldstprsgnkkegWttevst 75
                ++ll+++++l +C + + k+ ++   +   ++  vv+P+  pv +    ++d+ ++++  p+ + +  ++ ++ + 
  AHX11106.1  6 LVLLCMVIFLCSCLKDSEKEVESAvvESRYFKTAVVTPSLRPVVISGYGFVDTVQRYFLYPQVQAEVVQKVSKDGE 81
                6799999******8888888777799999999********************999976666665555444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      506  (0.0282224); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.38
# Mc/sec: 2672.84
//
Query:       AHX11107.1  [L=42]
Description: hypothetical protein NHE_0139 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       703  (0.0392102); expected 358.6 (0.02)
Passed bias filter:                      407  (0.0227007); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.23s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 380.35
//
Query:       AHX11108.1  [L=414]
Description: amino acid carrier family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-80  271.6  29.7    1.7e-80  271.3  29.7    1.0  1  Na_Ala_symp  Sodium:alanine symporter family


Domain annotation for each model (and alignments):
>> Na_Ala_symp  Sodium:alanine symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.3  29.7   9.2e-85   1.7e-80       8     378 ..      22     411 ..      16     413 .. 0.94

  Alignments for each domain:
  == domain 1  score: 271.3 bits;  conditional E-value: 9.2e-85
  Na_Ala_symp   8 ksegeissfqAlatalaarvGtGniaGvatAialGGpGAvfWmwvvallGmatkfvEstLaqlYkekdekgevrGGpayyiekglkkkwlavlfavll 105
                   s++++ssf+A+   l +  G+Gn+ G a+A+++GGpG+++Wm+++ l+ ++ k+v + L+ +++ ++   ++ GGp+y++++g+++k+la+lf++ +
   AHX11108.1  22 GSHRNMSSFSAFSAILGGNLGVGNLSGTAIALSIGGPGSIIWMVLIILFTASIKYVTCYLSLVHRIRR-GSRFIGGPMYFLRDGFGSKALAALFCLGT 118
                  46789**************************************************************9.789************************** PP

  Na_Ala_symp 106 iialglginavqansiasaleeafeveklvvgivlavllalvilggikriakvaevvvPvmailYillalvvillniekvpevlalifksAFgleava 203
                  i+++++g  +vq+ns+a  ++  +++++++ g+++a ++a+v lg+++  ++v ++vvP+mai+Y+ ++++++++n+ k+p++++lif+s +++++v 
   AHX11108.1 119 ICTAVIGGGLVQVNSLALPMDY-INIPRIYGGLFFASIVAVVTLGKLRVFTRVISFVVPFMAIAYLGISIYILVINAGKIPAAISLIFSSVWNTTDVQ 215
                  ****9999************99.77************************************************************************* PP

  Na_Ala_symp 204 gGilg.......aaialGvkRglfSneAGlGsapiaaAaaevsh....p..vkqGlvqalgvfidtlvvCtatalvills.......egvaltqaale 281
                  gG++g       a++++G+ Rg+f+++ G G   i +A  + ++    p  v+qGl+ ++++fi  l+vC +talv++++       e++++  +a++
   AHX11108.1 216 GGAIGfvwsqffATMQMGISRGIFASDIGFGLEGILHANVKHQEghtlPleVEQGLIGVISPFI-VLLVCFVTALVLMVTgvvagpfESTNMCFEAFK 312
                  ***************************************99965333324489***********.799***********5555555599********* PP

  Na_Ala_symp 282 svl.gsvgalfvaialllFafstilgnyyygeknleyllgkkkk.lliyrvlvlllvfvgavaslelvwnlaDialglmalvnliaillLskvvvkal 377
                    + ++++ +f+ ++l++Faf+t+l++++ ++ ++eyl++ + k l + +v+++l++ +ga+ ++  +w++ D+a ++m ++nli+i++L+k+vv+++
   AHX11108.1 313 VGTnSEFAGYFLIVVLFCFAFTTVLTWSFCAQCSFEYLTNYDPKvLKLWKVFFVLIMPLGALFDVYSLWRVVDLASAIMLITNLIGIAFLAKTVVHET 410
                  998678*********************************766666999***********************************************998 PP

  Na_Ala_symp 378 k 378
                  +
   AHX11108.1 411 N 411
                  6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1039  (0.0579508); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2980.73
//
Query:       AHX11109.1  [L=438]
Description: dihydroorotase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-30  106.8   2.7    3.5e-30  105.5   2.7    1.6  1  Amidohydro_1  Amidohydrolase family
    1.1e-12   48.2   0.0    1.6e-07   31.1   0.0    2.3  2  Amidohydro_3  Amidohydrolase family
    4.8e-10   39.5   0.0    1.4e-09   38.0   0.0    1.8  2  DHOase        Dihydro-orotase-like
     0.0046   16.4   0.1      0.042   13.2   0.0    2.0  2  TatD_DNase    TatD related DNase


Domain annotation for each model (and alignments):
>> Amidohydro_1  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.5   2.7   7.8e-34   3.5e-30       1     344 []      67     434 ..      67     434 .. 0.81

  Alignments for each domain:
  == domain 1  score: 105.5 bits;  conditional E-value: 7.8e-34
                   EEEE-EEEEEEECETTECSSSGHHHHHSTTHHHHHHHHHHHHHHHHTTEEEEEEEEHSSTH.HHHHHHHHHHTSSSEEEEEEESSEGGSGCCCSHHH CS
  Amidohydro_1   1 ivlPGlIDaHvHleqsllrgatledwlvppetaaealesgiktalksGtttvadmgattst.giealleaaeelplglrilggkvsldrgsaetska 96 
                   +++PG ID+HvHl+             +p++ + e + sg+k+a  +G+ttv   ++t ++ ++   l+ +++                   + + +
    AHX11109.1  67 FLIPGVIDIHVHLR-------------DPGQLYNEDIHSGTKAAAAGGVTTVVCQPNTKPPiNTVETLKYIRD-------------------KARTE 131
                   689**********9.............******************************9866644444444444...................44556 PP

                   HHHHHHHHHHHHHHHCTTTCEE.EEEEECGTCCSHHH........HHHHHHHHHHHHTTEEEEEE....TSSCHHHHHHHHHHTTTEEEETTTTSTC CS
  Amidohydro_1  97 sreklkagaaetikgkadgvvk.valapheapafsde........elkealkeakkrdlpvaiHa....letkgevedaeaafgetiehgthlevae 180
                     ++++ +a  +i  +++++++  al  ++a++f+d+        ++++a+  a+  ++pva Ha    l++ g + + +    ++   +++++ ae
    AHX11109.1 132 GFVNVLCYA--AITNDGNELTDmFALHKAGAVGFTDDglpvmnplLMRQAFANAAFLKVPVAQHAedlyLSNGGCINEGVM--SHKLNVPGITDLAE 224
                   666777777..6677788888889999999999999999999999********************8877666666644444..44477899****** PP

                   CHHTTTHCCEE.....EHCTCEEEHHHHHHHHHHHHHHCEE........HHHHHHHH...............SEHHHHHHHHHHHHTSCEEEEEECT CS
  Amidohydro_1 181 slglldeikli.....lahgvhltpteaellkerlkeagva........hcpfsnsi...............lrsgrealrkaldeGvkvglgtDga 249
                   s+++++++ l+       h  h++ ++a+ ++e +k+ g +        h   +++                 +++r  + +al+++++ ++++D+a
    AHX11109.1 225 SVMVARDVMLLdqldsHYHVLHVSTKKAVEIIETAKSRGMNvtcevtphHFLLTEEAvvdyntdakmnpplrTEQDRLYMIEALKNSTIDAIASDHA 321
                   *******888866655556666665577777777777777766788888555555557999999999999999999999****************** PP

                   ...TSSCCGGHHHH...HHHHHHHHHHCCTT.TTHCHCHHHHHHHHHTHHHHHHTT-TTTSSSS-TTSB--EEEECC..CT............CGGG CS
  Amidohydro_1 250 ...asgnslnllee...lrlalklqrgllye.deegglslkealrmaTingAkalglddkvGsievGkdADlvvvdl..di............laaf 325
                      +  ++l l +e   ++++l++  +l  e   +g ++l  +l++ T n+A++++    +G+i+vG +ADlv++dl   i            +++f
    AHX11109.1 322 phnGLYKNLPL-REaafGIIGLETILPLSLElYHDGVMDLHSLLAKLTCNPARIINS--SAGRIKVGAPADLVLLDLnaEIvidsakfvskskNSPF 415
                   87733333333.3357777777777777777766999*******************9..8*****************873366778999999***** PP

                   TTTCTSEEEEEEEETTEEE CS
  Amidohydro_1 326 vglkkdgnvkkvivkGklv 344
                   vg k +g+v ++iv+G+ v
    AHX11109.1 416 VGRKTKGKVLRTIVAGDSV 434
                   ****************876 PP

>> Amidohydro_3  Amidohydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.2e-06     0.014       1      47 [.      59     105 ..      59     114 .. 0.77
   2 !   31.1   0.0   3.7e-11   1.6e-07     399     473 .]     338     435 ..     286     435 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.2e-06
  Amidohydro_3   1 eviDakGrlvlPGFvDsHtHlagggvnl.rllrlpdarvtslegvlta 47 
                   evi+++G +++PG +D+H Hl   g+ +   + ++  ++ ++ gv+t+
    AHX11109.1  59 EVINCSGYFLIPGVIDIHVHLRDPGQLYnEDIHSGT-KAAAAGGVTTV 105
                   79******************9999966655555555.44455555555 PP

  == domain 2  score: 31.1 bits;  conditional E-value: 3.7e-11
  Amidohydro_3 399 g............evlrpdeelsleealalyTrgpAkalgledrkGtLevGadADlvvld.adpldvdppelaear.............vrltvvdG 469
                   g            e++  d  ++l+ +la +T +pA++++ +   G+++vGa+ADlv+ld ++ + +d ++ +++              v  t+v+G
    AHX11109.1 338 GiigletilplslELY-HDGVMDLHSLLAKLTCNPARIINSSA--GRIKVGAPADLVLLDlNAEIVIDSAKFVSKSknspfvgrktkgkVLRTIVAG 431
                   3444445566664444.45699*********************..***************777777777777777699******************* PP

  Amidohydro_3 470 rvvy 473
                     vy
    AHX11109.1 432 DSVY 435
                   9998 PP

>> DHOase  Dihydro-orotase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   3.1e-13   1.4e-09       3     141 ..      67     251 ..      65     252 .. 0.87
   2 ?   -3.2   0.0       1.6   7.1e+03      67      89 ..     303     325 ..     299     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 3.1e-13
      DHOase   3 llvpglidlavhlrelsgeakeliet...........tvaaygvtfkaP.......................aaitveddsee...........afilt 56 
                  l+pg+id++vhlr ++   +e i+            tv   ++t + P                           + +d++e           a  +t
  AHX11109.1  67 FLIPGVIDIHVHLRDPGQLYNEDIHSgtkaaaaggvtTVVCQPNTKP-PintvetlkyirdkartegfvnvlCYAAITNDGNEltdmfalhkagAVGFT 164
                 589*************9998888877777666666555555555543.379*****************99995556779999999*******999999* PP

      DHOase  57 ddtvyvtiqllefeglkk.aeLdqalkaiaeDDevtnqsavqdfelarfyGvqLkG...vCeaekivydvLlakaagcgfyvsiiytke 141
                 dd++ v   ll+ +++ + a L+  + ++aeD  + n++ ++++ +++     + G     e++ +++dv+l ++  ++++v +++tk+
  AHX11109.1 165 DDGLPVMNPLLMRQAFANaAFLKVPVAQHAEDLYLSNGGCINEGVMSHKLN--VPGitdLAESVMVARDVMLLDQLDSHYHVLHVSTKK 251
                 *****************97779999*********************99987..55655599**************************97 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.6
      DHOase  67 lefeglkkaeLdqalkaiaeDDe 89 
                  + e+lk++ +d    ++a  ++
  AHX11109.1 303 YMIEALKNSTIDAIASDHAPHNG 325
                 57899999998888888876655 PP

>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   9.4e-06     0.042       1      46 [.      73     122 ..      73     151 .. 0.75
   2 ?    0.9   0.1     0.052   2.3e+02       2      33 ..     239     269 ..     238     313 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.4e-06
                 EEEEE-TTS..CCCTTTHHHHHHHHHHTTEEEE.EEE-SSG.....GGHHHHHH CS
  TatD_DNase   1 iDaHcHlds..kefeedreeileraeeagvaav.vvvgtss.....kdskavle 46 
                 iD H+Hl +  ++++ed  +  ++a+++gv++v ++++t++     +    +l+
  AHX11109.1  73 IDIHVHLRDpgQLYNEDIHSGTKAAAAGGVTTVvCQPNTKPpintvE----TLK 122
                 8******9988889*****************9945666666433332....333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.052
                 EEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEE CS
  TatD_DNase   2 DaHcHldskefeedreeileraeeagvaavvv 33 
                 D+H H+ + + ++++ ei+e a+ +g+   + 
  AHX11109.1 239 DSHYHVLHVS-TKKAVEIIETAKSRGMNVTCE 269
                 9999999944.577888889888877766553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (438 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3329.72
//
Query:       AHX11110.1  [L=851]
Description: alanine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   8.3e-195  648.4   0.0   1.1e-194  648.0   0.0    1.2  1  tRNA-synt_2c  tRNA synthetases class II (A)
    1.7e-16   60.0   1.4    4.5e-16   58.7   1.4    1.8  1  tRNA_SAD      Threonyl and Alanyl tRNA synthetase second addi


Domain annotation for each model (and alignments):
>> tRNA-synt_2c  tRNA synthetases class II (A)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  648.0   0.0  1.3e-198  1.1e-194       1     551 [.       4     547 ..       4     548 .. 0.96

  Alignments for each domain:
  == domain 1  score: 648.0 bits;  conditional E-value: 1.3e-198
                   HHHHHHHHHHHCTT-EEE----SS-SSSTTCSS--SGGGGGHHHHTTSSCGGSSSEEEEEEEEE-EETTEEGGGGTTTSSS--SEEEEEEEEESSSS CS
  tRNA-synt_2c   1 eirekFldfFekkgHtvvksssvvpendptllfvnAgmaqfkpiflgkeakpklkravnsQkciRagGkhnDlenVGktarHhTfFeMlGnfsfgdY 97 
                   ++r++F++fF+++gH+ + s+s++p+nd +l+fvnAgm++fk++f+ ++ k++++ +v+sQkc+RagGkhnDlenVG+t rHhTfFeMlGnfsfg Y
    AHX11110.1   4 NVRKRFINFFAANGHKGLSSASLIPHNDSSLMFVNAGMVPFKEYFMDTR-KAPYTNIVTSQKCVRAGGKHNDLENVGHTKRHHTFFEMLGNFSFGGY 99 
                   59***********************************************.*********************************************** PP

                   -HHHHHHHHHHHHHTTTT--GGGEEEEEETTEHHHHHHHHHTTTTEGGGEEEE-HHHHEEESSSSEEEEEEEEEEEECETTSHHCHCCCCTTCTCCH CS
  tRNA-synt_2c  98 fkeeaiefawelltkelgldkerlyvtvfeeddeaveiweklvgvpeerilrfgekdnfwemgdtgpcgpcseiyydrgeeigkrkaaseveadddr 194
                   fke ai++awe++tkel+l+k+rly+t++++ddea+eiw  l+g  e+ri+r++++dnfw+mgdtgpcgpcsei+yd+g ++ ++ ++ +    ++r
    AHX11110.1 100 FKEGAIKLAWEFITKELKLEKNRLYITIYHTDDEAFEIWSTLTGFGEDRIIRISTDDNFWQMGDTGPCGPCSEIFYDHGSHLDGDLPGDTGD-TGER 195
                   ************************************************************************************88888887.9*** PP

                   EEEEEEEEEEEEEESTTSHEEEEEEEEEEEEEEHHHHHHHHTTHSSGGGSCCTHHHHHHHHHHHT--TCSTCCHHHHHHHHHHHHHHHHHHHHTT-- CS
  tRNA-synt_2c 195 vleiwnlvfmqfnreedgtlkpLpkksidtGmglerlvavLqevrsnydtdlfvpvieaieeisgatyedkdetdealrviaDHvralafaladGvv 291
                   ++eiwnlvfmq+ + +dg+l+ +++++idtGmgler++avL+ + +ny+  lf+++i++ ++i+      +++  +a+rvi+DH+r+++f++adGv+
    AHX11110.1 196 YVEIWNLVFMQYVKGQDGNLTRIEQPCIDTGMGLERIAAVLEGTDDNYEIALFRELIQESQRITR-----NKNNVTAHRVISDHIRSASFLIADGVL 287
                   *****************************************************************.....555689********************* PP

                   SSSSHHHHHHHHHHHHHHHHHHHTT-SSTHHHHHHHHHHHHHTTTGCCHHCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCSEEXHHHHH CS
  tRNA-synt_2c 292 psnegrgYvlRrllRravrhakkLglkekflaklvavvvevlgdvypelkekeekveeiieeEeerFakTlerGlklleelikklkkkkelsgedaf 388
                   p+n+g+gYvlRr+ Rravr+ ++Lg+++++l +l +++ +++g++ypel+++++ + e +e+Ee +F+ Tl+ G+k+l+e  ++lk++++l+g++af
    AHX11110.1 288 PGNTGKGYVLRRITRRAVRYSNMLGFEKPLLPELFHTLEKLMGQHYPELTRARDLILETLETEEISFRSTLKAGMKMLDEISNSLKEGDVLPGDVAF 384
                   ************************************************************************************************* PP

                   HHHHCHXXXHHHHHHHHHCTTXEEXHHHHHHHHHHHHHHHCCHHSXSS..XXXXXXXXTTSHCHHCCTSTTTXXXXXXTSXXXXXXSEEEEEEEEEE CS
  tRNA-synt_2c 389 kLydtyGfPvdltkeiaeekglkvdiegfekameeqrerskkekkekk..likkdvealkelkkteeflgyeeleaeakvlallkdkefveeveege 483
                   +Lydt+GfP+dlt +i++e+ ++v++++f ++m+ qr+ +++++++++  + +++++a+   + ++ef+gye+++ +a vl +++     e+v+ ++
    AHX11110.1 385 TLYDTHGFPLDLTIDILKERKISVNESEFMEKMQGQRALARASWTGNRidSSNNEIKAILLAHGKTEFIGYESFSGSAVVLSVIS----SESVQLSK 477
                   **********************************************9976777778888888888********999999997765....56778889 PP

                   TTEEEESEEXXXXSSSSCSXXXEEEEESSEEEEESEEEEET.TEEEEEXSS.XSX.XXTTSEEEEEEXHH CS
  tRNA-synt_2c 484 evgvvLdrTpfYaesGGqigDeGliekegaefrvkdvqkak.gvvlhkgkleegk.lkvgdkvkaevdee 551
                   + ++vLdrT fY+esGGq++D+G+i++++a++rv+ v k + g++lh + + +g+ ++  ++v++++d +
    AHX11110.1 478 KLTLVLDRTTFYPESGGQESDHGIIFAKSATLRVERVYKSAdGIILHDCCIVDGHtVRRDEQVSLQIDLD 547
                   99*************************************999*****99876664399999*****9966 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   1.4     5e-20   4.5e-16       1      44 []     645     687 ..     645     687 .. 0.98

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 5e-20
                 EEEEEETT.EEEEESS---SBGGGC-SEEEECCECCCTCEEEEE CS
    tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkilseesiakglrRIy 44 
                 vrvvsiG  svelCgGtHv +   Ig++kilse+sia g rRI+
  AHX11110.1 645 VRVVSIGG-SVELCGGTHVGSSASIGLVKILSESSIARGTRRIE 687
                 9******8.**********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      657  (0.0366445); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.73u 0.28s 00:00:01.01 Elapsed: 00:00:00.43
# Mc/sec: 5902.63
//
Query:       AHX11111.1  [L=531]
Description: citrate transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-28   99.4  55.0    1.1e-19   70.8  36.5    2.1  2  CitMHS           Citrate transporter
    1.6e-08   34.1  35.4    4.5e-07   29.3  11.8    2.6  2  Na_sulph_symp    Sodium:sulfate symporter transmembrane regio
  ------ inclusion threshold ------
       0.19   11.2   0.3       0.33   10.4   0.3    1.3  1  TPPII            Tripeptidyl peptidase II
        3.9    7.3   7.1        1.1    9.1   0.4    3.0  3  Phage_holin_2_4  Bacteriophage holin family, superfamily II-l


Domain annotation for each model (and alignments):
>> CitMHS  Citrate transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8  36.5   2.4e-23   1.1e-19       3     270 ..      24     440 ..      22     440 .. 0.86
   2 !   42.8  10.5   8.2e-15   3.7e-11       9     173 ..     349     522 ..     337     528 .. 0.83

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 2.4e-23
                 xxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx RF
      CitMHS   3 llileklrldvvallvlvll.......vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd.llvllvlltallsafvsndg 93 
                 +li+ek r  +va+  + ll       + ++ ++l+g+++++++++lg  ++g++++ tG+++  a   ++      + ++++l+l++ + saf++n++
  AHX11111.1  24 CLITEKFRAEAVAFTSIGLLafyqgiaFSKPLVLLEGMMNGTVITILGITVMGRMVACTGAINKFASLTMKTDY--VAlIPMILILVSYFSSAFINNTP 120
                 589999999999997777778888877777777**********************************9996444..47799****************** PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxxxxxxxxxxxxxxxxxxxxx RF
      CitMHS  94 vvlimipivlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll.................lalllvgllplvllfmfgvala 175
                 vv+++i  +    ++++  + ++++p+a+aa++gg+lt  G +            +nll+                 +++l++gl+ l++++  ++ + 
  AHX11111.1 121 VVVLLITFLSICSRKIGIANSSVMMPIAFAASLGGMLTVLGSS------------TNLLIyskagelgvdigffgffTPALFIGLFGLAYVV--ALTII 205
                 ******9888777877777777*********************............***********99999999999777888787766666..55666 PP

                 xxxxxx............................................................................................. RF
      CitMHS 176 lpvnap............................................................................................. 181
                 lpv  +                                                                                             
  AHX11111.1 206 LPVRGGqleyfrsfffalnpieetrsifssvslreiksilynrkfsknllideivitekseligldilsqrvinyfqalgigisgasrkivpgvrlviv 304
                 666666999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999 PP

                 ...........xxxxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      CitMHS 182 ...........kvkkqkaiieaiarsllpvatillla................................ykkveWsvlllfaGvfllvgaleqtGilea 237
                             vkk++a i ++  +l  v t ++++                                + ++e +++l+++  ++l++ le tG+le 
  AHX11111.1 305 heghtptledvIVKKNNAYILSHHNGLRVVFTFIAVIflsavfklplafgvsagltllvlsgtvdvaeiFGSIEVKLFLMLIYSLVLGKSLEMTGVLEV 403
                 9999999999988888888888888777554444444778888888888888888888899************************************** PP

                 xxxxx.xx..x.xxxxxxxxxxxxxxxxxxxxxxxxx RF
      CitMHS 238 ladll.ga..g.gplvalalvlgliallsafisnvav 270
                 + +ll +   + ++++++a+++++++ll  ++sn+av
  AHX11111.1 404 FTQLLyEWtyDsPLIALIAVTFLIVSLLNEIMSNNAV 440
                 *****6658634776666888889999********97 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 8.2e-15
                 xxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      CitMHS   9 lrldvvallvlvll....vltieealsgiaspiillllgamiigaaleetGlfdrlaakllrlaggkrd..llvllvlltallsafvsndgvvlimipi 101
                 l+l++ +  +l+ll    +++  e++  i + + l+l+   ++g+ le tG+ +  ++ l+ ++  ++   l+++++l++ ll  ++sn++v li++p+
  AHX11111.1 349 LPLAFGVSAGLTLLvlsgTVDVAEIFGSIEVKLFLMLIYSLVLGKSLEMTGVLEVFTQLLYEWTYDSPLiaLIAVTFLIVSLLNEIMSNNAVGLIFTPV 447
                 555555555555555589999999******************************************98864444588888888899************* PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxx RF
      CitMHS 102 vlslakrlkklppllliplalaaniggaltpiGtpttraaarpglslpnlll................lalllvgllplvllfmfgva 173
                 v++l + +  +p +l+  l++aan     tp+G               nl++                +  ++v+ ++l++l++f+++
  AHX11111.1 448 VFKLSNMMDIDPKYLVWTLVFAANSAF-STPFGYQ------------ANLIVmesgkykysdylkfgtPLNFIVLGAYLLYLYLFSNL 522
                 ******88888888************9.*******............******************99855566655777777766655 PP

>> Na_sulph_symp  Sodium:sulfate symporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0  15.6   6.9e-05      0.31     321     435 ..      62     171 ..       9     197 .. 0.71
   2 !   29.3  11.8     1e-10   4.5e-07     326     461 ..     383     515 ..     333     522 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 6.9e-05
  Na_sulph_symp 321 aWntllllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalats 416
                      +t++   g+ ++ ++   +g i+ ++   +++       ++i +il+l+ +    f  +t  ++ l+  l   +  i g+    v++++a+a s
     AHX11111.1  62 MNGTVITILGITVMGRMVACTGAINKFASLTMKT----DYVALIPMILILVSYFSSAFINNTPVVVLLITFLSICSRKI-GIANSSVMMPIAFAAS 152
                    5567777777888888888888776666532222....23344444444444555678888888887777777777777.999************* PP

  Na_sulph_symp 417 lagfllpyatgpnpivfga 435
                    l+g+l+ ++++ n ++++ 
     AHX11111.1 153 LGGMLTVLGSSTNLLIYSK 171
                    *****************85 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 1e-10
  Na_sulph_symp 326 lllgglialakllersgliewlgnklttslsglspavaiiiilslfvlvhylfaSatAttaallpillavaqaipgappllvalllalatslagfl 421
                    l+l   ++l k le +g++e + + l       sp +a+i++ +l+v +  ++ S+ A   ++ p++  +++ +  ++p +++ +l++a + a f 
     AHX11111.1 383 LMLIYSLVLGKSLEMTGVLEVFTQLLYEWTY-DSPLIALIAVTFLIVSLLNEIMSNNAVGLIFTPVVFKLSNMM-DIDPKYLVWTLVFAANSA-FS 475
                    444455677999**************99988.79****************************************.99***************9.** PP

  Na_sulph_symp 422 lpyatgpnpivfgagylkvkdywrlGfilsiigllillll 461
                    +p++  +n iv  +g+ k  dy + G +l++i l  +ll 
     AHX11111.1 476 TPFGYQANLIVMESGKYKYSDYLKFGTPLNFIVLGAYLLY 515
                    ********************************98766665 PP

>> TPPII  Tripeptidyl peptidase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.3   7.4e-05      0.33      47      84 ..     383     420 ..     377     428 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 7.4e-05
       TPPII  47 lvltYnfklskstevtprlplLsdlLYesefesqlwmi 84 
                 l+l Y++ l ks e+t  l ++++lLYe  ++s l+ +
  AHX11111.1 383 LMLIYSLVLGKSLEMTGVLEVFTQLLYEWTYDSPLIAL 420
                 7899*****************************99876 PP

>> Phage_holin_2_4  Bacteriophage holin family, superfamily II-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.3      0.14   6.2e+02      12      42 ..      75     105 ..      61     113 .. 0.66
   2 ?    9.1   0.4   0.00024       1.1      14      44 ..     170     200 ..     163     206 .. 0.86
   3 ?   -1.5   0.0      0.49   2.2e+03      22      38 ..     427     443 ..     424     447 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.14
  Phage_holin_2_4  12 agnkatggGavvsfaGflasselialvGlav 42 
                       g   +  Ga+  fa     ++ +al+ +++
       AHX11111.1  75 MGRMVACTGAINKFASLTMKTDYVALIPMIL 105
                      3444566788888888888888888776655 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00024
  Phage_holin_2_4  14 nkatggGavvsfaGflasselialvGlavAl 44 
                      +ka   G  ++f+Gf + + +i+l+Gla  +
       AHX11111.1 170 SKAGELGVDIGFFGFFTPALFIGLFGLAYVV 200
                      78999999******************98544 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.49
  Phage_holin_2_4  22 vvsfaGflasselialv 38 
                      +vs++  + s+++++l+
       AHX11111.1 427 IVSLLNEIMSNNAVGLI 443
                      68999999******996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (531 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       852  (0.0475208); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 3665.88
//
Query:       AHX11112.1  [L=181]
Description: ccmB family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-11   42.3   4.1    7.7e-11   41.9   4.1    1.1  1  CcmB      CcmB protein


Domain annotation for each model (and alignments):
>> CcmB  CcmB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   4.1   4.3e-15   7.7e-11      50     186 ..      13     150 ..       8     175 .. 0.84

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 4.3e-15
        CcmB  50 gilWvaallaslLsldrlfaadfedGsLellllapvplellvlaKalAhwlltglplvllapllallln...leaaalgllaltLllGtpalsllgavg 145
                  i+W++  +  l s+  +f+   ++G Le+l ++++ +   +   ++  w+  glpl+l a++l  ll+   ++   l +   +L+  t ++s++ga+ 
  AHX11112.1  13 HIIWISTNILYLASISSIFTRYWSSGVLEQLSTSNIHIRRFISRTIVDFWISIGLPLILFATILYCLLSyysIHLRDLLFFSGSLIYSTITFSFIGALC 111
                 69**************************************************************99996322667777777889*************** PP

        CcmB 146 aAltvgLkrgglLlslLvlPliiPvlifaveaveaaaegld 186
                    tv+  r   L  +++ P++iP ++++   ++   e+l 
  AHX11112.1 112 NCFTVTTDRITYL--IIAAPISIPGIVMSMFILNGSLENLG 150
                 ******9998887..6899******9998877766665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (181 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.42
# Mc/sec: 1282.84
//
Query:       AHX11113.1  [L=127]
Description: prokaryotic dksA/traR C4-type zinc finger family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-08   32.9   1.0      6e-08   32.5   0.1    1.7  2  zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
     0.0014   18.3   0.9      0.011   15.4   1.2    2.2  2  IDEAL         IDEAL domain
  ------ inclusion threshold ------
      0.086   13.0   0.0      0.094   12.8   0.0    1.4  1  DUF3683       Protein of unknown function (DUF3683)
       0.11   12.7   0.1       0.19   11.9   0.0    1.4  2  DUF5564       Family of unknown function (DUF5564)


Domain annotation for each model (and alignments):
>> zf-dskA_traR  Prokaryotic dksA/traR C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1         1   4.5e+03      29      35 ..      44      50 ..      43      51 .. 0.78
   2 !   32.5   0.1   1.3e-11     6e-08       1      35 [.      78     112 ..      78     113 .. 0.95

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
  zf-dskA_traR 29 eCqekae 35
                   C++ +e
    AHX11113.1 44 KCANSYE 50
                  6999998 PP

  == domain 2  score: 32.5 bits;  conditional E-value: 1.3e-11
  zf-dskA_traR   1 giygsCeeCGEpIpeaRlralPgarlCveCqekae 35 
                   g yg+Cee G++I++ Rl   P+ar  v+ qe+ +
    AHX11113.1  78 GVYGYCEETGDEIGFSRLDLEPTARCSVDVQERLD 112
                   68******************************987 PP

>> IDEAL  IDEAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   1.2   2.5e-06     0.011       6      24 ..      56      74 ..      54      74 .. 0.90
   2 ?   -1.7   0.0      0.56   2.5e+03      23      33 ..      85      95 ..      85      95 .. 0.86

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.5e-06
       IDEAL  6 lrkfrrekLlreIDeALdn 24
                l +++r+ Ll+eIDeAL++
  AHX11113.1 56 LSTQKRALLLKEIDEALER 74
                5689*************96 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.56
       IDEAL 23 dnrDkeaFleL 33
                +++D+  F +L
  AHX11113.1 85 ETGDEIGFSRL 95
                579**999998 PP

>> DUF3683  Protein of unknown function (DUF3683)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.094      50      91 ..      37      78 ..      11     120 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
     DUF3683 50 vlGdiwvvrRnpylqddlldnkkrrkalvealehrleeiekr 91
                v+ d +    n y  dd++ ++++r+ l++++++ le+ie+ 
  AHX11113.1 37 VVQDFLRKCANSYEADDIILSTQKRALLLKEIDEALERIEQG 78
                6667777788*****************************986 PP

>> DUF5564  Family of unknown function (DUF5564)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.2e-05      0.19      14      79 ..       5      71 ..       2      80 .. 0.83
   2 ?   -3.5   0.0       2.6   1.2e+04      15      26 ..     107     118 ..     101     122 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
     DUF5564 14 elkkklfkrrrvlsrekrkkrqvvGavvdeglitvhhlkkrsssara.nitlsGkkrrkllkqlrha 79
                e+k++ +   r++s  + k  ++   ++ eg +    l+k + s  a +i ls +kr  llk +  a
  AHX11113.1  5 EIKNAEYMGERMISYFRDKLLRLKSDLLSEGRVVQDFLRKCANSYEAdDIILSTQKRALLLKEIDEA 71
                56666677778888888888888899999***********999988846*************99765 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.6
     DUF5564  15 lkkklfkrrrvl 26 
                 ++ +l k++r l
  AHX11113.1 107 VQERLDKKNRFL 118
                 444444544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (127 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      488  (0.0272185); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 989.74
//
Query:       AHX11114.1  [L=291]
Description: thymidylate synthase, flavin-dependent [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-56  190.5   2.7    3.7e-56  189.9   2.7    1.3  1  Thy1      Thymidylate synthase complementing protein


Domain annotation for each model (and alignments):
>> Thy1  Thymidylate synthase complementing protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.9   2.7   2.1e-60   3.7e-56       1     187 [.      34     232 ..      34     233 .. 0.89

  Alignments for each domain:
  == domain 1  score: 189.9 bits;  conditional E-value: 2.1e-60
                 EEEEEECHHHHHHHHHHHHHTTCSSHHHH.SGCCHHHHHHHHHHTTGGGGGGG-EEEEEEEEEEHHHHHHHTT-TTSEEEE--TTTSGCCCTCBS--GG CS
        Thy1   1 kLldytdpeklvaaaarvcygsseeaeeleeeekkeklikkllkhghgsplehasftfeiegvSravlrqlvrHRiasfsqqSqRYvesskeafvippe 99 
                 +++dy+++++ +++aarv+yg+   ++++   ++ ++li++l++h h++p+e+++++f+i+ ++++v+rq++rHR+a+++++S RY+ +++e f+ip+ 
  AHX11114.1  34 RVVDYMGNDQSIVQAARVSYGKG--TKTV---NQDRALIHYLMRHSHTTPFEMCEIKFHIK-MPIFVARQWIRHRTANVNEYSARYSIVDNE-FYIPEM 125
                 589***99************985..3333...23469************************.***************************999.****99 PP

                 GC..............C.HHHH.........HHHHHHHHHHHHHHHHHHHTTCHHHHHGGGSBTTBEEEEEEEEEHHHHHHHHHHHSSTTS-HHHHHHH CS
        Thy1 100 ie..............qkeele.........elyeeamekaleaykelleagvarEdaryvLPlatktklvvtmNlrsLlhflelracsrAqwEirela 175
                 ++              q              ++ +e  ++ +e y +++++g+arE +r++LPl+ +t+++++++l++Llhfl+lr++s+Aq+Eir++a
  AHX11114.1 126 EKvcyqsatnaqggsdQ----VdqvlaqefnDALNENSRALYEGYTHFINSGLAREIVRIALPLNAYTEMYWKIDLHNLLHFLKLRSHSHAQYEIRRYA 220
                 99999877776655541....03555555557788889999999******************************************************* PP

                 HHHHHHHHHHSH CS
        Thy1 176 eemleelkkvaP 187
                 e m e++k ++P
  AHX11114.1 221 EVMEEIVKLWVP 232
                 ***********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2115.98
//
Query:       AHX11115.1  [L=346]
Description: hflK protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.9e-24   85.3   0.1      8e-24   84.6   0.1    1.3  1  Band_7      SPFH domain / Band 7 family
  ------ inclusion threshold ------
      0.074   12.7   0.0       0.16   11.6   0.0    1.6  1  Lambda_Kil  Bacteriophage lambda Kil protein
       0.15   12.1   1.1       0.28   11.2   0.1    1.9  2  Pam16       Pam16


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   0.1   1.3e-27     8e-24       2     174 ..      71     254 ..      70     257 .. 0.90

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 1.3e-27
      Band_7   2 iieegevgvvvrfGklsrvlepGlhfilP.fgrsvtvvsvr...vqtldvsv......sltvptkDglpvtidvtviyrvpddapklvaaveresanld 90 
                 ++++ e gv  +fGk++ + epGl + lP  + +v +v v      ++ +s       +  ++t D  +v+ ++ v++r+ ++a  + ++v  ++    
  AHX11115.1  71 VVNPEEQGVQLTFGKYVSTSEPGLRYHLPfPIGRVDKVKVAavnRDEIGFSSgrkgegEGIMLTGDENIVNANFEVQWRI-KNAYNFLYNV--KDYGFG 166
                 89*********************98888863444555555530144555555****************************.**********..9999** PP

      Band_7  91 nlirrvlesalrevisemtleellsn..reelaeelknelneqlrkyG..vevldvritdidpppevaqalaakqaaeaeaqaeiara 174
                 + ++ ++esa r +i+++++  +l++  r+++a++ k+ l++ l++y+  vevl+++ +++dpp++v++a++++q a+a+++ ei++a
  AHX11115.1 167 TSVKGAAESAMRDAIGKNEISFILRGegRAQIAADTKKNLQAILDGYNmgVEVLSIQMKKVDPPEKVINAFRDVQSARADKEREINQA 254
                 ************************8888******************9777***********************************998 PP

>> Lambda_Kil  Bacteriophage lambda Kil protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   2.8e-05      0.16      13      41 ..     283     311 ..     272     312 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 2.8e-05
  Lambda_Kil  13 vIArFlGDekMfleAvdayKkavlilklR 41 
                 vI r lGD k f e  ++yK    i k+R
  AHX11115.1 283 VINRALGDTKRFTEIYQQYKSYPEITKMR 311
                 899*****************988888877 PP

>> Pam16  Pam16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   4.7e-05      0.28      35      93 ..     111     168 ..     104     185 .. 0.83
   2 ?   -1.5   0.1       0.4   2.4e+03      47      70 ..     264     288 ..     231     309 .. 0.55

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 4.7e-05
                 XXXX.XXXXXXXXXXXXXXXX-HHHHHHHHT--G--SHHHHHHHHHHHHHHT-CCCTS- CS
       Pam16  35 aadartsasereaaksnlkGisleeslkilnveedlnreevekryehlfevndkskGGs 93 
                 aa  r++ +  +  k++ +Gi l    +i+n + +++  ++++ y++l++v d   G s
  AHX11115.1 111 AAVNRDEIGFSSGRKGEGEGIMLTGDENIVNANFEVQ-WRIKNAYNFLYNVKDYGFGTS 168
                 4555555666677789999************999665.68*************988876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 0.4
                 XXXXXXX.XX-HHHHHHHHT--G-- CS
       Pam16  47 aaksnlk.Gisleeslkilnveedl 70 
                  ak++++  i   e+ ki  +++ l
  AHX11115.1 264 RAKGEAEvAIQNAEAYKIEVINRAL 288
                 3566665566666666666665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (346 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       635  (0.0354175); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 2542.71
//
Query:       AHX11116.1  [L=287]
Description: hflC protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-30  106.5   1.0    2.1e-30  106.0   1.0    1.1  1  Band_7    SPFH domain / Band 7 family
    0.00087   19.4   0.1     0.0037   17.4   0.1    1.9  2  Gp49      Phage derived protein Gp49-like (DUF891)
  ------ inclusion threshold ------
      0.028   14.5   3.0      0.048   13.7   3.0    1.4  1  DivIVA    DivIVA protein
       0.35   11.3   3.6        1.1    9.7   3.6    1.8  2  HHH_8     Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> Band_7  SPFH domain / Band 7 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.0   1.0   4.7e-34   2.1e-30       2     176 ..      22     196 ..      21     198 .. 0.98

  Alignments for each domain:
  == domain 1  score: 106.0 bits;  conditional E-value: 4.7e-34
      Band_7   2 iieegevgvvvrfGklsr..vlepGlhfilPfgrsvtvvsvrvqtldvsvsltvptkDglpvtidvtviyrvpddapklvaaveresanldnlirrvle 98 
                 +++eg  ++v +fG+++   +l+pGlhf++Pf++ v+++++r+  l+    ++v+ +D+ ++ +  ++ yr+ +d+ +++++  +++ nl++ +++v+e
  AHX11116.1  22 VVPEGRQAIVLQFGEVVTsePLKPGLHFKIPFINNVVRIDTRILDLSSGS-IEVIAADQKRLIVSYYAKYRI-TDPVQFYRSA-KSITNLESRLSPVIE 117
                 89***************999******************************.*********************.**********.9************** PP

      Band_7  99 salrevisemtleellsn.reelaeelknelneqlrkyGvevldvritdidpppevaqalaakqaaeaeaqaeiaraea 176
                 s+ re+++   l+ +l + r+++ +++k +  + ++ +Gvev+dvri++ d+p e  +a+ ++++ e+e++a++ ra++
  AHX11116.1 118 SNMREQVGLVPLIGILTEeRGKVMSNIKLQADKVASDFGVEVVDVRIKRADLPGENSEAIFKRMQTEREKEAREIRAQG 196
                 ****************8879********************************************************996 PP

>> Gp49  Phage derived protein Gp49-like (DUF891)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.49   2.2e+03      55      70 ..      20      35 ..      19      36 .. 0.87
   2 !   17.4   0.1   8.3e-07    0.0037      28      74 ..     173     223 ..     157     236 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.49
        Gp49 55 lyafdpgrkvilLhaf 70
                ++++ +gr++i+L  +
  AHX11116.1 20 VFVVPEGRQAIVLQFG 35
                79999*******9865 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 8.3e-07
        Gp49  28 lgkplvkkle....dglwElrpksaggiiRvlyafdpgrkvilLhafqKkt 74 
                 + + ++k ++    ++ +E+r ++ +++ R++ ++d+++k+i+++a  K++
  AHX11116.1 173 NSEAIFKRMQtereKEAREIRAQGYQEAQRIISTADKEKKLIITNAYSKAQ 223
                 5667777777777799*********************************87 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   3.0   1.1e-05     0.048      73     116 ..     186     229 ..     172     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.1e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  73 qetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeei 116
                 ++ a e++a+  +ea+ ii+ A+k+++ i+ +a ++a+ i+ e 
  AHX11116.1 186 EKEAREIRAQGYQEAQRIISTADKEKKLIITNAYSKAQSIKGEG 229
                 78899999999999999999999999999999999999998775 PP

>> HHH_8  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.2   5.4e+03      28      42 ..      98     112 ..      96     125 .. 0.77
   2 ?    9.7   3.6   0.00024       1.1       7      65 ..     177     238 ..     173     240 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.2
                 HHHHHCCCCC-SS-H CS
       HHH_8  28 YrrAaraiealpeei 42 
                 + r a++i +l+ ++
  AHX11116.1  98 FYRSAKSITNLESRL 112
                 668888888888766 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00024
                 HHHHHHHHHHHCT--CCCHHHHHHHHCCCCC-SS-HHHH.TT...HCTTSTT--HHHHHHHHH CS
       HHH_8   7 aLeeladllelkgedpfrvraYrrAaraiealpeeitsl.ee...eltklpgiGkkiaakiee 65 
                 +++++ + +e++ + + r++ Y+ A r i   ++e + +      ++++++g G++ aaki  
  AHX11116.1 177 IFKRMQTEREKE-AREIRAQGYQEAQRIISTADKEKKLIiTNaysKAQSIKGEGDAEAAKIYS 238
                 789999999999.99*******************9888873347889*************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       916  (0.0510904); expected 358.6 (0.02)
Passed bias filter:                      547  (0.0305092); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2142.18
//
Query:       AHX11117.1  [L=474]
Description: trypsin family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-32  112.8   0.6    4.2e-32  112.1   0.6    1.3  1  Trypsin_2      Trypsin-like peptidase domain
    3.4e-20   72.1   4.3    1.9e-14   53.7   0.4    2.5  2  PDZ_2          PDZ domain
    3.9e-16   59.5   0.6    6.6e-16   58.8   0.6    1.3  1  Trypsin        Trypsin
    3.9e-12   45.8   0.5      2e-07   30.8   0.1    2.9  3  PDZ_6          PDZ domain
    8.4e-12   45.3   7.8    3.9e-08   33.5   0.8    2.7  2  PDZ            PDZ domain
    4.3e-05   22.4   1.1       0.13   10.9   0.0    2.2  2  Peptidase_S46  Peptidase S46
  ------ inclusion threshold ------
      0.013   14.9   0.1          2    7.7   0.0    2.4  2  Helo_like_N    Fungal N-terminal domain of STAND proteins
      0.014   15.3   0.3       0.25   11.3   0.1    2.5  2  Tricorn_PDZ    Tricorn protease PDZ domain
      0.021   14.0   1.3       0.71    9.0   0.3    2.2  2  Peptidase_S32  Equine arteritis virus serine endopeptidase S3
      0.031   14.1   0.3       0.13   12.0   0.5    1.9  2  Peptidase_S7   Peptidase S7, Flavivirus NS3 serine protease
      0.082   12.6   0.1       0.19   11.4   0.1    1.6  1  Peptidase_S29  Hepatitis C virus NS3 protease


Domain annotation for each model (and alignments):
>> Trypsin_2  Trypsin-like peptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.1   0.6   2.6e-35   4.2e-32       1     150 []      93     231 ..      93     231 .. 0.98

  Alignments for each domain:
  == domain 1  score: 112.1 bits;  conditional E-value: 2.6e-35
   Trypsin_2   1 GsGflvgsdglilTnaHvvdsadgaavkaikkkveeagadgrevpakvvaadpelDlAllkvssderaglpplplgpsealkggepvyvvGyplggeks 99 
                 GsGfl+++dgli+Tn+Hvv++a++  v     + ++ +++ ++++ak++++d  +DlA+lk+     +gl+ l++g+s++++ g+ v   G+p g ++ 
  AHX11117.1  93 GSGFLISDDGLIVTNYHVVSNAEKIKV-----VLSQCTENCQQYDAKIIGYDVKTDLAVLKI--PGVKGLAHLRFGDSSKVRAGDWVLTAGNPFGLGG- 183
                 9**************************.....899*****************999*******..9********************************9. PP

   Trypsin_2 100 gsvssGivsgvvesesaasgegesflqtdaatspGsSGGplfdsdGrvvGl 150
                  svs Givs++++  +   +++++f+qtd+a++pG+SGGpl +++G+v+G+
  AHX11117.1 184 -SVSVGIVSAISR--EIGLFRSSDFIQTDSALNPGNSGGPLCNTNGEVIGV 231
                 .9***********..***********************************8 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.7   0.4   1.2e-17   1.9e-14       1      74 [.     270     352 ..     270     364 .. 0.90
   2 !   19.4   0.3   6.2e-07     0.001       3      66 ..     382     455 ..     381     471 .. 0.81

  Alignments for each domain:
  == domain 1  score: 53.7 bits;  conditional E-value: 1.2e-17
                 ....XX------...........-EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTE CS
       PDZ_2   1 pylGvsvsdeed.........tggvlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgk 74 
                 +++Gv +++ ++          +gvlv+s++++gPa k+gl+ gDvi++v+g k++ ++ l +++++kk+Gd ++l+v Rd  
  AHX11117.1 270 GWIGVVMQEITNevrdslggdFSGVLVASIDKKGPAYKSGLRVGDVITAVGGEKISGSRRLVREVSSKKIGDSLTLSVVRDPL 352
                 57999999999999999999999*********************************************************743 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 6.2e-07
                 ..XX------.............-EEEEEE-TTSGGGGT.--TT-EEEEETT.B--SSHHHHHHHHH.TS-TT-EEE CS
       PDZ_2   3 lGvsvsdeed...........tggvlvvsVkeggPaakaglkagDvilkvdg.kkvksledlislll.kkkpGdtVk 66 
                 +G+ vs+++d           t+gv+v  V++++      l+agD+i+ ++g k++++ +++++++  ++k+G+   
  AHX11117.1 382 IGIVVSSLTDnirasfglgddTKGVIVLAVDPNKD---TFLRAGDIIVGIGGnKQISTVQEFKQYIEaTRKKGQRSV 455
                 788888888888888888888*****999999966...77**********9835689*********98777776544 PP

>> Trypsin  Trypsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.8   0.6   4.1e-19   6.6e-16      27     221 .]      93     258 ..      77     258 .. 0.84

  Alignments for each domain:
  == domain 1  score: 58.8 bits;  conditional E-value: 4.1e-19
                 EEEEEEETT.EEEEEGGGTTTGGGEEEEESESBTTSCTTTEEEEEEEEEEEETTEBTTTTTTTEEEEEESSSSTSBSSBHCCBBCSTTHTTSTTTEEEE CS
     Trypsin  27 CgGslisen.wvlTAaHCvsnasdvkvvlgehnlkksegkeqklkvekvivhpnynpstldnDiallklkepvklgdtvrpiclpaassslpvgttclv 124
                  +G+lis++  ++T+ H+vsna+++kvvl++   +++    q+++ + +    +y+ +t   D+a+lk+       +    ++  + ss  +v+++++v
  AHX11117.1  93 GSGFLISDDgLIVTNYHVVSNAEKIKVVLSQ--CTENC---QQYDAKII----GYDVKT---DLAVLKIPGV----KGLAHLRFGD-SS--KVRAGDWV 172
                 47*******99****************9997..33333...45555553....599999...********98....7778888888.44..79999*** PP

                 EESSBSSTSSBSSBEEEEEEEEEEHH.HHHHHTTTTSTTTEEEEESTTSSSBCTTTTTTSEEEETTTEEEEEEEEE.SSSSCTTSEEEEEEGGGGHHHH CS
     Trypsin 125 sGwgrtkekgksdtlqevevpvvsre.tcksaykgkvtenmlcagakeggkdacqGDSGGPlvcsdgelvGivswg.kgcakgnrpgvytkvssyldwi 221
                    g+++  g   ++  + v+++sre    +      +++++++++     + ++G+SGGPl + +ge++G+++++ ++ +++  +g++++ + ++++i
  AHX11117.1 173 LTAGNPFGLG--GSVSVGIVSAISREiGLFR------SSDFIQTDS-----ALNPGNSGGPLCNTNGEVIGVNTASmYSNGSNAGIGFAVPSNVAVPVI 258
                 **********..8888888888888855555......69*******.....9************************988888888****9998777665 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.5   7.4e+03      16      23 ..     166     173 ..     162     176 .. 0.84
   2 !   30.8   0.1   1.2e-10     2e-07       2      32 ..     296     326 ..     295     349 .. 0.86
   3 !   12.3   0.0   6.8e-05      0.11      16      45 ..     419     447 ..     419     461 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.5
       PDZ_6  16 lrvGDiil 23 
                 +r+GD +l
  AHX11117.1 166 VRAGDWVL 173
                 799**998 PP

  == domain 2  score: 30.8 bits;  conditional E-value: 1.2e-10
       PDZ_6   2 VtaVdpgsPAdrAGlrvGDiilsvNGqpveg 32 
                 V ++d+ +PA++ GlrvGD+i++v+G+ + g
  AHX11117.1 296 VASIDKKGPAYKSGLRVGDVITAVGGEKISG 326
                 899************************9944 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 6.8e-05
       PDZ_6  16 lrvGDiilsvNGqp.veglsladvaallrgs 45 
                 lr+GDii+ ++G   +   +++++++++++ 
  AHX11117.1 419 LRAGDIIVGIGGNKqI--STVQEFKQYIEAT 447
                 89**********9999..9999888888733 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.8   2.4e-11   3.9e-08       7      81 ..     266     347 ..     260     348 .. 0.86
   2 !   14.9   1.1   1.6e-05     0.026       9      81 ..     379     459 ..     372     460 .. 0.77

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 2.4e-11
                 S.TTSESSEEEEEETTSS......SSSSEEEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHHHHHHHTTTSEEEEEE CS
         PDZ   7 e.grgglGfslkggsdqr......gdkgifvsevlpggaaeadglkvGDkIlsvNgvdvenvsheeavqaikgskgkvtLti 81 
                 + +rg++G+  ++ +++       +  g+ v+++ ++g+a ++gl+vGD+I++v+g+++++ + +      k++++++tL +
  AHX11117.1 266 QvQRGWIGVVMQEITNEVrdslggDFSGVLVASIDKKGPAYKSGLRVGDVITAVGGEKISGSRRLVREVSSKKIGDSLTLSV 347
                 347899999999988888999998889*********************************9988877777777877888866 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-05
                 TSESSEEEEEETTSS........SSSSEEEEEECTTSHHHHHT.SSTTEEEEEETT.EETTTSHHHHHHHHHHTTTS..EEEEEE CS
         PDZ   9 rgglGfslkggsdqr........gdkgifvsevlpggaaeadg.lkvGDkIlsvNg.vdvenvsheeavqaikgskg..kvtLti 81 
                  + +G+ +++ +d+         + kg++v  v p+    +d  l++GD+I++++g + +++v++ ++ ++ + +kg  +v ++i
  AHX11117.1 379 LEIIGIVVSSLTDNIrasfglgdDTKGVIVLAVDPN----KDTfLRAGDIIVGIGGnKQISTVQEFKQYIEATRKKGqrSVLMLI 459
                 567888888888888888888888888888888886....6677**********9989999998877766666555558666655 PP

>> Peptidase_S46  Peptidase S46
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   8.1e-05      0.13      47      69 ..      91     113 ..      83     118 .. 0.88
   2 !    8.9   1.5   0.00032      0.52     633     656 ..     214     237 ..     203     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 8.1e-05
                    TTEE-EE-STT-EEEE-HHHHHH CS
  Peptidase_S46  47 ggCtasfVSpeGLvlTNHHCayg 69 
                    +  ++ ++S++GL++TN H++ +
     AHX11117.1  91 SRGSGFLISDDGLIVTNYHVVSN 113
                    56799**************9976 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00032
                    TT-TT-EEE-TTS-EEEEEEEE-G CS
  Peptidase_S46 633 GGNSGSPvlngkgelvGlaFDgni 656
                     GNSG P+ n++ge++G++  + +
     AHX11117.1 214 PGNSGGPLCNTNGEVIGVNTASMY 237
                    59****************976655 PP

>> Helo_like_N  Fungal N-terminal domain of STAND proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.0    0.0012         2      65      94 ..     112     141 ..     104     166 .. 0.82
   2 ?    4.4   0.0     0.013        21      11      58 ..     345     393 ..     340     398 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0012
  Helo_like_N  65 selalLklpllrCgkaCkefeqvikkcskk 94 
                  s+ +++k+ l++C++ C+++++ i+ +  k
   AHX11117.1 112 SNAEKIKVVLSQCTENCQQYDAKIIGYDVK 141
                  56788999***************9877666 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.013
  Helo_like_N  11 lalvtfalqssksLyetvksfrsrdktvreLkeeleaLeevLesLee.v 58 
                  l++v   l++  sL   v+  r  +k+v+e+++ele +  v++sL++ +
   AHX11117.1 345 LSVVRDPLKAKESLSLKVSVERAPKKHVNEIVSELEIIGIVVSSLTDnI 393
                  56777889999999999*999************************9855 PP

>> Tricorn_PDZ  Tricorn protease PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00016      0.25      29      79 ..     301     350 ..     296     358 .. 0.74
   2 ?    1.1   0.0      0.23   3.8e+02      41      67 ..     420     447 ..     418     465 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00016
                  -B-GGGGGS---.TT-EEEEETTEE-BTTB-H.HHHHHTTTTSEEEEEEE-S CS
  Tricorn_PDZ  29 arSPLaepGvnvreGdlilavdgepvskekgi.aelLvgkagkeveLtvkrk 79 
                  +++P  ++G++  +Gd+i+av ge++s ++ +  e+   k g++ +L+v r+
   AHX11117.1 301 KKGPAYKSGLR--VGDVITAVGGEKISGSRRLvREVSSKKIGDSLTLSVVRD 350
                  67888999999..7************98766514555556677777777665 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.23
                  .TT-EEEEETTE.E-BTTB-HHHHHHTT CS
  Tricorn_PDZ  41 reGdlilavdge.pvskekgiaelLvgk 67 
                  r+Gd+i+ + g+ ++s++++++++++ +
   AHX11117.1 420 RAGDIIVGIGGNkQISTVQEFKQYIEAT 447
                  78*******9962578888888777654 PP

>> Peptidase_S32  Equine arteritis virus serine endopeptidase S32
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.019        31     112     183 ..      91     168 ..      81     189 .. 0.60
   2 ?    9.0   0.3   0.00044      0.71     206     230 ..     213     237 ..     198     249 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.019
                    SEEEEEEEECTTEEEEEEEHHHH-.TSEEEEEETT.EEEEEE.......EEEETTEEEEEETTS-S---B--B----SEEE CS
  Peptidase_S32 112 slGsGgvftidgevvvvtashvlg.dnkarvsivg.asqtlt.......fktkGDyalavvaelkGaaPklklaqsttGra 183
                    s GsG +  i ++  +vt  hv++ ++k +v  ++ ++++ +       +++k D a+ +++ +kG a +l++ +s + ra
     AHX11117.1  91 SRGSGFL--ISDDGLIVTNYHVVSnAEKIKVVLSQcTENCQQydakiigYDVKTDLAVLKIPGVKGLA-HLRFGDSSKVRA 168
                    5566655..55556899******966666664333133333300111115566677777776666654.566666665555 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00044
                    -GGGTT-EEEETTE.EEEEEEEEET CS
  Peptidase_S32 206 kcGDsGspvvdedgelvGvhtGsnk 230
                    ++G+sG p+ + +ge++Gv t s  
     AHX11117.1 213 NPGNSGGPLCNTNGEVIGVNTASMY 237
                    79*******************9853 PP

>> Peptidase_S7  Peptidase S7, Flavivirus NS3 serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.5   8.2e-05      0.13      88     128 ..     207     247 ..     200     249 .. 0.86
   2 ?   -3.2   0.0       4.2   6.8e+03      21      45 ..     397     421 ..     381     428 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.2e-05
                   EEXXXXXTT-TTSEEE-TTSXEEEECEEEEEXTTSXEEEEE CS
  Peptidase_S7  88 itdlnlssGsSGSlvlnqnkqivgiYfatvevdkkeaevgl 128
                    td+ l++G SG ++ n n++++g+  a + ++  +a +g+
    AHX11117.1 207 QTDSALNPGNSGGPLCNTNGEVIGVNTASMYSNGSNAGIGF 247
                   57899********************9999999966666666 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.2
                   EEEEEEETTEEEEEHHHHTTXXEEE CS
  Peptidase_S7  21 rgvkvlqegvfvtlthvtrgakltt 45 
                    g + +++gv v   ++++ ++l+ 
    AHX11117.1 397 FGLGDDTKGVIVLAVDPNKDTFLRA 421
                   5667788899999999999999876 PP

>> Peptidase_S29  Hepatitis C virus NS3 protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.19     107     143 ..     214     251 ..     201     256 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
  Peptidase_S29 107 kGssGsPilCdsGhvvGllvaavcsggvvkavrfv.Pv 143
                     G sG+P+   +G v+G+ +a + s g+   + f  P 
     AHX11117.1 214 PGNSGGPLCNTNGEVIGVNTASMYSNGSNAGIGFAvPS 251
                    599****9999*****************9999997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       641  (0.0357521); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3334.07
//
Query:       AHX11118.1  [L=1032]
Description: DNA polymerase III subunit alpha [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.9e-102  341.0   0.0   5.9e-100  334.2   0.0    2.6  2  DNA_pol3_alpha   Bacterial DNA polymerase III alpha NTPase do
    8.8e-59  197.6   0.0    1.7e-58  196.7   0.0    1.5  1  DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit f
    7.7e-18   64.5   0.2    2.8e-17   62.8   0.1    2.2  2  HHH_6            Helix-hairpin-helix motif
    3.9e-08   33.8   0.0    8.5e-08   32.7   0.0    1.6  1  PHP              PHP domain


Domain annotation for each model (and alignments):
>> DNA_pol3_alpha  Bacterial DNA polymerase III alpha NTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  334.2   0.0  1.3e-103  5.9e-100       2     260 .]     227     485 ..     226     485 .. 0.99
   2 !    4.1   0.1    0.0066        30     139     222 ..     600     685 ..     568     721 .. 0.72

  Alignments for each domain:
  == domain 1  score: 334.2 bits;  conditional E-value: 1.3e-103
                     HHHHHHHHHHHHHSTT---TTHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHTT--B-S--GGGGG-HHHHHTTS----HHHHT--HHHHS-T CS
  DNA_pol3_alpha   2 yLrklveeglkerlkeelpeevkerlekElevIekmgfadyflivadlvkaakkkgilvGpgRGSaagslvayllgiTeidPlkydllFerFlnp 96 
                     +Lrklv++gl++r+k+++p ++ erle+El+vI++m++a+yflivad+++++k++gi vGpgRGS+ gs+va+ lgiT +dP+k+ l+FerFlnp
      AHX11118.1 227 ELRKLVYSGLRKRMKDNIPGNYLERLEYELSVIIEMKYAGYFLIVADFIRWSKENGIAVGPGRGSGVGSIVAWSLGITGLDPIKFALFFERFLNP 321
                     79********************************************************************************************* PP

                     TS-------EEEEGGGHHHHHHHHHHHH-TTTEEEEEEEEE--HHHHHHHHHHHH-GGHHHHHHHHHTS---SS..--GGGG-----SHHHHHHH CS
  DNA_pol3_alpha  97 ervsmPDiDidfekerreevidyvkekyGkenvaqiitfgtlaakaairdvgralglplkevdklaklipkelg..itlekaleeekelkeliee 189
                      rvsmPD+D+df++e+r+ vi+y+k+kyG  +vaqi+tfgtl+ +aa+rdvgr+l+lp++ vdk++k+ip++++  i+l++a++ +k+l+e  ++
      AHX11118.1 322 VRVSMPDFDVDFCQEKRHLVIEYIKKKYG--HVAQIVTFGTLQPRAALRDVGRVLQLPYSRVDKICKMIPNNPAnpISLQEAIDLDKDLQEERKN 414
                     ****************************9..6****************************************7769******************* PP

                     -HHHHHHHHHHHTTTT-EEEEEEEEEEEEE-SS-GGGTS-EEE-TTT--EEESS-HHHHHTTT-EEEEEEE CS
  DNA_pol3_alpha 190 deevkrlvelakkleglkrntgqHaaGvvispkeltdlvPlqkaekeeevvtqfdmedledlgllKlDfLG 260
                     de++++l++la kleg+ r++++HaaG+vis+k+++++ P++++++++ +vtq++m+++e++gl+K+DfLG
      AHX11118.1 415 DETMDKLLDLALKLEGTLRHSSTHAAGIVISDKPIEEYLPIYYDQDSDIPVTQYSMKYVEKAGLVKFDFLG 485
                     *******************************************999999*********************9 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.0066
                     -HHHHHHHHHHHH.-GGHHHHHHHHHTS---SS--GGGG---.--SHHHHHHH-HHHHHHHHHHHTTTT-EEEEEEEEEEEEE-SS CS
  DNA_pol3_alpha 139 aakaairdvgral.glplkevdklaklipkelgitlekalee.ekelkelieedeevkrlvelakkleglkrntgqHaaGvvispk 222
                       ++ + ++ + l g++l+e+d l +++ k+ + ++++++e+  +  k+   e+e++++++e+++k+ g   n +  aa  +is +
      AHX11118.1 600 IYQEQVMEIVKLLaGYTLAEADILRRVMGKKIRSEMAEQTEKfIEGAKQNGIESEKAREIFEMVEKFAGYGFNKSHAAAYALISYQ 685
                     44555556666654999999999999999997755555555521223333338999*************99999855555555544 PP

>> DNA_pol3_finger  Bacterial DNA polymerase III alpha subunit finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.7   0.0   3.7e-62   1.7e-58       1     166 []     488     650 ..     488     650 .. 0.97

  Alignments for each domain:
  == domain 1  score: 196.7 bits;  conditional E-value: 3.7e-62
                      HHHHHHHHHHHHHHHH-----GGG--S--HHHHHHHHHT--TTSTT--SHHHHHHHHHH---SHHHHHHHHHHSSHHHHHTTHHHHHHHHHTTS CS
  DNA_pol3_finger   1 tltiirralklikekkgkeidleeipleDkkvykllskgdtlGvfqlesrgmrqllkrlkPktfeDlvalvaLyRpgpvqggnvddyikrknge 94 
                      tlt+i++a++li+ek   ++d+e+ipl+D+k+y+lls g+++Gvfql+   m ++lkrl+P+++eD++al++L Rpgp++  n+++yi+rk+g+
       AHX11118.1 488 TLTVINQACSLIREK-IPDFDIESIPLNDRKTYELLSAGKAIGVFQLDNAYMCETLKRLHPDSLEDIIALISLNRPGPMA--NIPTYIARKHGK 578
                      79**********554.467*************************************************************..************ PP

                      S----SSHHHTTTTTTTTT---BHHHHHHHHHHHH---HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHTT CS
  DNA_pol3_finger  95 ekveyihpeleeiLketygvivyQEqvmqiaqvlagfslgeAdllrramgkkkeeeleklkekfiegakeng 166
                      ekvey+hp le+ Lket+gv++yQEqvm+i++ lag++l+eAd lrr mgkk + e+++++ekfiegak+ng
       AHX11118.1 579 EKVEYPHPLLESSLKETFGVVIYQEQVMEIVKLLAGYTLAEADILRRVMGKKIRSEMAEQTEKFIEGAKQNG 650
                      *********************************************************************996 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       3.4   1.5e+04      43      63 ..     408     428 ..     406     433 .. 0.82
   2 !   62.8   0.1   6.1e-21   2.8e-17       2      89 ..     724     807 ..     723     808 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 3.4
       HHH_6  43 ivaeRekegpfksledlarrv 63 
                 + +eR++++   +l dla ++
  AHX11118.1 408 LQEERKNDETMDKLLDLALKL 428
                 678999999999999998776 PP

  == domain 2  score: 62.8 bits;  conditional E-value: 6.1e-21
       HHH_6   2 vevlppdvnrSeadftveeedgairlGLaaikglgeaaaerivaeRekegpfksledlarrvds..lnkrqleaLakaGaldslglnRrq 89 
                 + +lppdv++S++ f++e  d+air++Laa+k++geaaa  + +eR+   +f+++e+++  +d+  +n+r++e+L+k+Ga+d+++ +R++
  AHX11118.1 724 ISILPPDVTKSKVLFSIE--DNAIRYSLAALKNVGEAAATFL-QERN---QFRTIEEFSGCIDAkiVNRRAVESLVKSGAMDAISPDRSN 807
                 78****************..999*************998765.5576...8************************************986 PP

>> PHP  PHP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   1.9e-11   8.5e-08      41     166 ..       2     112 ..       1     113 [. 0.78

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 1.9e-11
                 THHHHHHHHHHHHTTTTSEEEEEEE..................E....EHHHHHHHHHHHHH..........HHHHHHS..................TT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         PHP  41 fgyvefykaakkkykagikpiiGleayvaddsekerpshltllaknqeGyknllkllskaylegfyrkpridkellekhsegLivlsgclkGevfeald 139
                  g +ef+++a   +++g++piiG++++v  ++     s ++l+a+n+eGy+nl+kl+ +          +i+ e + + + gLivl g     + +a++
  AHX11118.1   2 AGTLEFAEYA---KSSGVQPIIGTDLSVFYKN---VDSSILLIARNEEGYRNLIKLSGAVSR------RKITLEDVFAWHRGLIVLLGNF---LIDAIN 85 
                 5789******...7788************987...6999**************998655444......566666666666******9955...444444 PP

                 GGHHHHHHHHHHHHHHHC...T-EEEEEG CS
                 xxxxxxxxxxxxxxxxxxx..xxxxxxxx RF
         PHP 140 lieveekaeealeelakif..gdyiEint 166
                  ++++e   + l  ++++f  + +iEi++
  AHX11118.1  86 SYSIDE--VALLSDFKQVFerDLFIEIQR 112
                 445555..5677888888888******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1032 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      518  (0.0288917); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.29s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 6945.63
//
Query:       AHX11119.1  [L=413]
Description: smr domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.8e-47  159.8   0.0    1.1e-46  159.3   0.0    1.2  1  Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
    1.5e-14   54.1   0.0    3.9e-14   52.8   0.0    1.7  1  Smr           Smr domain
  ------ inclusion threshold ------
       0.13   12.3   0.1       0.28   11.3   0.1    1.5  1  VHP           Villin headpiece domain


Domain annotation for each model (and alignments):
>> Cu-oxidase_4  Multi-copper polyphenol oxidoreductase laccase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.3   0.0   1.8e-50   1.1e-46      38     229 ..      42     227 ..      28     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 159.3 bits;  conditional E-value: 1.8e-50
                   HTTS.GEEE-B--SS--EEE-EE--GGCSSSS..B..-SEEEESSTTSEEEEEESSSEEEEEEETTSSEEEEEEE-HHHHHHTHHHHHHHHHCSTT- CS
  Cu-oxidase_4  38 algv.rlvlleqvHgtevvvvaeeaaakgsaeeeeleaDalvtdepgvalavltADCvPvlladpkgkvvaaaHaGwrGlvagvlektveamkelga 133
                   +l+  ++v+++qvH++ ++  ++   +    ++++l++Da+vtd+p+++l+v tADCvP+ll dp++++++++HaGw+Gl +gv+++++++m ++g+
    AHX11119.1  42 NLQRnEYVFPKQVHSNICMFTRT---P----SANSLKCDAIVTDQPNLTLVVKTADCVPILLSDPVNHIIGVVHAGWKGLNSGVIQNAIAKMIDIGS 131
                   33334589********9833332...2....234477************************************************************ PP

                   -GGGEEEEE-SB--TTT-EEEHHHHHHHHHHSGGGGEEEEETTEEEE-HHHHHHHHHHHTT-..SEEEE---BTTT-TTT---HHHH...SH..--- CS
  Cu-oxidase_4 134 kpedilaaiGPsIgpecyeVgeevaeafeaadpeaaaaaeeegkaylDLaalarlqLeeaGvkeenieasglCTvceedrfFSyRrd...gg..tGr 225
                   +++ i +aiGP+I +e+yeV+e++ eaf ++ +  ++++ ++gk+y+DL ++++ +L++ G+  ++i+ s+++T++++    SyRr+   ++  t r
    AHX11119.1 132 QSKYINVAIGPCILRENYEVQEDFLEAFGSTGK--EFSRLKQGKYYFDLLGCCQDILKKEGI--REIHTSEVDTYTNTG-ISSYRRTrhlNNpdTYR 223
                   ****************************87554..4799***********************..***********9986.99****95431234555 PP

                   EEEE CS
  Cu-oxidase_4 226 maal 229
                    +++
    AHX11119.1 224 NISA 227
                   5555 PP

>> Smr  Smr domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.8   0.0   6.5e-18   3.9e-14       1      80 []     328     410 ..     328     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 52.8 bits;  conditional E-value: 6.5e-18
                 EE-TT--HHHHHHHHHHHHHHHHHTT-SEEEEE--STTSTTHCHHHHHHHHHHHCS....TTEEEEEE--CCCTGGGEEEEEE- CS
         Smr   1 lDLhglrraealnvletfldaasakglrsvevihGkGahagvgvLrpavmgwLagk....eaveafreaekkeGgkGavvVlLk 80 
                 lDLh  + + a +    f+ +++++glr +++i+GkG+ +g+g+Lr+ + +w +++    e    ++ea +++Gg+Ga++V L+
  AHX11119.1 328 LDLHWETEESAYKKTIGFILESYEAGLRYLLIIVGKGK-NGKGKLRDSLASWVENHcktrELLMLVEEALPQHGGEGAYYVFLR 410
                 8*************************************.789***************9998899999**************997 PP

>> VHP  Villin headpiece domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   4.6e-05      0.28       4      23 ..     152     171 ..     151     173 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.6e-05
         VHP   4 dedFeevFgmtreeFykLPk 23 
                 +edF e+Fg t +eF++L++
  AHX11119.1 152 QEDFLEAFGSTGKEFSRLKQ 171
                 59****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       671  (0.0374254); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3172.78
//
Query:       AHX11120.1  [L=374]
Description: DNA polymerase III, beta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-28   99.2   2.4    2.2e-23   82.7   0.1    2.5  3  DNA_pol3_beta_2  DNA polymerase III beta subunit, central dom
    1.1e-24   86.6   1.0    1.1e-23   83.3   0.1    2.7  3  DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal 
    2.2e-20   73.0   5.5    7.3e-12   45.5   0.6    3.1  3  DNA_pol3_beta    DNA polymerase III beta subunit, N-terminal 
  ------ inclusion threshold ------
      0.062   12.5   0.0       0.14   11.4   0.0    1.6  1  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
       0.12   12.5   0.1       0.23   11.6   0.1    1.4  1  SGS              SGS domain


Domain annotation for each model (and alignments):
>> DNA_pol3_beta_2  DNA polymerase III beta subunit, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   2.8e-06    0.0099       2     113 ..      11     120 ..      10     124 .. 0.90
   2 !   82.7   0.1     6e-27   2.2e-23       3     116 .]     137     250 ..     135     250 .. 0.94
   3 ?   -3.3   0.0       2.8   9.9e+03      85     101 ..     286     302 ..     270     306 .. 0.60

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 2.8e-06
                      EEHHHHHHHHHCCGGGS-SSTTSGGGGEEEEEEECCEEEEEEE-SSEEEEEEEEEEECTTCEEEEEEEHHHHHHHHHHHTSSSSEEEEEEESSE CS
  DNA_pol3_beta_2   2 lkqkelkelieqvafaasedetrpvLtGvrleieedklllaaTdghRlavrkleleeeeedeasvivPaktlaelaklledneeqvklalsegk 95 
                      +kq+ l +++++      ++ t  +L  vr+ +++   ++++Td   l++  + ++ ++ d++++ v +  l e+ + l   + +v+l++++ +
       AHX11120.1  11 VKQEDLSRVLSNLVGVSTRKSTIAYLSQVRIFLSGGAAEFTTTDN-ELSLTDTVVDIANVDDVAISVDVFKLHEIVRHLPI-DAEVRLSIDQVN 102
                      577888888888776677888999********************8.7**********************************.9*********** PP

                      EEEEETTEEEEEE-BSS- CS
  DNA_pol3_beta_2  96 irfevgnvrltsrlldgk 113
                      + ++ g+  ++   ld++
       AHX11120.1 103 LAISSGKIEFALPYLDAA 120
                      *******99999888863 PP

  == domain 2  score: 82.7 bits;  conditional E-value: 6e-27
                      EHHHHHHHHHCCGGGS-SSTTSGGGGEEEEEEECCEEEEEEE-SSEEEEEEEEEEECTTCEEEEEEEHHHHHHHHHHHTSSSSEEEEEEE.... CS
  DNA_pol3_beta_2   3 kqkelkelieqvafaasedetrpvLtGvrleieedklllaaTdghRlavrkleleeeeedeasvivPaktlaelaklledneeqvklals.... 92 
                      +++e+k l ++v+fa+s++ tr+ L+G++le +++k+++aaTd hRlav++l  ++  +  +s ivP+kt++e+ kl +   ++v l+l     
       AHX11120.1 137 SKDEIKTLFNKVKFAISTESTRQHLNGIYLESDGEKITAAATDIHRLAVATLDKKTGFN--FSCIVPKKTVLEMIKLSTM--GKVLLSLHgrey 226
                      68999*********************************************999888877..9***************999..778888877899 PP

                      SSEEEEEETTEEEEEE-BSS---B CS
  DNA_pol3_beta_2  93 egkirfevgnvrltsrlldgkfPd 116
                      ++++++ vgnv+l s+l+ g fPd
       AHX11120.1 227 TNRVKVVVGNVYLNSKLVAGTFPD 250
                      99*********************8 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.8
                      SEEEEEEESSEEEEEET CS
  DNA_pol3_beta_2  85 eqvklalsegkirfevg 101
                       +++l++ e+ + +e+ 
       AHX11120.1 286 RAIRLTIREKTLSVEAS 302
                      44555555555555544 PP

>> DNA_pol3_beta_3  DNA polymerase III beta subunit, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.81   2.9e+03      82     114 ..      45      75 ..      21      83 .. 0.72
   2 ?    0.6   0.1      0.13   4.8e+02      33      54 ..      90     111 ..      61     114 .. 0.73
   3 !   83.3   0.1   3.1e-27   1.1e-23       2     121 .]     253     373 ..     252     373 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.81
                      HHHHHH-SSEEEEEESSTTS-EEEEETTEESEE CS
  DNA_pol3_beta_3  82 dalkaleteevelqltdstkpvllsevedesvk 114
                       + + ++t++ el+ltd++  v + +v d+ ++
       AHX11120.1  45 GGAAEFTTTDNELSLTDTV--VDIANVDDVAIS 75 
                      4555667777777777776..666666666555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                      STGEEEEEEETTEEEEEEEETT CS
  DNA_pol3_beta_3  33 knrkvrLsleegqlklsaense 54 
                        ++vrLs+++ +l++s+++ e
       AHX11120.1  90 IDAEVRLSIDQVNLAISSGKIE 111
                      4578999999999999988755 PP

  == domain 3  score: 83.3 bits;  conditional E-value: 3.1e-27
                      CCS-SS-SEEEEEEHHHHHHHHHHHHTTSSTSTGEEEEEEETTEEEEEEEETTSEEEEEEEEEBEE.SS-EEEEEEHHHHHHHHHHH-SSEEEE CS
  DNA_pol3_beta_3   2 rllPkefkkkvtvdlkelkealkRvalladeknrkvrLsleegqlklsaensevgeaeEevdvnye.GeeleiafNvsYlldalkaleteevel 94 
                       ++Pk fk  ++++ k+++ a++R+ l++ +++r++rL++ e+ l ++a+ns++    E+++ + e   +++i fN  Ylld  ++le+ee  +
       AHX11120.1 253 AVIPKTFKFSLSMNKKAIARAVERIGLVSPDQSRAIRLTIREKTLSVEASNSDASFGREALELDSEfDGDMSIHFNHAYLLDIFSVLESEEMVM 346
                      59*********************************************************9999999999************************* PP

                      EESSTTS-EEEEETTEESEEEEE--BB CS
  DNA_pol3_beta_3  95 qltdstkpvllsevedesvkyvilpmr 121
                      +++++t+ vl ++ +desv y+i+pm+
       AHX11120.1 347 CFNNPTSQVLFKDGSDESVLYIIMPMS 373
                      *************************95 PP

>> DNA_pol3_beta  DNA polymerase III beta subunit, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.6     2e-15   7.3e-12       3     120 ..       9     125 ..       7     126 .. 0.96
   2 !   20.3   0.1   1.3e-07   0.00046       6      94 ..     137     223 ..     133     251 .. 0.85
   3 !    8.4   0.0   0.00061       2.2      32     105 ..     287     362 ..     281     369 .. 0.77

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 2e-15
                    EEEEHHHHHHHHHHHHTTSSSTTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEEEEETTEEE CS
  DNA_pol3_beta   3 ftiereellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivkaLpndkkvkisvneqkll 98 
                    +++++e+l   l++  +v  ++ t+  Ls v +  +     +t tD e+s+ +t+    +  + ++ v   +l +iv++Lp d++v +s+++ +l+
     AHX11120.1   9 IVVKQEDLSRVLSNLVGVSTRKSTIAYLSQVRIFLSGGAAEFTTTDNELSLTDTVVDIANVDDVAISVDVFKLHEIVRHLPIDAEVRLSIDQVNLA 104
                    789***************************************************998888899********************************* PP

                    EEEETTEEEEEE-BEGGGS--- CS
  DNA_pol3_beta  99 iiksgssrfslstlsaeeypnl 120
                    i+ sg+ +f l+ l+a  +p +
     AHX11120.1 105 IS-SGKIEFALPYLDAATFPSI 125
                    **.*****************86 PP

  == domain 2  score: 20.3 bits;  conditional E-value: 1.3e-07
                    EHHHHHHHHHHHHTTSSSTTSSGGGGEEEEEEETTEEEEEEE-SSEEEEEEEESEEEEE-EEEEEEHHHHHHHHHHSSTTSEEEEEEET CS
  DNA_pol3_beta   6 ereellkelekvakvisnRntlpiLsgvllevkdsqlsltgtDleisiestisaeseeeegkvlvparllldivkaLpndkkvkisvne 94 
                    +++e+ +  +kv+ +is+  t   L+g++le + ++++  +tD    + +t+ ++    +++ +vp +++l+++k   +  kv +s+++
     AHX11120.1 137 SKDEIKTLFNKVKFAISTESTRQHLNGIYLESDGEKITAAATDIHRLAVATLDKKTG-FNFSCIVPKKTVLEMIKLSTM-GKVLLSLHG 223
                    678889999************************************************.99**************85444.888888877 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00061
                    EEEEEEETTEEEEEEE-SSEEEEEE.EESEEE.EE-EEEEEEHHHHHHHHHHSSTTSEEEEEEET.TEEEEEEETTE CS
  DNA_pol3_beta  32 gvllevkdsqlsltgtDleisiest.isaese.eeegkvlvparllldivkaLpndkkvkisvne.qklliiksgss 105
                    ++ l++ +++ls+ +++++ s+  + +++ se + + ++  +  +lldi + L+  ++  + +n+ + + + k gs+
     AHX11120.1 287 AIRLTIREKTLSVEASNSDASFGREaLELDSEfDGDMSIHFNHAYLLDIFSVLES-EEMVMCFNNpTSQVLFKDGSD 362
                    799*******************7661455555445667888999***********.555566666477777777766 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   3.8e-05      0.14     133     192 ..      60     121 ..      32     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 3.8e-05
                 XXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 133 gdtlftiadlstVWveaevye..qqlalvkvgqkvevtvealpgktfeGkvdyiyptvdpet 192
                  dt++ ia++++V + ++v+   + ++ + ++++v++++++++    +Gk+++ +p++d++t
  AHX11120.1  60 TDTVVDIANVDDVAISVDVFKlhEIVRHLPIDAEVRLSIDQVNLAISSGKIEFALPYLDAAT 121
                 6899***************97336799********************************998 PP

>> SGS  SGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   6.5e-05      0.23      12      68 ..     127     183 ..     119     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 6.5e-05
         SGS  12 keekeekkeeegeaalnklFkkl.YadadedtrrammKSyveSnGtvLstnWeevkkk 68 
                 +eek+ +  e +++++++lF+k+ +a ++e tr+ ++  y eS+G  ++   +++++ 
  AHX11120.1 127 EEEKQGEI-EFSKDEIKTLFNKVkFAISTESTRQHLNGIYLESDGEKITAAATDIHRL 183
                 33333333.589999*****99989********************9998877777665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (374 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       525  (0.0292822); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3068.10
//
Query:       AHX11121.1  [L=472]
Description: isocitrate dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      5e-89  298.9   0.5    6.3e-89  298.5   0.5    1.1  1  Iso_dh    Isocitrate/isopropylmalate dehydrogenase
    4.5e-20   71.8   0.0    1.5e-19   70.1   0.0    2.0  2  TT1725    Hypothetical protein TT1725
  ------ inclusion threshold ------
      0.026   15.2   1.2      0.035   14.8   0.2    1.7  2  DUF2712   Protein of unknown function (DUF2712)


Domain annotation for each model (and alignments):
>> Iso_dh  Isocitrate/isopropylmalate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  298.5   0.5     1e-92   6.3e-89       2     348 .]       4     331 ..       3     331 .. 0.95

  Alignments for each domain:
  == domain 1  score: 298.5 bits;  conditional E-value: 1e-92
                 EEEEEESTTHHHHHHHHHHHHHHHHHHHT-EEEEEE---THHHHHHHS.SSS-HHHHHHHHHSSEEEEEE---CSSSSSSHHHHHHHHHHHTTEEEEEE CS
      Iso_dh   2 iallegdgiGpevveaalkvlkaakekaglelefeevdvGgaaidetg.eplpeetleaikeadvvllgavgtpkekevrpengLlaLrkeldlfanlr 99 
                 +++  g+giG e+++++l+++ +a     + l++  +++G++ +++   + +p+ + + ik++++ l+g+++tp +++v++ n  ++Lrk+l+lfan+r
  AHX11121.1   4 LTVAYGNGIGAEIMTSVLEIIFEAG----AALQIDTIEIGQKIYKKGWpSGIPDSAWDTIKKNKILLKGPITTPRGGGVKSLN--VTLRKKLGLFANVR 96 
                 57788****************9998....4588999*******99954689********************************..9************* PP

                 EEE-BCCTTCCSSBTHHHHCT-EEEEEEE-SSCGGCSSEEEEETTG.GGGEEEEEEEEEHHHHHHHHHHHHHHHHHTTTSEEEEEESTTTTHHHH.HHH CS
      Iso_dh 100 pvkvfeklkvksplkrevveevdlvivReltggiYfgeekekkgsifteevavdtklyseeeieriaraafelAlkrgkkkvtlvdKanvlksse.lwr 197
                 p+ +      +s+ k     +vd+vi+Re+ +++Y+g+e+ ++       +   tk+++e+ +e+i r+afe+A+++++kkvt++ K n++k+++  ++
  AHX11121.1  97 PCVSH----LSSQDK-----KVDIVIIRENEEDLYSGIEYRQTRD-----TYNCTKVITEKTSEKICRYAFEYARNNNRKKVTVMVKDNIMKMTDgVFH 181
                 **998....344444.....59*******************9997.....355799***************************************9*** PP

                 HHHHHHHCCTTTTSEEEEEEHHHHHHHHHHSGGGGSEEEE-HHHHHHHHHHHHHHTTSGCC-EEEEEETSS-EEEEESS---CCCTTSS-S-THHHHHH CS
      Iso_dh 198 kiveevaeeeypdielehqlvDsaamqlvkspkqfdVivtkNlfGDilSDeaaalvGslGllpSaslgekkvaifEavHGsapdiagkdkaNpiavilS 296
                 + + +va+ ey+di+ e+ ++D  a+++ k p++fdVivt Nl+GDi+SD aa + Gs+Gl  S ++g ++ a+fEavHGsapdia +d+aNp++ + +
  AHX11121.1 182 RLFRDVAS-EYNDIQSENYIIDIGAARIAKTPEKFDVIVTLNLYGDIISDIAAEISGSVGLGGSINIG-EEYAMFEAVHGSAPDIADQDIANPSGLLNA 278
                 ********.***********************************************************.68**************************** PP

                 HHHHHHHTTT-HHHHHHHHHHHHHHHHHTSCCHHHCTTS..TCCCHHHHHHHHH CS
      Iso_dh 297 aalmLryslgleeaAdkiekAvekvleagivTkDlagea..akevstsefgdav 348
                 a+ mL y +g++e A+k+++A  k++++g+ T+D++  +  + +v t++f+++v
  AHX11121.1 279 ATYMLSY-IGQKEVAQKVYSAWLKTIKDGVHTADIYHPSwsKIKVGTKKFTEHV 331
                 *******.****************************999878899******987 PP

>> TT1725  Hypothetical protein TT1725
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.1   6.7e+03      56      80 ..     145     169 ..     137     181 .. 0.64
   2 !   70.1   0.0   2.5e-23   1.5e-19       1     105 [.     364     470 ..     364     472 .] 0.95

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.1
                 SEEEEEEEE-SSS---HHHHHHHHH CS
      TT1725  56 dhwrcRfvakegkkvskeeileLle 80 
                     cR+  + +++ ++++++ +++
  AHX11121.1 145 SEKICRYAFEYARNNNRKKVTVMVK 169
                 4556888877666666666665554 PP

  == domain 2  score: 70.1 bits;  conditional E-value: 2.5e-23
                 EEEEEEEEEEE.--S-HHHHHHHHHHHHTTT.EEEEEEEETTEEEES--S----.--SEEEEEEEE-SSS---HHHHHHHHHHH.HTTSEEEEEEEEEE CS
      TT1725   1 kelvGvDvfiewkekdpeelaekleklaeee.lkLkmitnrGvkvyPegleetf.ctdhwrcRfvakegkkvskeeileLlerlaeagldviktenLye 97 
                 k+l+GvD+fi+w++++ ++l + le ++ ++ + L  i+ +G+ ++P++ +  + ++d+  cRf+ + + ++++++i +L+e+++++ ++v+++e+Ly+
  AHX11121.1 364 KKLIGVDLFITWESTNLQKLLTLLEGIKVSKaIILGSISVKGISIWPDKSSIVLpYSDTLCCRFLGEPNGNLTTRDIYALMEEIENNAIEVTRMEKLYT 462
                 89*************************9887799**************999775379****************************************** PP

                 ETTEESB- CS
      TT1725  98 fdgkrgys 105
                 f +k g+s
  AHX11121.1 463 FGDKLGFS 470
                 *******9 PP

>> DUF2712  Protein of unknown function (DUF2712)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.2   5.8e-06     0.035      11      72 ..     113     174 ..     103     201 .. 0.81
   2 ?   -2.5   0.0       1.4   8.1e+03      72      90 ..     289     307 ..     273     318 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.8e-06
     DUF2712  11 klkankensytedryRqtkktdnpWkvnltkstEGkgsvatywlektGllkikvskthdvkq 72 
                  ++ n+e+ y++++yRqt++t n  kv  +k +E    +a  + +++  +k+ v  + ++ +
  AHX11121.1 113 IIRENEEDLYSGIEYRQTRDTYNCTKVITEKTSEKICRYAFEYARNNNRKKVTVMVKDNIMK 174
                 477899999*************************9999999999999888887776666655 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.4
     DUF2712  72 qgsgehkYsAyseasqqnv 90 
                 ++ ++ +YsA+ ++ +  v
  AHX11121.1 289 KEVAQKVYSAWLKTIKDGV 307
                 5566777888777666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (472 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       694  (0.0387082); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.28s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3480.33
//
Query:       AHX11122.1  [L=304]
Description: membrane transport family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.6e-10   40.0  21.5    2.9e-07   29.3   7.5    2.1  2  Mem_trans   Membrane transport protein
  ------ inclusion threshold ------
      0.064   13.7   1.7      0.064   13.7   1.7    3.2  3  ATP_synt_H  ATP synthase subunit H


Domain annotation for each model (and alignments):
>> Mem_trans  Membrane transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   7.5   3.2e-11   2.9e-07       2     128 ..       5     123 ..       4     146 .. 0.84
   2 !   16.9   6.2   1.8e-07    0.0016     240     386 ..     152     299 ..     139     300 .. 0.80

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 3.2e-11
   Mem_trans   2 vleavvplyvimllgYgsvkwvkiftpdqcsginrfVvlfavPllifhfisqnnpyemllrfiladvlvklivlillllgallskifkgslewtitlfs 100
                 vl +++ply+++llgY+++++     +  ++ i +f +++  Pl i++ + + + +    ++ l++++++li  ++  l + ++  + ++   ++++ +
  AHX11122.1   5 VLSKILPLYLMILLGYIAGRS----LNTDRNTIATFLLYLLSPLVILNGLLRVDGMG---KLFLLPIVILLISCFMCWLVYTVTY-LFYDNSLRNIIAF 95 
                 6789*****************....5567899********************77777...6667777777777777777777777.57899999***** PP

   Mem_trans 101 lstlpNtlvlgipllkalygeygvslmv 128
                  s ++Nt+  g+p+   +++ ++v + +
  AHX11122.1  96 SSGSSNTGHFGLPVALMIVDAETVGIYI 123
                 **************99998886665554 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.8e-07
   Mem_trans 240 lrklirnPntyssllglilslvsfkwnvimpkiiqksisil.gd.aglpmalfslGlfLalqpkkiacgnsvatfalavRlilgPlvmlvavla....v 332
                 +++ +r P++ ++l+++ + l     +    + ++  +  l g  ++l+m ++ lGl+ +   kk+++  +   + ++v+++l P++ l +v++    +
  AHX11122.1 152 IKRTLRLPPLHAVLIAFLMKLLDLDLP----QALDPFFLNLrGTyVTLGMSTIGLGLSTI---KKFEIDWKCIGITMFVKYFLWPALTLSLVYLdiyyL 243
                 6788999****************9999....55555544441433788888888888877...4566666666678***********999987443224 PP

   Mem_trans 333 gL..rgslllvaivqaAlPqgivlfviAkeynvherelstllifgmlialpitlvy 386
                 +L  + +++ ++++   +P ++  + i   +n+  + l++++++++l  ++ ++++
  AHX11122.1 244 HLfnNNKVYNAMLILSVVPISVSTMLIGCVFNYPAEKLAVVVLISTLTGILYIPLI 299
                 443245699999999********************************999988876 PP

>> ATP_synt_H  ATP synthase subunit H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   1.7   7.1e-06     0.064      28      49 ..      62      83 ..      31      89 .. 0.76
   2 ?    1.5   0.3     0.048   4.3e+02      23      38 ..     231     261 ..     212     268 .. 0.61
   3 ?   -0.7   0.2      0.23   2.1e+03       9      37 ..     262     290 ..     254     296 .. 0.50

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-06
                HHHHHHHHHHHHHHHTCHHTSS CS
  ATP_synt_H 28 lirvlviltavccWlfWlcvYl 49
                l +v++++++++cWl++ ++Yl
  AHX11122.1 62 LPIVILLISCFMCWLVYTVTYL 83
                568899***************9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.048
                 ................TTHHHHHHHHHHHHH CS
  ATP_synt_H  23 g...............enrglirvlviltav 38 
                                 +n+++ + ++il++v
  AHX11122.1 231 LtlslvyldiyylhlfNNNKVYNAMLILSVV 261
                 2222233333344444888899999999987 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.23
                 HHHHHTCSCSSS-S.TTHHHHHHHHHHHH CS
  ATP_synt_H   9 favlgvvatfvvpkgenrglirvlvilta 37 
                  + ++ ++  +v   + ++l  v++i t+
  AHX11122.1 262 PISVSTMLIGCVFNYPAEKLAVVVLISTL 290
                 33343333333334455566666666554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       828  (0.0461822); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2178.02
//
Query:       AHX11123.1  [L=292]
Description: hypothetical protein NHE_0158 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (292 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2185.62
//
Query:       AHX11124.1  [L=424]
Description: peptidase M16 inactive domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-39  136.2   0.0    2.7e-39  135.1   0.0    1.5  1  Peptidase_M16_C  Peptidase M16 inactive domain
    5.7e-39  133.5   0.0    4.7e-38  130.5   0.0    2.0  2  Peptidase_M16    Insulinase (Peptidase family M16)
  ------ inclusion threshold ------
       0.04   12.9   0.3       0.19   10.7   0.0    2.0  2  DDR              Diol dehydratase reactivase ATPase-like doma
      0.095   12.7   0.1        0.3   11.1   0.0    1.9  2  AAA_5            AAA domain (dynein-related subfamily)


Domain annotation for each model (and alignments):
>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.1   0.0   5.9e-43   2.7e-39       1     182 [.     167     342 ..     167     343 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.1 bits;  conditional E-value: 5.9e-43
                      CH-HHHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSHCSGSCTSSSSSGGGSSEEEEEEEESSSSSEEEEEEEEEECT.CTH CS
  Peptidase_M16_C   1 sltredlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaskappakptgepltpatlkkppvvlkkldeeqahlslafegpsk.end 93 
                      ++t++dl +f+ ++Y penm l++ G vd +  + l+ekyf d+k       + +++++ pa +++++++ +++  eq+h+ l+f+g+s+ ++ 
       AHX11124.1 167 NFTKNDLTSFISEHYYPENMMLIVSGGVDINVFLVLAEKYFADMK-----SVDVSKKDPAPAVYQPREYREERKL-EQTHIILGFPGVSYqDSI 254
                      6899*****************************************.....6678888888888999999999999.**************8888 PP

                      TTHHHHHHHHHHHHSSTTSHHHHHHHTTTTSESEEEEEEEEESSCEEEEEEEEEECTTHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
  Peptidase_M16_C  94 eddlalavlntlLgggmesrLytnlrekeglaysvsafndsyrdsglfgisatadpenveevvevilkelrklkkeglteeeleraknq 182
                       +++  ++l  lLg  m+srL++++rek+glays+saf++  + sg++gi+ +adp+++ e+v v+l+el +l ++ lt ee+erak+q
       AHX11124.1 255 AQIYSSKILTILLGASMSSRLFQEVREKRGLAYSISAFHSPAETSGIIGIYSSADPKKLTELVTVVLEELVRLEST-LTMEEIERAKKQ 342
                      9***************************************************************************.**********98 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.5   0.0     1e-41   4.7e-38       5     147 ..      18     160 ..      14     162 .. 0.97
   2 ?    0.6   0.0      0.11   5.1e+02      76     113 ..     305     344 ..     267     355 .. 0.64

  Alignments for each domain:
  == domain 1  score: 130.5 bits;  conditional E-value: 1e-41
                    EE-TSSSEEEEEEEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEEEEEEEGGGHHHHHHHHHHHHHSBTT CS
  Peptidase_M16   5 esdppaktsavglvvdaGSryepkdlnGlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvYyvevlskdlekaldvladvfkapll 100
                     + p + ++++ ++v aGS ye++++nG+AH+lehm+fkgTk+++++++a+ +++lGg++nA t + +t+Yy++vl+++l+k +++l+dv++++ +
     AHX11124.1  18 DNIPGNYSVSIKIWVRAGSNYEQQENNGIAHFLEHMIFKGTKTRTAEQIAKDFDELGGHFNACTGKGYTIYYAKVLAEYLDKGMELLSDVLNNSVF 113
                    56788889**************************************************************************************** PP

                    SHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHTTTSGGGSHSS- CS
  Peptidase_M16 101 eesevererkvvekeveavdaepekvveenlhaaayrekalgrsllg 147
                     + e++re++vv++e+ + ++ p+++++++  ++ y ++++gr++lg
     AHX11124.1 114 PDVELQREKMVVLEEILQTEDTPDDIIFDRFFETIYPDQPYGRPILG 160
                    ********************************************986 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.11
                    EEEEEGGGHHHHHHH.HHHHHH.SBTTSHHHHHHHHHHHH CS
  Peptidase_M16  76 yvevlskdlekaldv.ladvfk.aplleesevererkvve 113
                    y ++++k+l +++ v l + ++ +++l+ +e+er +k+++
     AHX11124.1 305 YSSADPKKLTELVTVvLEELVRlESTLTMEEIERAKKQIK 344
                    4455566666666541555554377999999999888776 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   4.3e-05      0.19     188     255 ..     281     348 ..     260     358 .. 0.86
   2 ?   -0.5   0.1       0.1   4.7e+02      49      74 ..     380     405 ..     372     411 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 4.3e-05
         DDR 188 KkyplakveslfhireEdgtvqFfdkpldpevfarvvllkedelvpleedlslekirsvRreaKekvf 255
                  k  la   s fh   E   +  + +++dp+ ++ +v++  +elv+le+ l++e+i + ++++K+  +
  AHX11124.1 281 EKRGLAYSISAFHSPAETSGIIGIYSSADPKKLTELVTVVLEELVRLESTLTMEEIERAKKQIKSSLL 348
                 46678888899999999999999999**************************************9765 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.1
         DDR  49 kvedikikDllavdtlvpqkvkgglA 74 
                  +++i+++D++a+ +l+ ++ k +lA
  AHX11124.1 380 VINEITVQDVAAIANLMLTEKKVSLA 405
                 56899999999999988887777766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.8e-05       0.3      14      93 ..     274     355 ..     261     365 .. 0.87
   2 ?   -2.8   0.0       1.3   5.6e+03      71     108 ..     381     416 ..     377     420 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.8e-05
                 HHHHHGGGGBS--EEEEE--TT--HHHHH--B--...........--------G-SEEEEESGGG--HHHHHHHHHHHHSSE CS
       AAA_5  14 elaerlaaalnreveyvqltrdtteedlkgrreik..ngttslvdsplvraaregeilvlDEveraesevlnsLlslleerr 93 
                 +l +++ +  +  + + ++++  +++ ++g ++ +  ++ t+lv  +l + +r  ++l ++E+era++++ +sLl+ le ++
  AHX11124.1 274 RLFQEVREKRGLAYSISAFHSPAETSGIIGIYSSAdpKKLTELVTVVLEELVRLESTLTMEEIERAKKQIKSSLLMGLESNE 355
                 56666666667777888899999999999999988999999***********************************999887 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.3
                 EESGGG--HHHHHHHHHHHHSSEEE..-SSSEEE---. CS
       AAA_5  71 lDEveraesevlnsLlslleerrllleeggelvkaknd 108
                 ++E++   ++v+++ + +l e++++l++ g   + +++
  AHX11124.1 381 INEIT--VQDVAAIANLMLTEKKVSLASIGAKDGLPEY 416
                 55666..4888888888999999998887776666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (424 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      594  (0.0331307); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.56u 0.22s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 3216.54
//
Query:       AHX11125.1  [L=183]
Description: ATP-dependent protease HslVU, peptidase subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    9.5e-26   90.5   2.3    3.3e-25   88.7   2.3    1.7  1  Proteasome  Proteasome subunit


Domain annotation for each model (and alignments):
>> Proteasome  Proteasome subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   2.3   1.9e-29   3.3e-25       3     190 .]       2     176 ..       1     176 [. 0.96

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 1.9e-29
                 HS-EEEEEEETTEEEEEEEEEEEETTEEEESSSSTSEEEE.ETTEEEEEEESHHHHHHHHHHHHHHHHHHHHHHSSGTCHHHHHHHHHHHHHHHHHHCT CS
  Proteasome   3 kGttvvGikgkdgvvlaadkratagskllskstveKifki.ddhigvafaGlaaDartlvrraraeaqlyrlrygrpipverlvarvaaklqaytqrsg 100
                 +Gtt++ i+ ++ vv+++d ++t+g+ ++ kst++K+ ++ + +i+ +faG++aDa tl++r++++++ +        ++         ++ +++++++
  AHX11125.1   2 HGTTILSIRKDNKVVIIGDGQVTMGNAVVVKSTAQKVKRLsNGKIISGFAGSTADAFTLFERLESKLEAHP------GQLL--------RACVELAKDW 86 
                 8***************************************99***************************98......5566........777******* PP

                 TTTTSEEEEEEEEETTTEEEEEEEETTSEEEEES.SEEEESTTHHHHHHHHHHHHSTTBSHHHHHHHHHHHHHHHHHHBTTSCSSEEEEEE CS
  Proteasome 101 rrpfgvslliagvdeeggpeLyqidpsGsyieek.davaiGsgseaaktalekeykedltleeavelavkalkealerdklsgknievavi 190
                 r + +++ l a++   ++   + ++ +G++ie++ +++aiGsg ++a +a +++     +  +a+++a++a+k a+  ++++++n++v +i
  AHX11125.1  87 RTDKYLRRLEAMMIVADARGTFILNGAGDVIEPEdNVAAIGSGGNYALAAAKALS-RYADNLDAYQIAESAMKIAAGICVFTNENFTVETI 176
                 *********************************99***************99988.889999*************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1384.67
//
Query:       AHX11126.1  [L=475]
Description: ATP-dependent protease HslVU, ATPase subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.8e-39  134.9   0.1    1.2e-30  106.9   0.1    2.5  2  AAA_2            AAA domain (Cdc48 subfamily)
    3.6e-14   53.3   0.1    6.3e-07   29.9   0.0    3.3  3  AAA              ATPase family associated with various cellul
    3.2e-06   27.2   0.3    0.00033   20.6   0.0    3.1  3  AAA_5            AAA domain (dynein-related subfamily)
    1.6e-05   24.8   1.8    0.00012   22.1   0.0    2.6  2  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    4.9e-05   23.6   0.1     0.0011   19.2   0.0    2.7  2  AAA_22           AAA domain
    0.00084   19.8   0.0     0.0027   18.1   0.0    1.9  2  AAA_16           AAA ATPase domain
    0.00094   19.0   0.5      0.013   15.2   0.0    2.6  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0017   18.1   0.0      0.067   12.9   0.0    2.9  3  Sigma54_activat  Sigma-54 interaction domain
     0.0034   16.8   0.1      0.019   14.4   0.0    2.3  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0038   16.5   0.0       0.16   11.3   0.0    2.4  2  Zeta_toxin       Zeta toxin
  ------ inclusion threshold ------
      0.011   14.8   0.2       0.79    8.8   0.0    2.4  2  MCM              MCM P-loop domain
      0.012   15.7   0.0      0.029   14.5   0.0    1.6  1  AAA_33           AAA domain
      0.015   15.4   0.0      0.057   13.5   0.0    1.9  2  Torsin           Torsin
      0.024   15.2   0.1      0.084   13.4   0.0    2.0  2  AAA_18           AAA domain
      0.026   13.9   0.2       0.12   11.8   0.0    2.0  2  TniB             Bacterial TniB protein
       0.04   13.7   0.1       0.33   10.7   0.0    2.3  2  IstB_IS21        IstB-like ATP binding protein
      0.051   13.1   0.0       0.38   10.2   0.0    2.2  2  AAA_7            P-loop containing dynein motor region
        0.1   12.9   0.1       0.27   11.5   0.0    1.7  2  AAA_28           AAA domain
       0.13   11.7   0.0       0.24   10.8   0.0    1.4  1  IPT              Isopentenyl transferase


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.0   1.4e-08   1.3e-05       5      66 ..      75     136 ..      73     140 .. 0.92
   2 !  106.9   0.1   1.3e-33   1.2e-30      29     171 .]     240     361 ..     214     361 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 1.4e-08
                 -EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---....----THHHHHHHHHTTT-HHH CS
       AAA_2   5 silllgptgvGktelakalaellfvkkekkliradaselle....eeevehlvsrligappgyvga 66 
                 +il++gptgvGkte+a+ +a+l  +    ++i ++a++++e    + +ve+++  l+ ++ + v+ 
  AHX11126.1  75 NILMIGPTGVGKTEIARRVANLSGA----PFIKVEATKFTEvgyvGRDVESIIRDLVDSAVAQVKD 136
                 89*********************96....****************9********999999888765 PP

  == domain 2  score: 106.9 bits;  conditional E-value: 1.3e-33
                 -.......-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTSEEEEETGGG-------------HHHHHHHHHHHH--EE-------EE-TT-EEE CS
       AAA_2  29 v...kkekkliradaselleeeevehlvsrligappgyvgaeegGivllDEidKihpkessgadvSregVqrdLLqileggtltdkqgrkvdtknilfI 124
                 +    k+k++ ++da ++l + eve+l +++ + +++   +  +G+v++DEidKi+++++ + +v regVqrdLL++leg+ + +k+g  v+t++ilf+
  AHX11126.1 240 AgkkFKKKRVKVKDAWKILIDAEVEELFDEDAIVKDALELVTTKGMVFIDEIDKICARSEVRGEVNREGVQRDLLPLLEGTAVVTKYG-VVKTDHILFV 337
                 24445899********************************************************************************.********** PP

                 EEE--TTHHHHTTTS-STTTTSGGG--HHHHHHTT--HHHHTT--EE CS
       AAA_2 125 mtgafgsskisdesrskeeeeekkkeeveeelkkglipEllgRlpei 171
                  +gaf+ +k+sd                       l pEl+gRlp++
  AHX11126.1 338 GSGAFHFAKPSD-----------------------LLPELQGRLPIR 361
                 ************.......................**********86 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.9   0.0   6.7e-10   6.3e-07       1      52 [.      76     129 ..      76     168 .. 0.74
   2 !   19.7   0.0   9.1e-07   0.00085      57     129 ..     276     363 ..     222     366 .. 0.75
   3 ?   -2.6   0.0       7.2   6.8e+03      66      97 ..     418     442 ..     404     450 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.9 bits;  conditional E-value: 6.7e-10
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.STTHH.HHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.yvges.ekkirelfke 52 
                 +l++Gp G+GKT +a+ va+ +g++f++++++++++  yvg   e+ ir+l+++
  AHX11126.1  76 ILMIGPTGVGKTEIARRVANLSGAPFIKVEATKFTEVgYVGRDvESIIRDLVDS 129
                 699********************************4454443302223333333 PP

  == domain 2  score: 19.7 bits;  conditional E-value: 9.1e-07
                 S.....TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS.......SSTEEEEEEESS....GGGSTHHHHSTTSSEEEE CS
         AAA  57 a.....kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk.......eskvivigatnr....pdkldpallrgRfdrkie 129
                 a     ++  +fiDEid+++ +++ + + ++e v+  Ll+ l+g           +++++++g +      p++l p+l  gR+ +++e
  AHX11126.1 276 AlelvtTKGMVFIDEIDKICARSEVRGEVNREGVQRDLLPLLEGTAVVtkygvvkTDHILFVGSGAFhfakPSDLLPELQ-GRLPIRVE 363
                 245555569************998889999999**********9988777788885558888877655455666666666.77766665 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 7.2
                 TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTT CS
         AAA  66 EidalaksrsgseseeeervvnqLlteldgvk 97 
                 E+++++ +r         +++++Ll+e++ ++
  AHX11126.1 418 EVENIGARR-------LHTIMETLLEEINFES 442
                 566666666.......6788888888887555 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   3.5e-07   0.00033       1      37 [.      75     111 ..      75     138 .. 0.90
   2 ?    2.3   0.0      0.16   1.5e+02      58      78 ..     272     295 ..     250     336 .. 0.76
   3 ?   -0.2   0.0         1   9.4e+02      60      98 ..     405     444 ..     378     451 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 3.5e-07
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT-- CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtt 37 
                 ++l++Gp+G+gK+e+a+r+a + ++++  v  t++t+
  AHX11126.1  75 NILMIGPTGVGKTEIARRVANLSGAPFIKVEATKFTE 111
                 689************************9999999987 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.16
                 -------...G-SEEEEESGGG-- CS
       AAA_5  58 plvraar...egeilvlDEverae 78 
                 ++++a +   ++ ++++DE++++ 
  AHX11126.1 272 IVKDALElvtTKGMVFIDEIDKIC 295
                 3334444666999********964 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 1
                 -----G-SEEEEESGGG--.HHHHHHHHHHHHSSEEE..- CS
       AAA_5  60 vraaregeilvlDEverae.sevlnsLlslleerrlllee 98 
                 v a+ e++i+v  Eve++  +    ++ +llee  +   e
  AHX11126.1 405 VSAIAEAAITVNSEVENIGaRRLHTIMETLLEEINFESGE 444
                 4578899999999999999888888899999998877554 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.4      0.49   4.6e+02       6      42 ..     123     162 ..     118     166 .. 0.74
   2 !   22.1   0.0   1.2e-07   0.00012       1      61 [.     367     436 ..     367     440 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.49
                    HHHHHHH...HHHHHHHHSCTTTEEEEEHHHHHHHHHHHT CS
  ClpB_D2-small   6 lkkIvdl...alkklekrlkergvelevtdealdalaekg 42 
                    +++ vd    ++k++++r  +++ e + ++++ldal+ k 
     AHX11126.1 123 IRDLVDSavaQVKDQKRREFAKEAESSAKEKILDALVGKK 162
                    5556666555788888888889999999999999888765 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 1.2e-07
                    SCHHHHHHHHHH...HHHHHHHHSCT.TTEEEEEHHHHHHHHHHHTSB.....TTTBTCCHHHHHHHHTH CS
  ClpB_D2-small   1 LtkeelkkIvdl...alkklekrlke.rgvelevtdealdalaekgyd.....peyGARpLrriiqreie 61 
                    L+  ++++I+++    l k++  l e +gv+le+t++ ++a+ae+++      ++ GAR L +i++  +e
     AHX11126.1 367 LDVGDMTRILTEtesSLLKQYCALLEtEGVSLEFTKDGVSAIAEAAITvnsevENIGARRLHTIMETLLE 436
                    5667999*****999666666666555*******************7622222578**********9987 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.2e-06    0.0011       8      66 ..      76     125 ..      73     161 .. 0.73
   2 ?    1.0   0.0      0.49   4.6e+02      12      51 ..     173     221 ..     173     304 .. 0.51

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.2e-06
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralgl 66 
                 ++ +G++G+GKT  +rr+++           ++++++v++++ t+   + r++ +++ +
  AHX11126.1  76 ILMIGPTGVGKTEIARRVANLS---------GAPFIKVEATKFTEVGYVGRDVESIIRD 125
                 7889*****************9.........************9665555555554443 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.49
      AAA_22  12 GesGtGKTtllrrlleqldeeakaee.........erpevvfvtlpsst 51 
                 G sG+GK  + + + ++lde +  e          ++ ++ ++++p+  
  AHX11126.1 173 GDSGSGKANTRAVFEKKLDEGSLDESeieinirdiPQNSFPTMDVPGMP 221
                 6778888777777777777666555566666655544444444444433 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   2.8e-06    0.0027      24     107 ..      73     162 ..      54     207 .. 0.62
   2 ?   -2.7   0.0         7   6.6e+03      80     123 ..     386     431 ..     371     439 .. 0.42

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 2.8e-06
      AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleeala..........a 107
                 p ++l +G+ GvGK+ ++r++++ l+++   f++ +++++ +++ y+   ++ + r +l+    ++ +++++++++++ e++++           
  AHX11126.1  73 PKNILMIGPTGVGKTEIARRVAN-LSGA--PFIKVEATKF-TEVGYVGrDVESIIR-DLVDSAVAQVKDQKRREFAKEAESSAKekildalvgkK 162
                 47899*****************6.5544..3777777777.333443333333333.44444444444434444444444444455444444441 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 7
      AAA_16  80 ellrqlldeaesaeleawrekleeala..avpelagaeasrllell 123
                 ++++ l++e  s e+  +     +++a    +e++  +a+rl+  +
  AHX11126.1 386 QYCALLETEGVSLEFTKDGVSAIAEAAitVNSEVENIGARRLHTIM 431
                 3333333333333333332222222223333344444445555555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   1.4e-05     0.013       8      66 ..      38     106 ..      32     168 .. 0.66
   2 ?    0.9   0.0      0.35   3.3e+02      79      99 ..     277     297 ..     263     306 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.4e-05
      RuvB_N   8 ey.igqekvkeklkifieaakkreea...l.d.....hvllyGpPGlGkttlakiiakelgvklkitsg 66 
                  + igq+  k+k++i+i+   +r++    l d      +l++Gp G+Gkt +a+ +a+  g+ +    +
  AHX11126.1  38 RFvIGQKLAKKKIAIAIRNRWRRNNVpkpLqDeiipkNILMIGPTGVGKTEIARRVANLSGAPFIKVEA 106
                 55279999*********99999986422222322222689*****************988876544333 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.35
      RuvB_N  79 ltnleekdvlfideihrlsra 99 
                 l  +++k ++fidei ++   
  AHX11126.1 277 LELVTTKGMVFIDEIDKICAR 297
                 556778899******998655 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.0   7.1e-05     0.067      23      60 ..      74     108 ..      61     112 .. 0.85
   2 ?   -0.4   0.0      0.85     8e+02      26      63 ..     170     209 ..     147     213 .. 0.65
   3 ?    0.5   0.0      0.45   4.2e+02      93     106 ..     282     295 ..     276     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 7.1e-05
                      S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTT CS
  Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaa 60 
                       ++l+ G +G+GK+ +ar + + s    +pf++v+ ++
       AHX11126.1  74 KNILMIGPTGVGKTEIARRVANLSG---APFIKVEATK 108
                      689****************998876...8999988766 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.85
                      EEECSTTSSHHHHHHHHHH...HSTTTTS-EEEEETTTS-T CS
  Sigma54_activat  26 litGesGtGKellaraihe...askrkekpfvavncaaipe 63 
                      l  G+sG+GK    ra++e    +   +++ +++n+ +ip+
       AHX11126.1 170 LEGGDSGSGKANT-RAVFEkklDEGSLDESEIEINIRDIPQ 209
                      55799*****865.455552222222355667777777776 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.45
                      TTSEEEEETGGGS- CS
  Sigma54_activat  93 dgGtlfLDeigelp 106
                       +G++f+Dei ++ 
       AHX11126.1 282 TKGMVFIDEIDKIC 295
                      68********9886 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.1       5.6   5.3e+03       5      19 ..      40      54 ..      38      55 .. 0.87
   2 !   14.4   0.0     2e-05     0.019      24      46 ..      75      97 ..      73     140 .. 0.83
   3 ?   -2.1   0.0       2.2   2.1e+03     106     118 ..     282     294 ..     279     298 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 5.6
  Mg_chelatase  5 vkGqeeakraleiaa 19
                  v+Gq+ ak+ + ia+
    AHX11126.1 40 VIGQKLAKKKIAIAI 54
                  89*******999996 PP

  == domain 2  score: 14.4 bits;  conditional E-value: 2e-05
  Mg_chelatase 24 nlllvGppGsGKtmlakrlpsll 46
                  n+l++Gp G GKt +a+r+++l 
    AHX11126.1 75 NILMIGPTGVGKTEIARRVANLS 97
                  9******************9885 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 2.2
  Mg_chelatase 106 hnGvLfLDElpef 118
                   ++G++f+DE+ ++
    AHX11126.1 282 TKGMVFIDEIDKI 294
                   79*******9765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.0   0.00017      0.16      14      91 ..      71     150 ..      56     164 .. 0.70
   2 ?    2.7   0.0     0.071        67      22      42 ..     172     192 ..     169     206 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00017
  Zeta_toxin  14 erPklillgGqpGAGKselaellkdelerqgnvvrldpDdlRel...hPeyeeilkadpkkaselt.qkdaselvekllqea 91 
                   Pk il+ G +G GK+e+a+ +++    +  +++++++++ e     +++e+i+++ +++a++++ ++  +e+++++   a
  AHX11126.1  71 IIPKNILMIGPTGVGKTEIARRVANLS--GAPFIKVEATKFTEVgyvGRDVESIIRDLVDSAVAQVkDQKRREFAKEAESSA 150
                 569********************9987..89999999988877522246677777764444444330344455555555555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.071
  Zeta_toxin  22 gGqpGAGKselaellkdeler 42 
                 gG +G+GK ++ + ++++l++
  AHX11126.1 172 GGDSGSGKANTRAVFEKKLDE 192
                 8****************9963 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0   0.00083      0.79      17      90 ..      31     105 ..      22     124 .. 0.72
   2 ?    3.6   0.1     0.032        30     119     135 ..     280     296 ..     255     304 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00083
                 HHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-...EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS CS
         MCM  17 klvksiapsiyghedvkkaillqlfggvkkkledktklrgdi...nvllvgdpgtaKsqlLkyveklapravytsgk 90 
                 ++v+++ + ++g++  kk i++++    ++++   + l+ +i   n+l++g  g++K+++ ++v++l+  a +++ +
  AHX11126.1  31 EIVSYLDRFVIGQKLAKKKIAIAIRNRWRRNNVP-KPLQDEIipkNILMIGPTGVGKTEIARRVANLS-GAPFIKVE 105
                 6777788888899999999988888877765444.3344444444*******************9654.44454444 PP

  == domain 2  score: 3.6 bits;  conditional E-value: 0.032
                 HTTTSEEEEESGGGSTC CS
         MCM 119 ladkGvcciDefdkmke 135
                 + +kG++ iDe+dk+  
  AHX11126.1 280 VTTKGMVFIDEIDKICA 296
                 5689**********865 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0     3e-05     0.029       2      43 ..      76     120 ..      76     162 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklgavllssdtlrrrlfg...tdqq 43 
                 +l++G+ G+GK+  a+r+++  ga ++   + +++ +g   +d++
  AHX11126.1  76 ILMIGPTGVGKTEIARRVANLSGAPFIKVEATKFTEVGyvgRDVE 120
                 69*****************88887777777744433332223333 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   6.1e-05     0.057      17      75 ..      30      95 ..      21      98 .. 0.81
   2 ?   -2.6   0.0         6   5.7e+03       6      36 ..     294     326 ..     291     331 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 6.1e-05
                HHHHHHHHHH--S-HHHHHHHHHHHHHHHT-SS-SS-E.......EEEEEE-TTSSHHHHHHHHHH CS
      Torsin 17 eeLekdlekklfGqhlvkklvvksvkaylenekpkkpL.......vlsfhGwtGtGknfvaeiiae 75
                +e+ + l++ ++Gq l+kk +  +++  ++++++ kpL        + + G tG Gk  +a+ +a+
  AHX11126.1 30 KEIVSYLDRFVIGQKLAKKKIAIAIRNRWRRNNVPKPLqdeiipkNILMIGPTGVGKTEIARRVAN 95
                56677899*****************************94443333366789999999988887775 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6
                 XXXXXX...---HHHHHHHHHHH--S-HHHHHH CS
      Torsin   6 cCeekri..sanleeLekdlekklfGqhlvkkl 36 
                 +C  +++  ++n e++++dl   l G  +v+k 
  AHX11126.1 294 ICARSEVrgEVNREGVQRDLLPLLEGTAVVTKY 326
                 566544422568889999999999999888764 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   8.9e-05     0.084       1      25 [.      76     113 ..      76     172 .. 0.55
   2 ?   -1.7   0.0       4.3   4.1e+03      47      47 ..     223     223 ..     170     275 .. 0.49

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 8.9e-05
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.............g 25 
                 Il  G+ GvGKt++a++++++ g              g
  AHX11126.1  76 ILMIGPTGVGKTEIARRVANLSGApfikveatkftevG 113
                 7889**************99863344433422223331 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 4.3
      AAA_18  47 d 47 
                  
  AHX11126.1 223 T 223
                 1 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00013      0.12      35      97 ..      73     137 ..      62     162 .. 0.70
   2 ?   -1.1   0.1       1.1   1.1e+03     117     133 ..     279     296 ..     264     305 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00013
        TniB  35 mpnlllvGdsnnGKtmivekFarlhppe..kdedaekvpvlvvqappkpdekrlyaaiLealgap 97 
                 ++n+l++G++ +GKt i+++ a+l  +   k e ++  +v +v    ++  ++l ++ +++++ +
  AHX11126.1  73 PKNILMIGPTGVGKTEIARRVANLSGAPfiKVEATKFTEVGYVGRDVESIIRDLVDSAVAQVKDQ 137
                 589******************99885541133444445777777777777777777666666655 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.1
        TniB 117 elkvr.vLiiDEihnlla 133
                  + ++ ++ iDEi+++ a
  AHX11126.1 279 LVTTKgMVFIDEIDKICA 296
                 555443888*****9986 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00035      0.33      48      66 ..      74      92 ..      67     110 .. 0.89
   2 ?   -0.4   0.0      0.89   8.4e+02      11      61 ..     132     180 ..     124     188 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00035
   IstB_IS21 48 enivllGpsGvGKshlaia 66
                +ni+++Gp+GvGK+ +a  
  AHX11126.1 74 KNILMIGPTGVGKTEIARR 92
                69************99965 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.89
   IstB_IS21  11 aklpaqktledidfraarsldkrkvkeLatlsfiekkenivllGpsGvGKs 61 
                 a+++ qk   +++ +a+ s++++++++L++ + +e+ e  +  G sG GK+
  AHX11126.1 132 AQVKDQKRR-EFAKEAESSAKEKILDALVGKK-VEDDEEDLEGGDSGSGKA 180
                 555555555.6777788889999999999887.555555567899999996 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00041      0.38      34      54 ..      74      94 ..      70     111 .. 0.85
   2 ?   -0.4   0.0      0.75   7.1e+02      33      70 ..     166     203 ..     151     211 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00041
       AAA_7 34 kpvllvGptGtGKtviikdll 54
                k++l++GptG+GKt i++++ 
  AHX11126.1 74 KNILMIGPTGVGKTEIARRVA 94
                799************998865 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.75
       AAA_7  33 kkpvllvGptGtGKtviikdllkkldkekylsltinfs 70 
                 + + l  G++G+GK  +   + kkld+ ++    i+++
  AHX11126.1 166 DEEDLEGGDSGSGKANTRAVFEKKLDEGSLDESEIEIN 203
                 55556679******999999999999888777777665 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.27       2      69 ..      76     143 ..      75     156 .. 0.74
   2 ?   -2.7   0.0       6.7   6.3e+03     136     149 ..     426     439 ..     399     460 .. 0.46

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
      AAA_28   2 ivitGgestGKTtlleaLaar.gypvvpEaareileeklakgedalpwv.edllafaervleeqleeeaa 69 
                 i ++G+ + GKT ++++ a+  g p ++  a++++e ++  +    ++  +dl++ a ++++ q+++e a
  AHX11126.1  76 ILMIGPTGVGKTEIARRVANLsGAPFIKVEATKFTEVGYVGRDV--ESIiRDLVDSAVAQVKDQKRREFA 143
                 899****************9889999988889999888866554..444467777776666666665533 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 6.7
      AAA_28 136 aiderlrealrelg 149
                 +++++++ +l+e++
  AHX11126.1 426 RLHTIMETLLEEIN 439
                 22222222222222 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00025      0.24       5      32 ..      77     104 ..      73     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00025
         IPT   5 lifGatttGKtaeaiklaketgapvivl 32 
                 l+ G+t++GKt+ a ++a+  gap i +
  AHX11126.1  77 LMIGPTGVGKTEIARRVANLSGAPFIKV 104
                 889*********************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (475 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      611  (0.0340789); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3234.36
//
Query:       AHX11127.1  [L=224]
Description: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      4e-53  180.4   0.0    4.5e-53  180.3   0.0    1.0  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    2.5e-11   44.2   0.0    2.8e-11   44.0   0.0    1.1  1  NTP_transf_3     MobA-like NTP transferase domain
    7.5e-05   22.4   0.0    8.7e-05   22.2   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase


Domain annotation for each model (and alignments):
>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.3   0.0   7.5e-57   4.5e-53       1     219 [.       4     223 ..       4     224 .] 0.94

  Alignments for each domain:
  == domain 1  score: 180.3 bits;  conditional E-value: 7.5e-57
                 EEEEEECTTSSCTT.-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGG...CCEEEEE--SSHHHHHHHHHHTTSSTT.SE CS
        IspD   1 vvvvipAAGsGkRm.kaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllld...ksiqlvaGGdeRaesVlnglkalegea.kf 94 
                 ++vvi+A GsG+Rm  +g pKq+l  +g+++l+ht++a+la++++++i +vv++ +  + +++l     + +   + G++RaesV+ gl  l+ ++ ++
  AHX11127.1   4 IAVVIVAGGSGSRMlSSGSPKQYLRFSGKAVLQHTIEAFLAHHEISRIQLVVNPLHDVYYSSILEIfdrRMVSSSKAGSTRAESVFSGLMDLKRHEpDY 102
                 689**********95689***********************************98877777777665568888899******************999** PP

                 EEE--TT-TT--HHHHHHHHHHHHTTCSEEEEEEE-SSEEEEEETTTBEEEEETGTTEEEEEEEEEEEHHHHHHHHHHHHHCT---SSHHHHHHHTT-- CS
        IspD  95 VLvHDaARpllkaadiaellaaaeqstqgailalpvkDtikrveadglvaetedRegLwaaqtPqgFrvdlllaahakgeqegaeitDdaslvekiGls 193
                 VL+HDa Rpl++   i+++++ + ++ qg+++a+ v+Dt+ +      v +  +Re+L   qtPqgF ++++l+a++++   + ++tDd+ l+e+ G +
  AHX11127.1 103 VLIHDAVRPLVSLGLIDAVIKHLLNGAQGVVPAIEVRDTVVKRR-SDYVEGVLEREELVFLQTPQGFIFKEILDAYTAS---SGSYTDDVTLAETSGIK 197
                 ***************************************98887.789*****************************99...678************** PP

                 EEEEE--TTG----SHHHHHHHHHHH CS
        IspD 194 vkvVeGeednlKittpeDlalAeail 219
                 vk+++G+++n+Kit p Dl +A  +l
  AHX11127.1 198 VKLIPGDQKNFKITFPFDLEVATLLL 223
                 *********************98776 PP

>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.0   0.0   4.7e-15   2.8e-11       1     127 [.       6     140 ..       6     185 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.0 bits;  conditional E-value: 4.7e-15
                   EEEEEESS-TTT...TTTHHHHCCCCCCHHHHHHHHHCTT..-CEEEEECSH.CHHHH..HHTTCTS-EEE-TTSS-SHHHHHHHHHHHH...SSSC CS
  NTP_transf_3   1 aviLAGGrSsRm...ggdKallplggkpllervldalraa.gvdevvvvggd.eevla..alarlgvrvvededpgkgplaslaaalraaa..dada 88 
                   +vi AGG +sRm   g++K+ l++ gk +l+++++a+ a+ +++++ +v+++ ++v+    l+ ++ r+v+ +++g   ++s+ ++l  ++  + d+
    AHX11127.1   6 VVIVAGGSGSRMlssGSPKQYLRFSGKAVLQHTIEAFLAHhEISRIQLVVNPlHDVYYssILEIFDRRMVSSSKAGSTRAESVFSGLMDLKrhEPDY 102
                   69**********88778*******************999957********99866553336788899********************8866558899 PP

                   EEEEETT-TT--HHHHHHHHHCHHHHTSSEEEEESSSEE CS
  NTP_transf_3  89 vlvlacDmPlltpelverllaaaaasgadvvvptyeger 127
                   vl+  +  Pl++  l++++++++  +ga+ vvp+ e + 
    AHX11127.1 103 VLIHDAVRPLVSLGLIDAVIKHLL-NGAQGVVPAIEVRD 140
                   99999999**************95.78888888877554 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   1.5e-08   8.7e-05       3      65 ..       7      67 ..       5     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 1.5e-08
                     EEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHH.TT-SEEEEEEETTTHHHHHHHH CS
  NTP_transferase  3 vILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlan.sgieeiivvltqehsflveeql 65
                     vI aGGsG+R+  L++ ++k+ + + gk  ++q+t+++ ++ ++i +i +v+++ h   + + l
       AHX11127.1  7 VIVAGGSGSRM--LSSGSPKQYLRFSGK-AVLQHTIEAFLAhHEISRIQLVVNPLHDVYYSSIL 67
                     9*********9..9**************.********987769**********99887766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (224 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       318  (0.0177366); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1713.15
//
Query:       AHX11128.1  [L=347]
Description: dihydroorotate dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      8e-88  294.4   0.2    9.2e-88  294.3   0.2    1.0  1  DHO_dh    Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
      0.033   13.5   3.1      0.058   12.7   3.1    1.4  1  Spiralin  Spiralin


Domain annotation for each model (and alignments):
>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  294.3   0.2     1e-91   9.2e-88       2     294 ..      42     330 ..      41     331 .. 0.96

  Alignments for each domain:
  == domain 1  score: 294.3 bits;  conditional E-value: 1e-91
                 G-EEETTEEESSSEEE-TTSSTTSSSHHHHHCTTSSEEEEEEE-SS-B--S-S--EEEETTCTEEEE---S-BS-HHHHHHHHHHHHHHHHCC.CEEEE CS
      DHO_dh   2 latkvlglkfknpiglAaGfdkegeeilkllklgfgaieigsvtpkpqeGnpkPrvfrlkedrsvlNslGlnneGldavlekllkrrkeqeekkelgin 100
                 l+ +v+gl fknp+g+AaGfdk++e+++ l   gfg++e+g+vt+kpq+GnpkPr+frl+edr+v+N+lG+nn+G+++ l++l k + ++   + +g+n
  AHX11128.1  42 LENEVCGLSFKNPVGIAAGFDKNAECVNPLSRTGFGFLELGTVTLKPQKGNPKPRLFRLPEDRAVINRLGFNNKGVEYFLKRLVKAKYNRS-LPPIGVN 139
                 8899*******************************************************************************99886655.489**** PP

                 EEE-TTSS.HHHHHHHHHHHHGGGESEEEEES-SCTCCTSCCCGCHHHHHHHHHHHHHHHH.SSEEEEEE-SSSSHHHHHHHHHHHHHHTECEEEE... CS
      DHO_dh 101 lskakktenavddyvevvrkigpfadilelNvSsPntpglrdlqekeelkaillkvvkevs.kvpvlvKlaPdltdeekkdiadvllelkldgiivtNt 198
                 ++k+ ++ +a+ dy+ ++++++++ad++ lN+SsPnt+ lrd+q+ e l++ l++v+++v   +p+++K+aPdltde+k di+++++++k++giiv+Nt
  AHX11128.1 140 IGKNATSLDAISDYARLAKRVSKVADYVTLNISSPNTAKLRDMQKIEILQQLLVSVKAAVVeGMPIFIKVAPDLTDEAKVDIMQLAVKQKVTGIIVANT 238
                 *********************************************************9987379*********************************** PP

                 BSEE--CTTCCGCCCCTTSSEEEEEGGGHHHHHHHHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCHHHHHHHHHHHH CS
      DHO_dh 199 tvqrlaidlkseknvkanktGGlsGkalkdialkvirelykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpkiakkikkeleel 294
                 t+     +lks+ +v+    GGlsG++l ++++ ++re+yk+  +++  Ig+GG++  e a+ ki+ GA+l+qvyta++++g  + ++ikk+l+++
  AHX11128.1 239 TIGCR-EKLKSKCKVE---YGGLSGAPLFELSTTLLREMYKYAGGRLVFIGCGGVSDVETAYIKIRNGATLIQVYTAFTYQGFGLLNEIKKGLAQR 330
                 98776.7899866666...8************************************************************************9875 PP

>> Spiralin  Spiralin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   3.1   6.5e-06     0.058     100     165 ..     182     246 ..     138     256 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-06
    Spiralin 100 agkvevyvqitpakdktvviGksgyikvtlpkasevkkvdisdvtvpeqtveikvadpkavtkdel 165
                   k+e+  q+  +   +vv G   +ikv+ p  ++  kvdi +++v++++ +i va+++   +++l
  AHX11128.1 182 MQKIEILQQLLVSVKAAVVEGMPIFIKVA-PDLTDEAKVDIMQLAVKQKVTGIIVANTTIGCREKL 246
                 4689999999999999************7.7778999*******************9987766666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (347 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2683.47
//
Query:       AHX11129.1  [L=399]
Description: EPSP synthase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-38  130.8   0.1      7e-38  130.4   0.1    1.1  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.4   0.1   3.9e-42     7e-38      32     400 ..       2     370 ..       1     375 [. 0.83

  Alignments for each domain:
  == domain 1  score: 130.4 bits;  conditional E-value: 3.9e-42
                    SSEEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHHHTT-GGGGGGHHHHHHHHSEESSEEEEE-SBTTCGS--HHHHH CS
  EPSP_synthase  32 gestitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeelvldlgnsgtalrlLtallalasgevvLtGdesirkRPidrlld 127
                    g+sti+    s+ + s++ +l++Lg+ei+++++   +v   g  + ++ap  +vl++gns +a+ lL++++a  s+++++tG          + ++
     AHX11129.1   2 GKSTISPSFISDSTVSTMCCLQHLGVEIKRISDSRIEVYGVG-VRGLSAP-TDVLNIGNSRIAMHLLLGVVASYSFQTIITGYGHFLDKFKIKGVK 95 
                    6789999999999******************99888888888.7778888.7******************************88777777777899 PP

                    HHHHTT-EEEEETTEEEEEESEETSS-BEEEEE.TSSTTHHHHHHHHHHHTTSBSEEEEES-TTHHHHHHHHHHHHHTT-EEEETTSSE..EEEEE CS
  EPSP_synthase 128 aLrqlGaeieveegenkaplkvkglklkgveik.aevsSqqvtsllllaallaegtteleelasepsiddtlkmlkkfgikietsgtee..sitvk 220
                     +  +G+ei       ++p +vkg      +i+ +e s  q++s+ll+a+l ++gtt+++e + + s ++t+ mlk++g++i+  +++e  ++t+ 
     AHX11129.1  96 HFSDIGIEIT----SCTLPTIVKGNDYCVPHIHiLEHSCSQIKSALLMAGLNTKGTTTIVE-PFSGSTNHTELMLKHLGADITIIRSKEntKTTIC 186
                    *********9....57889999**66665555526889999********************.78889************99887554443389999 PP

                    --SSB--EEEE--B-HHHHHHHHHHHHHTT-.EEEEES--GGGGHHH..HHHHHHHHTTEEEE........EESTSEEEEEET...TS--BEEEEE CS
  EPSP_synthase 221 GkeklpgteyvvegDassAayflvaAaitgg.evtvenvginslqGdiealdeilekmgaeit........qeedasivvgps...glklkdvdie 304
                    G ++l  ++++++gD+s + ++++aA++ +g e+t+e++ +n  +  +++++ il++m+a+i+         ++  si v++    g+++k+ di 
     AHX11129.1 187 GIPELRPQDIIIPGDPSITLFLVAAATLIPGsEITIEGICLNEDR--LRVYR-ILREMSADINttisgknlGNKIGSINVKSArlnGVTIKESDI- 278
                    ****9999*************************************..67777.888888888855556554333344444444333333333344. PP

                    BGSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEEETTEEEEEEEEE.EB-EEEE-TTSTTTTHHHHHHHHHSBSEEEE CS
  EPSP_synthase 305 tlpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaeveeeedgliiipaekqlkgaevesydDhRiamalalaglvaegevei 400
                      +d + +l  l + a+g+++ie+ + l  k++ +l+ +++ ++ lGa +e+++  ++i++ +    g  +++  D  ++  l+l g v++++++ 
     AHX11129.1 279 -SIDNFQILLFLLCTANGKSSIENNKGL--KISSKLHKFIEIMQELGAIIEVTDTSINIEGTTL-DGGKSINARYDYLLGNILILSGFVSRKPITM 370
                    .4999999****************9987..799********************87877666554.4556799999************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (399 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3154.76
//
Query:       AHX11130.1  [L=65]
Description: hypothetical protein NHE_0165 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (65 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       179  (0.00998383); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 562.96
//
Query:       AHX11131.1  [L=44]
Description: hypothetical protein NHE_0166 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      227  (0.0126611); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.34
# Mc/sec: 384.78
//
Query:       AHX11132.1  [L=947]
Description: asmA-like region family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-08   33.9   5.0    3.8e-07   29.9   0.4    4.0  3  AsmA_2    AsmA-like C-terminal region
    0.00017   21.2   0.4    0.00017   21.2   0.4    5.3  5  AsmA_1    AsmA-like C-terminal region


Domain annotation for each model (and alignments):
>> AsmA_2  AsmA-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    2.9   0.3    0.0076        68      13      64 ..     275     321 ..     258     510 .. 0.82
   2 ?   -1.3   0.0      0.15   1.3e+03      39      66 ..     476     504 ..     451     531 .. 0.59
   3 !   29.9   0.4   4.2e-11   3.8e-07      12     220 ..     719     916 ..     707     928 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.0076
      AsmA_2  13 eglrldnlrlrspggklsgsgswstkggaartnldlkldgvdlgallkrlgl 64 
                 e+l+l+n++++++g  + g+  +    g   ++l +k+++  +g++lk +g 
  AHX11132.1 275 ENLELNNVKIKIDGTEFRGRLLLKD--G---LSLEGKIENLVAGDILKYWGN 321
                 5788889999999888666655555..3...788888888888888888883 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.15
      AsmA_2  39 ggaa.rtnldlkldgvdlgallkrlglae 66 
                 +++  +t ++ k d+ ++++++k+++++ 
  AHX11132.1 476 ATQEiDTVINIKADNIQAARFYKAFHIEN 504
                 34333677777777777777777777654 PP

  == domain 3  score: 29.9 bits;  conditional E-value: 4.2e-11
      AsmA_2  12 deglrldnlrlrspggklsgsgswstk...ggaar..tnldlkldgvdlgallkrlglaevl.gGkgslelnlswqgaplspdlssLsGdlsleledgq 104
                 +++++++nl+l++ +g  s+sg  s +      ar   +   ++d+ ++g+llk lg ++ + gG+g l++      ++++ +      ++ l++e+  
  AHX11132.1 719 KNEISMNNLSLTLQEGDGSLSGIFSDDsilR--ARfsKDGGINVDSTNVGTLLKGLGFKSGIiGGRGALHMG----TKNMRTN------SGVLKIENFY 805
                 6799*******************99985541..34113556799*************888666998876655....8888877......8999999*** PP

      AsmA_2 105 ilgvsll.rdlgllkltldfrdlfgeglafddikgtftienGvvttkdfklkgpaaavtvsGtvdldtetldlnvvvvppisaslavvaalainlaala 202
                 i++ + l r l+l++l   ++ l+geg++fd++  +f++ + v+ +++ +l+   ++++v G +++ +e+l l+ +vvp    +  +  ++       +
  AHX11132.1 806 IQDAPILaRILSLASLNGIMNILNGEGIFFDRFFSEFKYADDVFYISESWLEATPIGLSVMGILSIPEEKLILHGSVVPLYRINQLISKMP------II 898
                 ***77333444555578899********************************************************999554433333333......34 PP

      AsmA_2 203 aqkllsddlekiaaleyr 220
                 +++l++    +++a ey+
  AHX11132.1 899 GTLLTGGRNRGVIAAEYT 916
                 555555555555555554 PP

>> AsmA_1  AsmA-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0      0.93   8.3e+03     101     113 ..     151     163 ..     130     172 .. 0.67
   2 !    2.6   0.1    0.0091        81     120     147 ..     214     241 ..     209     258 .. 0.86
   3 ?    1.2   0.3     0.025   2.2e+02     101     148 ..     336     383 ..     332     400 .. 0.86
   4 ?   -0.0   0.0     0.057   5.1e+02     101     127 ..     498     524 ..     477     536 .. 0.68
   5 !   21.2   0.4   1.9e-08   0.00017      34     176 ..     768     906 ..     739     937 .. 0.84

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 0.93
      AsmA_1 101 kGykikngkinfk 113
                 +Gy++++g i +k
  AHX11132.1 151 NGYTVSEGFIRIK 163
                 5777777777665 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.0091
      AsmA_1 120 viekiklkgdsidiegkGiielkkkkld 147
                  +++i+++ ds ++ g  +++l++kk++
  AHX11132.1 214 GLSNIDISNDSFTFSGYAVLNLNEKKIQ 241
                 5899**********************97 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.025
      AsmA_1 101 kGykikngkinfkikkdllviekiklkgdsidiegkGiielkkkkldl 148
                 +G  ik++ i+f+ k   l ie++ l+g ++ i+    ++++k+ +d+
  AHX11132.1 336 QGGIIKQADIKFESKSGDLKIEDAILEGVKARIAITEPADIEKRFIDV 383
                 78889************************9999988888888887776 PP

  == domain 4  score: -0.0 bits;  conditional E-value: 0.057
      AsmA_1 101 kGykikngkinfkikkdllviekiklk 127
                 k ++i+ng++++ki+++  ++ +  l+
  AHX11132.1 498 KAFHIENGSMELKITNNDAAMRATLLS 524
                 557778888888877776666655553 PP

  == domain 5  score: 21.2 bits;  conditional E-value: 1.9e-08
      AsmA_1  34 flnkllkkdilkkgrfelslklee.evfkgeikiqntilknlkilqnllafidtipsLltfksPgfskkGykikngkinfkikkdllviekiklkgdsi 131
                 +l+ l  k+ + +gr  l++ +++  + +g +ki+n ++++  il ++l++     sL  + +  ++ +G+  +    +fk+ +d+ +i++  l+++ i
  AHX11132.1 768 LLKGLGFKSGIIGGRGALHMGTKNmRTNSGVLKIENFYIQDAPILARILSLA----SLNGIMN-ILNGEGIFFDRFFSEFKYADDVFYISESWLEATPI 861
                 45555566777888888987776548999**************999999874....4444443.4899******************************* PP

      AsmA_1 132 diegkGiielkkkkldlklqlktlkslssilskiPllgyillGkd 176
                  +   Gi+++ ++kl l+ ++  l ++ + +sk+P++g +l G  
  AHX11132.1 862 GLSVMGILSIPEEKLILHGSVVPLYRINQLISKMPIIGTLLTGGR 906
                 ****************************************99964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (947 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       563  (0.0314016); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.71u 0.29s 00:00:01.00 Elapsed: 00:00:00.44
# Mc/sec: 6511.31
//
Query:       AHX11133.1  [L=74]
Description: putative multiple resistance and pH regulation protein F [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.1e-07   32.1   4.0    1.1e-07   32.1   4.0    1.6  2  MrpF_PhaF  Multiple resistance and pH regulation protein F (M
  ------ inclusion threshold ------
      0.035   14.1   2.0       0.04   13.9   2.0    1.1  1  DUF1304    Protein of unknown function (DUF1304)


Domain annotation for each model (and alignments):
>> MrpF_PhaF  Multiple resistance and pH regulation protein F (MrpF / PhaF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.1      0.36   3.2e+03      19      23 ..       4       8 ..       1      13 [. 0.40
   2 !   32.1   4.0   1.2e-11   1.1e-07       4      52 ..      18      66 ..      17      67 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.36
   MrpF_PhaF 19 allai 23
                +ll++
  AHX11133.1  4 LLLGV 8 
                22222 PP

  == domain 2  score: 32.1 bits;  conditional E-value: 1.2e-11
   MrpF_PhaF  4 vvAlDllgtllvallallailtgrpayldvalvlAllgFvgtvafarfl 52
                ++A++ l+t ++ l +l+  lt ++  +d+alv++l +F+g va++ f+
  AHX11133.1 18 ILAANSLATHAMILACLYPNLTVDSNSIDIALVYSLTAFIGLVAVTSFV 66
                8********************************************9996 PP

>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   2.0   4.4e-06      0.04      54     109 ..       2      62 ..       1      63 [. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4.4e-06
     DUF1304  54 agliwgl.ll.gseavglalvlfflgcvvvaglygaltask...killvQglpallAlvll 109
                 a+l++g+ ++ ++++  la+  + +  +++a ly  lt+++    i+lv +l a+++lv++
  AHX11133.1   2 AVLLLGViFFsEKHSKILAANSLATHAMILACLYPNLTVDSnsiDIALVYSLTAFIGLVAV 62 
                 577888844444555566777788889************665577**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (74 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 563.05
//
Query:       AHX11134.1  [L=444]
Description: UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-19   69.1   0.0    7.8e-19   68.6   0.0    1.2  1  NTP_transf_3     MobA-like NTP transferase domain
    8.3e-17   60.2  15.7    0.00013   21.6   1.3    4.4  4  Hexapep          Bacterial transferase hexapeptide (six repea
    5.4e-09   36.0   0.0    7.6e-09   35.5   0.0    1.2  1  NTP_transferase  Nucleotidyl transferase
    8.6e-07   28.9   0.0    1.7e-06   28.0   0.0    1.4  1  IspD             2-C-methyl-D-erythritol 4-phosphate cytidyly
    1.5e-05   24.3   0.0    0.00012   21.3   0.0    2.2  2  CofC             Guanylyl transferase CofC like
     0.0053   16.5  15.0       0.15   11.9   0.0    5.1  6  Hexapep_2        Hexapeptide repeat of succinyl-transferase
  ------ inclusion threshold ------
      0.011   14.8   0.0      0.021   13.8   0.0    1.4  1  Fucokinase       L-fucokinase


Domain annotation for each model (and alignments):
>> NTP_transf_3  MobA-like NTP transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.6   0.0   3.1e-22   7.8e-19       1     117 [.      22     138 ..      22     181 .. 0.88

  Alignments for each domain:
  == domain 1  score: 68.6 bits;  conditional E-value: 3.1e-22
                   EEEEEESS-TTTTT..THHHHCCCCCCHHHHHHHHHCTT.-CEEEEECSHCHHHHHHTTCTS-EEE-TTSS-SHHHHHHHHHHHH.SSSCEEEEETT CS
  NTP_transf_3   1 aviLAGGrSsRmgg..dKallplggkpllervldalraagvdevvvvggdeevlaalarlgvrvvededpgkgplaslaaalraaadadavlvlacD 95 
                   a+iLA+G+SsRm++  +K   ++gg  l+ + l  l+++g++e v+v+g++    ++ +  vr v +++  kg+++++++al ++ ++  vl+l +D
    AHX11134.1  22 ALILAAGNSSRMNSqlPKVVHRVGGLELINHNLLLLQELGFEEAVMVCGPQLDFVDVTHISVRKVFQRE-KKGTAHAVKCALPEL-HSRNVLILYGD 116
                   79***********88********************************9997655568888999999985.8*************9.9********** PP

                   -TT--HHHHHHHHHCHHHHTSS CS
  NTP_transf_3  96 mPlltpelverllaaaaasgad 117
                   +Pl+++ ++e+ll++ ++ +a 
    AHX11134.1 117 VPLISKGTIEALLESQEKYDAT 138
                   **************97655443 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00024      0.62       1      34 [.     277     310 ..     277     312 .. 0.88
   2 !   21.6   1.3     5e-08   0.00013       4      35 ..     315     346 ..     312     347 .. 0.94
   3 !   18.1   1.8   6.4e-07    0.0016       1      35 [.     347     380 ..     347     381 .. 0.94
   4 !   18.6   0.2   4.3e-07    0.0011       1      35 [.     389     423 ..     389     424 .. 0.96

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00024
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEE CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvi 34 
                 +t I+s+v+++p++++ ++Vk+ +++ I +++ +
  AHX11134.1 277 DTYIESDVIVHPNVIFFPGVKVFRGAEILPFSLL 310
                 589*******************999999888866 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 5e-08
                 EETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   4 IGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                 IGs +++gpfa i+g   IG n++Ig++v ++
  AHX11134.1 315 IGSAAKVGPFARIRGSSDIGGNAVIGNFVEVK 346
                 9****************************997 PP

  == domain 3  score: 18.1 bits;  conditional E-value: 6.4e-07
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                 +++IG++v++ + ++i g++ IGd + Ig g+vi 
  AHX11134.1 347 NSTIGQGVKVKHLSYI-GDASIGDQTNIGGGTVIC 380
                 579*************.99**************96 PP

  == domain 4  score: 18.6 bits;  conditional E-value: 4.3e-07
                 TEEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   1 stvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                 +t+I ++++Ig + +i ++V I+  ++ +ag++i+
  AHX11134.1 389 HTQIDKKCFIGGNNTIVAPVRIHAEARTAAGSTIT 423
                 68999*****************************8 PP

>> NTP_transferase  Nucleotidyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0     3e-12   7.6e-09       2     218 ..      22     225 ..      21     242 .. 0.83

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3e-12
                      EEEE--S--GGGTTCCTTSSGGGSEETTETETTHHHHHHHHHTT-SEEEEEEETTTHHHHHHHHTTSGGGTSEEEEEEESS--BGGHHHHHTHH CS
  NTP_transferase   2 avILaGGsGtRLwPLtrtlakklvpvlgkerliqatlsrlansgieeiivvltqehsflveeqlkegskfgvevlialepegkgtAdAvalaae 95 
                      a+ILa G+ +R+    +++ +k v+ +g+  li++ l  l + g+ee ++v+ ++  f   ++++  +        ++++e+kgtA+Av+ a+ 
       AHX11134.1  22 ALILAAGNSSRM----NSQLPKVVHRVGGLELINHNLLLLQELGFEEAVMVCGPQLDFVDVTHISVRK--------VFQREKKGTAHAVKCALP 103
                      79*********9....6899*****99999***************************99999988554........789*************** PP

                      HHTTSSE..EEEEETTEE.EEST.THHHHHHHHHTHSSTTSEEEEEEESS-CTTSEEEEECTTSBEEEEECS-SSHSH....CSEECCSEEEEE CS
  NTP_transferase  96 lledeksdelvlvLggDh.likd.ayeeavkkaiekaakgtvtfgivpveeateyGvieadeegrverfvEKPkeaka....selassGiYvfn 183
                       l+ ++    vl+L gD+ li++ ++e+++++ ++++a  t++ ++v +  ++eyG   + e g+v r++E  + +       ++a+sGi   +
       AHX11134.1 104 ELHSRN----VLILYGDVpLISKgTIEALLESQEKYDA--TLLGFPVMD-SSSEYGRLMITE-GKVSRIIEYSELEGEqkqvLNFANSGILCID 189
                      ***888....8******855555699999999999999..666666655.5789**888887.455555554444333333589********** PP

                      TTHHHHHHH.CCHHHTTSSCHHHHHHHHHHHTTEEE CS
  NTP_transferase 184 sevllflak.dleelkrgedeitdilpkaleegkva 218
                       + l++ ++   +  ++ge  +td+++ + +++++ 
       AHX11134.1 190 VKLLKEYISlVDASNRQGEYYLTDVVNLMARDSRNV 225
                      ****99999888888889999999999998887665 PP

>> IspD  2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0   6.5e-10   1.7e-06       3     133 ..      22     147 ..      20     163 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 6.5e-10
                 EEEECTTSSCTT-SSS-GGGSEETTEEHHHHHHHHHHCTTTEEEEEEEE-GGGHHHHHHHHGGCCEEEEE--SSHHHHHHHHHHTTSSTTSEEEE--TT CS
        IspD   3 vvipAAGsGkRmkaglpKqflelkgqtllehtvdallaskavdkivvvvseddteefeqllldksiqlvaGGdeRaesVlnglkalegeakfVLvHDaA 101
                 ++i AAG+ +Rm+++lpK    + g  l++h +  l++ +  + ++v  ++ d+  +++++  k  q  + G   a++V+ +l  l+     VL+  + 
  AHX11134.1  22 ALILAAGNSSRMNSQLPKVVHRVGGLELINHNLLLLQELGFEEAVMVCGPQLDFVDVTHISVRKVFQREKKG--TAHAVKCALPELHSR--NVLILYGD 116
                 799**********************************************************99855555555..4799******99887..78888999 PP

                 -TT--HHHHHHHHHHHHTTCSEEEEEEE-SSE CS
        IspD 102 RpllkaadiaellaaaeqstqgailalpvkDt 133
                  pl+++ +i++ll+ +e+ + +++l  pv D+
  AHX11134.1 117 VPLISKGTIEALLESQEK-YDATLLGFPVMDS 147
                 9*************9997.**********997 PP

>> CofC  Guanylyl transferase CofC like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.3   0.0   4.7e-08   0.00012      55     118 ..      75     137 ..      48     141 .. 0.83
   2 ?   -0.0   0.0      0.16   4.2e+02      62     122 ..     224     288 ..     191     290 .. 0.73

  Alignments for each domain:
  == domain 1  score: 21.3 bits;  conditional E-value: 4.7e-08
        CofC  55 vleyaldelgvevvkekekdlntavekafeeieekeviiipsdiPlikkedvkdllelekradv 118
                  ++  +     +v + ++k+   av+ a+ e    +v+i+  d+Pli+k +++ lle ++++d 
  AHX11134.1  75 FVDVTH-ISVRKVFQREKKGTAHAVKCALPELHSRNVLILYGDVPLISKGTIEALLESQEKYDA 137
                 555554.333467777789*******************************************96 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.16
        CofC  62 elgvevvkek.ekdlnta..veka..feeieekeviiipsdiPlikkedvkdllelekradvviaP 122
                 + g ++++e    ++nt   + +a  f   e k+   + + + li+ ++v   +++  + dv++ P
  AHX11134.1 224 NVGFNIIQESeGIGINTQadLSRAerFF-QERKRARFLSAGVRLIDPDTVYFAYDTYIESDVIVHP 288
                 4566677766345666641234445544.5888899999999999999999999999999999998 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.1   0.0    0.0077        20       2      20 ..     278     298 ..     277     304 .. 0.81
   2 ?   -0.9   0.0      0.58   1.5e+03      16      27 ..     311     322 ..     306     323 .. 0.77
   3 ?    0.4   2.8      0.22   5.6e+02       4      28 ..     315     341 ..     312     345 .. 0.66
   4 ?    1.1   2.0      0.13   3.3e+02      10      29 ..     333     353 ..     331     357 .. 0.63
   5 ?    2.7   0.8     0.041     1e+02       3      16 ..     366     379 ..     360     380 .. 0.72
   6 !   11.9   0.0   5.8e-05      0.15       4      33 ..     392     423 ..     390     424 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.0077
                 EEE-TT-EE-TT-EE..SEEE CS
   Hexapep_2   2 viIGdnCliGanagi..Gvsl 20 
                 + I+ ++++++n +   Gv++
  AHX11134.1 278 TYIESDVIVHPNVIFfpGVKV 298
                 67***********96589987 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.58
                 ESEEE-TT-EE- CS
   Hexapep_2  16 iGvslGdncvvg 27 
                  Gv +G  ++vg
  AHX11134.1 311 EGVAIGSAAKVG 322
                 4999*9999988 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.22
                 E-TT-EE-TT-EE.S.EEE-TT-EE-T CS
   Hexapep_2   4 IGdnCliGanagi.G.vslGdncvvga 28 
                 IG    +G++a i G  ++G n+v+g+
  AHX11134.1 315 IGSAAKVGPFARIrGsSDIGGNAVIGN 341
                 666666677777774367777777776 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.13
                 E-TT-EES..EEE-TT-EE-TT CS
   Hexapep_2  10 iGanagiG..vslGdncvvgaG 29 
                 iG na+iG  v++ +n+++g G
  AHX11134.1 333 IGGNAVIGnfVEV-KNSTIGQG 353
                 7888888766665.34555544 PP

  == domain 5  score: 2.7 bits;  conditional E-value: 0.041
                 EE-TT-EE-TT-EE CS
   Hexapep_2   3 iIGdnCliGanagi 16 
                 +IGd ++iG   +i
  AHX11134.1 366 SIGDQTNIGGGTVI 379
                 68888888877664 PP

  == domain 6  score: 11.9 bits;  conditional E-value: 5.8e-05
                 E-TT-EE-TT.-EE.SEEE-TT-EE-TT-EE- CS
   Hexapep_2   4 IGdnCliGan.agi.GvslGdncvvgaGvvit 33 
                 I + C+iG n  ++ +v +  ++  +aG++it
  AHX11134.1 392 IDKKCFIGGNnTIVaPVRIHAEARTAAGSTIT 423
                 6689******55559****************9 PP

>> Fucokinase  L-fucokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   8.3e-06     0.021     274     330 ..     343     398 ..     320     410 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 8.3e-06
  Fucokinase 274 avvinSvlessvsvgegsviehsslkgnvsigsnsivsglelesseeslelpddtil 330
                 + v nS + ++v+v+  s+i + s++++++ig ++++ + ++e++++  ++ +++++
  AHX11134.1 343 VEVKNSTIGQGVKVKHLSYIGDASIGDQTNIGGGTVICNFDFEKKHH-TQIDKKCFI 398
                 5588***************************************9876.999999988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (444 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 3122.36
//
Query:       AHX11135.1  [L=490]
Description: phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-100  336.0   0.4   2.7e-100  335.6   0.4    1.1  1  AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
    5.7e-21   74.5   1.0    1.4e-20   73.3   0.0    2.1  3  MGS              MGS-like domain


Domain annotation for each model (and alignments):
>> AICARFT_IMPCHas  AICARFT/IMPCHase bienzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  335.6   0.4  3.1e-104  2.7e-100       1     296 []     131     425 ..     131     425 .. 0.94

  Alignments for each domain:
  == domain 1  score: 335.6 bits;  conditional E-value: 3.1e-104
                      HHHTTTT-EEE-SGGGHHHHHHHHHCT.B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH..CSE...EEEEEEEEESSSSSTTS-EEEEE-TTS CS
  AICARFT_IMPCHas   1 AAKNhksVtvvvdpadYeevleelkkgevsletrkklaakaFahtaaYDaaiaeylskq..lpetlklslekkqkLrYGeNphQkaalyeeeee 92 
                      AAKN+++V+v++dp+dY+ +       +++l++r+k+a k+F ++a+YD  ia+++s++  lpe++++sl+k+++ rYGeNphQ+a++y++   
       AHX11135.1 131 AAKNFRNVCVLSDPSDYALFDV-----NCTLAFRTKMARKTFMRVARYDCKIADWFSSSltLPENINISLTKRTDFRYGENPHQNASFYSD--- 216
                      9****************97754.....579**************************998667799************************64... PP

                      TTHHH-EEEESS---HHHHHHHHHHHHHHCTS..EEEEEEETTEEEEEEEESS.HHHHHHHHHCCSHHHHTTEEEEECCEE-HHHHHHHTTS-E CS
  AICARFT_IMPCHas  93 eglakaeqlqGkelsynNllDadaalelvkef..aavaivKHanpcGvAvget.laeAyekAlaaDpvSaFGgiialnrevdaetaeeikkefl 183
                       g   ++++qGkelsynNllD+d+al++v++f   a+ai+KH+npcGv+v+++ l eAy++A+aaD++SaFGg++a+n+ v++++ae+i+k+f+
       AHX11135.1 217 -GELPFKKIQGKELSYNNLLDLDSALAIVANFssPACAIIKHNNPCGVSVSKDsLYEAYDNAFAADSLSAFGGVVAFNQIVTKDVAEKISKTFF 309
                      .456799*************************753788************98548*************************************** PP

                      CEEEECEE-CCHHHCCTTSSS-EEEE-SS..-...EEEEETTEEEEEE--G..TTCCCSEEECSC---HHHHHHHHHHHHHCCCS-SS-EEEEE CS
  AICARFT_IMPCHas 184 eviiApsfeeealeilkkkknlrvlelke..e...elrsvsgglLvqerdeakieeeelkvvtkkkpteeeledllfawkvvkhvkSNaivlak 272
                      ev++A +++++a  +l++k nlrvl +k+  +   ++ s+ gg+Lvq+ +++ ++  +++vvt+++p++ee+++l+fawkv+k+vkSNaiv a+
       AHX11135.1 310 EVVVATGITQDAELMLQTKTNLRVLIYKKytQpdrHFISLLGGFLVQSCNAKLFQ--DFEVVTNRAPDDEETNQLIFAWKVCKYVKSNAIVTAR 401
                      ***************************996516679999***********87765..6************************************ PP

                      TTEEEEEE-SSSSHHHHHHHHHHH CS
  AICARFT_IMPCHas 273 dgqtvgiGaGqmsRvdsarlAvek 296
                      + +tvgiGaGqmsRv+s+++A+ek
       AHX11135.1 402 NYTTVGIGAGQMSRVKSVEIALEK 425
                      *********************997 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.3   0.0   1.6e-24   1.4e-20       2      94 ..      15     125 ..      14     126 .. 0.93
   2 ?   -2.3   0.0      0.57   5.1e+03       5      24 ..     300     320 ..     298     343 .. 0.72
   3 ?   -2.9   0.0      0.92   8.2e+03      80      94 ..     467     481 ..     455     482 .. 0.75

  Alignments for each domain:
  == domain 1  score: 73.3 bits;  conditional E-value: 1.6e-24
                 HHHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCH................HHHHHHHTTSCC...EEEEE--THHHHHHCHHHH CS
         MGS   2 lvelakklkelgfellATgGTakllkeagipvtevvektgegerlggrv................eildaikngeid...lvintlypfkatvakdgyk 81 
                 l++la klk ++ e++ATg T+++l e+gi++++++++tg++e+l+grv                 +  +++++ei+   lv+++lypf++ v+ ++++
  AHX11135.1  15 LLSLANKLKVVNAEIIATGKTYEYLLENGIDAIRLSDYTGSPEILNGRVktlhptihvgiladpdLHSSEMAKYEIHsidLVVVNLYPFEEHVR-KSAS 112
                 799**************************************************************666666666666666*************9.9*** PP

                 HHHHHHHTTSHEE CS
         MGS  82 irraaenidIplp 94 
                   +++enidI+++
  AHX11135.1 113 ENEIIENIDIGGV 125
                 ***********97 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.57
                 HHHHHHHTTCEE.EEEHHHHH CS
         MGS   5 lakklkelgfel.lATgGTak 24 
                 +a+k ++  fe+ +ATg T++
  AHX11135.1 300 VAEKISKTFFEVvVATGITQD 320
                 677777777775268988876 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 0.92
                 HHHHHHHHHTTSHEE CS
         MGS  80 ykirraaenidIplp 94 
                  ++ +aa++++I+++
  AHX11135.1 467 NEVIEAANKHNIGMI 481
                 456678888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (490 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3777.57
//
Query:       AHX11136.1  [L=338]
Description: prokaryotic glutathione synthetase, N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.3e-38  129.9   0.2    1.8e-37  128.5   0.0    1.8  3  GSH-S_ATP       Prokaryotic glutathione synthetase, ATP-grasp
    7.1e-24   84.2   0.0    1.4e-23   83.3   0.0    1.5  1  GSH-S_N         Prokaryotic glutathione synthetase, N-termina
    1.6e-12   47.5   0.0    2.8e-12   46.6   0.0    1.3  1  RimK            RimK-like ATP-grasp domain
     0.0008   18.7   0.0     0.0092   15.3   0.0    2.1  2  ATPgrasp_YheCD  YheC/D like ATP-grasp


Domain annotation for each model (and alignments):
>> GSH-S_ATP  Prokaryotic glutathione synthetase, ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.2   5.4e+03     134     152 ..      21      39 ..      14      41 .. 0.74
   2 ?   -2.9   0.0      0.85   3.8e+03     109     132 ..      79     102 ..      76     110 .. 0.80
   3 !  128.5   0.0   3.9e-41   1.8e-37       8     173 ..     152     316 ..     147     318 .. 0.91

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.2
                 HHHHHHHHTT--EEEEEEE CS
   GSH-S_ATP 134 elapkLkekGllfvGlDvi 152
                   ++ L++k ++ +G+ vi
  AHX11136.1  21 LTSTDLRKKTVVKIGIQVI 39 
                 4567788888888999888 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.85
                 S---GGGTSCEEEEE--HHHHHHH CS
   GSH-S_ATP 109 vRsnlaaggraeatelterdreia 132
                  R+ + + +++ +++l+e+++e+ 
  AHX11136.1  79 ARGKMVTTSSEGKVSLSEKEEEVN 102
                 688899999999999999988874 PP

  == domain 3  score: 128.5 bits;  conditional E-value: 3.9e-41
                 GCCCS--EEEES-HHHHHHHHHHHSSEEEEESS--TTTT-EEE-TT-TTHHHHHHHHTTTTTS-EEEEE--GGG.GG-EEEEEEETTEE-SEEEEEE-- CS
   GSH-S_ATP   8 fpelipktlvskdkeeirafleeqgdvilKPldgkgGegvfrvkksdpnlksilellteegkepviaqrylpei.keGDkRillvdGepigyalaRvpa 105
                 + +  p+tl+s++ ++i+ f e++++v+lKPl++ gG+ v++ ++ d++ +  +  l++++ +p++aq++ + + ++GDkR++++dG+ +g + +R  +
  AHX11136.1 152 YYNDAPPTLISREIRNIQLFFEQYKSVVLKPLYEFGGDDVMKFESFDESTQEKIHELISKTGTPIVAQKFEESVlEDGDKRVVVLDGKLLG-CFRR-KK 248
                 455679***************************************988877666666666666********998468**************.8766.78 PP

                 SS-S---GGGTSCEEEEE--HHHHHHHHHHHHHHHHTT--EEEEEEETTEEEEEE-SS---HHHHHHH CS
   GSH-S_ATP 106 egevRsnlaaggraeatelterdreiaeelapkLkekGllfvGlDvigdkltEinvtsPtgireieel 173
                 eg + +n+  gg  ++  lt++++e + ++a+ Lke+G++++G+D+i +k+tEinvts +gi e+++l
  AHX11136.1 249 EGSFITNMCKGGDFSSCILTSNEEEKCYRIASDLKERGITLAGIDLIAEKITEINVTSIAGIAELHQL 316
                 99**************************************************************9987 PP

>> GSH-S_N  Prokaryotic glutathione synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.3   0.0   3.1e-27   1.4e-23      18     119 .]      46     143 ..      33     143 .. 0.90

  Alignments for each domain:
  == domain 1  score: 83.3 bits;  conditional E-value: 3.1e-27
     GSH-S_N  18 DttfalmleaqarghevfvleaadLslregkatararkvevkedkedwyelgeeeelaleeldvvlmRkDPPfdmeylyatylLelaeregvlvvNdpr 116
                  +t+ l+ ea +r+ ++f++ +++Ls+ +g+++ar + v+  +++ ++   ++eee++l++ld++lmR+DPPfdm+y++aty+Le++   g+lv+N+p+
  AHX11136.1  46 KSTTYLIGEALERECNIFIYPVETLSIWDGRVSARGKMVTT-SSEGKVSLSEKEEEVNLSTLDMLLMRNDPPFDMSYITATYMLERC---GTLVINEPE 140
                 58999**********************************97.44455666678999*******************************...9******** PP

     GSH-S_N 117 alR 119
                 a+R
  AHX11136.1 141 AVR 143
                 **9 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.0   6.2e-16   2.8e-12      18     185 ..     156     326 ..     150     329 .. 0.83

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 6.2e-16
                 ---EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-.....SHHHHHHHHHHGGG--EEEEE--SS.-SEEEEEEEETTEEEEEEEEE--SS CS
        RimK  18 vpntalardeedaekliekiklrfPvvvKsvegsqGikvvlak.....keqklkqvlealkeailvqeyieea.enediRvlvvddevvaalrrvskeG 110
                  p t ++r+  +++ + e++k    vv+K ++   G+ v+  +     +++k++++++ + + i+ q++ e   e+ d Rv+v+d++  + +rr+ keG
  AHX11136.1 156 APPTLISREIRNIQLFFEQYK---SVVLKPLYEFGGDDVMKFEsfdesTQEKIHELISKTGTPIVAQKFEESVlEDGDKRVVVLDGKLLGCFRRK-KEG 250
                 6789999999**********7...8**************98762222245567788999**********98752679*****************9.*** PP

                 S----TTTT-EEEE----HHHHHHHHHHHHHC...T-SEEEEEEEEETTEEEEEEEESS--SHHHHHHHT--HHHHHH CS
        RimK 111 dFRsnlhrGgvaeklqlseeekelAikaakam...elvvaGvDllrakrgllvlEvnsspglekiektlgidiakkli 185
                  F +n+ +Gg  +   l+ +e+e   ++a  +   ++ +aG+Dl+ +k     ++v s  g+ ++++   i+ a+k  
  AHX11136.1 251 SFITNMCKGGDFSSCILTSNEEEKCYRIASDLkerGITLAGIDLIAEKIT--EINVTSIAGIAELHQLYHINSAAKCF 326
                 ************999999988888888875431226899******98855..46788888999998999999888865 PP

>> ATPgrasp_YheCD  YheC/D like ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     2e-06    0.0092      30      70 ..     157     199 ..     153     225 .. 0.82
   2 ?    0.8   0.0     0.053   2.4e+02     146     167 ..     245     266 ..     241     299 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2e-06
  ATPgrasp_YheCD  30 PetellesledleemlekyksvylKpanGskGkgilriek..e 70 
                     P+t   +++++++ ++e+yksv+lKp +  +G ++++ e+  e
      AHX11136.1 157 PPTLISREIRNIQLFFEQYKSVVLKPLYEFGGDDVMKFESfdE 199
                     8999999******************************999331 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.053
  ATPgrasp_YheCD 146 RiagkgsittnlsrGGtalple 167
                     R  ++gs++tn+ +GG+  +  
      AHX11136.1 245 RRKKEGSFITNMCKGGDFSSCI 266
                     66689***********987654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (338 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       654  (0.0364772); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 2506.92
//
Query:       AHX11137.1  [L=48]
Description: hypothetical protein NHE_0172 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.014   15.7   0.0       0.03   14.6   0.0    1.6  2  DUF3243   Protein of unknown function (DUF3243)


Domain annotation for each model (and alignments):
>> DUF3243  Protein of unknown function (DUF3243)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.0      0.06   1.1e+03      19      33 ..       3      17 ..       1      22 [. 0.72
   2 ?   14.6   0.0   1.7e-06      0.03      20      44 ..      23      47 ..       9      48 .] 0.84

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.06
                HHHHHHHHTT----H CS
     DUF3243 19 qaeklGlseetiekl 33
                +a +lG+ +e++++l
  AHX11137.1  3 AASELGVLDENVTQL 17
                677888888888776 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 1.7e-06
                HHHHHHHTT----HHHHHHHHHHT- CS
     DUF3243 20 aeklGlseetieklAyevGdyLaek 44
                 + +G+s+++++++  +v+d+L+++
  AHX11137.1 23 HKLIGISQDAMQEYTLKVADFLSQH 47
                4568******************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 384.17
//
Query:       AHX11138.1  [L=465]
Description: nitronate monooxygenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-10   39.6   0.0    1.2e-09   38.1   0.0    1.9  2  NMO       Nitronate monooxygenase


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.4      0.15   2.7e+03      12      44 ..      15      47 ..      12      54 .. 0.82
   2 !   38.1   0.0   6.6e-14   1.2e-09     117     285 ..     129     318 ..     101     464 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.15
         NMO 12 ppvvqpgmgg.iskarLaaavsnaGgLGvlasgy 44
                +p++ +g g+ +s     +a + aG  G  + g+
  AHX11138.1 15 WPIIEGGKGVaVSDGVSSGAFAAAGCVGTFS-GV 47
                6899999999888888889999999999988.54 PP

  == domain 2  score: 38.1 bits;  conditional E-value: 6.6e-14
         NMO 117 vsfgfglpteevvarlkeagvvliptissvkearkvearG.......aDalivq.GpeaGGhqGtpevgd.kglfaLvpqvldavd.........iPvi 197
                 +  g+g+p  ++ +   +  v   p++ss+k+ r++ +r           ++ +    aGGh+G  +++   +     p+v++            +P++
  AHX11138.1 129 ITCGAGMP-YKLAEIATRYRVYYYPIVSSAKAFRILWKRSyrklsefLGGVVYEdPWLAGGHNGLSNTDRpDNIQDPHPRVVELRTlmnengltqVPIV 226
                 55566666.33334445677889999*********99999999988855555551569******4444334333334444444333555666677**** PP

         NMO 198 AaGGiidrrgvaaaL...alGAsgvqigtrfLltkesdakdahkkklleaklddtelts.avsGrpaRalatelleeleeakiatlalpeah 285
                  aGG++   + +  +    +GA + q gtr L+t+es+ +   k+kll  k  +++l +    G +   l++ +++el +  +  +++ e++
  AHX11138.1 227 MAGGVWSLSDWQHFIdsdEVGAIAFQFGTRPLITQESPISRQWKEKLLRTKKGEVLLHKfSPTGFYSSSLKNAFIRELVDRSERQVPYVEVE 318
                 **********9999844458***************************99998888886524468**************99999999998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (465 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3610.59
//
Query:       AHX11139.1  [L=230]
Description: bacterial dnaA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      6e-09   36.1   2.1    3.4e-08   33.6   1.0    2.0  2  Bac_DnaA         Bacterial dnaA  protein
  ------ inclusion threshold ------
      0.013   15.3   0.7      0.023   14.5   0.7    1.4  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
      0.035   14.4   0.3        5.9    7.2   0.0    2.4  2  AAA_22           AAA domain
       0.13   11.1   0.0       0.19   10.6   0.0    1.4  1  tRNA-synt_1f     tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.062   2.8e+02      33      50 ..      40      57 ..      20      68 .. 0.81
   2 !   33.6   1.0   7.5e-12   3.4e-08     101     204 ..      85     185 ..      72     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.062
                .S--EEEE-SSSSSHHHH CS
    Bac_DnaA 33 kynPlfiygevGlGktHL 50
                +  P++i g++  GktH+
  AHX11139.1 40 HQPPIIIKGDSKSGKTHI 57
                4579*************7 PP

  == domain 2  score: 33.6 bits;  conditional E-value: 7.5e-12
                 EEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT----TTHHHHHHHH-- CS
    Bac_DnaA 101 LliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevpeevlefiaervt 199
                  l+DDi  l+++ ++ e l+h++n+ +e++k +++++ rs  e++++   lrsr++a  +  i  pd e+   i++k+    ++ vpe ++ +i +rv+
  AHX11139.1  85 CLVDDIDELKTQAEI-EALLHIYNNAVENKKMLLMTT-RS-LEFSNVLPDLRSRLRATTTFTIPSPDDELLRVIVRKQFYLRQIRVPERIVDLILHRVE 180
                 59*******999866.7899*******9988887775.44.678888899************************************************9 PP

                 S-HHH CS
    Bac_DnaA 200 dnvRe 204
                 +++  
  AHX11139.1 181 RSIES 185
                 98865 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.7   5.2e-06     0.023      90     155 ..      68     137 ..      13     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.2e-06
  DNA_pol3_delta2  90 elieelsrkpreskkkiiiiedaekmtksAa.NalLktlEEPsenaifiLitsdtnkl...LktirSRcq 155
                      ++ ++l+++++ s +  ++++d+++++++A+  alL +  +  en  ++L+t+++ ++   L+ +rSR  
       AHX11139.1  68 RILSNLEKETTFSMYHNCLVDDIDELKTQAEiEALLHIYNNAVENKKMLLMTTRSLEFsnvLPDLRSRLR 137
                      577889999999******************7589******************987554455*******86 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0013       5.9       4      43 ..      40      79 ..      37      85 .. 0.80
   2 ?    4.8   0.1    0.0069        31      96     133 ..      86     123 ..      82     125 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0013
      AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevv 43
                ++  +++ G s +GKT+  r  ++++++++  + e+ +++
  AHX11139.1 40 HQPPIIIKGDSKSGKTHIGRIWVSKHNARILSNLEKETTF 79
                77889***************99999988877766555555 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0069
      AAA_22  96 iiDEaqhlrseealeeLrsllnlsrkgvqliLvGtpel 133
                 ++D+++ l +++ +e L +++n++  + +++L+ t++l
  AHX11139.1  86 LVDDIDELKTQAEIEALLHIYNNAVENKKMLLMTTRSL 123
                 69******55999*********9888888888888776 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.3e-05      0.19      23      76 ..      41      95 ..      24     144 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.3e-05
  tRNA-synt_1f 23 devvvesGispSGliHiGnlrevltadlvaralrkr.geevrlilisDdmDglRk 76
                  +  ++  G s SG+ HiG++        +  +l+k  + ++ + +++Dd+D l+ 
    AHX11139.1 41 QPPIIIKGDSKSGKTHIGRIWVSKHNARILSNLEKEtTFSMYHNCLVDDIDELKT 95
                  444566799**********9977776777777776637779***********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.27s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1723.51
//
Query:       AHX11140.1  [L=327]
Description: hypothetical protein NHE_0175 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-41  141.9  40.3    2.8e-41  141.7  40.3    1.0  1  AI-2E_transport  AI-2E family transporter


Domain annotation for each model (and alignments):
>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.7  40.3   1.6e-45   2.8e-41      22     323 ..       2     306 ..       1     310 [. 0.95

  Alignments for each domain:
  == domain 1  score: 141.7 bits;  conditional E-value: 1.6e-45
  AI-2E_transport  22 llplliAlvlayllnpvvkfLkkrgvkrvlavllvlllllvllvllvlllvplliaqltqlvkslpayidslqnilnelp.slleele.nliqa 113
                      ll +++A+++a  l+  +++L+ +  +r la +++++ll++l+v+++ l +pll  ql+ +++  p++++s++++l+++  +l+++le + i+ 
       AHX11140.1   2 LLAFVFAFIFACFLEGYTTKLAIMLGSRKLASFFIVTLLSILVVIILSLALPLLYHQLILFLSGAPQLLASINKHLQTVApNLYNFLEtQGIAS 95 
                      789**************************************************************************99615677777557777 PP

  AI-2E_transport 114 lkqslskilsnilssilnsllsllasllglilslvlvllllffllldgeklrqgilkllpervrervkailrelektlsgylrgqvlvaliigv 207
                      + + + + l ++ s+i++ l + +  ++++i+ +++++l++f+ll d+  ++  ++ ++p r+r+ +k  ++ ++ ++sgyl gq+ ++li ++
       AHX11140.1  96 VLDYTLALLPQLSSQITQHLWDSTLAVANGIILVIFTPLITFYLLDDWPVIVSSVREMVPLRYRKAFKIDAQLISASISGYLSGQAKISLILAI 189
                      7777778899999********************************************************************************* PP

  AI-2E_transport 208 lvfigllilgvpyalllailvglanliPyiGavivlipiaiialltgg.ikevlivlivvllvqliegnilePklmgkrlglhplvillsllag 300
                      l  ++l ++g+py +l+++ +g++ +iPy+G + +l+++ ++a+   + +  vl + +++++  ++e  il+Pkl++k+++lhpl+i++++ +g
       AHX11140.1 190 LYTVLLFFAGLPYYFLIGVSTGILTIIPYLGNITGLVIAHLVAFSNASnVLDVLPITLIFIACGITESMILSPKLLSKSVNLHPLWIIFAITIG 283
                      **************************************9999988888899******************************************* PP

  AI-2E_transport 301 gklfGlvGlilavpltavikail 323
                      g lfG+ G++lavp+++++  ++
       AHX11140.1 284 GILFGFTGILLAVPFASIAAGFV 306
                      ****************9987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1088  (0.0606838); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2364.08
//
Query:       AHX11141.1  [L=1023]
Description: acrB/AcrD/AcrF family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   1.8e-155  519.2  30.4   2.1e-155  519.0  30.4    1.0  1  ACR_tran        AcrB/AcrD/AcrF family
    8.6e-05   21.6  12.6    8.6e-05   21.6  12.6    3.2  2  MMPL            MMPL family
  ------ inclusion threshold ------
      0.067   13.2   0.6       0.86    9.6   0.0    3.2  5  AsnC_trans_reg  Lrp/AsnC ligand binding domain
       0.11   12.5   0.0       0.41   10.6   0.0    2.0  1  DUF2621         Protein of unknown function (DUF2621)
       0.65    9.3   6.8       0.19   11.0   0.4    2.9  2  CCB1            Cofactor assembly of complex C subunit B


Domain annotation for each model (and alignments):
>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  519.0  30.4  5.8e-159  2.1e-155       1    1019 [.       1    1015 [.       1    1017 [. 0.93

  Alignments for each domain:
  == domain 1  score: 519.0 bits;  conditional E-value: 5.8e-159
                  -HHHHHTSHHHHHHHHHHHHHHHHHHHCTSSBESSSS-S--EEEEEEE-TTC-HHHHHHHTHHHHHCTCTS-TTEEEEEEEETTSEEEEEEEESTTS CS
    ACR_tran    1 iikffikrpifalvlaliilllGilsilslPvdalPeiapptvqvstsypGaspevvesevtqplEqalngldglkyvsSqSseglssitltFedgt 97  
                  +++f +kr  +++vl li++ +G ++ + +P ++ P+ + p + v+t + G+s++  ++   q lE +l  ++ lk+++SqS e++s+i ++F+ g 
  AHX11141.1    1 MLDFLLKRNKAVIVLWLILIAFGSYACFVIPKEQAPSAEVPYILVNTVLGGISAKDSAKFLSQQLEDSLRSIEHLKEITSQSMENTSHILMEFDFGF 97  
                  68899******************************************************************************************** PP

                  -HHHHHHHHHHHHHHHGGGS-HHHHHH-EEEEEEECCECEEEEEEESSSSS-HHHHHHHHHHHTHHHHHTSTTEEEEEESS.-SEEEEEEE-HHHHH CS
    ACR_tran   98 didiArqqvqnrlqeaknkLPeevqepgiskiktssseilvlavtskdgsltktelrdlaetnikdqLsrveGVgdvqliGgsekavriwldpqkla 194 
                  d  +A   + ++l +++nkLP++  +p+i+ i+t++ +++ + v+s+    t+++l+  +++++++ L++++ V + ++iG+++  v i++dp+ l 
  AHX11141.1   98 DSAKAIASIRDELDKVMNKLPNNTFRPTIKRISTELIPVVAVVVSSD--LGTEETLK--IASKLQKRLNSLPNVLSTKMIGKRNTIVEITVDPKMLM 190 
                  **********************************************9..44444444..5689********************************** PP

                  CTT--HHHHHHHHHHHSSB-EEEEETT-SB-EEEEESB---SHHHHHTSEEEETTSCEEEHHHCEEEEEEESSSSSEEEETTEEEEEEEEEEETTSB CS
    ACR_tran  195 klgltltdvvsalkeqnvnvaaGqlegqeeelliraqgqlqsaediekiivknqdgskvrlrDvAkVelgaeeerlaatfngkpavllevkklpgan 291 
                  +++++++++v++l+++n  +++G+  g+  e++i+++g +++++ i+++ v  +  s + ++DvAkVe+  e+e+ ++++ng +++++ev k++g+n
  AHX11141.1  191 AYNISMHNIVQTLTQNNILIPSGSFPGT--EYSISVNGLVEQVNKIKELPVLAHGDSLLTIGDVAKVETVLEKEKSISRINGVDTIVVEVSKMIGKN 285 
                  ************************9887..57889999*************888888899************************************* PP

                  HHHHHHHHHHHHHCCGGGSSTTEEEEEEEESHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHHHH CS
    ACR_tran  292 aievakavkekleeLkeslPegveivvvydrtefvrasieeVvktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNlltL 388 
                   +e++++v++++ +Lk++l+egv i++ +d+++ v + + + +++ ++ ++Lvv v+ ++++ ++++ ++a ++P sll+++ +++++gf++N   L
  AHX11141.1  286 LLETIQQVNAEVISLKRTLSEGVRISIEFDTSKEVTEVLIDLKNNVILTTILVVGVMAIYIG-WKIAFMTAFTIPGSLLVGVLLIYVMGFTMNIVVL 381 
                  ************************************************************97.********************************** PP

                  HHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH CS
    ACR_tran  389 fgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkeiqgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPal 485 
                  f L + iG++vD A++v E   rk+   g++p  a ++++ ++  ++++++ + l+v++P+lf  G+ Gk+ + + +t+++ + +sv++++++tP+l
  AHX11141.1  382 FSLIMSIGMIVDAAVIVNEYADRKMLV-GLSPTLAYRAAAAKMFWPVLSSTGTTLIVLVPLLFWPGLAGKFMKFLPITLIFTLSASVVMSIVFTPVL 477 
                  ***************************.********************************************************************* PP

                  HHHHS---STT-CT.....SHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHCS-B..ESS----TSEEEEEEE-STTB-HHH CS
    ACR_tran  486 callLkerkeekek.....kffrefnrlfealeraYakllekvlrhravvllvalvllvlsvllfvripk..eflPeedegvlvtsvqlppgvsleq 575 
                   +++  ++ +  +k     ++       ++ ++++Y kll k+l  ++ +++++l++++l ++ + + +k  +flP+ d ++ ++ +++ +  +l+q
  AHX11141.1  478 GSMIGTPSTSDPDKikriaAIDSGDASAMSGIHAKYYKLLDKFLDYPKTLITSILMIVLLGIVGYWFFGKgfQFLPNVDPKSTTVLIKASDNLTLKQ 574 
                  ***9999999888887665455556778999*********************9999999999888888773368*********************** PP

                  HHHHHHHHHHHHHTTTTEEEEEEEECECSSE..ECCCEEEEEEEES-GCGS-SGGGSHHHHHHHHHHHCTTSTSSEEEEEETTSSCCCSSSSCEEEE CS
    ACR_tran  576 tqkvlkqvekilkekpevesvfavtGfaesgdtagpnsakvfisLkpekerkeeeksvealierlrkelkkipganvellapiqlreletlsgvrse 672 
                   ++++++ e+ +   p ++   ++ G+       +   +k++i+L ++k+r     +v ++ +++++++++i+g+++ell    ++ ++ ++   ++
  AHX11141.1  575 KRQIVESAEEKICSLPGIKTCYTTIGT-----LDNDAIGKIQIELIDWKKR----RTVREINSEVEEKIASIEGIQFELL----IQRDGPIQEKPIK 658 
                  **************************6.....56789************99....9********************7765....3444566666666 PP

                  EEE.SSSSHHHHHHHHHHHHHHHHCCSTTEEEEEESS-S-EEEEEEEE-HHHHHHCTCSHHHHHHHHHHHHTTEEEEEEEET..TEEEEEEEEE-GG CS
    ACR_tran  673 lqvklfgddleaLseaaeqllaalkelpelsdvrseqqedqpqlqveidrekaarlGvsisdindtletalggsyvndfiee..grrvkvvvrleed 767 
                  ++v   g+++e++++ a  +++ + ++++++++  ++ +++    + id++ka+ +Gv++++i++ +  a  g+ v++   +  +++ ++ + l+e+
  AHX11141.1  659 IAV--SGTSYENVRHGAMVIKSLITNIKGATSITDDAITEKLGWSIVIDKKKASLYGVDTATIGHYVMLATKGALVGEYRGDdyDEKLDILLVLPEK 753 
                  666..************************************************************************99865125788899999999 PP

                  GSSSGGGGCCSEEEETTSCEEEGGGTEEEEEEEE-SEEEEETTCEEEEEEEEESTTS-HHHHHHHHHHHCTT..SSTTEEEEEEHHHHHHHHHHCHH CS
    ACR_tran  768 lrsspedlkklkvrnkkgkmvplsavakieeekgpnsierengsrsvvisgnvaegdslseaeeavekiakkvklpegvtiewtgqaeqeqeasnsl 864 
                   r+ +  + ++ +++++g +vpls++ +i+ e+   s++r n+ +++ i ++v +g +  ++    ek+ k+    ++++i++ g+ ++++e+s  l
  AHX11141.1  754 ERN-VASVMNMMIPSHNG-LVPLSSFLTIKPENKVTSVKRVNSDPTIHIHADVLPGFLAHNIVSTLEKAIKNRPELSSLSIRFKGEQQEQEETSRFL 848 
                  886.66666788998877.9*************************************9999888777777774555799****************** PP

                  HHHHHHHHHHHHHHHHHHHTSSSTCHHHHTTHHHHHHHHHHHHHHTT--BS.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHH CS
    ACR_tran  865 lilvalalllvflvLaalyeslsepllilltvPlalvGallalllrglels.viaqvGlilliGlavkNaillvefakelrekegksleeaileaak 960 
                  l+ ++++++ + l+L ++++s+ + ++i+  v l+  G +l+ll++++++  v++ +G+i l G++v+N ill++ +++    e  + +  i++aa+
  AHX11141.1  849 LVAFVASVFCMILILLLQFNSFYQVFIIIAAVVLSTGGVILGLLITHQPFIvVMSGIGIISLAGIVVNNNILLIDAYNDYAS-ESEDKKHSIMRAAL 944 
                  ************************************************97516788************************99.8899********** PP

                  HCHHHHHHHHHHHHHHHHHHH.........CT-STTHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    ACR_tran  961 eRLrPiLMTalaailGvlPLa.........lstgaGselq...qplgivvlgGlvtstvLtLllvPvlYvl 1019
                   R+rPiL+T+ +++lG+lP++         ++   G+ +    q l ++v gGl   t+LtL+l+P+l +l
  AHX11141.1  945 SRFRPILLTSGTTVLGLLPMVgcitidfinFGITYGAPATqwwQSLSTTVAGGLSFTTILTLFLTPALLML 1015
                  ********************8666666655455677755422389**********************9887 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -8.1   9.8         5   1.8e+04     155     223 ..     362     399 ..     325     494 .. 0.54
   2 !   21.6  12.6   2.4e-08   8.6e-05     108     302 ..     815    1016 ..     808    1022 .. 0.75

  Alignments for each domain:
  == domain 1  score: -8.1 bits;  conditional E-value: 5
        MMPL 155 vilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgllvvlliavGtDYallLv 223
                 +++ +Lli    + + +++l +                                ++ i+  +D a+++ 
  AHX11141.1 362 LLVGVLLIYVMGFTMNIVVLFSL-------------------------------IMSIGMIVDAAVIVN 399
                 33333444444444444444444...............................444444555554433 PP

  == domain 2  score: 21.6 bits;  conditional E-value: 2.4e-08
        MMPL  108 aairaaveearpleglkvevtGpaatladlrdasdrdlklievvtlvvilviLlivyrSlvaallplltvvvsll.aalglvlilalllglelstfv 203 
                    +++a+++ ++l++l ++  G        ++ ++r l ++ v+++   ++iLl+ + S+  ++++++ vv+s + + lgl     l+ ++    ++
  AHX11141.1  815 STLEKAIKNRPELSSLSIRFKGEQQE----QEETSRFLLVAFVASVFCMILILLLQFNSFYQVFIIIAAVVLSTGgVILGL-----LITHQPFIVVM 902 
                  55677777777788888888884433....455888899999999999999********************9975255555.....66777888889 PP

        MMPL  204 lgllvvlliavGtDYallLvsRyreelaagedreeaviravastgkvv.taaGltvaia..mlg...Lvvarlpvl.........aqvGvaialGvl 285 
                   g+ ++ l ++ +  ++lL+  y +++ + ed++++++ra  s  + + + +G tv +   m+g     ++++++          +++ +++a G+ 
  AHX11141.1  903 SGIGIISLAGIVVNNNILLIDAYNDYASESEDKKHSIMRAALSRFRPIlLTSGTTVLGLlpMVGcitIDFINFGITygapatqwwQSLSTTVAGGLS 999 
                  9999999******************************9987666655516788888764113333332233333222222222227899******** PP

        MMPL  286 vdvlivlTllPAllvll 302 
                  +++ ++l l+PAll+l+
  AHX11141.1 1000 FTTILTLFLTPALLMLM 1016
                  *************9986 PP

>> AsnC_trans_reg  Lrp/AsnC ligand binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.8   6.5e+03      52      69 ..      63      80 ..      58      85 .. 0.63
   2 ?   -2.3   0.0       1.2   4.4e+03      55      68 ..     158     171 ..     154     173 .. 0.73
   3 ?   -2.8   0.0       1.8   6.6e+03      46      70 ..     251     274 ..     247     276 .. 0.61
   4 ?    9.6   0.0   0.00024      0.86       5      37 ..     572     603 ..     569     612 .. 0.83
   5 ?   -3.1   0.0       2.2   7.7e+03      50      65 ..     626     641 ..     620     641 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.8
                    HHHHHTTTTSTTEEEEEE CS
  AsnC_trans_reg 52 rflreklaslpgvartet 69
                    + l++ l+s+++++++++
      AHX11141.1 63 QQLEDSLRSIEHLKEITS 80
                    455556666666666554 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                     HHTTTTSTTEEEEE CS
  AsnC_trans_reg  55 reklaslpgvarte 68 
                     +++l+slp+v +t+
      AHX11141.1 158 QKRLNSLPNVLSTK 171
                     55688888888886 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 1.8
                     SHHHHHHHHHHTTTTSTTEEEEEEE CS
  AsnC_trans_reg  46 dlealerflreklaslpgvartets 70 
                     d++  e++l++   s+  +  ++t 
      AHX11141.1 251 DVAKVETVLEK-EKSISRINGVDTI 274
                     77788888777.4455555555555 PP

  == domain 4  score: 9.6 bits;  conditional E-value: 0.00024
                     E-GGGTTHHHHHHHHHHTSTTEEEEEEESSSSS CS
  AsnC_trans_reg   5 lepghpeqleefeealaelpeVvecyrvtGdyd 37 
                     l+++ ++ +e++ee+++ lp ++ cy++ G  d
      AHX11141.1 572 LKQK-RQIVESAEEKICSLPGIKTCYTTIGTLD 603
                     5533.5789*******************99755 PP

  == domain 5  score: -3.1 bits;  conditional E-value: 2.2
                     HHHHHHHTTTTSTTEE CS
  AsnC_trans_reg  50 lerflreklaslpgva 65 
                     ++  ++ek+as++g++
      AHX11141.1 626 INSEVEEKIASIEGIQ 641
                     4555667777777775 PP

>> DUF2621  Protein of unknown function (DUF2621)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00011      0.41      10      43 ..     528     561 ..     523     588 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00011
     DUF2621  10 lwvvvlvsllaiGGffmfrkflkrlpkedGksel 43 
                 + ++++++ll i G++ f k ++ lp+ d ks+ 
  AHX11141.1 528 ITSILMIVLLGIVGYWFFGKGFQFLPNVDPKSTT 561
                 66899*************************9974 PP

>> CCB1  Cofactor assembly of complex C subunit B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   1.3      0.18   6.5e+02       3      20 ..     528     545 ..     526     548 .. 0.88
   2 ?   11.0   0.4   5.3e-05      0.19      67     116 ..     831     880 ..     822     887 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.18
        CCB1   3 lsstLlLtlLllvGLfff 20 
                 ++s+L++ lL +vG +ff
  AHX11141.1 528 ITSILMIVLLGIVGYWFF 545
                 6899*************9 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 5.3e-05
        CCB1  67 tvtfeGlvapslflAifLtllaalgllclaLVlsilvpelgnlflllvll 116
                  ++f+G  + +     fL +  + +++c+ L+l ++++++ ++f++++++
  AHX11141.1 831 SIRFKGEQQEQEETSRFLLVAFVASVFCMILILLLQFNSFYQVFIIIAAV 880
                 699***************************************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1023 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1395  (0.0778069); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.86u 0.34s 00:00:01.20 Elapsed: 00:00:00.45
# Mc/sec: 6862.01
//
Query:       AHX11142.1  [L=459]
Description: amidophosphoribosyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-20   73.8   0.0      2e-20   72.9   0.0    1.5  1  GATase_7      Glutamine amidotransferase domain
    8.5e-20   71.3   0.0    1.3e-19   70.7   0.0    1.4  1  GATase_6      Glutamine amidotransferase domain
    3.2e-06   26.7   0.0    6.1e-06   25.8   0.0    1.4  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
      0.017   14.6   0.1       0.12   11.9   0.1    2.0  1  PRTase_2      Phosphoribosyl transferase


Domain annotation for each model (and alignments):
>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.9   0.0   4.5e-24     2e-20       1     121 [.      86     211 ..      86     213 .. 0.94

  Alignments for each domain:
  == domain 1  score: 72.9 bits;  conditional E-value: 4.5e-24
    GATase_7   1 hrrlsiidseagaQPmvs.sedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea.......ewgeealerlnGmfAfaiwdeeekrll 91 
                 h r s+   ++ +QP++     g+++i++nG + N +elre L+++g+ f+++ Dtevl++ll+         +++eal++++G ++++++ ++e  ++
  AHX11142.1  86 HVRYSTSGNASFSQPVYLrCPFGEIAIAHNGNLINADELREILKKRGCIFESDVDTEVLVHLLALskeetyiGKITEALQQVKGAYSLVLLINNE--VF 182
                 6677788888999**9987899****************************************9989999999899*****************999..** PP

    GATase_7  92 laRDrlGikPLyygedkgdallfaSelkal 121
                 ++RD+ G++PL +g+  gda++++Se  al
  AHX11142.1 183 AVRDPHGVRPLSLGRL-GDAIVITSETCAL 211
                 ****************.89********998 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.7   0.0     3e-23   1.3e-19      10     134 .]      78     207 ..      48     207 .. 0.91

  Alignments for each domain:
  == domain 1  score: 70.7 bits;  conditional E-value: 3e-23
    GATase_6  10 vedevalaHvRlaivglaeeegaqPf..psedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall......eelG..eevlerlrGmfaf 98 
                 ++++ a++HvR +++g+a  +  qP+    + g+++++hNG   n++elre l++ +g  f+s++Dtevl++ll      ++ G  +e+l++++G+++ 
  AHX11142.1  78 CSSDKAIGHVRYSTSGNA--SFSQPVylRCPFGEIAIAHNGNLINADELREILKK-RGCIFESDVDTEVLVHLLalskeeTYIGkiTEALQQVKGAYSL 173
                 456789***********9..777***777788***********************.****************888999888888***********7777 PP

    GATase_6  99 aiwdkrentlilardrlgvkplyyavdesglafase 134
                 +     +n+++ +rd +gv+pl+ +  +++++++se
  AHX11142.1 174 V--LLINNEVFAVRDPHGVRPLSLGRLGDAIVITSE 207
                 5..5579**************************998 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.0   1.4e-09   6.1e-06      22     120 ..     280     384 ..     260     403 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 1.4e-09
                   EEEE--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE...............EE----TTSEEEEE-SEESSSHHHHHHHHHHH CS
  Pribosyltran  22 ileeyngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdes.......rlledpagkkVliVDDildtGgTllaalelLk 111
                   ++e+ n k d+vv+++  G++    +a   ++pl     + y++++s   +++    +        + e++  kk++++DD +  G+Tl+  +  L 
    AHX11142.1 280 AHES-NTKSDMVVPVLDSGMVSSIGYAETSGIPLELAITKNYYSGRSFIEPTQDLRRIrvklkhnANRELLQSKKIILIDDSIVRGTTLKLLIAMLW 375
                   3444.889***************************888888888777666665555558*****99******************************* PP

                   CC-BSEEEE CS
  Pribosyltran 112 ekgpeevri 120
                   e+g ee+++
    AHX11142.1 376 EAGTEEIHV 384
                   *****8764 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.1   2.6e-05      0.12     113     153 ..     343     384 ..     266     391 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.6e-05
    PRTase_2 113 edeellaaakelvLvDDEistGktalnliralqeklpr.kry 153
                 + ++ l ++k+++L+DD i  G+t+  li  l e+ ++  ++
  AHX11142.1 343 NANRELLQSKKIILIDDSIVRGTTLKLLIAMLWEAGTEeIHV 384
                 44555667888**************99999988876553455 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (459 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3289.00
//
Query:       AHX11143.1  [L=191]
Description: translation elongation factor P [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.8e-21   74.3   0.7      9e-21   73.4   0.7    1.5  1  Elong-fact-P_C  Elongation factor P, C-terminal
      2e-18   66.1   0.4    5.1e-18   64.8   0.4    1.7  1  EFP_N           Elongation factor P (EF-P) KOW-like domain
    3.1e-13   49.6   1.1      1e-12   47.9   0.3    2.2  3  EFP             Elongation factor P (EF-P) OB domain


Domain annotation for each model (and alignments):
>> Elong-fact-P_C  Elongation factor P, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.4   0.7   1.5e-24     9e-21       3      56 .]     134     188 ..     132     188 .. 0.97

  Alignments for each domain:
  == domain 1  score: 73.4 bits;  conditional E-value: 1.5e-24
                     EEEEE--SSS--SSSSTTEEEEEETTS.-EEEEETT--TT-EEEEETTTTEEEEE CS
  Elong-fact-P_C   3 leVvetepgvkGdtasggtKpatletG.aevqVPlFIneGdkIkvdTrtgeYvsR 56 
                     ++V+etep +kG+t ++++Kpatl+ G ++v+VP+FI++Gd+++v+T++g+Yv+R
      AHX11143.1 134 YTVEETEPYIKGQTITSSYKPATLNGGlLKVMVPPFIKIGDQVVVKTEDGTYVER 188
                     79*************************889************************9 PP

>> EFP_N  Elongation factor P (EF-P) KOW-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.8   0.4   8.6e-22   5.1e-18       3      58 .]       8      63 ..       6      63 .. 0.97

  Alignments for each domain:
  == domain 1  score: 64.8 bits;  conditional E-value: 8.6e-22
                GG--TT-EEEETTEEEEEEEEEEEEETTS--EEEEEEEETTTS-EEEEEEETT-EE CS
       EFP_N  3 selkkGlvieidgklyvVlefehvkpGkGqafvrvklknlrtGakvektfkagdkv 58
                +++k G+++e+++ ly Vl+ ehvkpGkG+afv v++k++   +k++++f++++ v
  AHX11143.1  8 NDIKVGNILEHKNGLYYVLKREHVKPGKGGAFVNVEMKSIDGATKLNHRFRSEEVV 63
                9***************************************************9965 PP

>> EFP  Elongation factor P (EF-P) OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.9   0.3   1.7e-16     1e-12       2      54 .]      72     124 ..      71     124 .. 0.96
   2 ?   -2.6   0.0         1     6e+03      38      46 ..     128     136 ..     128     145 .. 0.67
   3 ?   -1.0   0.0       0.3   1.8e+03      35      51 ..     166     183 ..     149     186 .. 0.70

  Alignments for each domain:
  == domain 1  score: 47.9 bits;  conditional E-value: 1.7e-16
                 EEEEEEEETTEEEEEETTT--EEEEEHHHHTTGCGG--TT-EEEEEEETTEEE CS
         EFP   2 emqylYkdgdeyvFMdnetYeqielpkeqlgdaakfLkEgmevtvllyegepi 54 
                 e+qyl+++ +++++M+  +Yeqi+++++ ++  +k+LkE+  v++l ++++++
  AHX11143.1  72 EYQYLFSEAKSVILMNLSNYEQISIDASLFEGVSKYLKEDVCVKLLKHNEKVV 124
                 79****************************8888****************996 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1
                 --TT-EEEE CS
         EFP  38 LkEgmevtv 46 
                 Lk+++ +tv
  AHX11143.1 128 LKDNLVYTV 136
                 677777666 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.3
                 C.GG--TT-EEEEEEETT CS
         EFP  35 a.kfLkEgmevtvllyeg 51 
                 + +f+k g++v v + +g
  AHX11143.1 166 VpPFIKIGDQVVVKTEDG 183
                 458999999999887766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1509.25
//
Query:       AHX11144.1  [L=132]
Description: putative lipoprotein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0086   15.8   0.1      0.014   15.2   0.1    1.3  1  SmpA_OmlA  SmpA / OmlA family
  ------ inclusion threshold ------
       0.28   11.8   1.9        0.6   10.7   1.9    1.6  1  LPAM_1     Prokaryotic membrane lipoprotein lipid attachment 


Domain annotation for each model (and alignments):
>> SmpA_OmlA  SmpA / OmlA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.1   1.5e-06     0.014      12      67 ..      31      88 ..      29      92 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.5e-06
                --TT-BHHHHHHHH-S-SEE-SSSSSEEEEEEEETTE..........EEEEEEEE-TTSBE CS
   SmpA_OmlA 12 lkpGmtkeqVryllGsPsltdtfdpnrwdYvynfkrg.....gkaveqqvlavyFdddglv 67
                +k+G  k+ V+   G P+l    d n w+Yv  ++r+     +++ +++v+ v+Fd + + 
  AHX11144.1 31 IKIGERKAVVQIMSGDPTLI---DGNNWYYVRINTRSdsvglRNNYSSTVIQVTFDGEIVK 88
                67788888888888888875...6889*********85444444499*********97665 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   1.9   6.7e-05       0.6       1      13 [.       1      13 [.       1      13 [. 0.96

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.7e-05
      LPAM_1  1 MKKillalgalll 13
                MKK++++l++ll+
  AHX11144.1  1 MKKYIFTLLLLLV 13
                ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1097.63
//
Query:       AHX11145.1  [L=383]
Description: dicarboxylate symporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-28  100.3  46.8    4.3e-28   98.4  46.8    1.7  1  SDF       Sodium:dicarboxylate symporter family


Domain annotation for each model (and alignments):
>> SDF  Sodium:dicarboxylate symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.4  46.8   2.4e-32   4.3e-28       5     389 ..       7     370 ..       2     371 .. 0.81

  Alignments for each domain:
  == domain 1  score: 98.4 bits;  conditional E-value: 2.4e-32
         SDF   5 iliglvlGlviGllelvkelaalisplgdlfinllkmlivPl.vfasiisgiaslgdakklgklglktllyfllttliAaiiglilalllkpgselale 102
                 i i+l++ +++ l  +++  +   +++ +l i+ + ++i+P  +f++i   i++++  +k+  l++  ++ ++++ + A+++++++++++ p       
  AHX11145.1   7 ITISLIVAIILFL-GYIPMDVRSAMYAVSLTIQDVILMILPFiIFSFILDLIIKMR--AKASGLLFLFVVAVVISNTTAICLAYFIGNFFLPS------ 96 
                 4445555544433.57999999999999999*9999*****97888999999***5..55555666666677778888***************...... PP

         SDF 103 assakeaekketdslldlilslipsnifealaegnvlavivfailfGialaalgekgepllkffeslnevvmkvvkivmk.laPigvfaliaslvaskg 200
                     ++  + +t +l  + + ++p+ +        +  ++ +++++G++l      ge++ ++ +++++++  +++ v+  + P+ +++l +++v++k 
  AHX11145.1  97 ---VENVVSGSTVKLIPMWRLYLPQLL-------PTEYAMPLSVVIGVMLLVF--FGEKVNSLNTKIYNACDFLLNKVVMpVIPVFIAGLAVKIVSDKM 183
                 ...333333344456666666666666.......4445888999****99999..88889999999999998888766655****************99 PP

         SDF 201 lgalsslakflltvylglai.hllivlpllllvltkknplkflkkilpalltAfsTaSSaAtLPvtlecaeknlgvsesiasfvlPlGatinmdGtaly 298
                 l+ ++   +++l+++l+  i +  i +++l     +k++  +l +i+p l+tAf+T+SSa tLP  l +++kn   ++ +as +lP  ++++ +G +  
  AHX11145.1 184 LQPIVDHYSVILLIVLLSSItYSSIWYLAL----VGKRIGSVLVNIAPSLVTAFTTMSSAVTLPSLLVATRKN-TDDSYVASAILPPAVNFHVMGDTFN 277
                 998886666666655555550444444444....3569**********************************7.889999******************* PP

         SDF 299 eavaaifi.aqlfgvelslgqllllvlvatlasiGaagvPgaglva.lllvlsalglpvegialilaidrllDmfrTavNvtGdavaalivak 389
                 +++++i i + ++g  l++++l++ ++  ++  +++ g+Pg+g+++ l +  + +g+  e ++li ++++++D f+T++N++G+ ++a+  +k
  AHX11145.1 278 ITITVIAIlFTFTGKVLGISDLMIYIFYFIIYRFATVGIPGGGIIIlLPFFSEKFGFTPEMLTLITTLYVVFDPFQTVLNIFGNGAFAIFFSK 370
                 *99999994556666699****************************45555559**********************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (383 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       968  (0.0539907); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.21s 00:00:00.73 Elapsed: 00:00:00.37
# Mc/sec: 3085.84
//
Query:       AHX11146.1  [L=351]
Description: recF/RecN/SMC N terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.2e-11   42.4   3.5    5.2e-05   22.8   0.4    2.1  2  SMC_N        RecF/RecN/SMC N terminal domain
    3.6e-07   30.3   2.8     0.0058   16.5   0.3    2.3  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.3e-05   24.9   0.2     0.0017   18.8   0.2    2.4  1  ABC_tran     ABC transporter
    3.7e-05   24.3   0.2    7.7e-05   23.3   0.2    1.6  1  AAA_23       AAA domain
    6.8e-05   22.7   1.1    0.00012   22.0   1.1    1.3  1  AAA_15       AAA ATPase domain
     0.0026   18.2   0.2      0.047   14.1   0.0    2.3  2  AAA          ATPase family associated with various cellular a
     0.0065   16.2   0.0      0.015   15.1   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.025   14.2   0.1       0.32   10.6   0.0    2.2  2  AAA_27       AAA domain
      0.045   13.2   0.1       0.14   11.7   0.0    1.7  2  AAA_7        P-loop containing dynein motor region
      0.069   13.4   0.8       0.45   10.8   0.8    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
      0.072   12.2   0.0       0.17   11.0   0.0    1.6  1  DUF815       Protein of unknown function (DUF815)
       0.11   12.4   0.2       0.27   11.1   0.1    1.7  2  RsgA_GTPase  RsgA GTPase


Domain annotation for each model (and alignments):
>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.8   0.4   3.5e-08   5.2e-05       1      67 [.       4      65 ..       4     104 .. 0.83
   2 !   21.0   0.2   1.2e-07   0.00018     114     202 ..     229     339 ..     123     350 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.8 bits;  conditional E-value: 3.5e-08
                EEEEEEEESETTEECEEEEEETTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC-- CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  1 vlkrleienFksyagktvilpfsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk 67
                +++++ +++F++   +  +++f++++    G+NG GK+++l+A+   L+      +rs+k s++i+ 
  AHX11146.1  4 YITEILLKDFRNH--SFYKTKFNSKHVLFFGRNGVGKTSILEAV-SKLS--PGLGIRSAKNSEIISI 65
                6999********9..69999************************.5666..4446888888888875 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 1.2e-07
                 TTEEE-HHHHHHHHHCTT-STT..........................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxx..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 114 ngkevtkkevsellesagiske..........................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                  +k+v+ +++s++l++++ + +                          + S Ge++ + la+l+A  +     ++llD+i ++LD++n + + e + +k
  AHX11146.1 229 TDKQVHVEDISRILRDSRAKDSitgkmdfgihradflvihgrnantakSCSTGEQKSLILAILLAASELV--DIMLLDDIFSHLDQRNLELFLEEVMQK 325
                 46777777788888777777778888888888888888888888888899*************9988775..5899*****************999887 PP

                 CTTSEEEEE-SSHHHC CS
                 xxxxxxxxxxxxxxxx RF
       SMC_N 187 sknaQfivislreeml 202
                    +Qf+   l+++ +
  AHX11146.1 326 D--CQFFFSDLESNKI 339
                 7..***9988877655 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.1   2.1e-05     0.032       3      22 ..      29      48 ..      28      84 .. 0.73
   2 !   16.5   0.3   3.9e-06    0.0058     229     294 ..     270     331 ..     155     332 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.1e-05
      AAA_21  3 vliGpNgsGKSnLLdaldll 22
                ++ G+Ng+GK+++L+a + l
  AHX11146.1 29 LFFGRNGVGKTSILEAVSKL 48
                579*************9655 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 3.9e-06
      AAA_21 229 gqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQvil 294
                 ++  +a + S G ++   +l++ll+a +  ++ l+D++ ++L+ + l+ +le + +   ++ Q+++
  AHX11146.1 270 RNANTAKSCSTGEQKS-LILAILLAASELVDIMLLDDIFSHLDQRNLELFLEEVMQ---KDCQFFF 331
                 44444455599*****.7777777777777*********************66633...3567776 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.2e-06    0.0017      11     134 ..      25     305 ..      19     308 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.2e-06
                 TSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.............................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
    ABC_tran  11 gekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.............................. 79 
                 ++ v ++G+nG GK+++l+++++l+ p  G    ++ ++ ++  +s+++++++++ ++    ++   +n                              
  AHX11146.1  25 SKHVLFFGRNGVGKTSILEAVSKLS-PGLGIRSAKNSEIISIGATSWEASFKFVSDNHLSEIGTGYCSNrrilklnkqpiigfgdilslvrvmwftpqm 122
                 678999****************996.6788877888888888888888888888888444444444455577877788888888888888888888888 PP

                 ................................................................................................... CS
                 ................................................................................................... RF
    ABC_tran  80 ................................................................................................... 79 
                                                                                                                    
  AHX11146.1 123 gnvfitdksvrrkffdrlvalsdpqhldnlvtyeklrsdrlrilstqpskrwldvierkiatlcvnisasresfidlleghsfsehfasprvklictva 221
                 888888888888888888888888888888888888888888888888888888888888888888887777777777777777777777777777777 PP

                 ........HHHTCHHHHHHHSTTGG....................TTCBGESTTSGGS-HHHHHHHHHHHHHHHTS..SEEEEES CS
                 ........xxxxxxxxxxxxxxxxx....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxx RF
    ABC_tran  80 ........esdeeiekalsklglke....................lkdtvvksspssLSgGqkqrvalarallkkp..kllllDE 134
                         ++++++e++ + l+++                     ++ +++ + ++s S G+++ + la +l+     +++llD+
  AHX11146.1 222 ndimtvstDKQVHVEDISRILRDSRakdsitgkmdfgihradflvIHGRNA-NTAKSCSTGEQKSLILAILLAASElvDIMLLDD 305
                 777777663333333333333333344466666666666666665555555.555888888888777777766553226777776 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.2   5.1e-08   7.7e-05       3      39 ..       9      45 ..       7      85 .. 0.91

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 5.1e-08
      AAA_23  3 kienfrsfrdqeidFskgltlItGpNGaGKTTildAi 39
                 ++ fr ++  +  F+++ +l++G NG GKT+il+A+
  AHX11146.1  9 LLKDFRNHSFYKTKFNSKHVLFFGRNGVGKTSILEAV 45
                57777777777789*********************97 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   1.1   7.8e-08   0.00012       2      46 ..       4      48 ..       4     101 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 7.8e-08
      AAA_15  2 kIkkikikNFRslkdveidlseeltvliGkNnsGKSsilealdlF 46
                +I++i +k FR ++  + +++++  ++ G+N++GK+silea  ++
  AHX11146.1  4 YITEILLKDFRNHSFYKTKFNSKHVLFFGRNGVGKTSILEAVSKL 48
                699**************************************8766 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   3.2e-05     0.047       1      32 [.      28      68 ..      28     113 .. 0.74
   2 ?    1.9   0.1      0.19   2.8e+02      36      74 ..     277     313 ..     245     340 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 3.2e-05
                EEEESSTTSSHHHHHHHHHHHH.........THEEEEEETT CS
         AAA  1 vllyGppGtGKTllakavakel.........gvefleisgs 32
                vl++G  G+GKT++ +av k +         ++e+++i ++
  AHX11146.1 28 VLFFGRNGVGKTSILEAVSKLSpglgirsakNSEIISIGAT 68
                79****************99865333333333444444444 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.19
                 SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH CS
         AAA  36 skyvgesekkirelfkeakekakpsilfiDEidalaksr 74 
                 s   ge+++ i +++ +a+e     i+++D+i +   +r
  AHX11146.1 277 SCSTGEQKSLILAILLAASELV--DIMLLDDIFSHLDQR 313
                 3478999999999999998886..9******98888777 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   9.8e-06     0.015      17      45 ..      21      48 ..      11      54 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 9.8e-06
      AAA_29 17 ieidlkgatlltGpsGsGKSTllDAiqal 45
                 +++ k  +l+ G++G+GK+++l A++ l
  AHX11146.1 21 TKFNSK-HVLFFGRNGVGKTSILEAVSKL 48
                355545.59****************9865 PP

>> AAA_27  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   0.00021      0.32      27      60 ..      26      59 ..      11      63 .. 0.81
   2 ?    0.9   0.0      0.19   2.8e+02      18      36 ..     254     272 ..     251     291 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00021
      AAA_27 27 dlhliyGpNEAGKstalrAisdllfGipertkdn 60
                +  l +G N  GK+++l+A+s+l  G+  r+ +n
  AHX11146.1 26 KHVLFFGRNGVGKTSILEAVSKLSPGLGIRSAKN 59
                455789*****************99999888776 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.19
      AAA_27  18 sldfsaeeadlhliyGpNE 36 
                 ++df+ ++ad+ +i+G N 
  AHX11146.1 254 KMDFGIHRADFLVIHGRNA 272
                 689999***********94 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   9.4e-05      0.14      32      53 ..      24      45 ..      13      53 .. 0.84
   2 ?   -2.3   0.0       1.8   2.8e+03      80     110 ..     304     335 ..     278     345 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 9.4e-05
       AAA_7 32 nkkpvllvGptGtGKtviikdl 53
                n+k+vl+ G  G+GKt+i++ +
  AHX11146.1 24 NSKHVLFFGRNGVGKTSILEAV 45
                689**************99875 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.8
       AAA_7  80 diiesklekrrkgvygPp.ggkklvvFvDDln 110
                 d i s+l++r+ +++    ++k + +F  Dl 
  AHX11146.1 304 DDIFSHLDQRNLELFLEEvMQKDCQFFFSDLE 335
                 44566666666666654325666777777765 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.8    0.0003      0.45      28      85 ..     273     319 ..     255     324 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0003
     SbcCD_C  28 rssgtlSGGekqflaylalaaalaalyssaegrepalrlvfLDEAFsklDeesiatll 85 
                 + +++ S+Ge+ + + la+++a++ l++          +++LD+ Fs lD+++++  l
  AHX11146.1 273 NTAKSCSTGEQ-KSLILAILLAASELVD----------IMLLDDIFSHLDQRNLELFL 319
                 567899****9.6666666666666555..........59************998665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00011      0.17      42      75 ..      14      47 ..       8      59 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00011
      DUF815 42 enteqfleglpannvLLwGarGtGKSslvkalln 75
                +n + + ++ ++++vL++G  G+GK s++ a+ +
  AHX11146.1 14 RNHSFYKTKFNSKHVLFFGRNGVGKTSILEAVSK 47
                57777788899******************99875 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   0.00018      0.27      94     120 ..      20      46 ..       6      68 .. 0.82
   2 ?   -3.9   0.0       7.5   1.1e+04      79      98 ..     224     243 ..     215     247 .. 0.58

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
                  HHHCTTSEEEEECSTTSSHHHHHHHHC CS
  RsgA_GTPase  94 kellkdktsvlvGqSGvGKStLinall 120
                  k+++++k +++ G  GvGK+++++a+ 
   AHX11146.1  20 KTKFNSKHVLFFGRNGVGKTSILEAVS 46 
                  66788999**************98764 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 7.5
                  EEE--TTTHTTHHHHHHHCT CS
  RsgA_GTPase  79 vllvsaktkegleelkellk 98 
                  +++vs++++ ++e++++ l+
   AHX11146.1 224 IMTVSTDKQVHVEDISRILR 243
                  45555555555555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (351 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 2602.28
//
Query:       AHX11147.1  [L=41]
Description: hypothetical protein NHE_0182 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       180  (0.0100396); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.26s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 325.03
//
Query:       AHX11148.1  [L=192]
Description: RNA methyltransferase, RsmD family [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-43  147.3   0.0    4.4e-43  147.0   0.0    1.0  1  Cons_hypoth95    Conserved hypothetical protein 95
      1e-05   25.4   0.0    1.4e-05   24.9   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    1.6e-05   24.5   0.0      2e-05   24.2   0.0    1.2  1  MTS              Methyltransferase small domain
      2e-05   24.4   0.3       0.13   12.0   0.0    2.2  2  MethyltransfD12  D12 class N6 adenine-specific DNA methyltran
    2.4e-05   24.9   0.0    3.7e-05   24.3   0.0    1.3  1  Methyltransf_25  Methyltransferase domain
    0.00011   22.0   0.1     0.0034   17.1   0.1    2.1  1  UPF0020          Putative RNA methylase family UPF0020
     0.0027   17.1   0.0     0.0043   16.5   0.0    1.3  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
  ------ inclusion threshold ------
       0.01   16.5   0.0      0.017   15.9   0.0    1.4  1  Methyltransf_12  Methyltransferase domain
      0.073   12.9   0.0      0.085   12.7   0.0    1.3  1  N6-adenineMlase  Probable N6-adenine methyltransferase


Domain annotation for each model (and alignments):
>> Cons_hypoth95  Conserved hypothetical protein 95
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.0   2.2e-46   4.4e-43       1     181 [.       1     186 [.       1     187 [. 0.92

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 2.2e-46
                    EEXXSCCCTTXEEEXTTXXXXXSSSHHHHHHHHHHHCCC......HCC-EEEETT-TTSHHHHHHHHTT-SEEEEEES-HHHHHHHHHHHCCCT-- CS
  Cons_hypoth95   1 lriigGkakgrkLkvlegkstRPttdrvrealFnilaae......iegarvLDlfaGsGalglEAlSRgakkavlvekdkeavkilkenleelkle 90 
                    +r+i+Gk++++k+ + +g ++RPt+ +vrealFnila+       +e+ ++LDlf G+G++++EAlSRg++++++v+ d +    +++nle+l ++
     AHX11148.1   1 MRVISGKYREKKIDLIKGVTIRPTMGKVREALFNILAHSslmskaFEEIHFLDLFTGTGSISIEALSRGCRSITAVDIDTR---CIRANLERLAIS 93 
                    9*************************************99*9999**********************************86...6899******99 PP

                    TTTEEEEES-HHHHCTS--SS-EEEEEEE--SSSTTCH........HHHHHHHHHTT-EEEEEEEEEEEECCSSS--.-TTEEEEEEEEETTEEEE CS
  Cons_hypoth95  91 eetaelkedaleallklakkkeefdivflDPPyakell.......ieevlelleekkllkenalvvvetekekelpespenlelvkekkygettla 179
                    + +++l   +  +l++      ++d+vf+DPPy+ke++       +e+ ++ l+++++l+ +++v++e++++ +   + +++e++++++yg ++l 
     AHX11148.1  94 D-ITVLD-RNIINLDSS---LIQYDVVFMDPPYMKEAVkyrpatiVEKSFDNLHKHHWLASGSIVILEKDRKDNSEMNHQGFEVLDRRRYGTSELL 184
                    7.55554.444445444...589*************98888888889**********************************************998 PP

                    EE CS
  Cons_hypoth95 180 ly 181
                    ++
     AHX11148.1 185 IF 186
                    76 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.9   0.0   7.1e-09   1.4e-05       4     116 ..      48     156 ..      46     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 24.9 bits;  conditional E-value: 7.1e-09
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieelekl.ledekfDlilsnevl...naladpdki 93 
                      ++++lDl +GtG +++e+ ++ +    ++ +Di+ + i+   e   +l ++ +++   +i +l+++ ++   +D+++ + +    +  + p+ i
       AHX11148.1  48 EIHFLDLFTGTGSISIEALSRGCR--SITAVDIDTRCIRANLE---RLAISDITVLDRNIINLDSSlIQ---YDVVFMDPPYmkeAVKYRPATI 133
                      6789***************87654..699*********76555...688***************98777...******9777666666778888 PP

  Methyltransf_31  94 leeiervlkpggilliedprlla 116
                       e+ +++l+++  l++ ++ +l+
       AHX11148.1 134 VEKSFDNLHKHHWLASGSIVILE 156
                      88888888888888777777333 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0     1e-08     2e-05      23     112 ..      42     126 ..      34     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1e-08
                 HHHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTSTTS-EEEEEE---STTTCH CS
         MTS  23 LletlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeveekkfdlivsNPPfhagka 112
                 + +++++    + lDl +G+G ++++++++  + ++t+vd+d+r +++  e l+ +++  ++    ++ + +   ++d++ + PP+ ++  
  AHX11148.1  42 MSKAFEE---IHFLDLFTGTGSISIEALSRGCR-SITAVDIDTRCIRANLERLAISDITvLDRNIINLDSSLI--QYDVVFMDPPYMKEAV 126
                 4444444...458***************99888.8********999776666666665544445555555555..9*********988765 PP

>> MethyltransfD12  D12 class N6 adenine-specific DNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   6.3e-05      0.13      19      46 ..      45      73 ..      34      87 .. 0.75
   2 !   10.8   0.1   0.00014      0.28     162     189 ..      95     123 ..      80     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                     ..--SEEEETT-TTSCCHHCS...SSCEE CS
  MethyltransfD12 19 d.kgktfvepFaGggaVffeakkqgkkvl 46
                        + +f ++F+G+g++++ea+++g + +
       AHX11148.1 45 AfEEIHFLDLFTGTGSISIEALSRGCRSI 73
                     455668***************99665443 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00014
                      EEEC-CHHHHTT-.-TTE.EEEE--S-T. CS
  MethyltransfD12 162 iecgdfdavllka.kieddivYlDPPYnp 189
                      i++ d + + l+   i+ d+v++DPPY  
       AHX11148.1  95 ITVLDRNIINLDSsLIQYDVVFMDPPYMK 123
                      555555555555558999*********87 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.9e-08   3.7e-05       2      70 ..      52     117 ..      51     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.9e-08
                      EEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEE CS
  Methyltransf_25   2 LdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvs 70 
                      Ldl +GtG ++++++ r g  ++t+vDi+ ++++a  er++   + +++++  ++ +l+    ++D+v++
       AHX11148.1  52 LDLFTGTGSISIEALSR-GCRSITAVDIDTRCIRANLERLA---IsDITVLDRNIINLDSSLIQYDVVFM 117
                      9**************99.69**************9999995...349*********************98 PP

>> UPF0020  Putative RNA methylase family UPF0020
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.1   1.7e-06    0.0034      25     171 ..      44     161 ..      30     181 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.7e-06
                 T--TTS-EEETT-TTSHHHHHHHHHHTT--TTTT----SSHHHHHHHHHHHH--EEEEES-HHHHHHHHHHHHHTT-GGGEEEEE--GGG--STTS--- CS
     UPF0020  25 gwkpgepllDPmCGsGtilIEaallganiapgllrefvlelkaeaeeearaelklygsDldrrvvqgareNaekagvgdliefsqadaakLrlkegevd 123
                 ++ ++  +lD + G+G+i IEa   g + +                          ++D+d r ++    N+e+  ++d+  +   ++ +L  +  ++d
  AHX11148.1  44 KAFEEIHFLDLFTGTGSISIEALSRGCRSI-------------------------TAVDIDTRCIR---ANLERLAISDITVLDR-NIINLDSSLIQYD 113
                 555667788899999999999866666655.........................7*****99985...7*******99777766.9999**55569** PP

                 EEEE----------HHHHHHHHHHHHHHHHHH-TT..-EEEEEESSHH CS
     UPF0020 124 vivtnpPYGerlgskkalekLYseflrelkrvlrgggrlvlltsenka 171
                 v+  +pPY +   + +      ++f +  k++   +g +v+l +++k+
  AHX11148.1 114 VVFMDPPYMKEAVKYRPATIVEKSFDNLHKHHWLASGSIVILEKDRKD 161
                 ********9999988888888888888777777776777766666655 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   2.1e-06    0.0043     164     211 ..      50      97 ..      36     118 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 2.1e-06
        PrmA 164 evlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkvea 211
                 ++lD+ tG+G ++i a+  g ++++avDiD   +++  e +++ +++ 
  AHX11148.1  50 HFLDLFTGTGSISIEALSRGCRSITAVDIDTRCIRANLERLAISDITV 97 
                 689*******************************99888777665554 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.9   0.0   8.3e-06     0.017       1      72 [.      52     117 ..      52     145 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 8.3e-06
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldgg.ssfDlvva 72 
                      L++ +GtGs++ + l +    ++t+vDi+++ i +a  +  ++++   ++++ + ++   ld++  ++D+v++
       AHX11148.1  52 LDLFTGTGSISIEALSR-GCRSITAVDIDTRCI-RANLERLAISD--ITVLDRNIIN---LDSSlIQYDVVFM 117
                      67778*********999.666677*********.44444444443..3344444444...3333349****97 PP

>> N6-adenineMlase  Probable N6-adenine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   4.3e-05     0.085      87     121 ..     110     155 ..      34     184 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.3e-05
  N6-adenineMlase  87 gkfdviviDPPFlseeclkklaktaklllk...........klilc 121
                       ++dv+ +DPP++ e +  + a+++++              +++++
       AHX11148.1 110 IQYDVVFMDPPYMKEAVKYRPATIVEKSFDnlhkhhwlasgSIVIL 155
                      479*************999988888766555665655554444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1468.00
//
Query:       AHX11149.1  [L=81]
Description: bolA-like family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.8e-12   47.4   0.0      2e-12   47.2   0.0    1.1  1  BolA      BolA-like protein


Domain annotation for each model (and alignments):
>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.2   0.0   1.1e-16     2e-12      26      72 ..      32      78 ..      18      81 .] 0.91

  Alignments for each domain:
  == domain 1  score: 47.2 bits;  conditional E-value: 1.1e-16
        BolA 26 ggetHFkvvivseaFegkslvarhRlvyalLkeelakgiHALslktk 72
                g + H++++i s++F gk +++rhRlv ++L e l++++H++s++t 
  AHX11149.1 32 GDGDHYHLRIRSSRFIGKASIQRHRLVVSALGELLKSRLHSISIETE 78
                6899****************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 610.67
//
Query:       AHX11150.1  [L=111]
Description: monothiol glutaredoxin, Grx4 family [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.1e-17   63.1   0.0    3.1e-17   62.5   0.0    1.3  1  Glutaredoxin  Glutaredoxin
  ------ inclusion threshold ------
      0.057   13.6   0.0       0.12   12.5   0.0    1.6  1  SH3BGR        SH3-binding, glutamic acid-rich protein


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   3.5e-21   3.1e-17       1      60 []      17      81 ..      17      81 .. 0.99

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 3.5e-21
                  EEEEES.....TSSHHHHHHHHHHHHTTGGEEEEEGCCSHHHHHHHHHHHTSSSSSEEEETTEEE CS
  Glutaredoxin  1 vvlftk.....ptCpyCkkakrlLkelgvkfeeidvdkdeeireelkelsgvrtvPqvfidgkhv 60
                  vvlf+k     p+C+++  ++ +L+ lgvkf+ +++++d+e+re +k+++++ t+Pq++++g++v
    AHX11150.1 17 VVLFMKgapemPMCGFSGVVVSILNALGVKFHSVNILEDQEMREGIKKFADWLTIPQLYVKGEFV 81
                  89*************************************************************97 PP

>> SH3BGR  SH3-binding, glutamic acid-rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.4e-05      0.12      23      53 ..      36      66 ..      33     103 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                HHHHHHHTT--EEEEETTT-HHHHHHHHHCS CS
      SH3BGR 23 vlriLdakkiefdevDitkdeeerelmrena 53
                v+ iL+a  ++f++v+i +d+e re +++ a
  AHX11150.1 36 VVSILNALGVKFHSVNILEDQEMREGIKKFA 66
                899*****************99999888654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       340  (0.0189637); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 841.53
//
Query:       AHX11151.1  [L=258]
Description: phosphate ABC transporter, permease protein PstC [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-17   64.4  16.0    1.1e-17   64.4  16.0    1.5  1  BPD_transp_1  Binding-protein-dependent transport system inne
  ------ inclusion threshold ------
       0.13   11.9   0.6       0.21   11.3   0.6    1.2  1  RTX           N-terminal domain in RTX protein
        2.6    8.3   7.0         14    6.0   0.8    2.6  2  MscL          Large-conductance mechanosensitive channel, Msc


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.4  16.0   1.9e-21   1.1e-17       1     175 [.      51     252 ..      47     257 .. 0.85

  Alignments for each domain:
  == domain 1  score: 64.4 bits;  conditional E-value: 1.9e-21
  BPD_transp_1   1 gillGilaalnrnkkldkllrpliivllslPsfvlaillvlvf..........vilsilghlilpviillllsaapyvrlirraalrslpkdlveaa 87 
                   gi+++i + ++ +k++++++ pli+v+ ++P+++ + + + ++           + si   ++l++ i++ ++++p+++ ++ + lr+ pk+l+  a
    AHX11151.1  51 GIGVAIAMTYFVSKRVRRFIKPLIEVMAGIPTIIYGYFSLTFIsklvqdlghlLHVSISSESALSAGIVIGIMIIPLITSMTDDLLRTTPKSLYYGA 147
                   444555555*************************99998877788899999999999999************************************* PP

  BPD_transp_1  88 ralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG.lgtllleailgydyseis................nggvlalviavll 167
                    alG +  +i+++v+lP  +p ++  ++laf ++lg+++++++l++ ++ l + +l++i    ++  +                +++ ++l +++++
    AHX11151.1 148 AALGSTQTEIIFRVILPYCFPGMVGVVLLAFSRALGETMVVLMLTGVSAnLDYNVLQPITTITVQIVTtltgdqtfnskeslsaYALGITLFALTWA 244
                   *********************************************8777955555555555544444455668888889988777777777777888 PP

  BPD_transp_1 168 lnlvadil 175
                   ln++++ +
    AHX11151.1 245 LNAISMSM 252
                   88777765 PP

>> RTX  N-terminal domain in RTX protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.6   3.5e-05      0.21      72     131 ..      18      78 ..      12      80 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 3.5e-05
         RTX  72 tieaaltaistvldvvsavvsaaaaasgVGaPvallva.litglisgileaskqailekvA 131
                 +i++ ++    +l  v + + +a+ as++GaP+++ va ++t  +s  ++ + ++++e +A
  AHX11151.1  18 IINGQVVKLFGILPLVFGTTMIALLASIIGAPIGIGVAiAMTYFVSKRVRRFIKPLIEVMA 78 
                 566677777789999********************99934566778778877777777776 PP

>> MscL  Large-conductance mechanosensitive channel, MscL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.8    0.0024        14      15      49 ..      46      80 ..      36     110 .. 0.71
   2 ?    5.3   0.2    0.0039        23      17      42 ..     114     139 ..     111     165 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0024
        MscL 15 idLAvgviiGaaftkiVtslvkdiimpliglllgg 49
                i   +g+ ++ a+t  V++ v+ +i+pli+++ g 
  AHX11151.1 46 IGAPIGIGVAIAMTYFVSKRVRRFIKPLIEVMAGI 80
                555688889999******************99853 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0039
        MscL  17 LAvgviiGaaftkiVtslvkdiimpl 42 
                 L+ g++iG  +  ++ts+++d++   
  AHX11151.1 114 LSAGIVIGIMIIPLITSMTDDLLRTT 139
                 789******************99765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       807  (0.0450109); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 1969.93
//
Query:       AHX11152.1  [L=71]
Description: hypothetical protein NHE_0187 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1169  (0.0652016); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 606.33
//
Query:       AHX11153.1  [L=317]
Description: hypothetical protein NHE_0188 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    0.00054   19.8   0.0     0.0083   15.9   0.0    2.1  1  GATase         Glutamine amidotransferase class-I
     0.0036   17.1   0.0      0.017   14.9   0.0    1.9  1  Peptidase_C26  Peptidase C26
  ------ inclusion threshold ------
      0.036   13.7   0.0      0.064   12.8   0.0    1.3  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma


Domain annotation for each model (and alignments):
>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.4e-06    0.0083      62     173 ..     134     281 ..      67     293 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.4e-06
                 HHHHHHCT.STS-EEEETHHHHHHHHHTTTEEEEEECEEEEEEEEEEEETTT....................................CGGTTTTSEEE CS
      GATase  62 eaikeare.nkiPiLGICLGmQllaiefgrkvvkekekehhggtmrlgddet....................................allyglknevi 123
                 +a  ++r+  k+ i+ IC GmQ ++++ g  +v  ++ +     +r+ dd+t                                    + +      + 
  AHX11153.1 134 DAMVKLRNeGKVSIFAICGGMQQTLDSDGIRIVDLSRIGITESHSRISDDSTnygargvfntllkkvminpsskiasiisdvsvevtpNGWL--VLYLP 230
                 33333443479**********************99999999999999998889999999999998888888888888888877655442222..23567 PP

                 EEEEEEEEEESG...CHHHTTEEEEEEEETTEEEEEEEEETT.TEEEESSBTTS CS
      GATase 124 erhrHryevnpk...elepaglevtakseddeelmeiiekkn.pfvgvQFHPEs 173
                 e+h  +  +++     l +ag  +++ sed+  ++e+ e+k+ +f+ +Q HPE 
  AHX11153.1 231 EWHLEGVDLDKGnlkVLREAGYNIVGFSEDG--VIEVLEDKYgNFY-FQSHPEN 281
                 7888888777668867788899999999877..9999999994577.9999996 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   2.9e-06     0.017      88     216 .]     127     280 ..     100     280 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.9e-06
  Peptidase_C26  88 peRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhrehe.....q......saashavkvekgsllaellgsee..... 167
                    ++R +++ a+++  +e +v i++iC G+q       G    d++++  ++ h + +                ++v ++++s +a+++++ +     
     AHX11153.1 127 QNRRRVTDAMVKLRNEGKVSIFAICGGMQQT-LDSDGIRIVDLSRIGITESHSRISddstnYgargvfNTLLKKVMINPSSKIASIISDVSvevtp 221
                    5677788899*******************98.8899999999998665555554444555504556656667899999999999999644411111 PP

  Peptidase_C26 168 .....ievnslHhqaike........laeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                               H  +++          + +++++  +eDgviE +e +  + f+   Q HPE
     AHX11153.1 222 ngwlvLYLPEWHLEGVDLdkgnlkvlREAGYNIVGFSEDGVIEVLEDKYGN-FY--FQSHPE 280
                    112223334566666666888888866778999999999999999888755.33..477776 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   1.1e-05     0.064      23      86 ..      87     155 ..      82     169 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 1.1e-05
    GATase_3  23 pevrvrfvplkdeslg.edadlvilpGgkdtiqdlall...resgldeaikeaae.aggpvlgiCGGlq 86 
                 +++ v  v+l +++l+ + ++ vi+pG +  +++  ++   +++++ +a+ ++ +  ++ +++iCGG+q
  AHX11153.1  87 GRKSVPLVTLLERELQaKGVNKVIIPGDYYNLDKPPFSpvqNRRRVTDAMVKLRNeGKVSIFAICGGMQ 155
                 5667788888888888777999*****9999998765411144555556555555145689*******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      438  (0.0244297); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2647.10
//
Query:       AHX11154.1  [L=44]
Description: hypothetical protein NHE_0189 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       159  (0.00886831); expected 358.6 (0.02)
Passed bias filter:                      146  (0.00814323); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 345.31
//
Query:       AHX11155.1  [L=712]
Description: primosomal protein N' [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.3e-17   63.6   0.1      2e-16   60.6   0.0    2.4  2  PriA_C          Primosomal protein N C-terminal domain
    4.4e-16   58.6   0.1      1e-15   57.4   0.1    1.7  1  PriA_3primeBD   3′ DNA-binding domain (3′BD)
    1.8e-14   53.9   0.0    9.3e-13   48.3   0.0    2.3  2  DEAD            DEAD/DEAH box helicase
      2e-11   44.2   0.3    4.1e-07   30.3   0.0    3.0  2  Helicase_C      Helicase conserved C-terminal domain
    1.9e-09   37.3   0.7    1.9e-09   37.3   0.7    2.5  3  PriA_CRR        PriA DNA helicase Cys-rich region (CRR) domai
    1.6e-07   31.5   0.1    2.8e-07   30.7   0.1    1.4  1  ResIII          Type III restriction enzyme, res subunit
     0.0032   17.0   0.0     0.0069   15.9   0.0    1.5  1  PhoH            PhoH-like protein
  ------ inclusion threshold ------
      0.025   14.4   0.0        0.1   12.5   0.0    2.0  2  Cbl_N3          CBL proto-oncogene N-terminus, SH2-like domai
      0.028   14.1   0.0      0.064   13.0   0.0    1.6  1  AAA_30          AAA domain
      0.065   13.4   0.3       0.14   12.4   0.3    1.6  1  AbiEi_4         Transcriptional regulator, AbiEi antitoxin
      0.084   13.1   0.0       0.28   11.4   0.0    1.9  1  AAA_22          AAA domain
       0.09   12.0   0.0       0.14   11.4   0.0    1.2  1  DUF2075         Uncharacterized conserved protein (DUF2075)
       0.11   13.0   2.7       0.22   12.0   2.7    1.4  1  zf-CHY          CHY zinc finger


Domain annotation for each model (and alignments):
>> PriA_C  Primosomal protein N C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.0       1.5   2.1e+03      44      89 ..     219     265 ..     186     270 .. 0.73
   2 !   60.6   0.0   1.4e-19     2e-16       1      94 []     618     708 ..     618     708 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 1.5
      PriA_C  44 apapiakikgryryqillksksrkalqkllkellekleklkk.vrvs 89 
                  ++ ++ +k +  +qi++  ++ +  + + +++++++  + + ++++
  AHX11155.1 219 LASALEILKREENAQIIIILSEIALTSYIFEKIKSHFAGKIEiIEWH 265
                 56678889999999999999988888888888888887554336665 PP

  == domain 2  score: 60.6 bits;  conditional E-value: 1.4e-19
      PriA_C   1 PFsrlalirvsgkdeekveeaaeelaellkealkleeveilgpapapiakikgryryqillksksrkalqkllkellekleklkkvrvsiDvDP 94 
                 PFsrl+ i++sg  e++v+++a+ + ++++     +ev+++gp+papi  +++r+ry+ill ++++ +++++l +  ++l  +k+v+v++DvDP
  AHX11155.1 618 PFSRLIAIVISGLVESEVISQARYMEQTISLI---KEVTMFGPCPAPIGVRNNRFRYRILLVTPKSYRIHNILMASFKQLPIRKGVSVQVDVDP 708
                 9**************************99983...6799***********************************99999987779********9 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.4   0.1   7.4e-19     1e-15       1      95 [.       4      95 ..       4      96 .. 0.97

  Alignments for each domain:
  == domain 1  score: 57.4 bits;  conditional E-value: 7.4e-19
  PriA_3primeBD  1 eVavdlpldrtfdYrvpeelevkiGsrVlVpfgkrklvGiVvalkeeseveeeklkpieevldeepllteellelaewlaeyylaplgevlkaal 95
                   +V+++l+ld+ f Y+   el+v++G  V+V+f++r+++G+V+++  e++  ++ +k+i++vl    ll+++++e++ w+a+y +a++g vl+ a+
     AHX11155.1  4 KVVLPLALDEEFLYSS-GELMVQVGNLVMVNFNGRNIIGLVISVGPETS-VQYTVKEITSVLP-FKLLQASYIEFLFWVARYNFAKIGLVLRSAI 95
                   69*************9.899***************************99.78**********9.99*************************9986 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.0   6.8e-16   9.3e-13      18     173 ..     205     353 ..     187     356 .. 0.77
   2 ?    3.1   0.0     0.053        73      61     105 ..     482     525 ..     475     537 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 6.8e-16
                 EEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTT.ST.SEEEEEET.TSSHHHHHHHHHTTCSEEEEEHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx.xxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  18 lvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkky.id.lrvlliig.gvaardqlskldngvdivvgtpgrlddlls 113
                 l+ + TGsGKT+++l  +l+i+   k++++ +++i+    +L+  +++++k+ +   i+ +++++ ++ +++ar+ +++++n+++ivvg  + ++    
  AHX11155.1 205 LLDGITGSGKTMVYLASALEIL---KREENAQIIIILSEIALTSYIFEKIKSHFAGkIEiIEWHSNMSpSHRARNWRRVVNNKARIVVGARSAIFL--- 297
                 66778*****************...789999********************99997687666666666366666777777788*******988885... PP

                 CTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHS...HHHCTTSTTTSEEEEEESSBS.HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxx.xxx RF
        DEAD 114 tgklnlsqvrflVlDEadrlldqgfsdfinrilnql...pqitcdgklqrqvivlSATlp.kdv 173
                        ++r++++DE +  + ++ + ++   ++ l   + + cd +    +i+ SAT++ ++v
  AHX11155.1 298 ----PAPNLRMIIVDEEHDQSFKQDQGELTYNARDLaimRAKLCDIP----IILSSATPSlESV 353
                 ....4789********9988766444444444555400044555555....********97776 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.053
                 HHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHH.TTCSEEEEEH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
        DEAD  61 eqtlnnlkkfkkyidlrvlliiggvaardqlskld.ngvdivvgtp 105
                 e++ +++++++ +   rv+++ ++++ +++l+k++ n+vdi++gt 
  AHX11155.1 482 EKISEEIEELFPK--RRVVVMSSDSQLTENLRKIEaNEVDIIIGTQ 525
                 5566667777764..577777888888*******8566******96 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.7   0.1   0.00037      0.51       6      72 ..     222     290 ..     217     295 .. 0.82
   2 !   30.3   0.0   2.9e-10   4.1e-07      24     110 ..     479     573 ..     459     574 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00037
                 HHHHHHHTTTTSEEEEEESSHH.HHHHHHHHHHHT..TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEE CS
  Helicase_C   6 llellkleeeggkilifvntid.rlekvklllekk..gikvavlhgelpqnereeileqfnkgesdvLia 72 
                  le+l ++ee+ +i+i++  i  + + ++ +++++  +i+++  h++++ ++r +  ++  +++ ++++ 
  AHX11155.1 222 ALEIL-KREENAQIIIILSEIAlTSYIFEKIKSHFagKIEIIEWHSNMSPSHRARNWRRVVNNKARIVVG 290
                 56777.89999***********5443367776666889******************99999888888775 PP

  == domain 2  score: 30.3 bits;  conditional E-value: 2.9e-10
                 SSHHHHHHHHHHHHHT.TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH............HHHHHHHTTSSS CS
  Helicase_C  24 ntidrlekvklllekk.gikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv............tsyiqriGRtgR 109
                 + i++++  + ++e + + +v+v+ +    ++  e l++  ++e+d++i t+++++G d+pk++l+ ++d + +v            + ++q +GR+gR
  AHX11155.1 479 PGIEKIS--EEIEELFpKRRVVVMSS---DSQLTENLRKIEANEVDIIIGTQIISKGYDFPKLTLLAIIDSDASVcagdlrsaeknfHILQQVMGRVGR 572
                 5555554..44444444566666666...45666888999999*****************************776666677777777************ PP

                 T CS
  Helicase_C 110 a 110
                  
  AHX11155.1 573 R 573
                 6 PP

>> PriA_CRR  PriA DNA helicase Cys-rich region (CRR) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.48   6.7e+02      17      26 ..     424     433 ..     420     434 .. 0.80
   2 !   37.3   0.7   1.4e-12   1.9e-09       1      27 []     435     461 ..     435     461 .. 0.99
   3 ?   -3.4   0.4       7.7   1.1e+04       1       5 [.     466     470 ..     466     472 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.48
    PriA_CRR  17 LrCHyCgyte 26 
                 ++C  Cg++ 
  AHX11155.1 424 VVCASCGHRI 433
                 78******85 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 1.4e-12
    PriA_CRR   1 CpnCdvsltyHksrnrLrCHyCgyteP 27 
                 Cp+C ++l+ Hk +n+L CH Cg+++P
  AHX11155.1 435 CPDCVAWLVEHKWNNSLLCHLCGFKRP 461
                 *************************99 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 7.7
    PriA_CRR   1 CpnCd 5  
                 C +C+
  AHX11155.1 466 CERCA 470
                 99**7 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.7   0.1     2e-10   2.8e-07       4     149 ..     185     323 ..     144     350 .. 0.78

  Alignments for each domain:
  == domain 1  score: 30.7 bits;  conditional E-value: 2e-10
                 E-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG....GEEEESSS-B--...... CS
      ResIII   4 lreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseaykeigkkvsgdkkkakekdst 102
                 l e Q ++ +++   l  ++ +  l+   TG+GKT+v+++ + ++lk +++ +++++  +++l++   e++k+ +  +     ++++  ++++ ++++ 
  AHX11155.1 185 LSEEQRQVKDRIF--L--EKFTAHLLDGITGSGKTMVYLASALEILKREENAQIIIILSEIALTSYIFEKIKSHFAGK----IEIIEWHSNMSPSHRAR 275
                 4455555555553..2..6788999**********************99999*********************99997....46666666666679999 PP

                 .-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.T.....T CS
      ResIII 103 nkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakk.....s 149
                 n++ +v +  ++        +    l   +  +ii+DE H  + k+     +
  AHX11155.1 276 NWRRVVNNKARIVVGA----RSAIFLPAPNLRMIIVDEEHDQSFKQdqgelT 323
                 *********9999999....667777777888********988753334442 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0     5e-06    0.0069       6      56 ..     186     238 ..     184     247 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 5e-06
                 SHHHHHHHHHHH..H-SEEEEE--TTSSTTHHHHHHHHHHHHTTS-SEEEEEE CS
        PhoH   6 tkeQkeylealk..kndivfaiGpaGtGKtylavalavealkkkkvkriiltr 56 
                 ++eQ+++ + +   k +     G +G+GKt++ +a a+e+lk+++  +ii++ 
  AHX11155.1 186 SEEQRQVKDRIFleKFTAHLLDGITGSGKTMVYLASALEILKREENAQIIIIL 238
                 5678888888774355566778*************************999975 PP

>> Cbl_N3  CBL proto-oncogene N-terminus, SH2-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.8   3.8e+03      49      79 ..     387     419 ..     380     422 .. 0.74
   2 ?   12.5   0.0   7.4e-05       0.1      48      82 ..     578     612 ..     564     616 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.8
                 S-EEEE--TT..--HHHHHHHHHHTTS--EETT CS
      Cbl_N3  49 kkilqtipqn..kslvqalidGereglylyPdG 79 
                  k+ q i ++   sl q l  G +  l+l  +G
  AHX11155.1 387 SKVSQHISEElyESLKQNLDSGMQSLLFLNRRG 419
                 677788877644699999999999888876665 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7.4e-05
                 TS-EEEE--TT--HHHHHHHHHHTTS--EETT-S- CS
      Cbl_N3  48 dkkilqtipqnkslvqalidGereglylyPdGkek 82 
                  + i+q+   + s+vqal +G reg+y    G++k
  AHX11155.1 578 GTAIMQSYSPDGSVVQALKNGDREGFYAEELGTRK 612
                 5789***********************98888765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   4.6e-05     0.064       2      64 ..     185     253 ..     184     328 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.6e-05
      AAA_30   2 lnaeQaaavealltsgdrvavltGpAGtGKtta.lkalreaweaa.ggrvig....lAptgkaAkvLae 64 
                 l++eQ+++ +++  ++   ++l G  G+GKt++ l+++ e+++++ + ++i+    +A t+   ++++ 
  AHX11155.1 185 LSEEQRQVKDRIFLEKFTAHLLDGITGSGKTMVyLASALEILKREeNAQIIIilseIALTSYIFEKIKS 253
                 89*****************************97477778888888666666411113555555555553 PP

>> AbiEi_4  Transcriptional regulator, AbiEi antitoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.3    0.0001      0.14       1      41 [.     123     162 ..     123     163 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
     AbiEi_4   1 erlpelasrqvGlfttreleaaGispsalrrLvrkGwLvrl 41 
                 +rl+e++ r++ ++t ++l +a i  +++ +++++G++ r+
  AHX11155.1 123 RRLLEFF-RRNEYLTADDLHEAKIQKRTVQKMLESGLIRRV 162
                 79*****.6669**************************997 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00021      0.28       9     130 ..     205     346 ..     202     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00021
      AAA_22   9 vvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka...........erlsseellealeqalrarav..... 91 
                 ++ G +G+GKT+++   + +  +++     +  ++ + l++    + +++++ + +  + +            +  + +++++  ++ +  ++      
  AHX11155.1 205 LLDGITGSGKTMVYLASALEILKRE-----ENAQIIIILSEIALTSYIFEKIKSHFAGKIEIiewhsnmspshRARNWRRVVNNKARIVVGARSaiflp 298
                 6789*********999999886654.....444444555555544556666666666544446666666666555678888877777777777789999 PP

      AAA_22  92 ...ielliiDEaqhlr....seealeeLrsllnl..srkgvqliLvGt 130
                     +++i+DE +  +    + e+  + r+l+    + +++++iL   
  AHX11155.1 299 apnLRMIIVDEEHDQSfkqdQGELTYNARDLAIMraKLCDIPIILSSA 346
                 9999*******9996444433888888899988899999999999754 PP

>> DUF2075  Uncharacterized conserved protein (DUF2075)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0    0.0001      0.14       5     105 ..     205     318 ..     202     342 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
     DUF2075   5 lVtGvaGtGKtvvllnllaeleddeeertavylsvNhplvlvlrealakke..........ekkkkkeafeklssfinnlsef...kkaeekkeepked 90 
                 l  G +G+GKt+v l+ + e+ + ee+ + ++++   +l   + e+++++           ++++ ++++++ + ++nn  +     + +   + p+++
  AHX11155.1 205 LLDGITGSGKTMVYLASALEILKREENAQIIIILSEIALTSYIFEKIKSHFagkieiiewhSNMSPSHRARNWRRVVNNKARIvvgARSAIFLPAPNLR 303
                 5689*****************999999999999999999998888888777777799998888888888888888888888778887777778999999 PP

     DUF2075  91 vvivDEAhrlltksd 105
                 ++ivDE h    k+d
  AHX11155.1 304 MIIVDEEHDQSFKQD 318
                 999999886555555 PP

>> zf-CHY  CHY zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   2.7   0.00016      0.22      11      62 ..     424     471 ..     417     483 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00016
      zf-CHY  11 irapcCkklyaCreCHeeledhelerlevkevlcllCeteqekavlCkkCkk 62 
                 + ++ C +  +C  C + l +h+   ++ +++lc lC  +++  ++C++C +
  AHX11155.1 424 VVCASCGHRIKCPDCVAWLVEHK---WN-NSLLCHLCGFKRPMIIQCERCAS 471
                 678999**********9788884...44.4578*****************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (712 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       658  (0.0367003); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        77  (0.00429472); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.67u 0.27s 00:00:00.94 Elapsed: 00:00:00.44
# Mc/sec: 4813.66
//
Query:       AHX11156.1  [L=321]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.4e-05   21.4   1.0    0.00017   20.5   1.0    1.4  1  Anoctamin        Calcium-activated chloride channel
  ------ inclusion threshold ------
      0.068   13.3   0.0      0.068   13.3   0.0    2.7  3  YtpI             YtpI-like protein
       0.11   12.5   0.7        2.7    7.9   0.2    2.2  2  Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
       0.34   11.2   2.1        0.4   11.0   0.2    2.1  3  MLANA            Protein melan-A
        1.9    8.4  12.2        1.1    9.1   5.3    3.1  3  Claudin_3        Tight junction protein, Claudin-like
        4.8    6.2   8.0        1.3    8.1   2.0    2.5  2  TMEM192          TMEM192 family


Domain annotation for each model (and alignments):
>> Anoctamin  Calcium-activated chloride channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   1.0   5.8e-08   0.00017      98     198 ..       6     116 ..       2     122 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 5.8e-08
   Anoctamin  98 krespvtgeeefyyppwkrrlfrllvslplvllliclavvgvlilrclalqelvssvke..........llsflptvlnlvlililne.....vykkla 181
                 k+ sp t +   yy   kr+++rll+ ++ +   ++l +v+v++++ +++ +++ + k+          + ++l tv + +l ++++e        kl 
  AHX11156.1   6 KQHSPTTTSLYRYYLCEKRKIRRLLCAMVAL--EVLLTLVFVVVYA-VSVFTFL-KPKHltsalikgieM-TVLVTVALSLLTFLVKEcalakYCGKLK 99 
                 4456889999********9*****9999444..4445677777776.3332232.233334444333321.2333333322222222223333888888 PP

   Anoctamin 182 iwltdlEnhrtqseyek 198
                  +l+++En  ++ e ++
  AHX11156.1 100 NRLNEFENVSHNPEEDE 116
                 ********988766555 PP

>> YtpI  YtpI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.5      0.29   8.6e+02       5      19 ..      39      53 ..      29      85 .. 0.66
   2 ?   -2.4   0.0       1.9   5.6e+03      32      44 ..     138     150 ..     128     159 .. 0.55
   3 ?   13.3   0.0   2.3e-05     0.068       2      52 ..     194     249 ..     193     260 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.29
        YtpI  5 vlslvlyvyykvkaf 19
                +l+lv+ v+y v  f
  AHX11156.1 39 LLTLVFVVVYAVSVF 53
                455555555554443 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.9
        YtpI  32 akasialGlflil 44 
                 +k   alGlf ++
  AHX11156.1 138 GKVTTALGLFTLS 150
                 3334444444433 PP

  == domain 3  score: 13.3 bits;  conditional E-value: 2.3e-05
        YtpI   2 ilivlslvlyvyykvkafrtkdplekk....llsakasialGlflilfgin.qlll 52 
                 ++i l l+ y+y +++ +r+  + ek+    +l+  as+++++fl++++++  ++ 
  AHX11156.1 194 FCIGLHLCQYFYSRRRGYRSLGEKEKGaeslMLMPPASLCMSFFLATLALVtKVFK 249
                 689999**************9998887444478899**************955544 PP

>> Abhydrolase_9_N  Alpha/beta-hydrolase family N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00092       2.7      91     159 ..      27      96 ..      20     116 .. 0.77
   2 ?    3.1   0.0     0.027        80      46     121 ..     178     252 ..     125     286 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00092
  Abhydrolase_9_N  91 eyllvllvallvfalllllgrllralvrlla.rllgrvlprrvaavlgvlvvvvlvvllvdgvvvrgvla 159
                        ll+++val v++ l+ ++     ++ +l+ ++l+  l + + +++ v+v++ l+ +lv++  +     
       AHX11156.1  27 RRLLCAMVALEVLLTLVFVVVYAVSVFTFLKpKHLTSALIKGIEMTVLVTVALSLLTFLVKECALAKYCG 96 
                      5678999999999999999999999999999988999888888888888888888877777766655544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.027
  Abhydrolase_9_N  46 rrvrrrlrlalavvalvvllvalvlaarwQrelralmgaeplgaaeyllvllvallvfalllllgrllralvrlla 121
                       rv+ +++ ++a+++l ++ + l +    +r+  + +g ++ ga + +l+ +++l + ++l +l+ l+ +++++l+
       AHX11156.1 178 SRVEDACEFIFATIGLFCIGLHLCQYFYSRRRGYRSLGEKEKGAESLMLMPPASLCMSFFLATLA-LVTKVFKALE 252
                      67888889999999999999999999999999999999999999999999888887776665554.5555666555 PP

>> MLANA  Protein melan-A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.7     5e+03      54      54 ..      94      94 ..      60     140 .. 0.51
   2 ?   -2.1   0.0       1.5   4.4e+03      24      42 ..     142     162 ..     122     174 .. 0.69
   3 ?   11.0   0.2   0.00013       0.4      22      63 ..     180     222 ..     162     234 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.7
       MLANA 54 s 54
                 
  AHX11156.1 94 Y 94
                2 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
       MLANA  24 eaaGigll..vvvLaillllg 42 
                  a+G+  l   +vL ill++ 
  AHX11156.1 142 TALGLFTLsaSLVLEILLVID 162
                 455555542237888888875 PP

  == domain 3  score: 11.0 bits;  conditional E-value: 0.00013
       MLANA  22 aeeaaGigllvvvL.aillllgCwyykrrsGYkslrskslkvs 63 
                 +e+a      ++ L  i l l  ++y rr+GY+sl +k+  ++
  AHX11156.1 180 VEDACEFIFATIGLfCIGLHLCQYFYSRRRGYRSLGEKEKGAE 222
                 55555544444433144456666889*********99987655 PP

>> Claudin_3  Tight junction protein, Claudin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   5.3   0.00038       1.1      54     127 ..      28      99 ..      18     105 .. 0.81
   2 ?   -1.2   0.0      0.57   1.7e+03      56      71 ..     183     198 ..     165     214 .. 0.71
   3 ?    0.9   0.1      0.13   3.8e+02      12      47 ..     232     262 ..     220     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00038
   Claudin_3  54 eaasimmyislalflvviliyivivrkvkkngysksvrklffliallslliviltviaviliavnvskfndsfn 127
                  + + m+ + ++l+lv +++y+v v+ + k +    +  l+++i +++l++v+l ++++ + +  + k++ + +
  AHX11156.1  28 RLLCAMVALEVLLTLVFVVVYAVSVFTFLKPKHL--TSALIKGIEMTVLVTVALSLLTFLVKECALAKYCGKLK 99 
                 6789999999999999999999999999998877..67789999999999999999999999999998887765 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.57
   Claudin_3  56 asimmyislalflvvi 71 
                 a+ +++++++lf++ +
  AHX11156.1 183 ACEFIFATIGLFCIGL 198
                 7888888888887755 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.13
   Claudin_3  12 vvisfilnivglftpaWiteestkkeksiGivPfss 47 
                 +++sf l +++l+t+ +   e+t     + ++P ++
  AHX11156.1 232 LCMSFFLATLALVTKVFKALEGT-----NTVMPLKV 262
                 56777788888888777776666.....55666555 PP

>> TMEM192  TMEM192 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   2.0   0.00044       1.3     145     176 ..      28      59 ..      13      65 .. 0.87
   2 ?    0.1   0.1      0.12   3.5e+02     106     166 ..     143     206 ..     128     211 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00044
     TMEM192 145 lfvliilllEllvllivlviYivkvvrFNkar 176
                  +++++++lE+l++l++ v+Y v v  F k +
  AHX11156.1  28 RLLCAMVALEVLLTLVFVVVYAVSVFTFLKPK 59 
                 6899*********************9997655 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.12
     TMEM192 106 pLiivSlgnavLLlvlavlrslykkek...aeqalsealspllfvliilllEllvllivlviYi 166
                 +L +++l+  ++L +l v++ +++        +  s       f+++ ++l ++ l +++  Y 
  AHX11156.1 143 ALGLFTLSASLVLEILLVIDLYCPFGMqtaHGDFISRVEDACEFIFATIGLFCIGLHLCQYFYS 206
                 5677788888888888888888876664434556666667788999999999999999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       988  (0.0551063); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2353.88
//
Query:       AHX11157.1  [L=208]
Description: exopolysaccharide synthesis, ExoD family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-56  188.3   6.2    9.6e-56  188.0   6.2    1.1  1  ExoD      Exopolysaccharide synthesis, ExoD


Domain annotation for each model (and alignments):
>> ExoD  Exopolysaccharide synthesis, ExoD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.0   6.2   5.3e-60   9.6e-56       2     178 ..       9     186 ..       8     188 .. 0.98

  Alignments for each domain:
  == domain 1  score: 188.0 bits;  conditional E-value: 5.3e-60
        ExoD   2 sdlLerlaeeaeseevtlgelldalgergfgllllllalplllPlpa.pgvstifGllilllalqmllgrrtpwLPkklarrsisrkklqkllkklrpl 99 
                 sd+Le ++ +  ++++tl e+   l+ergf+lllll++lpl +Plp+ pg++ti++l+il++++q++lg ++pwLPk+l+++ i+rk+l+ l++k  p+
  AHX11157.1   9 SDVLESVVVQGVRDTITLFEIKRILHERGFALLLLLFSLPLSIPLPVpPGYTTILSLPILFFSIQITLGCDSPWLPKFLENKAIKRKSLAFLIEKTVPI 107
                 89************************************************************************************************* PP

        ExoD 100 lrrlerllrpRltfltsrlaerllglailllaillalPiPftntlpalailllalGllerDGllvllglllallavall 178
                 lr++e+++rpR+++l++ ++e++ g++ +++a+++a+P+P+tn++pa +i+l++lG+l++DG++ +lg++++++++++ 
  AHX11157.1 108 LRKVEKFTRPRFPVLNNAFGEKIYGIISFICAVSIAIPLPLTNFIPAGGIALMSLGMLNKDGVISILGIVVSFTGIFIS 186
                 ***********************************************************************99988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1650.74
//
Query:       AHX11158.1  [L=269]
Description: P-type conjugative transfer protein VirB9 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-64  216.4   0.0    4.1e-64  216.2   0.0    1.0  1  CagX      Conjugal transfer protein


Domain annotation for each model (and alignments):
>> CagX  Conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  216.2   0.0   2.3e-68   4.1e-64       2     211 .]      32     246 ..      31     246 .. 0.92

  Alignments for each domain:
  == domain 1  score: 216.2 bits;  conditional E-value: 2.3e-68
        CagX   2 riqtvvYspgavvrvraapgyvtdielepgEkivevalGdtvrWeveptkgnhlfvkPteaglktnlvvvTdkRtYsfeLrste...kekkklmyrvsf 97 
                 +i+++vY+p+a+++ ++  gy+++i++e+gE i ++++Gd+++W+++p +gn+lf+kPt+++ +tn++++T+kR+Y+f +r +e    ++++l y+v+f
  AHX11158.1  32 QIKEIVYNPNAIHTYTGFFGYQSSIVFEDGEIIGTISMGDSTAWQLNP-QGNRLFLKPTDDNSTTNVTILTNKRVYHFVFRGKEakdIDDPELSYEVRF 129
                 6999********************************************.*******************************99998889999******** PP

        CagX  98 rypdeeaaaaaaaaaaaaaekkeaqek.....apeklnfdYsvsgsaeiaPervfdDgrfTyirfpsankelPavfvvdedgkeelvnyrvegnylvvd 191
                 ryp++  + +++ +a+ + +++ +        +++ lnf+Y++sgs++i+P +vfdDg+fTy++f+s n++lPa+f+vd++g e+lvny+++g+ylv++
  AHX11158.1 130 RYPASSVSVQNTGMADMQGSDRVE--PgldiaKKDYLNFEYKLSGSDNIKPLKVFDDGHFTYMQFHSVNANLPAIFLVDSKGYESLVNYHISGKYLVIQ 226
                 *****9999933333333333333..144666******************************************************************* PP

        CagX 192 rvakklvLrlGkevvriene 211
                 +va++++Lr+G+e v+++n+
  AHX11158.1 227 QVASRFTLRHGDEYVCVFNT 246
                 *****************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2210.21
//
Query:       AHX11159.1  [L=220]
Description: putative type IV secretion system protein VirB8 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.041   13.8   0.4       0.08   12.8   0.4    1.4  1  Chordopox_A35R  Chordopoxvirus A35R protein
       0.13   11.9   2.7       0.23   11.2   2.7    1.3  1  Doppel          Prion-like protein Doppel


Domain annotation for each model (and alignments):
>> Chordopox_A35R  Chordopoxvirus A35R protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.4     9e-06      0.08      57     137 ..      15      97 ..       3     107 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 9e-06
  Chordopox_A35R  57 ledCYiavnGvilkcsednklrlp..vtkiyaayrsknsiilccdkdpklsideklqpfyistsiviaeari.lEvYnlykkgd 137
                     l++     +G + +cs+++++ ++     i++a +  + +il ++ + +l +++ +  f++ t+ +  e +i + +Y+ly+k+d
      AHX11159.1  15 LQQGRYYEEGLLWHCSKNYYVFIErsWLIIFCALLFSTLCILSFNVYSMLPTKTSV-TFIRYTDDIHNEISIpIRLYDLYRKND 97 
                     555555679***********9887225689********************998765.57777777777777769******8765 PP

>> Doppel  Prion-like protein Doppel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   2.7   2.5e-05      0.23       9      21 ..      41      53 ..      38      56 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 2.5e-05
                CHHHHHHHHHHHC CS
      Doppel  9 wlAivCvLLfShL 21
                wl i+C+LLfS L
  AHX11159.1 41 WLIIFCALLFSTL 53
                999********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       702  (0.0391544); expected 358.6 (0.02)
Passed bias filter:                      389  (0.0216967); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1767.36
//
Query:       AHX11160.1  [L=192]
Description: grpE family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-46  156.5   5.9    5.5e-46  156.3   5.9    1.1  1  GrpE      GrpE


Domain annotation for each model (and alignments):
>> GrpE  GrpE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.3   5.9   3.1e-50   5.5e-46      23     165 ..      26     186 ..       2     187 .. 0.85

  Alignments for each domain:
  == domain 1  score: 156.3 bits;  conditional E-value: 3.1e-50
                 C..................HHHCTTSCCCCCCTTTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..HHH-HHHHHHHHHHHHHHHH CS
        GrpE  23 e..................lekevkelkekllrllaefenlrkrtekekeeakkfaiekfakdLLpvlDnleralksakeneeekslleGvemtlkqll 103
                 e                  ++kev+ +k+kl+++lae enl+k++++e+e+ ++fai+++ak++L  +++le+a++++ en+ e +lleG ++tl+ + 
  AHX11160.1  26 ErapkneessgagfiseedFKKEVDLWKKKLMYALAEQENLKKNVAREIEKTRDFAISDLAKEILTSVESLEKAVAHMVENKIEGPLLEGSKLTLEAIF 124
                 1333333333444444444******************************************************************************** PP

                 HHHHHTT-EE---TTSB--TTTEEEEEEECSSC...TBEEEEEE--EEETTEEEE-EEEEEE CS
        GrpE 104 kiLekhgvekiepkgepFDpnlheavstveddekeegtvvevvqkGYklkdrvlRpAmVkVs 165
                 ++L+k gvekie+kg  FD+n+h+avstv++de +++tv+ev+q+GY +k+r+lRpA V+V+
  AHX11160.1 125 SALKKGGVEKIEAKGVLFDHNVHQAVSTVKNDELPNNTVFEVLQDGYIIKGRLLRPAIVVVV 186
                 *************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1152  (0.0642534); expected 358.6 (0.02)
Passed bias filter:                      610  (0.0340231); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1415.62
//
Query:       AHX11161.1  [L=332]
Description: tryptophan--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.4e-61  206.2   0.0    1.4e-60  205.1   0.0    1.6  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.1   0.0   7.9e-65   1.4e-60       7     252 ..      11     256 ..       7     318 .. 0.86

  Alignments for each domain:
  == domain 1  score: 205.1 bits;  conditional E-value: 7.9e-65
                   EEEEEEETSSS-BGG.GHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT-SSHHHHHHHHHHHHHHHHHHHHHTCHTTTEEEEETHHHHTTHHHHHH CS
  tRNA-synt_1b   7 rvysGidPTgklHlG.ylvplkklvelqkaghevffliaDlhAiigdpskaeerklrkreevlenaikaqlakgldpekaevvlqsewlehlelael 102
                   +v+s ++PTg++HlG  ++++  +v+lq++  + f +iaDlh + g      + + r ++ev + +   ++a+g+dp+++++++qs++++h el +l
    AHX11161.1  11 IVLSAVQPTGSVHLGnLFGAIDLWVDLQSKYKTKFYCIADLHSLDGGGA---ADTARLSVEV-ACI---YIACGIDPTDSHIFVQSHIPQHAELCWL 100
                   68899**********99***********88888899********99999...5555555554.455...8*************************** PP

                   HHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHSEEEEEGGGHHHHHHHHHHHHHHHHH...STTSS-EEEEET....... CS
  tRNA-synt_1b 103 lrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkadlvpgGsDQkqnielgrdlarrfnkk...evfkkpegltvp....... 189
                   l++++++g+lnrm+q+k+  k++++ e+  l++ +Yp+L+aaDill++a+l p+G+DQ+q++el rd+a rfn+    +      +lt p       
    AHX11161.1 101 LSCITPTGWLNRMTQYKE--KSAAR-ESTMLSLYSYPVLMAADILLYNAELIPVGDDQSQHVELVRDIAARFNQLygvD------HLTLPatlkcel 188
                   ******************..77777.5789********************************************95554......555555555558 PP

                   ...-BBSTTSSSBTTCETTC..GC-BTTCCHHHHHHHHHHCHCSTTCSHHH.HHHHHHTHHHCHHHHHH CS
  tRNA-synt_1b 190 ...lltgldGekKmSKSagn..saIfLddekesvkkkiqkavtdsdeevek.llklktelsnelierle 252
                      ++ + d++kKmSKS++   s+I+L+d+k+ + +ki+ a+tds  ++     + ++e sn l+   +
    AHX11161.1 189 vtrVMGLRDPTKKMSKSDPAdfSRINLSDSKDLIAEKINAAKTDSIMGFSVeNIEDRPEASN-LLRMAS 256
                   888******************************************98443302344566666.444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       616  (0.0343577); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2503.71
//
Query:       AHX11162.1  [L=117]
Description: ribosomal protein L20 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-47  160.4   3.7    1.4e-47  160.2   3.7    1.0  1  Ribosomal_L20  Ribosomal protein L20
  ------ inclusion threshold ------
       0.14   11.7   0.0       0.14   11.6   0.0    1.1  1  ApbE           ApbE family


Domain annotation for each model (and alignments):
>> Ribosomal_L20  Ribosomal protein L20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.2   3.7   1.6e-51   1.4e-47       1     106 [.       3     108 ..       3     109 .. 0.99

  Alignments for each domain:
  == domain 1  score: 160.2 bits;  conditional E-value: 1.6e-51
                    XXX.XXXXXXXXXXXXX--SSS---SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTT--HHHHHHHHCCTTS---HHHHHHH CS
  Ribosomal_L20   1 RvkrgvaarkrrkkilklakgyrgrrsklyrvakqavekalqyayrdRkkkkrdfrklwitrinaaarenglsYskfingLkkanielnRkvLadl 96 
                    Rvkrgv+ r+r+kk++k+akg+ gr++++yr+a +++ek++qyayrdR+ +krdfr+lwi+rinaa+r+ g+ Ys+f++gLk a+i++nRk+L++l
     AHX11162.1   3 RVKRGVQVRQRHKKVIKQAKGFHGRSKNCYRIALRRLEKSWQYAYRDRRVRKRDFRSLWIQRINAAVRSCGMVYSTFMKGLKDAGIDINRKMLSEL 98 
                    9*********************************************************************************************** PP

                    HHH-HHHHHH CS
  Ribosomal_L20  97 AindpeaFka 106
                    Ai++p+aF +
     AHX11162.1  99 AITQPDAFGE 108
                    ********87 PP

>> ApbE  ApbE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.6e-05      0.14      45     104 ..       7      73 ..       1      98 [. 0.69

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.6e-05
                 -EEE-HHHHHHHHHHHHHHHHTTTSS-TTTHHHHHHHCTTSGG.----H.......HHHHHHHTT.- CS
        ApbE  45 evkvspelaellkaaleiseltdgafdptvgplvklwgfgeekarvpsa.......eeidaalalvg 104
                  v+v +   +++k+a+ ++ ++++++ +++  l k w+   +++rv ++       ++i+aa++ +g
  AHX11162.1   7 GVQVRQRHKKVIKQAKGFHGRSKNCYRIALRRLEKSWQYAYRDRRVRKRdfrslwiQRINAAVRSCG 73 
                 38999999*****************************965544444333122222244555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 920.72
//
Query:       AHX11163.1  [L=322]
Description: phenylalanine--tRNA ligase, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-90  303.2   0.0    1.6e-90  302.9   0.0    1.0  1  tRNA-synt_2d     tRNA synthetases class II core domain (F)
  ------ inclusion threshold ------
       0.02   14.3   0.0       0.59    9.5   0.0    2.4  2  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
      0.053   13.5   0.3       0.14   12.1   0.0    1.7  2  Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-termin


Domain annotation for each model (and alignments):
>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  302.9   0.0   2.7e-94   1.6e-90       2     241 ..      89     319 ..      88     321 .. 0.98

  Alignments for each domain:
  == domain 1  score: 302.9 bits;  conditional E-value: 2.7e-94
                   .-TSSCTSCTSHSB-SHHHHHHHHHHHHHHCTTCEESSTTSEEEHHHHTSTTTSTTTSHHHCHTTSEBTCTSSS-ECESEEE-SSTHHHHHHHHTTS CS
  tRNA-synt_2d   2 idvtlpgkrieagklhpltkvleeikeiflelgfeevegpevesefynfdaLnvpqdhpaRdmqdtFylkkpekaveekllLRthttavqirtlekk 98 
                   idvt+p+++ + g  hpl kv++  ++i+++lg e vegpe+e+e+++fdaLn+p +hp R+mqd+Fyl       +  +lLRtht++vqir++e +
    AHX11163.1  89 IDVTYPARPASLGVEHPLCKVIDSTRRILTALGMEYVEGPEIEDEYHVFDALNTPTHHPSRQMQDSFYL------CDPARLLRTHTSSVQIRAMEGS 179
                   8********************************************************************......35567***************** PP

                   -SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHHHHHHHHHHCTSTEEEEEEECEETTEEEEEEEEEEECCSSSSEEEEEEEEEE CS
  tRNA-synt_2d  99 kppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgvleellkklfgaevkvrfrpsyfpftePsaevdvylvekkkkwlEllgaGmv 195
                   +pp++i+s+g+v+R+d  Dath+++Fhqve l+vd +++++++k +++ +l++lfg   +vr+rpsyfpftePsaevd+    k+++wlE++g+Gmv
    AHX11163.1 180 RPPFYIFSLGKVYRNDW-DATHTPMFHQVEVLCVDVGINMSHMKYCVSFFLEQLFGSI-EVRMRPSYFPFTEPSAEVDIKD--KNGNWLEVMGCGMV 272
                   ****************9.**************************************97.********************77..************** PP

                   -HHHHHHTT-..TTSEEEEEEEEHHHHHHHHHT-SSGHHHHTT.HHH CS
  tRNA-synt_2d 196 rpevleavgid.eevsgfafGlGveRlamlkygieDiRelvendlrf 241
                   +p+vl++v+i  +e++gfafG G+eRl+ml+y+i D+R+l+ ndlr+
    AHX11163.1 273 HPNVLSKVDISpNEYTGFAFGAGLERLTMLRYDIRDLRNLYLNDLRW 319
                   *********************************************98 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.0     0.019   1.1e+02       1      34 [.      89     122 ..      89     127 .. 0.93
   2 ?    9.5   0.0   9.8e-05      0.59      99     205 ..     185     284 ..     176     290 .. 0.66

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.019
  tRNA_synthFbeta   1 IpstlPkapttegelnkeqklrrklrdllagaGl 34 
                      I  t P  p+  g +++  k+ + +r++l+++G+
       AHX11163.1  89 IDVTYPARPASLGVEHPLCKVIDSTRRILTALGM 122
                      67899***************************98 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 9.8e-05
  tRNA_synthFbeta  99 lFEigkvflkd.seeelpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgi.ekvefepaehpalhpgrsAeikvdgk..... 185
                      +F +gkv+++d +++      +++ ++ +               ++ ++k  v  +le+l    +v+++p+  p+ +p   Ae+ +++k     
       AHX11163.1 185 IFSLGKVYRNDwDATHT-PMFHQVEVLCVDV-----------GINMSHMKYCVSFFLEQLFGsIEVRMRPSYFPFTEPS--AEVDIKDKngnwl 264
                      67777777777422222.2222222222222...........2556777777777777775545678899999999995..6666666666899 PP

  tRNA_synthFbeta 186 evGvlGelhpevleafdlkq 205
                      ev   G +hp+vl + d++ 
       AHX11163.1 265 EVMGCGMVHPNVLSKVDISP 284
                      88889************986 PP

>> Phe_tRNA-synt_N  Aminoacyl tRNA synthetase class II, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   2.3e-05      0.14       2      24 ..      19      41 ..      18      47 .. 0.86
   2 ?   -2.1   0.0      0.63   3.8e+03      43      69 .]      58      84 ..      55      84 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 2.3e-05
                     CCCCCCCCHHHHHCCCCCCCCCC CS
  Phe_tRNA-synt_N  2 dleeLeelRvkyLGkkGeltell 24
                     ++e+L +lR++yL+++G +++ l
       AHX11163.1 19 SAESLRQLRIEYLSRNGLIKQGL 41
                     7899***************9865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.63
                     HHHHCCCCCCCCCHHHCCHCCHHHHHC CS
  Phe_tRNA-synt_N 43 NelKqeieealeerkeeleaaeleakl 69
                     N+   ++++a+ e+++ +   ele++l
       AHX11163.1 58 NAFLRDASAAITEKQNLVHCVELERRL 84
                     555567889999999988888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2366.60
//
Query:       AHX11164.1  [L=146]
Description: ribose 5-phosphate isomerase B [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-47  161.3   0.1    1.4e-47  161.2   0.1    1.0  1  LacAB_rpiB  Ribose/Galactose Isomerase


Domain annotation for each model (and alignments):
>> LacAB_rpiB  Ribose/Galactose Isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.2   0.1   7.7e-52   1.4e-47       1     139 []       3     141 ..       3     141 .. 0.99

  Alignments for each domain:
  == domain 1  score: 161.2 bits;  conditional E-value: 7.7e-52
                 EEEEE-GCGHHHHHHHHHHHHHTTTEEEEECESSSS---HHHHHHHHHHHHHTTSSSEEEEEESSSHHHHHHHHTSTT--EEE-SSHHHHHHHHHTT-- CS
  LacAB_rpiB   1 iaigsDhagfelkekikeyLkekghevidvgteseesvdYpdfakkvaeavasgeadlgiliCgtGiGmsiaaNkvkgiraalchdeesAklarehnna 99 
                 i ig Dhagf+lk+ +++++kekg  + d g++ +   dYpdfak+va +va+g++d+giliCg+GiGmsi+aN++k++raalc d +sAklarehn+a
  AHX11164.1   3 ISIGVDHAGFNLKSSLLAFFKEKGWALLDRGAHCSGISDYPDFAKAVAMDVAEGNVDFGILICGSGIGMSIVANRYKKVRAALCGDVQSAKLAREHNDA 101
                 78********************************9899************************************************************* PP

                 SEEEEETTTS-HHHHHHHHHHHHHS---.HTHHHHHHHHH CS
  LacAB_rpiB 100 nvlalGarvigeelakeivkaFletefeeggrharrvdki 139
                 n+l+l++r ++  +  eiv+ F++++f+ + rh++r++ki
  AHX11164.1 102 NILCLSGRSLTVAECFEIVQVFIDSKFSFEDRHKQRIEKI 141
                 ***************************989********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (146 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1094.54
//
Query:       AHX11165.1  [L=413]
Description: serine hydroxymethyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.5e-168  559.0   0.0   5.3e-168  558.7   0.0    1.0  1  SHMT             Serine hydroxymethyltransferase
    6.2e-13   48.6   0.0    8.2e-13   48.2   0.0    1.1  1  Aminotran_1_2    Aminotransferase class I and II
    3.3e-07   29.9   0.0    2.8e-06   26.9   0.0    2.1  1  Beta_elim_lyase  Beta-eliminating lyase
    6.3e-05   22.5   0.1    9.1e-05   21.9   0.1    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> SHMT  Serine hydroxymethyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  558.7   0.0  1.2e-171  5.3e-168       2     399 .]       8     384 ..       7     384 .. 0.99

  Alignments for each domain:
  == domain 1  score: 558.7 bits;  conditional E-value: 1.2e-171
                 HHHTHHHHHHHHHHHHHHHHSEE-STT-----HHHHHHHTSGGGG----EETTEESSST-HHHHHHHHHHHHHHHHHCT-STTTEEEE---SSHHHHHH CS
        SHMT   2 eesdpevaeiikkekerqkeeieliasenftskavlealGsvltnkyaeGyPGkryyGGcefvdeveelaqdrakelfkldpakwgvnvqplsGsqanl 100
                 ++ dp+v eiikke +rq+++i+liasenf+s avlea+Gsv+tnkyaeGyPGkryy Gce+ d+ve+la++r  +lf+      ++nvqp+sGsqan+
  AHX11165.1   8 STIDPQVSEIIKKEANRQRSGIQLIASENFASAAVLEAQGSVFTNKYAEGYPGKRYYCGCEYADQVERLAIERICKLFNSS----YANVQPHSGSQANQ 102
                 678******************************************************************************....************** PP

                 HHHHHHT-TT-EEEEESCTTTSTGGGT-BTSS-B-SHHHHHSEEEEE-B-TTTSSB-HHHHHHHHHHH--SEEEEE-SST-S---HHHHHHHHHHTT-E CS
        SHMT 101 avytallepgdrilgldladGGhlthGakveskkisassklfesveykvdketglidydelekkakefkPklivaGtsaysrlidyarlreiadevgay 199
                 av+ +ll+pgd+ilg++la GGhlthG++v+      s+k+f++++y+v++++  id+de+++ ak++ Pkli+aG+say++++d+  +reiadevgay
  AHX11165.1 103 AVFFSLLKPGDTILGFSLASGGHLTHGSSVNL-----SGKWFNAIHYTVRRDDFEIDMDEVRELAKKHSPKLIIAGASAYAKKMDFPLFREIADEVGAY 196
                 *******************************9.....************************************************************** PP

                 EEEE-GGGHHHHHTTSS--GCCTSSEEEEESSSTT-S-S-EEEEEC-SEEEEETTTEEEEHHHHHHHHHHHTTTT-SS--HHHHHHHHHHHHHCTSHHH CS
        SHMT 200 llvdmahiaGlvaagvipsPfeyadvvtttthktlrGprgglillrkgvksvdktgkevleelekkinsavfPglqGGPlnhviaakavalkealepef 298
                 ll+dmah aGl+aag +psPf+y d++t+tthktlrGprg++il++             +eel kkinsa+fPglqGGP +h+iaakava++eal pef
  AHX11165.1 197 LLADMAHYAGLIAAGEYPSPFPYVDIMTSTTHKTLRGPRGAIILTN-------------SEELIKKINSAIFPGLQGGPQMHAIAAKAVAFGEALAPEF 282
                 **********************************************.............79************************************** PP

                 HHHHHHHHHHHHHHHHHHHHTT-EEGGGS-SSSEEEEEGGGGTS-HHHHHHHHHHTTEE-EEE--TTS.STTTT-SEEEEESHHHHHTT--HHHHHHHH CS
        SHMT 299 kvyqkqvlknakalaealkekgyklvsgGtdnhlvlvdlrekgldGkraekvlekvnitankntvPgd.ksalvtsGlrlGtpaltsrgfkeedlekva 396
                 k y ++v+knak+la+al+++g+ ++sgGt++h+v+vdlr  +l+G+++ + le++ i +nkn++P+d ++++vtsGlr+G+pa t+rg++e ++++++
  AHX11165.1 283 KDYIRNVIKNAKVLAKALEDRGFVILSGGTETHIVMVDLRTLNLKGNTSAAKLESAGIICNKNAIPFDeEKPFVTSGLRFGSPAETTRGMRETEFSQIG 381
                 ********************************************************************99****************************9 PP

                 HHH CS
        SHMT 397 kfi 399
                 ++i
  AHX11165.1 382 EMI 384
                 987 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.2   0.0   1.8e-16   8.2e-13      49     316 ..      77     327 ..      68     374 .. 0.80

  Alignments for each domain:
  == domain 1  score: 48.2 bits;  conditional E-value: 1.8e-16
                    HHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EEEEEES...S-THHHHHHHHTTSEEEEEEBEET.TTTEE-HHHHHHHHT CS
  Aminotran_1_2  49 leealakflgrseklklkreaavvvgsGagaliealifllklnpgdeilvpdp...tyasyknilrlsggevvryplyse.edfhldlealeealk 140
                    + e+++k+++          a+v+  sG++a++++++ llk  pgd il +++    +  +   ++lsg  +  ++++   +df++d++++ e+ k
     AHX11165.1  77 AIERICKLFN-------SSYANVQPHSGSQANQAVFFSLLK--PGDTILGFSLasgGHLTHGSSVNLSGKWFNAIHYTVRrDDFEIDMDEVRELAK 163
                    5688999999.......6667*******************9..******998722257778889*****999999998878************888 PP

                    THHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTT.SSGGG-EEEEEE CS
  Aminotran_1_2 141 eapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKaf.GlaGeRvGyilg 235
                    +   +++  k+i ++++ +   + ++ +  +++   a++ +++l+ D+a+ ++   +    + ++   ++++ + +++  K + G  G   ++il 
     AHX11165.1 164 K---HSP--KLI-IAGA-SAYAKKMDFPLFREI---ADEVGAYLLADMAHYAGLIAAG---E-YPSPFPYVD-IMTSTTHKTLrGPRG---AIILT 241
                    8...455..444.4554.56799**********...*****************99933...3.788888888.777777777635555...88888 PP

                    .EHHHHHHHHHHHHHHTS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEECCS.CSSEEEEEETHH..C CS
  Aminotran_1_2 236 .naavvsqlrklsrpfls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvlasq.sgmflltdlsae..t 316
                     ++++++ ++++  p+l    ++ a++a+a+   +  + e+++  + ++k++k+l ++L++ g+ +l+    + ++++dl+ +  +
     AHX11165.1 242 nSEELIKKINSAIFPGLQgGPQMHAIAAKAVAFGEALAPEFKDYIRNVIKNAKVLAKALEDRGFVILSGGtETHIVMVDLRTLnlK 327
                    667***************988899999999999999999********************999*99998776777777788777653 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   6.2e-10   2.8e-06      39     274 ..      79     339 ..      67     352 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 6.2e-10
                      HHHHHHTT-S.EEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTT...TBE-HHHHHHHS--S-TTS-EE CS
  Beta_elim_lyase  39 davaelfgke.aalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkea...Gkmdlekleaaikevgaheeki 128
                      +++++lf    a +  ++G +An+  +  ll++g+ ++  + a +   + g  + l+g  ++ +         ++d+++++++ k+   h   +
       AHX11165.1  79 ERICKLFNSSyANVQPHSGSQANQAVFFSLLKPGDTILGFSLASGGHLTHGSSVNLSGKWFNAIHYTVRrddFEIDMDEVRELAKK---H--SP 167
                      667777777724456799*****************999999988888899999999888777665333333388899999999998...3..45 PP

                      EEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-EEEEE-HH......... CS
  Beta_elim_lyase 129 klisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvGgvlafrddel....... 215
                      kli+             +       ++ia++ g  l+ D A +a    + ge + + f yvD++t    K l  + G++++++ +el       
       AHX11165.1 168 KLIIAGASAY------AKKMDFPLFREIADEVGAYLLADMAHYAGLI-AAGEYP-SPFPYVDIMTSTTHKTLRGPRGAIILTNSEELikkinsa 253
                      6665544444......344556788999*************999877.445544.579***************************99******* PP

                      ...............................HHHHHHHHHHHHT---SSTHHHHH..HHHHHHHHSSTTHHHHHHHHHHHHHHHHHCT CS
  Beta_elim_lyase 216 .............................edylaerveqrkylggglrqagvlaaleagiraleeglaslerdhktaeqlaeklelvr 274
                                                   +dy+++ ++ +k l++ l++ g+++    g    ++ +  l+  + ++++ a+kle   
       AHX11165.1 254 ifpglqggpqmhaiaakavafgealapefKDYIRNVIKNAKVLAKALEDRGFVIL--SGGTETHIVMVDLRTLNLKGNTSAAKLESAG 339
                      ******************************************************9..5555555555555555555555555555544 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1     2e-08   9.1e-05      92     204 ..     146     260 ..     139     319 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 2e-08
                      B-TTTSSB-GGGCGGG--TTE.EEEEE.B-GGGB---HHHHHHHHHHCT-EEEEE-TT-TT-EETTEECCCSSSEEEEE-BTTSSS-SSS-EEE CS
  DegT_DnrJ_EryC1  92 vdpdtynidpaaieaaitert.kaIlp.VhlyGqvadmdalkaiaakhglkvieDaAhAlGatykgkkvGalgdaavfSFyptKnlttGeGGav 183
                      v +d++ id ++++++  + + k I++ + +y + +d++  ++ia++ g +++ D Ah  G   +g++   +  + ++     K+l    G ++
       AHX11165.1 146 VRRDDFEIDMDEVRELAKKHSpKLIIAgASAYAKKMDFPLFREIADEVGAYLLADMAHYAGLIAAGEYPSPFPYVDIMTSTTHKTLRGPRGAII 239
                      77899*************9998665543899*************************************************************** PP

                      EESTHHHHHHHHHHHBTTCEC CS
  DegT_DnrJ_EryC1 184 vtndeelaekarvlrnhGlkr 204
                      +tn+eel +k++     Gl+ 
       AHX11165.1 240 LTNSEELIKKINSAIFPGLQG 260
                      ***********9888888774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       630  (0.0351386); expected 358.6 (0.02)
Passed bias filter:                      575  (0.0320709); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.41
# Mc/sec: 3059.41
//
Query:       AHX11166.1  [L=125]
Description: hypothetical protein NHE_0201 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.024   15.2   2.1      0.035   14.7   2.0    1.5  1  MCM_N          MCM N-terminal domain
      0.055   13.6   0.1      0.086   13.0   0.1    1.3  1  UPF0047        Uncharacterised protein family UPF0047
       0.15   12.1   0.0       0.27   11.3   0.0    1.3  1  Col_cuticle_N  Nematode cuticle collagen N-terminal domain


Domain annotation for each model (and alignments):
>> MCM_N  MCM N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   2.0   5.9e-06     0.035      46      87 ..      14      59 ..      11     108 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 5.9e-06
       MCM_N 46 LaafdeeLaeailenpkeylplleealkevv.kklepsykdd...a 87
                +++f+++La+ i++++++y+p + +a++  + ++ +psy++    +
  AHX11166.1 14 INEFQSDLADDIESYTEKYVPRFYNATDFDMyQQAQPSYNQYehqE 59
                7899***********************9655155566554443330 PP

>> UPF0047  Uncharacterised protein family UPF0047
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   1.4e-05     0.086      32      63 ..      13      59 ..       9      92 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                EEEESSSHHHHHHHHHHHHHHSTT...............T..T-GGGTT CS
     UPF0047 32 tinEnadpdvqeDleealeklvpe...............e..eYrhnae 63
                tinE  ++d+++D+e++ ek vp+               +  +Y+h+ e
  AHX11166.1 13 TINEF-QSDLADDIESYTEKYVPRfynatdfdmyqqaqpSynQYEHQ-E 59
                79999.9*****************88888887777665415578887.3 PP

>> Col_cuticle_N  Nematode cuticle collagen N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   4.4e-05      0.27      17      37 ..       6      26 ..       2      30 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 4.4e-05
  Col_cuticle_N 17 tlpsiyndiqsfqsevldemd 37
                   +++++ n i++fqs++ d+++
     AHX11166.1  6 SMGMVGNTINEFQSDLADDIE 26
                   68999**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (125 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 895.47
//
Query:       AHX11167.1  [L=206]
Description: thiamine monophosphate synthase/TENI family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-33  115.7   0.0    1.5e-33  115.6   0.0    1.0  1  TMP-TENI  Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   0.0   8.4e-38   1.5e-33      21     177 ..      29     184 ..       7     188 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 8.4e-38
    TMP-TENI  21 ealkggvtlvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvHlgqddlpvaearellgpdliiGlSvhsleeaeeaealgadY 119
                 + +++   ++qlR k+  +++l + +     lc++y +pl+ind  dl  +++adgvH+g++d   +++r ll++++iiG+S++ +   +e+  + a+Y
  AHX11167.1  29 REFSAYLYAFQLRIKD--RESLMKAIPTFLVLCKEYMIPLVINDFPDLVTEFNADGVHIGESDSIFEDCRSLLPKEKIIGVSCYADVGKAEMY-KSASY 124
                 555666789*****99..99***************************************************************9776544444.678** PP

    TMP-TENI 120 igvGpifpTdtKkda.eplgleglkelaeale.iPvvaiGGitlenvaevleagadgvav 177
                 + +G +f+++tK+++ + + ++ l+e+++     P+v iGGi+ +n  ++++agad va+
  AHX11167.1 125 VSFGCFFESATKPNPvARATVTVLEEWKSLGYqTPCVCIGGINNDNFMSLIHAGADIVAI 184
                 ****************************99877*************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1658.05
//
Query:       AHX11168.1  [L=44]
Description: hypothetical protein NHE_0203 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       239  (0.0133304); expected 358.6 (0.02)
Passed bias filter:                      192  (0.0107089); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 379.15
//
Query:       AHX11169.1  [L=1073]
Description: carbamoyl-phosphate synthase, large subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-90  300.3   0.0    6.2e-58  195.8   0.0    2.2  2  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
      1e-34  119.5   0.0    2.8e-34  118.1   0.0    1.8  1  CPSase_L_D3      Carbamoyl-phosphate synthetase large chain, 
    4.6e-16   58.8   0.1    4.2e-15   55.7   0.0    2.8  2  MGS              MGS-like domain
      1e-11   44.7   0.0    1.8e-05   24.4   0.0    2.3  2  ATP-grasp        ATP-grasp domain
    3.8e-11   42.8   0.0    1.3e-06   28.1   0.0    2.6  2  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
    2.1e-09   37.7   1.4      4e-06   27.0   0.0    3.5  3  ATP-grasp_3      ATP-grasp domain
      3e-07   30.2   0.0      0.001   18.7   0.0    2.5  2  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    3.9e-06   26.6   0.0      0.074   12.7   0.0    3.7  3  ATP-grasp_4      ATP-grasp domain
    0.00064   20.2   0.1      0.013   16.0   0.0    3.2  4  CoA_binding_2    CoA binding domain
  ------ inclusion threshold ------
      0.024   14.2   0.0       0.21   11.2   0.0    2.5  2  RimK             RimK-like ATP-grasp domain
      0.084   12.4   0.0        2.3    7.8   0.0    2.9  3  ATP-grasp_2      ATP-grasp domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.8   0.0   3.8e-61   6.2e-58       2     210 ..     127     332 ..     126     333 .. 0.96
   2 !  102.5   0.0   1.4e-32   2.2e-29       1     209 [.     675     876 ..     675     878 .. 0.94

  Alignments for each domain:
  == domain 1  score: 195.8 bits;  conditional E-value: 3.8e-61
                  HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEE CS
  CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvev 99 
                  ++ +++++++i+ +v + + +  ++++e  ++ + ig P ii+++f+lGG+G++va+++ e+ ++++++l+ ++     ++v v++s+ g++e E+ev
   AHX11169.1 127 RSLFNSIMREIGLQVPKNMVV--THVNEIEQALEFIGIPAIIRPSFTLGGLGGGVATTRFEFFKIINEGLKFSP----VSEVQVDESVLGWQEFELEV 218
                  77899***********99988..6666666677779*************************************7....89****************** PP

                  EEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEE.EEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS-- CS
  CPSase_L_D2 100 lrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgag.tveflldpkskeyyviEvNtRlsvesalaekaTGld 194
                  +rD++gn+i+vc +en +++  +t+++++v P  tL dee+q +r aa kv++ +gv ++g +v+f+++p+++e+ viE+N+R+s++sala+kaTG++
   AHX11169.1 219 VRDSAGNAIVVCPIENTDPMgvHTGDSVTVSPIFTLRDEEYQLMRDAAFKVLNRIGVNTGGaNVQFAVNPENGEIRVIEMNPRVSRSSALASKATGYP 316
                  *********************************************************98777************************************ PP

                  HHHHHHHHHTT--GCG CS
  CPSase_L_D2 195 lvkeaakialgekLee 210
                  ++k+aa++a+g +L+e
   AHX11169.1 317 IAKVAAQLATGLTLPE 332
                  **************97 PP

  == domain 2  score: 102.5 bits;  conditional E-value: 1.4e-32
                  SHHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEE CS
  CPSase_L_D2   1 DkesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEve 98 
                  D+es++++++k+++   + ++a   + e++ + ++eig+P+i+++++ lGG+ m++++++e la+ + k  +     f  +++l++++l    e++v+
   AHX11169.1 675 DRESFNQLIAKLDMSQPNNTIA--FSREDVARGVDEIGFPMIVRPSYVLGGESMQIIYDTEMLADYLGKHNQ----IFNGSSLLLDRFLLDAIELDVD 766
                  9**************9999999..9999************************************99877654....47899***************** PP

                  EEEETTS-EEEEEEEEECCEC..TCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS-- CS
  CPSase_L_D2  99 vlrDakgnvitvcerenslql..rtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGld 194
                   ++D ++  +  + +e + +   + +++  v P q L+++  ++++  + +++ +++v+g  +++f++++  +e+yv+EvN+R s+  +   ka G++
   AHX11169.1 767 AISDGEDVYV-AGIMEHIEEAgvHSGDSAFVFPPQKLSSQLLRKIKDYTRRIALTLNVIGFLNIQFAIEE--DEIYVLEVNPRSSRTIPFVAKALGIP 861
                  ****998665.577888888778**********************************************5..9************************* PP

                  HHHHHHHHHTT--GC CS
  CPSase_L_D2 195 lvkeaakialgekLe 209
                  l+k+a k+ lg+kL+
   AHX11169.1 862 LAKIATKVMLGKKLK 876
                  *************97 PP

>> CPSase_L_D3  Carbamoyl-phosphate synthetase large chain, oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.1   0.0   1.7e-37   2.8e-34       4     122 .]     424     539 ..     422     539 .. 0.95

  Alignments for each domain:
  == domain 1  score: 118.1 bits;  conditional E-value: 1.7e-37
  CPSase_L_D3   4 keptdeRifaiaealrrglsveeiheltkidpwFLekleelvelekelkkkkkeldeellreakklGfsDkqiaelleeeeeeevrelrkklgilpvy 101
                  ++  +++i++ia+a+r g+s+eei++l+k+++wFL +++ lvele+e+k+++  l++ ++ + kk GfsD++ia+l +  +e+e+r++rk++++lpv+
   AHX11169.1 424 SSLIPNKILIIADAMRMGFSIEEIAKLSKYNEWFLLQIQVLVELENEIKTAN--LSPIVVLKWKKRGFSDSRIATLRG-CNESEIRKIRKEMSVLPVF 518
                  5566899******************************************997..9*********************65.88899************** PP

  CPSase_L_D3 102 krvDtcAaeFeaetpYlYstY 122
                  k+vDtcAaeFe++  YlYstY
   AHX11169.1 519 KKVDTCAAEFESDIMYLYSTY 539
                  ********************9 PP

>> MGS  MGS-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.9   6.3e+03      51      92 ..     778     824 ..     763     827 .. 0.70
   2 !   55.7   0.0   2.6e-18   4.2e-15       3      95 .]     960    1045 ..     958    1045 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
                 HHHHHHHTTSCC....EEEEE--THHHHHH.CHHHHHHHHHHHTTSH CS
         MGS  51 eildaikngeid....lvintlypfkatva.kdgykirraaenidIp 92 
                  i+++i++ +++    + ++ +++++++   k +  +rr+a+  ++ 
  AHX11169.1 778 GIMEHIEEAGVHsgdsAFVFPPQKLSSQLLrKIKDYTRRIALTLNVI 824
                 58899999999888888888888888887743333477777777765 PP

  == domain 2  score: 55.7 bits;  conditional E-value: 2.6e-18
                  HHHHHHHHHTTCEEEEEHHHHHHHHHTT--EEECCCCHSTGSGGTHCHHHHHHHHTTSCCEEEEE--THHHHHHCHHHHHHHHHHHTTSHEES CS
         MGS    3 velakklkelgfellATgGTakllkeagipvtevvektgegerlggrveildaikngeidlvintlypfkatvakdgykirraaenidIplpt 95  
                  ve+ak l+el f+++AT+G a++lk+++i+ +  v+k++eg +++    ++d+i+n ei+lvint ++  + v+ d+ +ir   + ++Ip+ t
  AHX11169.1  960 VEIAKILSELRFTIFATKGSAAFLKDHNID-AIAVNKVKEG-SPH----VVDMIMNSEICLVINTCSHVIESVR-DSMSIRSSSIINQIPCCT 1045
                  89****************************.88999*****.***....************************9.****************87 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   1.1e-06    0.0018       2     161 ..     135     303 ..     134     311 .. 0.74
   2 !   24.4   0.0   1.1e-08   1.8e-05       4     160 ..     686     847 ..     683     850 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE--EE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafypvv 96 
                 ++ gl+vp+ ++v++ +e+e+a+e +g+p++++ +     G G  v   + +  +++++        +v v e v   +E  + vvr+  G+  ++ ++
  AHX11169.1 135 REIGLQVPKNMVVTHVNEIEQALEFIGIPAIIR-PSFTLGGLGGGVATTRFEFFKIINEGlkfsPVSEVQVDESVLGWQEFELEVVRDSAGNAIVVCPI 232
                 5789****************************9.777777777777777666655555544544889999***999999*************999999* PP

                 EEEEETTEEE.EEEECEE-SCHHHHHHHHHHHHHHHHHTSSEE....EEEEEEEE.TTCTEEEEEEESS-- CS
   ATP-grasp  97 etvqedgilr.lsvapaevsekaqkkaeeiakkiveeLggvGv....favElFvl.edgellvnElapRpH 161
                 e++   g+    sv  +++ +   ++ + +   + + L+ +Gv      v + v  e+ge+ v E+ pR+ 
  AHX11169.1 233 ENTDPMGVHTgDSVTVSPIFTLRDEEYQLMRDAAFKVLNRIGVntggANVQFAVNpENGEIRVIEMNPRVS 303
                 **999998752344444444444444444444555555555541111567766666788899999999985 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 1.1e-08
                 TT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC....GTTCEEEEE----SEEEEEEEEEETTC-EEE--EEEE CS
   ATP-grasp   4 lglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal....keekvivEefvpfekElsvlvvrsaeGetafypvvet 98 
                 l ++ p+ +++ s+e++ + ++e+g+p++v+ +     G   +++ + e l + l  +    ++ ++++  f     El v ++ + e  +++  ++e+
  AHX11169.1 686 LDMSQPNNTIAFSREDVARGVDEIGFPMIVR-PSYVLGGESMQIIYDTEMLADYLGKHnqifNGSSLLLDRFLLDAIELDVDAISDGED-VYVAGIMEH 782
                 556667777778889999999**********.999999**************9998888888999***************999998776.999999999 PP

                 EEETTEE....EEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS- CS
   ATP-grasp  99 vqedgil....rlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRp 160
                 ++e g+       ++ p+++s++ ++k+++++++i+ +L+++G + + +  +e++e++v E+ pR 
  AHX11169.1 783 IEEAGVHsgdsAFVFPPQKLSSQLLRKIKDYTRRIALTLNVIGFLNIQF-AIEEDEIYVLEVNPRS 847
                 9987664111178999*******************************85.555888********96 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.0    0.0001      0.16      51     115 ..     264     332 ..     251     347 .. 0.77
   2 !   28.1   0.0   8.2e-10   1.3e-06      49     118 ..     810     880 ..     800     890 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.0001
  ATPgrasp_Ter  51 elaerlaeefgld.glvnvQvrededg..pkLLEiNpRasGGlg.ysalaGvnlpylalklllgletee 115
                   ++a ++ +++g++ g  nvQ+  + ++   +++E+NpR+s      s ++G  ++++a++l++gl  +e
    AHX11169.1 264 DAAFKVLNRIGVNtGGANVQFAVNPENgeIRVIEMNPRVSRSSAlASKATGYPIAKVAAQLATGLTLPE 332
                   67778888888863579***9987555479*********96555156777************9985554 PP

  == domain 2  score: 28.1 bits;  conditional E-value: 8.2e-10
  ATPgrasp_Ter  49 lielaerlaeefgldglvnvQvrededgpkLLEiNpRasGGlgysala.Gvnlpylalklllgleteevee 118
                   + ++++r+a ++++ g  n+Q+  +ed+ ++LE+NpR s ++   a a G+ l+++a k +lg++ ++ + 
    AHX11169.1 810 IKDYTRRIALTLNVIGFLNIQFAIEEDEIYVLEVNPRSSRTIPFVAKAlGIPLAKIATKVMLGKKLKDFRL 880
                   5578899999*********************************999888**************87766654 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.1     0.004       6.4       3     158 ..     125     302 ..     123     305 .. 0.61
   2 !   27.0   0.0   2.5e-09     4e-06      28     157 ..     707     846 ..     673     850 .. 0.74
   3 ?    0.3   0.1       0.4   6.6e+02      67     101 ..     994    1028 ..     972    1042 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.004
                  SHHHHHHHHTTT..S---...........-EESS--SSSEEEEESS-------B--SS--TTE................EEEE---SEEEEEEEEE.S CS
  ATP-grasp_3   3 dKlktykkLkea.gvkvP.......tkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve.........lvqefieGkplSvsllsdg 83 
                  +K+ +++ ++++ g++vP        +  ++ le+   + ++ p+   gg +  v+  + e +++i+e           +    +  +++ ++++ d 
   AHX11169.1 125 EKRSLFNSIMREiGLQVPknmvvthVNEIEQALEFIGIPAIIRPSFTLGGLGGGVATTRFEFFKIINEGLkfspvsevqVDESVLGWQEFELEVVRDS 222
                  57777777766668888855544321122223334477888888888888877777777666666665446677776645555555577888888888 PP

                  SSEEEEEEEEEEEET....TEEEEE...EES-...---HHHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEESS- CS
  ATP-grasp_3  84 ekvlvlavnrqliekaekefvyaGn...vtpi...etelkeevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNPRl 158
                    + +++++ +  +      v +G    v+pi   + e+ + ++++a +v++++    G + v + ++   +e+ viE NPR+
   AHX11169.1 223 AGNAIVVCPIENTDP---MGVHTGDsvtVSPIftlRDEEYQLMRDAAFKVLNRIGVNTGGANVQFAVNPenGEIRVIEMNPRV 302
                  888888777665554...3455554111344411144555567777777777774334666688887766699*********8 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 2.5e-09
                  S--SSSEEEEESS-------B--SS--TTE...............EEEE-.--SEEEEEEEEE.SSSEEEEEEEEEEEET......TEEEEEEES--- CS
  ATP-grasp_3  28 eeeekklvvKprdGaggesvrvveekeeaeaaieeve........lvqef.ieGkplSvsllsdgekvlvlavnrqliekaeke..fvyaGnvtpiet 114
                  +e   +++v p++  gges+ ++ + e +   + + +        l+ +f ++  +l v+++sdge+v+v  + + + e + ++   +++    +   
   AHX11169.1 707 DEIGFPMIVRPSYVLGGESMQIIYDTEMLADYLGKHNqifngsslLLDRFlLDAIELDVDAISDGEDVYVAGIMEHIEEAGVHSgdSAFVFPPQKLSS 804
                  344779*****************99999988887777899****955555279****************99999887776443344222223334444 PP

                  -HHHHHHHHHHHHHTTSTT--EEEEEEEEESS.SEEEEEEESS CS
  ATP-grasp_3 115 elkeevvelaeevvekleglaGyvGvDlvlkdeepyviEvNPR 157
                  +l +++ +  +++   l ++ G++ + + ++++e+yv+EvNPR
   AHX11169.1 805 QLLRKIKDYTRRIALTL-NVIGFLNIQFAIEEDEIYVLEVNPR 846
                  45666666667777777.************************* PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.4
                   EE---SEEEEEEEEE.SSSEEEEEEEEEEEET... CS
  ATP-grasp_3   67 qefieGkplSvsllsdgekvlvlavnrqliekaek 101 
                    +  eG+p+ v+++++ e  lv+ ++  +ie  ++
   AHX11169.1  994 NKVKEGSPHVVDMIMNSEICLVINTCSHVIESVRD 1028
                   55569**********99999999999999987665 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.0   0.00062         1       4     174 ..     136     300 ..     133     307 .. 0.81
   2 !   18.7   0.0   6.2e-07     0.001      26     174 ..     700     845 ..     684     860 .. 0.86

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00062
                      HTT--B--EEEEETTHHCH-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-..SCEEEEE--.ESEEEEEEEEETS CS
  Dala_Dala_lig_C   4 aaGlpvvpyvvlekeeakeekkellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafkyd..ekvlvEeai.egreievavlgne 94 
                      + Gl+v++ +v+++ +        +e+  e +g p++++p+ +   +G   ++++ e+ + i+e +k+   ++v v+e +   +e+e  v+ + 
       AHX11169.1 136 EIGLQVPKNMVVTHVNE-------IEQALEFIGIPAIIRPSFTLGGLGGGVATTRFEFFKIINEGLKFSpvSEVQVDESVlGWQEFELEVVRDS 222
                      55666666666555443.......3455788999******999999999999999********99998733689998888799********988 PP

                      SCEEEEEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT-.-SEEEEEEEE.ETTTEEEEEEEES CS
  Dala_Dala_lig_C  95 klevsevgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldl.rGlaRvDffl.teegeivlnEvNt 174
                      + ++ +v  i  ++ +      +++d++++    +l +e+++ ++++a+k+ + +++ +G a v f +  e+gei + E+N+
       AHX11169.1 223 AGNAIVVCPIENTDPM----GVHTGDSVTVSPIFTLRDEEYQLMRDAAFKVLNRIGVnTGGANVQFAVnPENGEIRVIEMNP 300
                      8888877777766543....334678888988899********************973699*******8899*********6 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 6.2e-07
                      HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT..-SCEEEEE--.ESEEEEE.EEEETSSCEEEEEEEEE-SSSSS-HHH CS
  Dala_Dala_lig_C  26 ellekveeelgypvfVKpareGSSvGvskveseeelkeaieeafky..dekvlvEeai.egreiev.avlgneklevsevgeivvkkgfydyea 115
                      e +++ ++e+g+p++V+p+       ++ +  +e l++++ +  +    ++ l ++++ ++ e++v a+ + e++ v+ + e++ + g+     
       AHX11169.1 700 EDVARGVDEIGFPMIVRPSYVLGGESMQIIYDTEMLADYLGKHNQIfnGSSLLLDRFLlDAIELDVdAISDGEDVYVAGIMEHIEEAGVHS--- 790
                      456777899*********976444457889**********888775226789*****99*******55666788************99975... PP

                      HHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
  Dala_Dala_lig_C 116 kysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                         +d+a ++ p kl+++  +ki+++  ++  +l++ G+  + f ++ e+ei++ EvN+
       AHX11169.1 791 ---GDSAFVFPPQKLSSQLLRKIKDYTRRIALTLNVIGFLNIQFAIE-EDEIYVLEVNP 845
                      ...56666899*********************************998.899*******7 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   4.5e-05     0.074      58     151 ..     206     301 ..     160     307 .. 0.86
   2 ?    0.4   0.0      0.27   4.3e+02      76     105 ..     590     620 ..     582     638 .. 0.71
   3 !    8.2   0.0     0.001       1.7      50     152 ..     746     847 ..     710     850 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.5e-05
  ATP-grasp_4  58 EeyieGeEfavdayfdeeGepvilnilkkefaseedvsdrlyvtsakvieetleal.eellkevnallglknfpvHiElrvs.edgkiipiEvnpl 151
                  E+++  +Ef +++  d+ G+++++  ++ +  +  ++ d + v +   +++++++l  ++  +v +++g++ + + + + v+ e+g+i +iE+np+
   AHX11169.1 206 ESVLGWQEFELEVVRDSAGNAIVVCPIENTDPMGVHTGDSVTVSPIFTLRDEEYQLmRDAAFKVLNRIGVNTGGANVQFAVNpENGEIRVIEMNPR 301
                  5666669**************999999999999999*******9998777777666488999*******************94667*********6 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.27
  ATP-grasp_4  76 Gepvi.lnilkkefaseedvsdrlyvtsakv 105
                  G++ i ln    + +++ d+sd+ly+t+  v
   AHX11169.1 590 GYEAImLNCNPETVSTDYDISDKLYFTPITV 620
                  5544414555555666778*********887 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.001
  ATP-grasp_4  50 veeesflvEey.ieGeEfavdayfdeeGepvilnilkkefaseedvsdrlyvts.akvieetlealeellkevnallglknfpvHiElrvsedgkiip 145
                   +++s l+  + ++  E  vda  d e    ++ i+++      +  d  +v + +k++++ l+++++++++++  l++  f + i + ++ed +i++
   AHX11169.1 746 FNGSSLLLDRFlLDAIELDVDAISDGE-DVYVAGIMEHIEEAGVHSGDSAFVFPpQKLSSQLLRKIKDYTRRIALTLNVIGF-LNIQFAIEED-EIYV 840
                  556666666652577788999988655.566899**99999999999999998626899***************88888766.78*****998.7*** PP

  ATP-grasp_4 146 iEvnplr 152
                  +Evnp++
   AHX11169.1 841 LEVNPRS 847
                  *****75 PP

>> CoA_binding_2  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   8.1e-06     0.013      14      79 ..      26      95 ..       9     136 .. 0.75
   2 ?   -1.9   0.0       2.8   4.6e+03      66     110 ..     621     667 ..     613     672 .. 0.72
   3 ?   -3.6   0.0       9.3   1.5e+04      55      76 ..     790     811 ..     778     819 .. 0.52
   4 ?   -2.0   0.0       2.9   4.8e+03      32      67 ..     992    1012 ..     979    1017 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 8.1e-06
                   SHHHHHHHHHHHHT--EEEESSS-SEETTEES----T........T--EEEE-S-HHHHGGGHHHHHHH- CS
  CoA_binding_2 14 kfgykvlryllehglpvvpVnpkeeeilgekvyaslae.d...pepvdlvdvftppeatpeivkealalg 79
                     g ++ r l++hg++vv +np+  +i   ++ a++   +    + ++++ ++ +p++++++v    al+
     AHX11169.1 26 YSGTQACRVLKKHGHRVVLINPNPATIMTDPETADVVYiEpitSKMIESIIILEKPDKLLPTVGGQTALN 95
                   56889999***********************99999953334566677********99999987666555 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 2.8
                    HHHGGGHHHHHHH-.-SEEEE-TT---H.HHHHHHHHTT-EEE.ES- CS
  CoA_binding_2  66 eatpeivkealalg.akavwlqpgsede.eaaelaeeagirvvgdrC 110
                    ea+++i+++ +++g   +v+lq g + + ++a++ e+ + r++g + 
     AHX11169.1 621 EAVLDILEKESERGeLLGVILQCGGQTPlKLAKAIEASDTRIIGTSF 667
                    56777777777775699999999965542777777778888887665 PP

  == domain 3  score: -3.6 bits;  conditional E-value: 9.3
                    T--EEEE-S-HHHHGGGHHHHH CS
  CoA_binding_2  55 pvdlvdvftppeatpeivkeal 76 
                      d+++vf p++   +++++++
     AHX11169.1 790 SGDSAFVFPPQKLSSQLLRKIK 811
                    3345555555555555555554 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 2.9
                     EESSS-SEETTEES----T....T--EEEE-S-HHH CS
  CoA_binding_2   32 pVnpkeeeilgekvyaslaedpepvdlvdvftppea 67  
                     +Vn             +++  ++ +++vd+++++e+
     AHX11169.1  992 AVN-------------KVK--EGSPHVVDMIMNSEI 1012
                     333.............333..245556666666665 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0      0.62     1e+03      13      62 ..     136     183 ..     124     197 .. 0.78
   2 ?   11.2   0.0   0.00013      0.21       2     178 ..     674     860 ..     673     869 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.62
                 HTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SH CS
        RimK  13 kakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakke 62 
                   +++vp+  ++ + +++e+ +e i  + P +++ +++  G++  +a ++
  AHX11169.1 136 EIGLQVPKNMVVTHVNEIEQALEFI--GIPAIIRPSFTLGGLGGGVATTR 183
                 4568899999999999*******99..69****99998888776666555 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                 H-HHHHHHHHHHTT-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHHGGG--......EEEEE--SS-SEEEEEEE CS
        RimK   2 rdKlkslklLakakikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlealkeai......lvqeyieeaenediRvlv 94 
                 +d+    +l+ak ++  pn ++a + ed+ + +++i  +fP++v+ ++   G  + +  +++ l + l   +++i      l+  ++  a + d+  + 
  AHX11169.1 674 EDRESFNQLIAKLDMSQPNNTIAFSREDVARGVDEI--GFPMIVRPSYVLGGESMQIIYDTEMLADYLGK-HNQIfngsslLLDRFLLDAIELDVDAIS 769
                 56666789****************************..6*********9999999888888888887655.3333344444888888888888888877 PP

                 ETTEE.EEEEEEE--SSS----TTTT-EE...EE----HHHHHHHHHHHH..HCT-SEEE...EEEEEETTEEEEEEEE..SS--SHHHHHHHT- CS
        RimK  95 vddev.vaalrrvskeGdFRsnlhrGgva...eklqlseeekelAikaak..amelvvaG...vDllrakrgllvlEvn..sspglekiektlgi 178
                  +++v va++    +e    + +h G  a    + +ls ++ +     ++  a+ l v+G   +    ++++++vlEvn  ss  +  + k lgi
  AHX11169.1 770 DGEDVyVAGIMEHIEE----AGVHSGDSAfvfPPQKLSSQLLRKIKDYTRriALTLNVIGflnIQFAIEEDEIYVLEVNprSSRTIPFVAKALGI 860
                 7777656666555555....556666544111233444443222222233112233344321133444566667777764444445555555555 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.7   4.4e+03       4      18 ..      99     113 ..      98     128 .. 0.68
   2 ?    7.8   0.0    0.0014       2.3       9      60 ..     132     180 ..     129     205 .. 0.89
   3 ?    0.5   0.0      0.23   3.7e+02       9      43 ..     681     715 ..     678     724 .. 0.83

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.7
                  HHHHHHHHHCTT--- CS
  ATP-grasp_2   4 Eyqakeilakygvkv 18 
                  E  ak ilakygv+ 
   AHX11169.1  99 ELVAKGILAKYGVQL 113
                  6679999****9985 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0014
                  HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEE CS
  ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvk 60 
                   i+++ g++vp+++v+++ +e+e+a++ +g  + +++     GG G  gGv 
   AHX11169.1 132 SIMREIGLQVPKNMVVTHVNEIEQALEFIGIPA-IIRPSFTLGGLG--GGVA 180
                  699***************************999.999999999876..6665 PP

  == domain 3  score: 0.5 bits;  conditional E-value: 0.23
                  HHHHCTT----SEEEESSHHHHHHHHHHHTSSSEE CS
  ATP-grasp_2   9 eilakygvkvpegevaesaeeaeeaakklgekelv 43 
                  +++ak +++ p++++a+s+e++++ ++++g   +v
   AHX11169.1 681 QLIAKLDMSQPNNTIAFSREDVARGVDEIGFPMIV 715
                  8999************************9988854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1073 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      565  (0.0315132); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.74u 0.26s 00:00:01.00 Elapsed: 00:00:00.38
# Mc/sec: 8379.79
//
Query:       AHX11170.1  [L=464]
Description: modulator of DNA gyrase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-53  181.9   0.3    3.4e-53  181.3   0.3    1.3  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.3   0.3   1.9e-57   3.4e-53       3     279 .]      22     315 ..      20     315 .. 0.88

  Alignments for each domain:
  == domain 1  score: 181.3 bits;  conditional E-value: 1.9e-57
                 EEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-.......................... CS
   PmbA_TldD   3 evrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea.......................... 75 
                 e+++e   s+s++f +g +  +++ ++sg+g+r+++g ++ +++++d s    ++ v++ + i + +     a                          
  AHX11170.1  22 ELFIEYLCSESLKFQDGGLVASTYADSSGFGLRAFYGDKVLYTHSSDVS---YKSIVKATEFILRNKF----Aataggisetshsdtavrdslyssglq 113
                 78899999**********************************9966766...6666665444443222....12233555666668888999999**** PP

                 .GGS-HHHHHHHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE...STCS..ET.EEEEEEEE....S CS
   PmbA_TldD  76 .eevsaeekielleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsvia.d.dggs..gd.gmgggsgy....e 164
                  ++ + e++++ll+++ + + s+          +i+++sa+ sas +++ i+ ++G  +++ r+   l++sv+    dg+s  ++ g+gg++g     e
  AHX11170.1 114 dDDFPFEKRVALLKDMYDYALSKGG--------NIASISATFSASIQKVEIIKNTGEILTDDRPMLKLGFSVVLrGeDGRSigATsGKGGRFGIprliE 204
                 9999999999*******88777776........*****************************************6645666987778888888755555 PP

                 SHHHS..SSHHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT-......-SB-TTS CS
   PmbA_TldD 165 dleeedleeiaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavlegrSflkdklGekvaselltivddpts.gglgsypfDdEG 262
                 +     +++++++a +ka  +l a+p+p+g+++Vvl++++ g llhea+gh+lead++++g S++++ +G kvas+ +++vdd+t+  ++gs+++DdEG
  AHX11170.1 205 N-----WKDLVDRAFRKAEVNLIAVPCPSGEMTVVLGNGWPGILLHEAIGHGLEADFNRKGASAFSGLVGGKVASDVVSVVDDGTIeAARGSINVDDEG 298
                 5.....555********************************************************667*****************99************ PP

                 BB---EEEEETTEE--- CS
   PmbA_TldD 263 vptqrtvlIenGvLkny 279
                 +p++ +vlIe+GvLkny
  AHX11170.1 299 TPSSYNVLIERGVLKNY 315
                 ****************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (464 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 3428.28
//
Query:       AHX11171.1  [L=419]
Description: adenylosuccinate synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.2e-150  501.3   0.0   2.4e-150  501.1   0.0    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  501.1   0.0  1.4e-154  2.4e-150       2     418 ..       4     414 ..       3     415 .. 0.96

  Alignments for each domain:
  == domain 1  score: 501.1 bits;  conditional E-value: 1.4e-154
                      EEEE-SSS-S-HHHHHHHHHTT-SEEEE-SB-TTSSEEEEETTEEEEESSS-GGGGSTT-EEEE-TTBEE-HHHHHHHHTTSS-TT......TE CS
  Adenylsucc_synt   2 vvvGaqwGDEGKGkivDllaeeadvvvRfqGGanAGHtvvvdgkkyklhllpSGilnpgvvnviGngvvvdpealleEieeleakgvelskerl 95 
                      +v+G+qwGDEGKGkivD+la ++d v+Rf+GG+nAGHtv+v++kk+kl++lpSGil+++v++viGngvv+dp +ll+Ei+ l ++gv+++ e+l
       AHX11171.1   4 AVIGLQWGDEGKGKIVDYLAGSFDSVIRFNGGNNAGHTVIVGEKKHKLRILPSGILRDDVTSVIGNGVVLDPYSLLDEIRLLGENGVSITPEKL 97 
                      79******************************************************************************************** PP

                      EEETTSEE--HHHHHHHHHHHHH----------TTHHHHHHHHHTT---BGGGGGSHHHHHHHHHHHHHHTHHHHHHT...T-----HHHHHHH CS
  Adenylsucc_synt  96 lisdrahlvlpyhkalDkleeaakgkkkiGtTkkGiGpayadkvarrgirvgdlldeeeleeklekllelknkllekldkeeleveelleellk 189
                      li d++hl+lp+hk+lD+l e+    +kiGtTk G+Gp+y+dkvarrgir++dl +e+ l++ + kll ++n + +  + +e++v+e+l++l++
       AHX11171.1  98 LIVDSCHLILPLHKELDELFERT---QKIGTTKCGVGPCYQDKVARRGIRLCDLRSEKYLKDAIGKLLCYHNIIRRGASLAEVQVDEVLDSLMA 188
                      *********************94...59********************************************8877666699************ PP

                      HHHHHGGGEE-HHHHHHHHHHTT--EEEE--S-GGG-TTTSSTTSS-SS--SHHHHHHHTT--GGGEEEEEEEEESSEEESSSS--TTB--SHH CS
  Adenylsucc_synt 190 yaerlkpyvvdtvallnealkegkkvLfEGaqgtllDidhGtYPfvTsSnttaggaltglglapkkidevlgvvKAyttrvGeGpfptelkdev 283
                      +++++ +y +    +l+  l +gk+ LfEGaqg+llDidhGtYPfvTsS+  +g+++ g+ l+p k  +v+g++K+y trvGeG+fpte ++++
       AHX11171.1 189 IRDEVIHYAIS-PCELQVRL-SGKRKLFEGAQGMLLDIDHGTYPFVTSSSSGVGQVANGAALGPVK--SVIGIMKSYATRVGEGAFPTEQNNSI 278
                      *******9995.67777777.67899**********************************999876..6************************* PP

                      HHHHHHHTT-B-TTT--B-EEE-EEHHHHHHHHHHHT-SEEEEE-GGGGTT-SEEEEEEEEE.ETTEEESS--S.....-GEEEEEEEEE--.S CS
  Adenylsucc_synt 284 geklrekGkEfgtttgrpRrcGwlDlvllryavrvngvtelaltklDvldgldeikvcvaYk.ldgkeldefpasleelekvepvyeelpgWke 376
                      g++l+++G+E+gt++gr RrcGw Dlvl+rya+ + gvt+l++tklDvld+++ei +c +Yk  +gk ld +  sl + +++ep+y  l+gW++
       AHX11171.1 279 GTELQKRGREIGTVSGRIRRCGWCDLVLVRYACITAGVTALVVTKLDVLDSFNEISLCYGYKtKEGKVLDVCSPSLLSSTECEPQYLRLKGWNS 372
                      *************************************************************96677888877667777889************* PP

                      --TT---GGGS-HHHHHHHHHHHHHHTS-EEEEE-SSSTT-E CS
  Adenylsucc_synt 377 disgvrsfedlpenakkyvefieellgvpvkiisvGpereqt 418
                      ++ +v+sfe+lp++a+++v  ieellg+pv ++s+Gp+req+
       AHX11171.1 373 STVDVTSFEKLPSEAREFVGKIEELLGLPVLMVSTGPGREQV 414
                      ****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (419 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3264.01
//
Query:       AHX11172.1  [L=245]
Description: phosphatidylglycerophosphatase A family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-10   40.4  10.0    1.2e-09   38.3  10.0    1.9  1  PgpA       Phosphatidylglycerophosphatase A
  ------ inclusion threshold ------
      0.026   14.5   2.5      0.026   14.5   2.5    2.0  3  RseC_MucC  Positive regulator of sigma(E), RseC/MucC
      0.069   13.2   0.5      0.069   13.2   0.5    2.7  4  DUF1290    Protein of unknown function (DUF1290)


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3  10.0     2e-13   1.2e-09       2     142 ..      41     221 ..      40     222 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 2e-13
                 HHHHHHHHTT......--HHHHHHHHHHHTT.........HHHHH.HHHHHHHHHHHHHHHHHHHHHT-S-HHT-TT--HHHHTTHHHHH......... CS
        PgpA   2 ellatlfgsGllpvaPgtvgslaalllallll........lleslslllllilllflvGiwackktekelgekDpgeiviDEvvgqwiallll..pa.. 88 
                 +++at+f +G+lp     +  +++++l+ l+         l++ ++ ll+  ++l+l+G+     ++k++ ++   e+ i  v gq ++l+l   p+  
  AHX11172.1  41 RMIATFFWIGYLPEWQSHWAAFFTIPLVSLIVyftvgfssLVSIAQVLLITSAALLLLGLLGIYTFQKTIFSENRYEVTIHVVFGQCLMLALSvpPVtq 139
                 789***********************999887777765543333333336777789999999999999999******************9555451155 PP

                 ..............................TT.HHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHHHHH CS
        PgpA  89 ...........................tllal.llafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvlali 142
                                            t++++ l+  ++Frl+DivKp+p  w++r  ++++  m+  ++ +++a l+l+l+
  AHX11172.1 140 ivaqvflfnsflcdrflncagwflrvsTYFVAgLIPYFTFRLIDIVKPWPSCWIERDYHNAVSNMFEGFCNAVYATLLLYLV 221
                 555556666666666677776666665444556999****************************************999875 PP

>> RseC_MucC  Positive regulator of sigma(E), RseC/MucC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   2.5   4.4e-06     0.026      68     128 ..      60     120 ..      55     122 .. 0.90
   2 ?   -2.6   0.3      0.84     5e+03      74      97 ..     136     158 ..     126     179 .. 0.55
   3 ?   -3.8   0.6         2   1.2e+04      66      76 ..     214     224 ..     210     234 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 4.4e-06
   RseC_MucC  68 llvYllPllllilgallgsallgssellaalgallglvlgflivrllskrlkkkskfqpvi 128
                 + ++ +Pl+ li+   +g + l+s   + ++++ ++l+lg+l ++ ++k++ ++++++++i
  AHX11172.1  60 AAFFTIPLVSLIVYFTVGFSSLVSIAQVLLITSAALLLLGLLGIYTFQKTIFSENRYEVTI 120
                 56899*******998888777789999999***************************9887 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.84
   RseC_MucC  74 Pllllilgallgsallgssellaa 97 
                 P+  +++ ++l++++l  + +l  
  AHX11172.1 136 PVTQIVAQVFLFNSFL-CDRFLNC 158
                 5555666666666664.3333333 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 2
   RseC_MucC  66 aallvYllPll 76 
                 a+ll+Yl+ ++
  AHX11172.1 214 ATLLLYLVTFM 224
                 55555655443 PP

>> DUF1290  Protein of unknown function (DUF1290)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1      0.46   2.7e+03      37      55 ..      74      92 ..      70     115 .. 0.62
   2 ?   -1.2   0.2      0.38   2.3e+03      50      75 ..     120     145 ..      99     156 .. 0.69
   3 ?   -1.4   0.1      0.44   2.6e+03      39      66 ..     143     171 ..     134     185 .. 0.60
   4 ?   13.2   0.5   1.2e-05     0.069      42      76 ..     208     242 ..     190     244 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.46
     DUF1290 37 fisgffsnvllAalLvylG 55
                f +gf s v +A +L    
  AHX11172.1 74 FTVGFSSLVSIAQVLLITS 92
                6677777777776665443 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.38
     DUF1290  50 lLvylGdklgvdlylaavvvfgirif 75 
                 + v +G+ l + l++  v  +++++f
  AHX11172.1 120 IHVVFGQCLMLALSVPPVTQIVAQVF 145
                 44566777777777777766666665 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 0.44
     DUF1290  39 sgffsnvllA.alLvylGdklgvdlylaa 66 
                   f++n+ l   +L   G  l v+ y++a
  AHX11172.1 143 QVFLFNSFLCdRFLNCAGWFLRVSTYFVA 171
                 55666766542567777777777666654 PP

  == domain 4  score: 13.2 bits;  conditional E-value: 1.2e-05
     DUF1290  42 fsnvllAalLvylGdklgvdlylaavvvfgirifq 76 
                 f+n++ A+lL yl + +  dl l  vv f +r+f+
  AHX11172.1 208 FCNAVYATLLLYLVTFMVFDLLLIDVVEFYTRVFH 242
                 79********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (245 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       879  (0.0490267); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1975.45
//
Query:       AHX11173.1  [L=63]
Description: putative thioredoxin [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 550.13
//
Query:       AHX11174.1  [L=327]
Description: NAD-dependent glycerol-3-phosphate dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.9e-42  144.9   0.2    5.4e-42  143.4   0.2    1.7  2  NAD_Gly3P_dh_N   NAD-dependent glycerol-3-phosphate dehydroge
      3e-32  111.8   0.3    5.8e-32  110.9   0.3    1.5  1  NAD_Gly3P_dh_C   NAD-dependent glycerol-3-phosphate dehydroge
    2.8e-08   33.5   0.1    5.4e-08   32.6   0.1    1.5  1  ApbA             Ketopantoate reductase PanE/ApbA
    3.4e-07   30.8   0.6    1.2e-06   29.0   0.1    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
     0.0017   17.4   0.0     0.0034   16.4   0.0    1.5  1  PDH              Prephenate dehydrogenase
     0.0018   18.5   0.5      0.012   15.8   0.0    2.5  3  TrkA_N           TrkA-N domain
     0.0024   18.0   0.0     0.0043   17.2   0.0    1.5  1  NAD_binding_2    NAD binding domain of 6-phosphogluconate deh
     0.0057   17.1   0.0      0.055   13.9   0.0    2.4  3  NAD_binding_7    Putative NAD(P)-binding
  ------ inclusion threshold ------
      0.018   15.6   0.0       0.14   12.8   0.0    2.4  2  Pyr_redox        Pyridine nucleotide-disulphide oxidoreductas
      0.023   14.6   0.0       0.07   13.0   0.0    2.0  1  3HCDH_N          3-hydroxyacyl-CoA dehydrogenase, NAD binding
      0.026   14.1   0.1      0.073   12.6   0.1    1.8  1  IlvN             Acetohydroxy acid isomeroreductase, NADPH-bi
      0.028   14.9   0.1       0.23   11.9   0.0    2.3  2  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
      0.034   14.4   0.1       0.29   11.4   0.0    2.5  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      0.037   12.7   0.1          2    7.0   0.0    2.2  2  HI0933_like      HI0933-like protein
      0.052   13.2   0.4        3.6    7.3   0.0    2.7  2  STAS             STAS domain
      0.062   13.5   0.0       0.12   12.6   0.0    1.5  1  NAD_binding_8    NAD(P)-binding Rossmann-like domain
      0.067   13.9   0.6        3.8    8.2   0.0    2.8  3  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer


Domain annotation for each model (and alignments):
>> NAD_Gly3P_dh_N  NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.4   0.2   5.2e-45   5.4e-42       4     155 ..       5     154 ..       3     156 .. 0.97
   2 ?   -1.7   0.0       2.4   2.5e+03      33      62 ..     158     187 ..     151     194 .. 0.74

  Alignments for each domain:
  == domain 1  score: 143.4 bits;  conditional E-value: 5.2e-45
                     EE--SHHHHHHHHHHHTTT--EEEE-S-HHHHHHHHHHSSBTTTBTT----TTEEEES-HHHHHTT--EEEE---HHHHHHHHHHHCCC--TT-E CS
  NAD_Gly3P_dh_N   4 vlGaGswGtalAkvlaenghevrlwvreeelieeineehenvkyLpgiklpenlvattdlaealkgadiivlvvPsqalrevlkklkgllkkkai 98 
                     v+G+G+wGta+A++la+n ++v++ +r+++ i++in++h+n  y++g++l++ + at+d a  l++a+ +++++Psq +r vlk++k+ +kk+a+
      AHX11174.1   5 VIGGGAWGTAIANLLASNSPKVHILSRNHKIIDSINNSHTNPVYFDGFQLNQGIIATNDPA-ILTQAESVFIAIPSQSTRAVLKEIKKNIKKDAQ 98 
                     9**********************************************************97.6778***************************** PP

                     EEE---SEET.TTEEHHHHHHHHH-S--EEEEESS--HHHHHTT--EEEEEEES-HH CS
  NAD_Gly3P_dh_N  99 lvsliKGieegtlkllsevieeelkeekvavlsGpslAeEvakgkptavviaskdke 155
                     ++ + KGie+g+++l+sev+++e+k++ + +lsGp++A+Ev+++k + + +as+d+e
      AHX11174.1  99 IILCNKGIEKGSMMLISEVVQDEIKNN-IFFLSGPNFAHEVIAEKYSFANLASADSE 154
                     ***************************.*****************999999998865 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
                     HHHHHHHHHSSBTTTBTT----TTEEEES- CS
  NAD_Gly3P_dh_N  33 elieeineehenvkyLpgiklpenlvattd 62 
                     el e+i+++   +ky+++i+  + + a ++
      AHX11174.1 158 ELSEAISTRTFFTKYIKDINGAQVIAAFKN 187
                     678888888888899998887777766655 PP

>> NAD_Gly3P_dh_C  NAD-dependent glycerol-3-phosphate dehydrogenase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.3   5.5e-35   5.8e-32       1     135 [.     175     302 ..     175     308 .. 0.95

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 5.5e-35
                     -HHHHHHHHHHHHHHHHHHHHHHHTTH-HHHHHHHHHHHHHHHHHHHHHHTSSGGGGGSTTTHHHHHHHHHSCT.HHHHHHHHHHCT--HHHHHH CS
  NAD_Gly3P_dh_C   1 DviGvelagalKNviAiaaGivdglglgdntkaalitrglaEmarlakalgakpetflglaglgDlivtctsgksRNrrfGeelgkgesleeiek 95 
                     D+ G+++ +a+KN +Ai +G++  lg + nt aal++++l E++ +++  +++p+t+++ +g+gDl++tc+s+ksRN++fG+el++g       k
      AHX11174.1 175 DINGAQVIAAFKNAVAILCGLLVRLGSEFNTLAALVSIALTEVKGFVEVKNGDPNTITEFCGIGDLVLTCFSDKSRNFKFGYELIDG-------K 262
                     899***********************************************************************************9.......3 PP

                     HHCC--HHHHHHHHHHHHHHHTT.G.HHHHHHHHHHHS-- CS
  NAD_Gly3P_dh_C  96 elnqvleGvetakevyellkkkgvemplleavykilyegk 135
                     e n+ +eG  t++++yel+kk+++++ l++++++i++ + 
      AHX11174.1 263 ENNTLVEGRATLESLYELAKKHDINCILINTLHDIITSRT 302
                     456799******************************9875 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.1   5.2e-11   5.4e-08       2     107 ..       4     108 ..       3     137 .. 0.89

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 5.2e-11
                 EEES-SHHHHHHHHHHHHHTHCEEEE-SCH.HHHHHHHHCEEEEETTCEEEEEECEEECCHSCCCCS-ESEEEE-SSGGGHHHHHHHHGGGECTCEEEE CS
        ApbA   2 ailGaGaiGsllaakLakagadvtlilrsr.rlealkknGlrltseggeeilrppealsaeekselepidlvivtvKayqteealeeikplldpntvvl 99 
                 +++G Ga G+ +a  La +  +v+++ r+   ++++++   +    +g + ++   a++++  + l++++ v++++++++t ++l+eik+ +++++ ++
  AHX11174.1   4 VVIGGGAWGTAIANLLASNSPKVHILSRNHkIIDSINNSHTNPVYFDGFQLNQGIIATNDP--AILTQAESVFIAIPSQSTRAVLKEIKKNIKKDAQII 100
                 69****************************9999999999888888889999999999999..9*********************************** PP

                 EESSSSCH CS
        ApbA 100 llqNGlgh 107
                 l+  G+++
  AHX11174.1 101 LCNKGIEK 108
                 *9999654 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.1   1.1e-09   1.2e-06       4      92 ..       5     100 ..       3     105 .. 0.89
   2 ?   -1.9   0.0       4.9   5.1e+03      33      50 ..     150     167 ..     131     193 .. 0.56

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 1.1e-09
                    EETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC...........-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTT CS
  F420_oxidored   4 iiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg...........vkvtavdneeaaeeadvvvlavkpedveevlselakdalkg 88 
                    +iG+G  g a+a+ l+++     ++ +  srn + ++++ ++              +++a++    +++a+ v++a++ + + +vl+e++k+ +k+
     AHX11174.1   5 VIGGGAWGTAIANLLASNS---PKVHIL-SRNHKIIDSINNSHTnpvyfdgfqlnQGIIATNDPAILTQAESVFIAIPSQSTRAVLKEIKKNIKKD 96 
                    89***********999998...788855.9********99887789********98888867777778***************************9 PP

                    SEEE CS
  F420_oxidored  89 klvi 92 
                      +i
     AHX11174.1  97 AQII 100
                    9998 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 4.9
                    ESSCCCHHHHHHHHC-EE CS
  F420_oxidored  33 srnpekaeelaeelgvkv 50 
                    s + ek +el e+++ ++
     AHX11174.1 150 SADSEKYKELSEAISTRT 167
                    566677777777776333 PP

>> PDH  Prephenate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   3.2e-06    0.0034      34      76 ..      58     100 ..      31     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.2e-06
                 SEEES-GGGGCCGSEEEE-S-GGGHHHHHHHHHHHS-TT-EEE CS
         PDH  34 deatddieavkeadivvlavPvevilevlkelaphlkedalit 76 
                   at+d + + +a+ v++a+P + ++ vlke+++ +k+da i+
  AHX11174.1  58 IIATNDPAILTQAESVFIAIPSQSTRAVLKEIKKNIKKDAQII 100
                 44555557899***************************98654 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   1.1e-05     0.012       2      93 ..       4     100 ..       3     104 .. 0.80
   2 ?   -2.6   0.0       6.2   6.6e+03      76      99 ..     166     188 ..     159     194 .. 0.74
   3 ?   -1.6   0.0       3.1   3.2e+03      44      73 ..     267     296 ..     261     309 .. 0.73

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 1.1e-05
                 EEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTS.....HHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEE CS
      TrkA_N   2 iiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatd.....eevLeeagiekadaviaatgddeanilavllakelnpkkkii 93 
                 ++iG G  G+++a+ L +++++v +  ++++ ++++ +  ++ v+ d+ +      ++ + a + +a++v +a+++  + +++ ++ k++ ++++ii
  AHX11174.1   4 VVIGGGAWGTAIANLLASNSPKVHILSRNHKIIDSINNSHTNPVYFDGFQlnqgiIATNDPAILTQAESVFIAIPSQSTRAVLKEIKKNIKKDAQII 100
                 8*****************9999**************9999886665554411111345566888899999999999888888888888888778777 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 6.2
                 HHHHHHHHHHHTSSSEEEEEESSG CS
      TrkA_N  76 nilavllakelnpkkkiiaraqdp 99 
                  ++ ++++k++n+ +++ia  +++
  AHX11174.1 166 RTFFTKYIKDING-AQVIAAFKNA 188
                 5677888888888.5788876665 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.1
                 EEES-TTSHHHHHHTTGGGESEEEE-SSSH CS
      TrkA_N  44 vvvgdatdeevLeeagiekadaviaatgdd 73 
                  v g at e++ e a+  +++++++ t +d
  AHX11174.1 267 LVEGRATLESLYELAKKHDINCILINTLHD 296
                 567778888888888888888777777655 PP

>> NAD_binding_2  NAD binding domain of 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   4.1e-06    0.0043       4      90 ..       5     103 ..       2     167 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-06
                    EE--SHHHHHHHHHHHHTT-EEEEE-SSHHHHHHHHHTT.............EEE-SSHHHHHHHCSEEEE-SSSHHHHHHHHHSHCCC--TT-EE CS
  NAD_binding_2   4 fiGlGvMGsnmalnllkagykvavynrtkekveelvaeg.............akaaesieelvasldvvitmvkagkavdeviegllealkkgdil 86 
                    +iG G  G+ +a+ l+++  kv++  r+++ ++++ +++               +a++  +++++++ v++ +++ + +++v++++++++kk++ +
     AHX11174.1   5 VIGGGAWGTAIANLLASNSPKVHILSRNHKIIDSINNSHtnpvyfdgfqlnqGIIATNDPAILTQAESVFIAIPS-QSTRAVLKEIKKNIKKDAQI 99 
                    89********************************9999999*********9955666666799999********8.789***************99 PP

                    EE-S CS
  NAD_binding_2  87 idgs 90 
                    i + 
     AHX11174.1 100 ILCN 103
                    9775 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   5.2e-05     0.055      11      84 ..       4      95 ..       1     112 [. 0.61
   2 ?   -1.2   0.0       2.7   2.8e+03      44      67 ..     156     183 ..     110     190 .. 0.51
   3 ?   -0.9   0.0       2.1   2.2e+03      55      78 ..     231     254 ..     196     272 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.2e-05
  NAD_binding_7 11 lvvGgGevAarkvrklleagakvtvvapevkeele............elvklaeeelekd.........legadlviaatddrelneriaeaaka 84
                   +v+GgG  ++  ++ l++++ kv++++ + +++++            + ++l++  +             e ++++i   + r++ ++i +++k+
     AHX11174.1  4 VVIGGGAWGTAIANLLASNSPKVHILSRN-HKIIDsinnshtnpvyfDGFQLNQGII--AtndpailtqAESVFIAIPSQSTRAVLKEIKKNIKK 95
                   8****************************.566664544445555552222332222..022344422244455555555556677777777744 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 2.7
  NAD_binding_7  44 leelvkla.eee.l...ekdlegadlvia 67 
                     +el +++  ++ +    kd++ga+++ a
     AHX11174.1 156 YKELSEAIsTRTfFtkyIKDINGAQVI-A 183
                    223333221122222214555555544.3 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 2.1
  NAD_binding_7  55 lekdlegadlviaatddrelneri 78 
                    + + +   dlv+++ +d++ n + 
     AHX11174.1 231 ITEFCGIGDLVLTCFSDKSRNFKF 254
                    444455568999999999988765 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   0.00013      0.14       3      37 ..       4      38 ..       2      56 .. 0.90
   2 ?   -1.4   0.0       3.4   3.6e+03      28      55 ..     106     126 ..      92     134 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 0.00013
                EEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTT CS
   Pyr_redox  3 vvvGgGyiglElAgalaelgkkVtvversdkllrl 37
                vv+GgG  g   A+ la    kV+++ r+ k+   
  AHX11174.1  4 VVIGGGAWGTAIANLLASNSPKVHILSRNHKIIDS 38
                9*****************************99844 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3.4
                 EESSSSSSTTSSHHHHHHHHHHHHHTTE CS
   Pyr_redox  28 versdkllrllDeeaskilqeklekngi 55 
                 +e ++++l      +s+++q+++++n i
  AHX11174.1 106 IEKGSMML------ISEVVQDEIKNN-I 126
                 56677777......999999999887.5 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.6e-05      0.07       4      43 ..       5      44 ..       2     100 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.6e-05
                EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHH CS
     3HCDH_N  4 viGaGtmGagiaavfasagleVvlvdiseealekalekie 43
                viG G  G+ ia+++as+  +V+++ ++++++++ +++ +
  AHX11174.1  5 VIGGGAWGTAIANLLASNSPKVHILSRNHKIIDSINNSHT 44
                9****************************99988777655 PP

>> IlvN  Acetohydroxy acid isomeroreductase, NADPH-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1     7e-05     0.073       8      92 ..       4     100 ..       1     119 [. 0.73

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 7e-05
                 EEES-SHHHHHHHHHHHHTT--EEEEE-TT-.......HHHHHHHHTT-EEEE......HHHHHHT-SEEEE-S-HHHHHHHHHHHTGGG--TT-EEE CS
        IlvN   8 aviGyGsqGhaqalnlrdsgldvvvglregs.......ksvkkAkeegfevlt......vaeavkkadvvmiliPDelqkevyeeeiepnlkegkala 92 
                 +viG G+ G a a+ l  +  +v +  r+++       + ++    +gf+  +         + ++a+ v+i iP +  ++v+ +ei++n+k+++ + 
  AHX11174.1   4 VVIGGGAWGTAIANLLASNSPKVHILSRNHKiidsinnSHTNPVYFDGFQLNQgiiatnDPAILTQAESVFIAIPSQSTRAVL-KEIKKNIKKDAQII 100
                 699999999999999999999999988888866444322222333467765431111003345689*****************.99******998654 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.23       4      94 ..       5     100 ..       3     125 .. 0.65
   2 ?    1.1   0.0       0.5   5.2e+02      49      89 ..     107     146 ..      94     156 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
                     EETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSG.....GGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHH...HHT CS
  Semialdhyde_dh   4 ivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavk.....aleegkdlkvedvdeeelkevdivflalpagvskelapkl...aea 89 
                     ++G  G+ G+++++lL++ +p+v   ++ls++++    +++ +         + ++  + + d+++l +++ vf a p++ ++++ +++   +++
      AHX11174.1   5 VIG-GGAWGTAIANLLASnSPKV---HILSRNHKIIDSINNSHTnpvyfDGFQLNQGIIATNDPAILTQAESVFIAIPSQSTRAVLKEIkknIKK 95 
                     677.7999********9955654...55556555555555555533333222334444444699999*******************999544555 PP

                     TSEEE CS
  Semialdhyde_dh  90 gvkvi 94 
                     ++++i
      AHX11174.1  96 DAQII 100
                     55666 PP

  == domain 2  score: 1.1 bits;  conditional E-value: 0.5
                     TTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHT CS
  Semialdhyde_dh  49 eegkdlkvedvdeeelkevdivflalpagvskelapklaea 89 
                     e+g+ + +++v ++e+ + +i fl+ p+ +++ +a+k+  a
      AHX11174.1 107 EKGSMMLISEVVQDEI-KNNIFFLSGPNFAHEVIAEKYSFA 146
                     5666777778777777.78999******9999999998655 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00027      0.29       2      44 ..       4      43 ..       3      87 .. 0.82
   2 ?    0.2   0.0      0.82   8.7e+02      47      71 ..     144     167 ..      80     190 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00027
                     EEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHH CS
  Sacchrp_dh_NADP  2 liiGaGsvGqavaellarhfdvdaeitvadrskeklealaaka 44
                     ++iG+G+ G a+a lla +++   ++++ +r+++  + + ++ 
       AHX11174.1  4 VVIGGGAWGTAIANLLASNSP---KVHILSRNHKIIDSINNSH 43
                     79*****************97...6*******99888776544 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.82
                      TCEEEEE--TTTHHHHHHHHHTTSS CS
  Sacchrp_dh_NADP  47 vrfeaialdaenyeavLaallkegd 71 
                      + ++ ++ d e+y++ L+++++ ++
       AHX11174.1 144 SFANLASADSEKYKE-LSEAISTRT 167
                      223334455555555.555555555 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0019         2       3      36 ..       3      36 ..       1      42 [. 0.89
   2 ?    3.7   0.0     0.019        20     222     258 ..      88     124 ..      63     187 .. 0.79

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0019
                 EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  3 viviGgGaAGlmaAisaakrgkrVlllekakklg 36
                  +viGgGa G   A  +a++  +V +l +++k+ 
   AHX11174.1  3 SVVIGGGAWGTAIANLLASNSPKVHILSRNHKII 36
                 69**************************999986 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.019
                  .ECTTEEEEEEEEE-SSEEESHHHHHHTTT-...... CS
  HI0933_like 222 kkkkkatekgellfThrGlsGpailqlSsyvakalek 258
                  + kk++++  ++++ + G++ ++++ +S++v++++++
   AHX11174.1  88 EIKKNIKKDAQIILCNKGIEKGSMMLISEVVQDEIKN 124
                  4578889999*********************887764 PP

>> STAS  STAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.056        59      67     106 ..      84     122 ..      79     131 .. 0.73
   2 ?    7.3   0.0    0.0034       3.6      65     105 ..     270     312 ..     268     322 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.056
                 HHHHHHHHHHHHTT-EEEEES--HHHHHHHHHTTCGGCC. CS
        STAS  67 raLkeilkelkrigvevvlvnikpevreklektgffdeve 106
                 ++Lkei+k++k ++ +++l+n   e   ++  +++ ++++
  AHX11174.1  84 AVLKEIKKNIK-KDAQIILCNKGIEKGSMMLISEVVQDEI 122
                 69********9.9*******97766665555555555555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
                 HHHHHHHHHHHHHHTT-EEEEES--HHHHHH..HHHTTCGGCC CS
        STAS  65 GvraLkeilkelkrigvevvlvnikpevrek..lektgffdev 105
                 G ++L+++++  k+++++++l n+  +++     + t + dev
  AHX11174.1 270 GRATLESLYELAKKHDINCILINTLHDIITSrtKNLTSLKDEV 312
                 5579********************9988876545555665555 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   0.00012      0.12       1      31 [.       5      35 ..       5      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 0.00012
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31
                   ++G+G+ G ++A lLa +  +v++l +++++
     AHX11174.1  5 VIGGGAWGTAIANLLASNSPKVHILSRNHKI 35
                   8*****************9999999887765 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0       0.2   2.1e+02      78     122 ..      57     104 ..       9     108 .. 0.70
   2 ?    8.2   0.0    0.0036       3.8      42     104 ..     139     201 ..     114     216 .. 0.84
   3 ?   -1.0   0.0       2.6   2.7e+03      33      58 ..     271     296 ..     260     315 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.2
                      SHHHHHHHHCHTT-SEEEE--...SSGGGHHHHHHHHHTTSEEEE--S CS
  DXP_reductoisom  78 Geealkelaeeeeadvvvaai...vGaaGLkptlaaikagkriaLANK 122
                      G  a ++ a  ++a+ v  ai   +  a Lk   + ik++++i L NK
       AHX11174.1  57 GIIATNDPAILTQAESVFIAIpsqSTRAVLKEIKKNIKKDAQIILCNK 104
                      444555555556777777777222345778888999999999999999 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0036
                      HHHHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SEEEE--SSGGGH CS
  DXP_reductoisom  42 qakefkpklvavadeeaaeelkealkekelktevlvGeealkelaeeeeadvvvaaivGaaGL 104
                      +a++++ + +a ad+e+++el+ea++++ + t+++ + ++++ +a+ ++a +++ ++    G 
       AHX11174.1 139 IAEKYSFANLASADSEKYKELSEAISTRTFFTKYIKDINGAQVIAAFKNAVAILCGLLVRLGS 201
                      45778889999************************************9999999998776664 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 2.6
                      SSTHHHHHHHHHHHT-SEEEESSHHH CS
  DXP_reductoisom  33 gsnvellaeqakefkpklvavadeea 58 
                         +e+l+e+ak++ ++++ ++  ++
       AHX11174.1 271 RATLESLYELAKKHDINCILINTLHD 296
                      45667788888888888887766554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      660  (0.0368119); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.37
# Mc/sec: 2645.00
//
Query:       AHX11175.1  [L=157]
Description: radC-like JAB domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-33  115.4   0.0      2e-33  114.9   0.0    1.2  1  RadC      RadC-like JAB domain
     0.0035   17.1   0.0     0.0052   16.5   0.0    1.3  1  Prok-JAB  Prokaryotic homologs of the JAB domain
  ------ inclusion threshold ------
      0.036   14.6   0.0      0.051   14.1   0.0    1.3  1  RNase_T   Exonuclease


Domain annotation for each model (and alignments):
>> RadC  RadC-like JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  114.9   0.0   3.4e-37     2e-33       2     120 ..      37     154 ..      36     156 .. 0.96

  Alignments for each domain:
  == domain 1  score: 114.9 bits;  conditional E-value: 3.4e-37
                 SSHHHHHHHHTTTSS-TTS-EEEEEEE-TTSBEEEEEEEEESTT-GGGCSHHHHHHHHHHTT-SEEEEEEE-TTS--S--HHHHHHHHHHHHHHHHHT- CS
        RadC   2 sspedvaeylkeeladleqEefvvllLdsknrliadeelseGtlnstlvdprevfkealklnAaavilaHnhPsgdlepSeeDieltkrlkealkllgi 100
                 +s+++v++yl+ ++ +++ E ++vllL++k  li++     G +++t++  re++k++l++ A+a++l+HnhPsg++ pSe D+ + ++l+++++ ++i
  AHX11175.1  37 KSWKSVVDYLRISIGNRPIEAICVLLLNKKYTLIKEYIQDFGAVDHTMICTREIIKRCLSCGASAIVLTHNHPSGNPLPSEPDLVIIRQLQKICQKVDI 135
                 799***********99999******************************************************************************** PP

                 EEEEEEEEESSE.EEETCCC CS
        RadC 101 ellDhiIigdeeeyySfaee 120
                 +l+Dh+Ii+ +e ++Sf  +
  AHX11175.1 136 QLIDHFIITPDE-HFSFVVN 154
                 *********776.89*9655 PP

>> Prok-JAB  Prokaryotic homologs of the JAB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   8.8e-07    0.0052      59     107 ..      86     146 ..      45     154 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 8.8e-07
    Prok-JAB  59 lkf....earerglevvgiwHSHpggsarPSetDrrdaaalar.........vkalliivgd 107
                 +++    ++ + g + ++  H Hp g + PSe D+   ++l +            ++ii++d
  AHX11175.1  86 CTReiikRCLSCGASAIVLTHNHPSGNPLPSEPDLVIIRQLQKicqkvdiqlI-DHFIITPD 146
                 33355556677888999******************999998778877777753.56666665 PP

>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   8.6e-06     0.051      56     134 ..      18     124 ..       2     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 8.6e-06
                 HHHHCHHHHHTCEBHHHHHHHHHHHHHHHTCCCETT.TCEEEESSHHHHHHHHHHHHH....HHHHCSEHCECHHHHHHHHHC................ CS
     RNase_T  56 ftgitqemldeapsfkevleefkellrklallvahn.aafdvgflraadkrilkkevp....krnqfldtlildkatlkelar................ 133
                 ++   q+ l+e  +++ vl+ +k+++++l++ +++   ++++  l ++ + ++k++++     ++ +++t++++k++l+  a+                
  AHX11175.1  18 VHESMQAILREDLETQPVLKSWKSVVDYLRISIGNRpIEAICVLLLNKKYTLIKEYIQdfgaVDHTMICTREIIKRCLSCGASaivlthnhpsgnplps 116
                 355557779*************************************************88888888899999988888766666655555555555555 PP

                 .......H CS
     RNase_T 134 .......t 134
                        +
  AHX11175.1 117 epdlviiR 124
                 55555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      587  (0.0327403); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1345.53
//
Query:       AHX11176.1  [L=151]
Description: helix-turn-helix family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-08   33.2   0.0    8.7e-08   32.1   0.0    1.6  1  HTH_19          Helix-turn-helix domain
    1.3e-07   31.6   0.0    3.1e-07   30.4   0.0    1.7  2  HTH_3           Helix-turn-helix
      1e-05   25.8   0.0    1.8e-05   25.0   0.0    1.3  1  HTH_31          Helix-turn-helix domain
     0.0033   17.5   0.1     0.0065   16.6   0.0    1.5  2  MqsA_antitoxin  Antitoxin component of bacterial toxin-antito
      0.009   15.8   0.1      0.023   14.4   0.1    1.8  1  HTH_38          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.015   15.1   0.0       0.28   11.0   0.0    2.4  2  HTH_23          Homeodomain-like domain
      0.045   13.9   0.1        3.9    7.7   0.0    3.3  3  HTH_AraC        Bacterial regulatory helix-turn-helix protein
      0.063   13.7   0.0       0.12   12.9   0.0    1.4  1  HTH_26          Cro/C1-type HTH DNA-binding domain
      0.076   13.4   0.0       0.18   12.2   0.0    1.6  2  Linker_histone  linker histone H1 and H5 family


Domain annotation for each model (and alignments):
>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   0.0   4.4e-11   8.7e-08       1      63 [.      19      80 ..      19      82 .. 0.95

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.4e-11
      HTH_19  1 GerLkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllqge 63
                G+ ++++R  +g++q+++a+++g++  +  ++E g +  +  ++ll+i++++++++ y+++  
  AHX11176.1 19 GKQIRRLRTLKGYSQAAIAKEIGVTFQQFQKYECGVN-RLCVSRLLDICKFCKVSPSYFFDSL 80
                7789*******************************88.899*******************976 PP

>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   0.0   1.5e-10   3.1e-07       1      55 []      22      76 ..      22      76 .. 0.98
   2 ?   -2.2   0.0       2.3   4.6e+03      34      42 ..     141     149 ..     135     151 .] 0.65

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 1.5e-10
                HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTTSSCSBHHHHHHHHHHHTSEHHHH CS
       HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnGernPsletlkklakaLgvsldel 55
                +++lR  +g+sq+ +A+++Gv+ ++ +++E G  +  +++l+ ++k+++vs++++
  AHX11176.1 22 IRRLRTLKGYSQAAIAKEIGVTFQQFQKYECGVNRLCVSRLLDICKFCKVSPSYF 76
                89**************************************************997 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                 SCSBHHHHH CS
       HTH_3  34 rnPsletlk 42 
                  +Ps+e + 
  AHX11176.1 141 KSPSQEEMS 149
                 556666654 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.2e-09   1.8e-05       2      58 ..      18      73 ..      18      75 .. 0.95

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.2e-09
      HTH_31  2 LGalLralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgldp 58
                +G + r+lR+  G sq++ A+ +gv+  +  ++E G + r   + l  ++  + ++p
  AHX11176.1 18 IGKQIRRLRTLKGYSQAAIAKEIGVTFQQFQKYECGVN-RLCVSRLLDICKFCKVSP 73
                5899**********************************.899*********999987 PP

>> MqsA_antitoxin  Antitoxin component of bacterial toxin-antitoxin system, MqsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.0   3.3e-06    0.0065      58     112 ..       6      60 ..       1      75 [. 0.89
   2 ?   -2.4   0.0       2.3   4.6e+03      54      66 ..     105     117 ..      88     137 .. 0.53

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 3.3e-06
  MqsA_antitoxin  58 lefrkkvnaelvdpafiarvrkkleldqreaaeifGgGvnafsryekGkvrppla 112
                      +f+k+ +++++ +++i+r+r   + +q+ +a+  G+  + f +ye G  r  ++
      AHX11176.1   6 DNFKKHAETDVMIGKQIRRLRTLKGYSQAAIAKEIGVTFQQFQKYECGVNRLCVS 60 
                     589*********************************************9986655 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.3
  MqsA_antitoxin  54 seellefrkkvna 66 
                      +ell + +  +a
      AHX11176.1 105 NKELLVLVRAFKA 117
                     3333333333333 PP

>> HTH_38  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.2e-05     0.023      12      32 ..      21      42 ..      20      45 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.2e-05
      HTH_38 12 eIerll.aeGlslreIArrLgr 32
                +I rl+  +G+s+++IA+++g+
  AHX11176.1 21 QIRRLRtLKGYSQAAIAKEIGV 42
                79999845************97 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00014      0.28      14      37 ..      25      50 ..      20      62 .. 0.83
   2 ?    1.6   0.0      0.13   2.6e+02      22      33 ..      64      75 ..      54      80 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00014
      HTH_23 14 lae..GlsvreIAreLgvsrrTvyrw 37
                l+   G+s+++IA+e gv+ ++ +++
  AHX11176.1 25 LRTlkGYSQAAIAKEIGVTFQQFQKY 50
                44444*************98888765 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.13
      HTH_23 22 eIAreLgvsrrT 33
                +I++ + vs++ 
  AHX11176.1 64 DICKFCKVSPSY 75
                79*******986 PP

>> HTH_AraC  Bacterial regulatory helix-turn-helix proteins, AraC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.22   4.4e+02      31      41 ..      38      48 ..      36      49 .. 0.83
   2 ?    7.7   0.0    0.0019       3.9      10      25 ..      61      76 ..      60      82 .. 0.92
   3 ?   -0.2   0.0       0.6   1.2e+03      25      33 ..     111     119 ..     110     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.22
                HHSSS-HHHHH CS
    HTH_AraC 31 ketGmtPsqyr 41
                ke G+t++q+ 
  AHX11176.1 38 KEIGVTFQQFQ 48
                677******96 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0019
                -HHHHHHHTTSSHHHH CS
    HTH_AraC 10 tiediAdelgfSrsyF 25
                ++ di+  + +S+syF
  AHX11176.1 61 RLLDICKFCKVSPSYF 76
                588************9 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.6
                 HHHHHHHHS CS
    HTH_AraC  25 FsrlFkket 33 
                 + r+Fk++t
  AHX11176.1 111 LVRAFKAIT 119
                 689***998 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   5.9e-05      0.12       2      55 ..      22      74 ..      21      78 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.9e-05
      HTH_26  2 LrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpg 55
                +r+l   +g++++  a+ +g++ ++++++  g ++r+  ++L  iC+  +++p+
  AHX11176.1 22 IRRLRTLKGYSQAAIAKEIGVTFQQFQKYECG-VNRLCVSRLLDICKFCKVSPS 74
                67888889************************.89*************999997 PP

>> Linker_histone  linker histone H1 and H5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   8.8e-05      0.18       1      34 [.      11      44 ..      11      57 .. 0.87
   2 ?   -2.9   0.0       4.7   9.4e+03      53      63 ..     122     132 ..     110     138 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.8e-05
  Linker_histone  1 hpsykdMikeAIkalkerkGsSrqaIkkyikaky 34
                    h  ++ Mi + I  l + kG S +aI k i  ++
      AHX11176.1 11 HAETDVMIGKQIRRLRTLKGYSQAAIAKEIGVTF 44
                    678899**********************997655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 4.7
  Linker_histone  53 gvekgelvqpk 63 
                      v +++l  +k
      AHX11176.1 122 SVRSKVLSLVK 132
                     34445555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       825  (0.0460148); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1314.88
//
Query:       AHX11177.1  [L=807]
Description: preprotein translocase, SecA subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.7e-128  428.0   3.5   1.7e-128  428.0   3.5    1.9  2  SecA_DEAD      SecA DEAD-like domain
    1.1e-44  152.9   8.9    1.1e-44  152.9   8.9    2.6  3  SecA_SW        SecA Wing and Scaffold domain
    1.6e-38  131.7   0.4    1.6e-38  131.7   0.4    2.6  3  SecA_PP_bind   SecA preprotein cross-linking domain
    2.2e-07   30.8   0.3    1.9e-06   27.8   0.0    2.4  2  DEAD           DEAD/DEAH box helicase
     0.0077   16.6   2.1      0.044   14.1   0.2    3.3  3  Helicase_C     Helicase conserved C-terminal domain
  ------ inclusion threshold ------
      0.039   14.1   0.2        0.2   11.9   0.0    2.4  2  YchF-GTPase_C  Protein of unknown function (DUF933)


Domain annotation for each model (and alignments):
>> SecA_DEAD  SecA DEAD-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  428.0   3.5  5.7e-132  1.7e-128       2     289 ..       6     389 ..       5     390 .. 0.97
   2 ?   -2.1   0.1      0.63   1.9e+03      21      69 ..     445     494 ..     422     548 .. 0.61

  Alignments for each domain:
  == domain 1  score: 428.0 bits;  conditional E-value: 5.7e-132
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SecA_DEAD   2 kkllgsknerelkklkkiveeineleeelkalsdeeLrakteelkerlaeg.ealdellpeafalvreaakrvlgmrhydvQliGglvlhegkiaemkT 99 
                 ++++ s+n++ + +lk+ v+ in+le e+++ls+++Lr kt+e+++r+ ++ ++l +llpeafa+vrea+ r+lgmrh+dvQl+Gg+vlh+g+i+em+T
  AHX11177.1   6 HRIFDSRNRKIMDQLKSSVRCINSLEGEIQRLSSDALRGKTNEFRDRILNQdSKLADLLPEAFACVREASIRTLGMRHFDVQLMGGIVLHQGMISEMHT 104
                 689999*****************************************9666168********************************************* PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SecA_DEAD 100 GEGKtlvatlpaylnaltgkgvhvvtvndYLakrdaewmgpvyeflGlsvgvieseleseerreaYeaditYgtnnelgfdyLrDnlalskeelvqrgl 198
                 GEGKtlvatl+aylnal g+gvh+vtvndYLa+rdaewm+++y++lGl+v++i+s+++++er +aY+aditY+tnnelgfdyLrDn++++k+e+vqrgl
  AHX11177.1 105 GEGKTLVATLAAYLNALLGEGVHIVTVNDYLARRDAEWMKQIYRYLGLTVSCITSDMQDSERINAYKADITYATNNELGFDYLRDNMKFTKKEMVQRGL 203
                 *************************************************************************************************** PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
   SecA_DEAD 199 nfaivDEvDsvLiDeArtpLiisgpaeeeselyeeakklvkeleeeed................................................... 246
                 n+ai+DEvDs+LiDeArtpLiisg a++++ ly++a+k++k+l+++                                                     
  AHX11177.1 204 NYAIIDEVDSILIDEARTPLIISGAASSSTYLYSRANKIAKKLDSNLYtvdekyksvflteegqevaekllleeklieassslyeaknlplvhclnqsl 302
                 ****************************************98888544555678888999999999999****************************** PP

                 ............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   SecA_DEAD 247 ............................................akegveieeesqtlatitlqnffrlYeklaGmtGTaeteaeef 289
                                                             ake++++++e+qtla+it+qn+frlY+kl+GmtGTa+te+ee+
  AHX11177.1 303 kanklfhkdkdyivkdgqiviideftgrmmegrryseglhqaleAKENLKVQNENQTLASITFQNYFRLYNKLSGMTGTAATEKEEL 389
                 **************************************************************************************8 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.63
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
   SecA_DEAD  21 eeineleeelkalsdeeLrakteelkerlaegealdel.lpeafalvrea 69 
                 ++i++ e+  +al +++L++++ + k+++ e e + ++  p a+++  ++
  AHX11177.1 445 TSIEQSETISSALRKAKLKHSVLNAKQHAFEAEIIAQAgKPGAITIATNM 494
                 45666666666666666666666666666544443332133344443333 PP

>> SecA_SW  SecA Wing and Scaffold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.3      0.56   1.7e+03      99      99 ..     191     191 ..      42     315 .. 0.64
   2 ?   -2.0   0.1       1.1   3.1e+03     104     123 ..     398     428 ..     320     477 .. 0.57
   3 !  152.9   8.9   3.7e-48   1.1e-44       1     198 [.     597     796 ..     597     797 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.56
                 S CS
     SecA_SW  99 f 99 
                 +
  AHX11177.1 191 M 191
                 0 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
                 T...........HHHHHHHHHHHHHHHHHHH CS
     SecA_SW 104 e...........elaeellekaekayekkee 123
                             +  +e++++ e++y++  e
  AHX11177.1 398 VqipthlpirrmDHDDEIYATKEEKYQAILE 428
                 1444444444444444444444444443333 PP

  == domain 3  score: 152.9 bits;  conditional E-value: 3.7e-48
                 -B-SCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTHHCHHHHHHHHHHHHHHHHHCHHHHS.SS.CSHHHHHHHHHCCCSS CS
     SecA_SW   1 piesklvsksienaQkkvEernfdiRknlleYDdVmnkQRkviYkqRrevLegesedlrerildliedvveeiveesvpeeekeewdleglleelkeef 99 
                 +i+++ +++s+e+aQkkvE+rn++iRknll++DdV+n+QRkvi++qR++++++e    + ++l + +dv ++++e+  +++     d+ +l++++++++
  AHX11177.1 597 AIKHSYITRSLEKAQKKVENRNYEIRKNLLKFDDVINEQRKVIFEQRNSIIDSE----SIDLLPIARDVNSQLLENARSKN---FYDIPSLTKAMHSVY 688
                 59*************************************************777....45677777777777774444433...578899999999988 PP

                 STSST......HHHHHHHHHHHHHHHHHHHHC...HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTTSSSS-CCHHHHHHHHHHHHHHHHHHHH CS
     SecA_SW 100 svele......elaeellekaekayekkeeei...ellrelervvlLevlDkaWkehLdamdeLregiglrgygqkdPlqeYkkegfelFeemlarike 189
                   ++e      ++ e +  k+e+ ++kke+e+   +ll  +++ +++ +lD+ WkehL+ +++Lr + +lr+++qk+Pl e+k+++f+ F+++ +r +e
  AHX11177.1 689 DEDFEalakteDIVELIERKTEEIISKKEKEYtdpKLLLLVKKRIMIGILDQLWKEHLQFLENLRLSTNLRAVAQKNPLIEFKHDAFHAFQKLSKRWHE 787
                 8877788888899999999999999999999999888999*********************************************************** PP

                 HHHHHCCCT CS
     SecA_SW 190 evvkkllkv 198
                 +v+ ++++v
  AHX11177.1 788 NVLASFIRV 796
                 ***999987 PP

>> SecA_PP_bind  SecA preprotein cross-linking domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.7   0.4   5.5e-42   1.6e-38       2     111 .]     232     346 ..     231     346 .. 0.92
   2 ?   -2.7   0.0       3.1   9.3e+03      24      69 ..     418     459 ..     401     469 .. 0.58
   3 ?   -2.5   0.1       2.7   7.9e+03      60      69 ..     674     683 ..     605     722 .. 0.54

  Alignments for each domain:
  == domain 1  score: 131.7 bits;  conditional E-value: 5.5e-42
                   HHHHHHHHHHHHCCCHTTCCECCCTTTSEEEESHHHHHHHHHCCT-......SSSTTSCCHCCHHHHHHHHHHHHHCSTTTTTEEECTTCEEEBSTT CS
  SecA_PP_bind   2 seelyekanklvkklkeeedyevdekkktveltekGvekvekllkv......keelydeenlelvhhvnqaLkAhtlferdvdYivkdgeviivDef 92 
                   s+ ly +ank++kkl+++  y+vdek k+v lte+G+e +ekll        +++ly+++nl lvh +nq+LkA++lf++d+dYivkdg+++i+Def
    AHX11177.1 232 STYLYSRANKIAKKLDSN-LYTVDEKYKSVFLTEEGQEVAEKLLLEeklieaSSSLYEAKNLPLVHCLNQSLKANKLFHKDKDYIVKDGQIVIIDEF 327
                   5679************96.8***********************63233445589999**************************************** PP

                   TSSEBTS--SSTTHHHHHH CS
  SecA_PP_bind  93 tGRlmegrrysdGLhqaie 111
                   tGR+megrrys+GLhqa+e
    AHX11177.1 328 TGRMMEGRRYSEGLHQALE 346
                   *****************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.1
                   CCTTTSEEEESHHHHHHHHHCCT-SSSTTSCCHCCHHHHHHHHHHH CS
  SecA_PP_bind  24 vdekkktveltekGvekvekllkvkeelydeenlelvhhvnqaLkA 69 
                    +e+k ++ l  + v+++++ l+    l+ ++++e  +++++aL+ 
    AHX11177.1 418 TKEEKYQAIL--ESVKECQNKLQ--PVLIGTTSIEQSETISSALRK 459
                   4444433333..34455555542..355666666666777776664 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 2.7
                   HHHHHHHHHH CS
  SecA_PP_bind  60 vhhvnqaLkA 69 
                      + ++ kA
    AHX11177.1 674 FYDIPSLTKA 683
                   3333333333 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.0   6.4e-10   1.9e-06      15     134 ..      96     215 ..      86     227 .. 0.82
   2 ?   -0.3   0.0      0.25   7.6e+02     113     155 ..     310     354 ..     263     371 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 6.4e-10
                 CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEETTSSHHHHHHHHHTTCSEEEEEHHHHHH.HH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
        DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliiggvaardqlskldngvdivvgtpgrldd.ll 112
                 + ++ +++TG GKTl++ ++++ +        g  + iv+    La+  ++ +k++  y++l+v++i+++ + ++ +++   ++di+++t   l    l
  AHX11177.1  96 QGMISEMHTGEGKTLVATLAAYLNA-----LLGEGVHIVTVNDYLARRDAEWMKQIYRYLGLTVSCITSDMQDSERINAY--KADITYATNNELGFdYL 187
                 568899***********99999333.....5566788899999**********************998877777777777..89*******77754255 PP

                 ......HCTSSHCTTEEEEEEETHHHHH CS
                 ......xxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 113 ......stgklnlsqvrflVlDEadrll 134
                       +++++  + +++ ++DE+d +l
  AHX11177.1 188 rdnmkfTKKEMVQRGLNYAIIDEVDSIL 215
                 676677677788999**********987 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.25
                 HCTSSHCTTEEEEEEETHHHHHHT..TTHHHHHHHHHHSHHHCTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxx RF
        DEAD 113 stgklnlsqvrflVlDEadrlldq..gfsdfinrilnqlpqitcd 155
                 +++   +++ +++++DE  + + +   +s+ +++ l++ ++ + +
  AHX11177.1 310 KDKDYIVKDGQIVIIDEFTGRMMEgrRYSEGLHQALEAKENLKVQ 354
                 445556888899*****9876666235555555555554333333 PP

>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.67     2e+03      32      58 ..     143     169 ..     101     172 .. 0.66
   2 !   14.1   0.2   1.5e-05     0.044       2     109 ..     422     558 ..     421     560 .. 0.73
   3 ?   -2.8   0.1       2.7   8.1e+03      50      63 ..     631     644 ..     585     667 .. 0.50

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.67
                 HHHHHHHTTSTEEEESTTSTHHHHHHH CS
  Helicase_C  32 vklllekkgikvavlhgelpqnereei 58 
                 +k + +  g++v +++++++ +er+ +
  AHX11177.1 143 MKQIYRYLGLTVSCITSDMQDSERINA 169
                 333333339999999999999999865 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.5e-05
                 HHHHHHHHH.HHTTTTSEEEEEESSHHHHHHHHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEESSSSSSH.. CS
  Helicase_C   2 kleallell.kleeeggkilifvntidrlekvklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVinfdlprnv.. 97 
                 k++a+le + + +++ + +li +++i++ e ++  l+k ++k  vl+++  + e e i ++ + g   + iat++a+rG di+   l  n+d++++   
  AHX11177.1 422 KYQAILESVkECQNKLQPVLIGTTSIEQSETISSALRKAKLKHSVLNAKQHAFEAEIIAQAGKPGA--ITIATNMAGRGTDIQ---LGGNIDFQTSAnd 515
                 667777777667778888999******9987666678889********888888877777777766..99************6...4444444433333 PP

                 ...............................HHHHHHHTTSSS CS
  Helicase_C  98 ...............................tsyiqriGRtgR 109
                                                +  +q +GR gR
  AHX11177.1 516 dsmkeeyaknkeivqnagglyvigterhesrRIDNQLRGRSGR 558
                 4456666777777777777777777777777777777777777 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 2.7
                 STHHHHHHHHHHHH CS
  Helicase_C  50 lpqnereeileqfn 63 
                   +++r+ i+eq n
  AHX11177.1 631 VINEQRKVIFEQRN 644
                 33445555555555 PP

>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.6e-05       0.2      48      81 ..     291     324 ..     275     326 .. 0.76
   2 ?   -3.2   0.1       3.5     1e+04      29      60 ..     683     715 ..     675     722 .. 0.50

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.6e-05
  YchF-GTPase_C  48 dlvelgseaaakeagklrlegkdyvvqdgDiilf 81 
                    +l  ++  ++  +a+kl +++kdy+v+dg+i+++
     AHX11177.1 291 NLPLVHCLNQSLKANKLFHKDKDYIVKDGQIVII 324
                    44445667777889999**************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.5
  YchF-GTPase_C  29 viHsDfekgFir.aevikyedlvelgseaaake 60 
                    ++Hs   + F   a++ ++ +l+e ++e+ + +
     AHX11177.1 683 AMHSVYDEDFEAlAKTEDIVELIERKTEEIISK 715
                    566666666643244444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (807 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1153  (0.0643092); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.66u 0.26s 00:00:00.92 Elapsed: 00:00:00.39
# Mc/sec: 6260.42
//
Query:       AHX11178.1  [L=264]
Description: cell cycle transcriptional regulator CtrA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-20   73.4   0.0    2.9e-20   72.5   0.0    1.5  1  Response_reg  Response regulator receiver domain
    2.3e-15   56.4   0.0    4.3e-15   55.5   0.0    1.5  1  Trans_reg_C   Transcriptional regulatory protein, C terminal


Domain annotation for each model (and alignments):
>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.5   0.0   3.2e-24   2.9e-20       1     104 [.       3     110 ..       3     118 .. 0.93

  Alignments for each domain:
  == domain 1  score: 72.5 bits;  conditional E-value: 3.2e-24
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHH....ESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCT CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeek....vdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkag 93 
                   +l+vdD+++v + +++++++ gy ++++a+  ++a +l++++k    +dli+lD  +p+ dGl+++ ++r ++ ++pvi+++a s+ e++++a++ g
    AHX11178.1   3 ILVVDDEQKVTDCVKSIITSVGY-VCDTASCCRDASALINSSKgdyqYDLIILDRVLPDGDGLDMILNLRCKNIKTPVIFFSALSSYENKIKAFDFG 98 
                   8**********************.***************88888889************************************************** PP

                   ESEEEESSG.-H CS
  Response_reg  94 addflsKpf.dp 104
                   addf++K   ++
    AHX11178.1  99 ADDFIAKSElHK 110
                   *******85355 PP

>> Trans_reg_C  Transcriptional regulatory protein, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.5   0.0   4.8e-19   4.3e-15       1      77 []     150     227 ..     150     227 .. 0.94

  Alignments for each domain:
  == domain 1  score: 55.5 bits;  conditional E-value: 4.8e-19
                  TEEEE-SHHHHHHHHHHHHT.TTSEEEHHHHHHHHTTTTSTSHTHHHHHHHHHHHHHHHTTTTSSSSEEEETTTEEEE CS
  Trans_reg_C   1 geeveltpkefklLelLlen.pgrvvsreeLleevwgededvddrtvdvhisrLRkkLeddekkprlIetvrgvGYrl 77 
                  g+ v+lt+ke+++Lel++ + +g ++s+++ +++++ ++e ++++ +dv  ++LR kL+++++  ++Ietv+g+GY l
   AHX11178.1 150 GKVVQLTNKEYSMLELMCLHgRGAIISKDKFISHLYSNNEPTEQKIIDVFACKLRSKLAAHNDGVSYIETVWGRGYTL 227
                  5679**************98689*************************************87777***********86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       600  (0.0334653); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1989.11
//
Query:       AHX11179.1  [L=164]
Description: N5-carboxyaminoimidazole ribonucleotide mutase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-58  196.7   0.2    1.5e-58  196.6   0.2    1.0  1  AIRC      AIR carboxylase


Domain annotation for each model (and alignments):
>> AIRC  AIR carboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  196.6   0.2   8.4e-63   1.5e-58       1     146 [.       5     152 ..       5     154 .. 0.97

  Alignments for each domain:
  == domain 1  score: 196.6 bits;  conditional E-value: 8.4e-63
                 EEEEEESSGGGHHHHHHHHHHHHHTT-EEEEEE--TTTSHHHHHHHHHHCHTTTEEEEEEEEESS--HHHHHHHHSSS-EEEEEE--STTCCHHHHHHH CS
        AIRC   1 kVgiimGSdsDlevmkkaaeilkelgveyevrvvSahrtpeelleyaeeaeerglkviIagAGgaahLpgvvaslttlPVigvPvkskalkgldsllSi 99 
                 kV +imGS+sD+ vm +a +ilkel++ +e+ v+Sahrtpe+l+++a++ae+rg+++iIagAGgaahLpg+vas+t++PV+gvP++ + l+g+dsllSi
  AHX11179.1   5 KVSVIMGSTSDYTVMCHAERILKELDILFETMVISAHRTPERLYTFARNAENRGIEIIIAGAGGAAHLPGMVASMTSVPVLGVPIEGRVLHGIDSLLSI 103
                 699************************************************************************************************ PP

                 HT--TTS--EE-SST..HHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHH CS
        AIRC 100 vqmPsgvpvatvaig..kaknAallAaqilalkdeelaekleeyreelk 146
                  qmPsg pvat++ig  +a+nAal+A +il+++++el++++ +  ++++
  AHX11179.1 104 CQMPSGTPVATFSIGkaGAENAALFAGRILGMNNKELKKRVLKRTTQQS 152
                 ***************9999*********************998877765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       476  (0.0265492); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1197.65
//
Query:       AHX11180.1  [L=328]
Description: tRNA threonylcarbamoyl adenosine modification protein YgjD [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-83  279.9   0.0    2.9e-83  279.7   0.0    1.0  1  Peptidase_M22   Glycoprotease family
    0.00014   21.6   0.0    0.00021   21.1   0.0    1.4  1  Carbam_trans_N  Carbamoyltransferase N-terminus
  ------ inclusion threshold ------
       0.14   11.5   0.0       0.52    9.7   0.0    1.7  2  DUF2066         Uncharacterized protein conserved in bacteria


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.7   0.0   4.9e-87   2.9e-83       2     271 .]      23     302 ..      22     302 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.7 bits;  conditional E-value: 4.9e-87
                    CEXEEEEEEEEE....SSSSHHHHHHHHHHHHHHHHHHHHHHHTSTGGGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHHHHHHHCC CS
  Peptidase_M22   2 vlanvvasqkelhakyGGvvPelasraHserllplieealaeaglsledldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhleahalaa 97 
                    vl +++ +q+  h+ y Gv Pe asr+H ++l+ l+e+a  + +l+   ldaIa+tkgPGl+++L vG ++A+gla++l+k ++++nhle+h+la 
     AHX11180.1  23 VLFHEIFTQD--HRIYNGVYPEFASREHLKILPLLLEKASLAHDLK--SLDAIAYTKGPGLIGSLIVGTMMAQGLAFSLGKRILAINHLEGHILAS 114
                    6778888887..***************************9998888..8*********************************************** PP

                    HCTSECSSC.EEEEESSSTEEEEEECT.TEEEEEEEESSSEHHHHHHHHHHHHT..SSCCHHHHHHHCTC..S.......EET...TEEE.CHHHH CS
  Peptidase_M22  98 rleekeefP.vvllvsGghtqvylvke.gryeilgetlddaagealdkvarllglpypggpkieklakeg..kkiefprplkg...ldfsfsGlkt 186
                    rl  + +fP ++ll+sGgh+q+++ +  g+y +lgetldda ge++dk+a +lg+pypgg+ iek+a +g  +++++p ++++   ++fs+sG+kt
     AHX11180.1 115 RLFYEIDFPfIALLISGGHSQLVCTERiGKYNVLGETLDDAFGETFDKLATMLGFPYPGGKTIEKFALNGnpSRFHLPGAMINqsnCNFSLSGIKT 210
                    **9767****************************************************************9888********************** PP

                    HHHHHHSTT.......HHHHHHHHHHHHHHHHHHHHHHHHHHCTBSEEEEESGGGGXHHHHHCHCCHHHHTTSEEEXXXHHHHSSXCHHHHH CS
  Peptidase_M22 187 avlkeleke.......vedlaasfqeavvdhlvekteralklpkakelvilGGvaankrLrealeeeaeelglkliiPplkyctdnaamiaw 271
                    a+ k + +        ++d++asfq+ vv+ +++k+e+a+k  + +++v+ GGv++n ++re ++e a+e+gl+l++Pp ++ctdnaamiaw
     AHX11180.1 211 ALKKIIDSLpivtsedKADICASFQACVVKIITSKLEQAVKISGHRRIVLTGGVGSNLYIRESIQEFANERGLSLYFPPVQLCTDNAAMIAW 302
                    ******5424677899*************************************************99999*********************9 PP

>> Carbam_trans_N  Carbamoyltransferase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.5e-08   0.00021     247     312 ..     208     274 ..      97     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.5e-08
  Carbam_trans_N 247 vhdffeasalrlkearekde.dlaAsiqvflErlvvevlnivyeklkirnLclaGGvalNiklNsal 312
                     ++  ++++   l  + ++d+ d+ As+q  + +++ + l+++ ++ + r++ l+GGv+ N+ +   +
      AHX11180.1 208 IKTALKKIIDSLPIVTSEDKaDICASFQACVVKIITSKLEQAVKISGHRRIVLTGGVGSNLYIRESI 274
                     333333333222223333333***************************************9877666 PP

>> DUF2066  Uncharacterized protein conserved in bacteria (DUF2066)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.18   1.1e+03     196     229 ..     135     168 ..     131     171 .. 0.83
   2 ?    9.7   0.0   8.7e-05      0.52     116     151 ..     258     295 ..     248     306 .. 0.73

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.18
     DUF2066 196 qlldggdtsegsvegedlealaeavlddladala 229
                 ql+ +++  +++v ge+l++++ +  d+la +l 
  AHX11180.1 135 QLVCTERIGKYNVLGETLDDAFGETFDKLATMLG 168
                 56666777889999***************99885 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 8.7e-05
     DUF2066 116 sllgee..sssellaalkaaakerGlplvlPllDledq 151
                  +l+ +  s+  +++++++ a+erGl l++P   l  +
  AHX11180.1 258 IVLTGGvgSNLYIRESIQEFANERGLSLYFPPVQLCTD 295
                 4444335578889******************8887544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2488.83
//
Query:       AHX11181.1  [L=339]
Description: TRAP transporter solute receptor, TAXI family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      4e-87  292.3   0.0    4.6e-87  292.1   0.0    1.0  1  NMT1_3    NMT1-like family
    3.2e-05   24.0   0.0    5.5e-05   23.2   0.0    1.3  1  NMT1      NMT1/THI5 like


Domain annotation for each model (and alignments):
>> NMT1_3  NMT1-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  292.1   0.0   5.1e-91   4.6e-87       1     289 []      40     334 ..      40     334 .. 0.96

  Alignments for each domain:
  == domain 1  score: 292.1 bits;  conditional E-value: 5.1e-91
      NMT1_3   1 igTastgGtyYpvGvaiatliseklakdq..kvkasaqssaGsveNiqllkkgeadlailqsdvayeAyeGegefegkkplknlraitmlyaevfqlvv 97 
                 igT+s++G+yY++G+a++++++++   d+   + +s+qs+ G+++N+++l+ g++++a +q+d+ay+ y+G g+f+++kp+++lr+++++++e+f+++v
  AHX11181.1  40 IGTGSISGVYYATGNAVCRFLKKHSVADKtlDIFCSVQSTPGAMYNLNALRHGDLEIAASQGDWAYDIYHGVGQFSSMKPMTSLRSLFATHKEAFTVLV 138
                 8********************9998877623599***************************************************************** PP

      NMT1_3  98 skdsgigsiadlkgkrvsvGpegsGtegsarailealglsekdlklleelgygesadalkdgqldgaalvaGvPvsavtqlaasedikliplddeqldk 196
                 +++s+i+s++++kgk v++G++g+G +g+ ++i++a g++ +d+k+++el+ +e+++al+dg++d++++v G+P++ ++++ a++ +++++ld+e+ +k
  AHX11181.1 139 RTNSNIKSFDEIKGKIVNIGAPGTGVRGTIENIMRAKGWTTRDFKVATELNSSEQVQALCDGKIDVMTTVIGHPSGLFQEALATCGVQFLSLDEETQQK 237
                 *************************************************************************************************** PP

      NMT1_3 197 llkeypvftkyvipagtypq...dedikTiavpnflvvradldeelvYeitkaifenldelnsihkaakeislekal.aglpvplHpGAerYYkEqG 289
                 l+++yp++++y ip ++yp+   +e ikT+av+++++vr+d++e+ +Y+++ +if n++ l+sih+a+ ++ + +++ +++ +p+HpGA++YYk +G
  AHX11181.1 238 LVSDYPYYYSYHIPIDLYPGvtpQESIKTVAVKSVFYVRKDFPEDKAYKLVGSIFQNFSTLQSIHPAFANLIKVDLVpENVDAPIHPGAQKYYKHIG 334
                 ******************96524467******************************************99777777747777************988 PP

>> NMT1  NMT1/THI5 like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   6.1e-09   5.5e-05      62     146 ..     119     207 ..     111     219 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 6.1e-09
                 -EEEEEEEE-S..--EEEEEECCC--SSGGGGTTSEEEE-S.-TTHHHHHHHHHHHTT--GGG-EEEE.-.TT-HHHHHHCTSSSEEEC CS
        NMT1  62 pvvsvaallqe..plsglivlkdsgikspkDLkGkrigyvg.spfekallkallakdggdpsdvtlvn.vggtslakalltgkvDaaig 146
                 p++s+ +l+ +  + ++++v+++s+iks+ ++kGk + +   +   + +++ +++++g +  d+++ +  + ++ ++al +gk+D+++ 
  AHX11181.1 119 PMTSLRSLFAThkEAFTVLVRTNSNIKSFDEIKGKIVNIGApGTGVRGTIENIMRAKGWTTRDFKVATeLNSSEQVQALCDGKIDVMTT 207
                 6666666665400566778899999**********8764332467899***********999999865155566677********9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (339 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2525.25
//
Query:       AHX11182.1  [L=51]
Description: hypothetical protein NHE_0218 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       141  (0.00786435); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 397.15
//
Query:       AHX11183.1  [L=429]
Description: UDP-N-acetylmuramoylalanine--D-glutamate ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-18   67.6   0.3    3.4e-18   66.3   0.3    1.7  1  Mur_ligase_M  Mur ligase middle domain
    7.9e-06   26.0   0.0    2.4e-05   24.5   0.0    1.8  2  Mur_ligase_C  Mur ligase family, glutamate ligase domain
  ------ inclusion threshold ------
      0.038   14.6   0.1        1.1    9.9   0.0    2.9  3  PglD_N        PglD N-terminal domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.3   5.7e-22   3.4e-18       1     130 [.     100     214 ..     100     264 .. 0.74

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 5.7e-22
                   EESSS-HHHHHHHHHHHHHCTEEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE---TSTTHHHHSSHHHHHH CS
  Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvgttnneiglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitnispdHldfhgtlenyae 96 
                   +TGtnGK+Ttt +i +il ++   + +vg+    ig p + ++  + ++  +++E+ss+   + +  ++ l+   av++ i+pdH+d++ +l++y +
    AHX11183.1 100 ITGTNGKSTTTAMISHILGNN---FISVGN----IGRPVM-EHIND-GV-GYIIELSSY---QlEMCSD-LPLSSAVLLDITPDHMDRYASLDDYVK 182
                   8*****************998...777887....666654.45555.45.5689*****...4255556.899************************ PP

                   HHHHHHHTSETTCEEEEETTSC...CHHHHHCTC CS
  Mur_ligase_M  97 aKaelferlkeegiavinaddpyakelikklkka 130
                   aK ++f++l+  +i+ +n   +  k+++++l+++
    AHX11183.1 183 AKVRIFDNLETTAIVALNSCVN--KRIFSELSNR 214
                   **********876666664444..5555555544 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.8   1.1e+04      41      52 ..      17      27 ..       6      35 .. 0.58
   2 !   24.5   0.0     4e-09   2.4e-05       2      56 ..     285     335 ..     284     355 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.8
                  SEEEEEEEESTT CS
  Mur_ligase_C 41 krlilvfgpgge 52
                   ++ilvf + +e
    AHX11183.1 17 AKKILVFDD-KE 27
                  456666654.44 PP

  == domain 2  score: 24.5 bits;  conditional E-value: 4e-09
                   TTSSEEEEETTTEEEEEE.T--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCS CS
  Mur_ligase_C   2 kgRlevvgeadgvtvidD.yahnpdslsaalkalreiapdkrlilvfgpggelger 56 
                   ++R e  g+ ++vt+++D +a+n++sl++a++++    + ++l l++g g+e+ ++
    AHX11183.1 285 PHRTEKCGSYKNVTFVNDsKATNIESLQKAISLY----SGSNLYLLAG-GREKHKN 335
                   8*********************************....8899999999.8884444 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.0   0.00019       1.1      11      63 ..       5      56 ..       2      61 .. 0.80
   2 ?   -2.3   0.0       1.3   7.5e+03      25      67 ..      84     126 ..      66     127 .. 0.41
   3 ?    1.0   0.0      0.11   6.7e+02      19      41 ..     289     311 ..     286     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00019
      PglD_N 11 gkvvadiieangeyeiigflDdnkktevegypvlgkaiellkslseeeyevvi 63
                gk  +    a+g  + i ++Dd++k++  gyp + + ++ ++   +++ +v++
  AHX11183.1  5 GKSLLSFFAARG-AKKILVFDDKEKSADFGYPQIVEHVDHKNLDWKKVRNVFV 56
                666677777888.89999****************9998877765567777877 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.3
      PglD_N  25 eiigflDdnkktevegypvlgkaiellkslseeeyevviAIGn 67 
                 ++  flD  + +   g+ +  + ++  + +s+   + +i++Gn
  AHX11183.1  84 DVQFFLDLLEGKIAVGITGTNGKSTTTAMISHILGNNFISVGN 126
                 4445555544333233333333333333332222234566666 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.11
      PglD_N  19 eangeyeiigflDdnkktevegy 41 
                 e++g y+ + f+ d+k+t++e +
  AHX11183.1 289 EKCGSYKNVTFVNDSKATNIESL 311
                 68899**********99887764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (429 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 3342.00
//
Query:       AHX11184.1  [L=321]
Description: polyprenyl synthetase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-54  182.6   0.7    8.4e-54  182.3   0.7    1.1  1  polyprenyl_synt  Polyprenyl synthetase
  ------ inclusion threshold ------
      0.016   14.8   0.3      0.032   13.8   0.3    1.5  1  HEPPP_synt_1     Heptaprenyl diphosphate synthase (HEPPP synt


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.3   0.7   9.3e-58   8.4e-54      10     237 ..      40     253 ..      34     276 .. 0.88

  Alignments for each domain:
  == domain 1  score: 182.3 bits;  conditional E-value: 9.3e-58
                      HHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEETTEE-HHHCTCHHHHHHHHHHHHHHHHHHHHHHHS CS
  polyprenyl_synt  10 ylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDimDdsetRRGqpcahrlvGnklAindgdfllarafellaklfe 103
                       +v a GK++R+ll l ++ ++++ +   ++  ++a+ +el+h+a+L+hDD++D+  +RRG+  +++++Gnk+++++gdf+l+ afe++ ++  
       AHX11184.1  40 KMV-AAGKKVRALLALISFALCGNAD--QDTEIRAAATIELIHNATLMHDDVIDENYMRRGRANIKSIYGNKISVLTGDFILSVAFEIILEC-- 128
                      567.89*****************444..5788************************************************************.. PP

                      TTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt 104 kslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaFQiqDDylDlf 197
                      k+l +++l+s+++ q+ eG++l+l +     +   +++eylei+ +KTa lf++++++aa+l++  +e +  ++++g+ +G+aFQi+DD++D+ 
       AHX11184.1 129 KNLAAVSLLSKTAKQLSEGEMLQLCTI-GRIV---TESEYLEIIGKKTAILFSAATEIAAILSNR-KEHILLFREVGHLIGIAFQIIDDVIDYD 217
                      99**********************555.2444...59***************************6.6779**********************99 PP

                      S-HHHHSS-TSHHHHTT---HHHHHHHHCT-HHHHHHHHH CS
  polyprenyl_synt 198 gdpevlgKpagtDiqegkctlpilkalelaspeqrkvlke 237
                       +++++gK+ g+D +e ++tlp + a++ a+++     k+
       AHX11184.1 218 -SSSKIGKEEGNDFRESRFTLPCMIAYRDAKSKA---AKK 253
                      .56889**********************554433...333 PP

>> HEPPP_synt_1  Heptaprenyl diphosphate synthase (HEPPP synthase) subunit 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.3   3.5e-06     0.032      19     111 ..      53     149 ..      46     187 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.5e-06
  HEPPP_synt_1  19 llllslleeaeltekekeeyiltamlvqiAldtHdkvsek..keeeeeekkn...rqLtVLAGdyYSglYYklLaevkdielirllaeaikeinehk 110
                   +l+ ++l + +++++ + +++ t+ l++ A  +Hd v ++   ++  ++ k+    ++ VL Gd+  ++ ++++ e k+++ + ll+++ k+  e  
    AHX11184.1  53 ALISFALCG-NADQDTEIRAAATIELIHNATLMHDDVIDEnyMRRGRANIKSiygNKISVLTGDFILSVAFEIILECKNLAAVSLLSKTAKQLSEGE 148
                   455556666.78888889999***************9887333333444454333799*******************************99998876 PP

  HEPPP_synt_1 111 i 111
                   +
    AHX11184.1 149 M 149
                   5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       652  (0.0363657); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 2367.91
//
Query:       AHX11185.1  [L=312]
Description: sulfite exporter TauE/SafE family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-38  132.8  32.2    1.8e-38  132.5  32.2    1.1  1  TauE      Sulfite exporter TauE/SafE
  ------ inclusion threshold ------
          8    6.9   6.5        3.9    7.9   0.2    2.6  2  FtsH_ext  FtsH Extracellular


Domain annotation for each model (and alignments):
>> TauE  Sulfite exporter TauE/SafE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5  32.2     2e-42   1.8e-38       2     233 ..      18     291 ..      17     294 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 2e-42
        TauE   2 llagllaGfvagllGiGggliavPlLlll.lppavavatsllavvatslsgalahrrrgnvdwrlllllllgsliGallGallllllpse.llkllfgv 98 
                 +++gl+ G++agl+GiGg +i++P L+++ ++p va+ +++   va+s++++l +++++nvd++++ +l+l+++ G+llG++ll +l ++  + +++ +
  AHX11185.1  18 MVVGLISGVMAGLFGIGGNFITIPTLIFMnIAPTVALSSAINQTVASSFASFLNQLKQKNVDLSIAFYLFLSGACGTLLGSFLLMYLQEKgNIDIVIFL 116
                 689*************************98899*******************************************************99534444444 PP

        TauE  99 lllllallm..llrkkr.........................................srak..grerrptaillvligglvGllsGllGiGgGfllvp 152
                 + + + ++m  +    +                                         +     +++++ + ++l+++g++vGl+ +l G+GgGfllvp
  AHX11185.1 117 IYIGMLASMgsI----IsvdsvcklfamrlakttyhespskesvagkcsrfvnklplrR--YfhSAKTEISIVALFIVGLIVGLILSLSGVGGGFLLVP 209
                 444444444332....244457888899999*******999999999998887777652..0447779999999****999****************** PP

        TauE 153 llllllglplkkavatslllilvislagalgyal.agavdwpllllllpgallGallGarlarrlsertlrrlfallllvlg 233
                 +l++l++lp++ a++ts++ ++++s+++++ +a+ ++ vd+ l+++l +ga++G+ lGarl+  l++  lr+l+ +++++  
  AHX11185.1 210 TLIYLFNLPTRMAIGTSVFQSVLVSASATFLHAItLHTVDVLLGFFLSLGAIFGVALGARLNLTLHPLILRLLLSAVMFAGV 291
                 *******************************977799999999999*********************99**99999998865 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.9   0.2   0.00044       3.9      12      45 ..      24      79 ..      13      80 .. 0.67
   2 ?    0.8   1.6     0.071   6.3e+02       2      35 ..     182     228 ..     181     236 .. 0.67

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00044
    FtsH_ext 12 lllllslfg......................gsgtgstkeisyseFledleqgnve 45
                 ++ + lfg                      +s  ++t+  s++ Fl++l+q+nv+
  AHX11185.1 24 SGVMAGLFGiggnfitiptlifmniaptvalSSAINQTVASSFASFLNQLKQKNVD 79
                444444444555555556666555566777777777******************96 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.071
    FtsH_ext   2 llwlllallllllllslfg.............gsgtgstkeisyseF 35 
                 ++ l +++l+++l+lsl+g             +++ +++  i  s F
  AHX11185.1 182 IVALFIVGLIVGLILSLSGvgggfllvptliyLFNLPTRMAIGTSVF 228
                 56788999999999998876666666666666555556655555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (312 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1049  (0.0585086); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2237.06
//
Query:       AHX11186.1  [L=246]
Description: transmembrane family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.5e-60  202.4   0.1    1.5e-59  201.6   0.1    1.4  1  Alph_Pro_TM  Putative transmembrane protein (Alph_Pro_TM)


Domain annotation for each model (and alignments):
>> Alph_Pro_TM  Putative transmembrane protein (Alph_Pro_TM)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  201.6   0.1   8.4e-64   1.5e-59       2     227 .]      24     237 ..      23     237 .. 0.91

  Alignments for each domain:
  == domain 1  score: 201.6 bits;  conditional E-value: 8.4e-64
  Alph_Pro_TM   2 lvadlskervaitssFtGtelllfGaverpdqsssdvvvvveGpkesvvvrrKervlgiWvnsdsvefesvPsfyavass.rpldeiaseeelkrlei 98 
                  ++adls++r++i+s+FtG+++l+fGa+++++   +++v++++Gp++s+++++K +vlg+W+n ++v +++vP f+++ s   p ++i         +i
   AHX11186.1  24 VIADLSPSRIEIHSKFTGKNILIFGALMEKT---DNIVIIIHGPETSMAIHKKVKVLGLWTNGAKVLVNRVPYFFSFSSAtMPYRKI--------KQI 110
                  789***************************6...89****************************************99872344444........556 PP

  Alph_Pro_TM  99 gldalklsaeaeaadaeeaeefrealirlkeraglYreeeggvefldgtlfraevalPanvpeGkytvevyllrdgkvvaeestelevekvGlerfia 196
                   +++++    +e+  +++++e++eali++k r++lY+ e++ ve+++++lfr ++ lP n+++Gkytve+++l+d+++v+ es +l v k+Gl+++i+
   AHX11186.1 111 FYEEFIPFS-HERDLSNDEREMVEALIQNKIRSSLYQFENA-VEIINDRLFRGNIFLPGNIVRGKYTVEIIALDDNRIVGIESIPLVVVKTGLDAWIF 206
                  666665555.3444455699*****************9877.******************************************************** PP

  Alph_Pro_TM 197 elAheqpllYGllavllAlaaGwlaslvfrr 227
                  +++h++p+lYG++a++ A+++Gwl  ++++r
   AHX11186.1 207 DMNHSHPILYGFAAIIGAIFIGWLGFFATNR 237
                  *************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       660  (0.0368119); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1914.64
//
Query:       AHX11187.1  [L=44]
Description: hypothetical protein NHE_0223 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       378  (0.0210832); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 369.25
//
Query:       AHX11188.1  [L=473]
Description: gram-negative porin family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.4   1.6    2.9e-10   40.4   0.7    1.8  2  Porin_4   Gram-negative porin


Domain annotation for each model (and alignments):
>> Porin_4  Gram-negative porin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0     0.057     1e+03      80     114 ..      64      99 ..      55     160 .. 0.66
   2 !   40.4   0.7   1.6e-14   2.9e-10      66     296 ..     151     433 ..     125     449 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.057
     Porin_4  80 gtsgarqayvglsg.gfGkvtlGrqdgafdeagvdl 114
                 g ++ +q  ++++g +++++ +G++  +f+ + + l
  AHX11188.1  64 GHNTINQPSFTIKGsSVFSFHYGKNEDFFELSKNLL 99 
                 445578888999999999999999998887766643 PP

  == domain 2  score: 40.4 bits;  conditional E-value: 1.6e-14
     Porin_4  66 lkasfeleagdngagtsgarqayvglsggfGkvtlGrqdgafdeagv..dlafesgsladtgtalsgvsgsagf......................... 137
                 +++ + le  +++  t   r+ay++l+ ++G++++G+ +  + +a    + ++++++++    +++ v++  g                          
  AHX11188.1 151 FSYGVLLEPMFDMSKTVSTRNAYIFLEAPYGRFEMGQVNDSATSALKidASSVAATGAGIRDLDWTEVANLEGRpehavfdtstsstqhkrhknvthpf 249
                 5566667766778788889******************97755555554422355555555555777776554445555667777777777777776666 PP

     Porin_4 138 ....d....srdsnsiiyyspkfgGftagasyafgeddntnglagsvagdsddndafglgagya..fggvglavaaaysqgdneada....dldawglg 222
                     +     ++  ++  ++  +g f++++sy+ + +++               d++++g gy+  +++ ++ v+++ +++  e ++     l+   +g
  AHX11188.1 250 lvhpNyyvaYDAPIRANFTTTGLGAFKLAVSYT-NRTAD-----------GIYRDILDFGCGYTgiAKNLNYGVSITGQTSLIEPTGnlhhPLKRFEIG 336
                 6665266545666666777888**********6.32222...........2369**********98888889999888855444434588866778899 PP

     Porin_4 223 asvslggfklgasyadaendaaaaa.........................adadlygvgasytvgaltvgaaygnydd..agandadatsyglgatYnL 294
                 + + + g+kl +s+++       ++                            + +++g +++ g++ ++++y + d+  +++++++ + +++g  Y+L
  AHX11188.1 337 GMAEMYGIKLAGSFGNSF----LSGikinknmqldlskgiddpkqfvstnGQLTYMTLGTAFESGPMMFSVNYMKSDNmlKKSDKSTLHVISIGTHYRL 431
                 999999999999988322....22234456666778889999999999887788899**********************999****************9 PP

     Porin_4 295 sk 296
                 ++
  AHX11188.1 432 TG 433
                 87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (473 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       404  (0.0225333); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3853.91
//
Query:       AHX11189.1  [L=43]
Description: hypothetical protein NHE_0225 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       403  (0.0224776); expected 358.6 (0.02)
Passed bias filter:                      268  (0.0149478); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 336.17
//
Query:       AHX11190.1  [L=476]
Description: UDP-N-acetylmuramyl-tripeptide synthetase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-37  129.5   0.0    2.5e-37  128.7   0.0    1.4  1  Mur_ligase_M   Mur ligase middle domain
    2.2e-21   75.9   0.0    4.7e-20   71.6   0.0    2.8  3  Mur_ligase_C   Mur ligase family, glutamate ligase domain
  ------ inclusion threshold ------
       0.11   12.7   0.3       0.69   10.1   0.1    2.2  2  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
       0.14   12.5   0.0       0.51   10.7   0.0    2.0  1  Mur_ligase     Mur ligase family, catalytic domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.0   5.6e-41   2.5e-37       2     192 .]     103     304 ..     102     304 .. 0.89

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 5.6e-41
                   ESSS-HHHHHHHHHHHHHCTEEEEETTC.................SS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE---T CS
  Mur_ligase_M   2 TGtnGKTTtteliaailekagkvigtvg.................ttnneiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitnis 81 
                   TGtnGKT+++++  +i+  ag++++++g                 tt+++ +l+k+l +++++ ++y+ lE+ss+g+++krl++ ++ +++++ n++
    AHX11190.1 103 TGTNGKTSISSFFSQICVLAGEKAASLGtlgvssnvrelnqplklTTPDAADLHKLLDKLAQSAVQYCCLEASSQGIEQKRLDS-VRLKAVAFSNLT 198
                   9****************99966666666666*****************************************************.************ PP

                   STTHHHHSSHHHHHHHHHHHHHT.SETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSC CS
  Mur_ligase_M  82 pdHldfhgtlenyaeaKaelfer.lkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipll 177
                   ++Hld+h+++++y++aK +lf+  l+++g++v+   d+ya ++++   +++  vvt+g  ++ +    +++  ++ g+ +++  v ++el i ++++
    AHX11190.1 199 HEHLDYHENMDKYFQAKLRLFSDiLPDDGTMVLPTLDEYAVRIRQICPNKH--VVTYGNTGDIQI--ISQL-PNQIGQVLKVK-VLDKELIIPLKVF 289
                   *********************66267778*********9999999999996..9*******8743..2233.33556666665.78999******** PP

                   SCHHHHHHHHHHHHH CS
  Mur_ligase_M 178 GkhnvyNalaaiaaa 192
                   Gk++ +N++aai++a
    AHX11190.1 290 GKFQGNNLIAAIGLA 304
                   ************875 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       0.5   2.2e+03      56      79 ..     151     173 ..     143     183 .. 0.73
   2 !   71.6   0.0   1.1e-23   4.7e-20       3      89 ..     324     408 ..     321     410 .. 0.95
   3 ?   -0.2   0.0      0.27   1.2e+03      27      58 ..     430     453 ..     420     470 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.5
                   SCHCTHHHHHHHHCCHSSEEEEEE CS
  Mur_ligase_C  56 rtrtfhdefgrlasaladslvvlg 79 
                   +++++h+++++la++ a+ ++ l+
    AHX11190.1 151 DAADLHKLLDKLAQS-AVQYCCLE 173
                   568899999999998.55555444 PP

  == domain 2  score: 71.6 bits;  conditional E-value: 1.1e-23
                   TSSEEEEE.TTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEESS-TTSTHHH CS
  Mur_ligase_C   3 gRlevvge.adgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvvlgdypraedsia 89 
                   gR+e ++  +d  ++++Dyah+pd+l+++l +l++++p++ + lvfg+gg+   r+++++++++r+as++  ++++++d+pr+e +++
    AHX11190.1 324 GRMEFIKHpGDRCKIMIDYAHTPDGLQHLLLSLKWHFPYNDITLVFGCGGD---RDKQKRPLMARIASKMTSKVIITDDNPRSEAPEK 408
                   9****9998999***************************************...***************9999**********99865 PP

  == domain 3  score: -0.2 bits;  conditional E-value: 0.27
                   HHHHHHHHHHHSSSSEEEEEEEESTT.CCSCH CS
  Mur_ligase_C  27 lsaalkalreiapdkrlilvfgpggelgertr 58 
                   ++ a++++    + +++i++ g g e    ++
    AHX11190.1 430 IKYAIRTA----KPSEIIVITGRGHE----SK 453
                   33344444....56899999997554....33 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.1   0.00015      0.69       8     138 ..     310     460 ..     309     464 .. 0.63
   2 ?    0.4   0.2      0.15   6.6e+02       2      11 ..     459     468 ..     459     475 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
  Metallophos_2   8 DlHsnldaleavlealkevgvdaiihaGD.....l.eeeepevleellela.......pvlaVrGNnDeev..veedvlreaaelgtdl...peea 85 
                    D+H n+++ + v+ +  +   + i h GD     + ++ +p+ l+ ll  +       +++ V+G+  +++   +  ++r a +++ ++    +  
     AHX11190.1 310 DVH-NIEYDKIVAPI-GRM--EFIKHPGDrckimIdYAHTPDGLQHLLLSLkwhfpynDITLVFGCGGDRDkqKRPLMARIASKMTSKViitDDNP 401
                    666.55555544444.444..788899998887636666665333333222355555599999999874445344444445555555557742333 PP

  Metallophos_2  86 elel.agekvlliHgdpl.....gvkdalaellkeaeegsdvvvcGHtHvpevekeggv 138
                    + e+ ++ +  l+H+ p+     g ++a+++++++a+  + +v+ G  H+ +   ++ +
     AHX11190.1 402 RSEApEKIRKELLHHCPKaleidGRQNAIKYAIRTAKPSEIIVITGRGHESKQVLKDRI 460
                    3443345557899999889***999**********666666********9866555555 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.15
  Metallophos_2   2 klaiiSDlHs 11 
                    ++++iSD+H 
     AHX11190.1 459 RILHISDVHT 468
                    699******3 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00011      0.51       5      50 ..      24      66 ..      20      99 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00011
                ESTTSCCHHHHHHHHHHTTSEEEEEESSHCHHHTT-EEEES-HGGG CS
  Mur_ligase  5 igidgrgmsagalflalkGykvdGsdfieslialGaaavvghdaan 50
                i++d+r++++  lf a   +k   +++ie+++++Ga++v++ ++ +
  AHX11190.1 24 ITMDSREVEKDFLFCAPS-EKS--HSYIEDALKRGAKIVLTKQEPQ 66
                899999999999988654.444..79**************998874 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (476 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       551  (0.0307323); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3690.77
//
Query:       AHX11191.1  [L=220]
Description: endonuclease III [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.5e-19   68.6   0.0      9e-19   67.9   0.0    1.3  1  HhH-GPD         HhH-GPD superfamily base excision DNA repair 
    4.7e-07   29.3   0.0    1.4e-06   27.9   0.0    1.8  1  HHH             Helix-hairpin-helix motif
    0.00062   20.3   0.2      0.032   14.8   0.0    2.3  2  HHH_5           Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.025   14.2   0.0      0.098   12.3   0.0    1.9  2  IL11            Interleukin 11
      0.048   14.0   4.3      0.079   13.3   4.3    1.4  1  EndIII_4Fe-2S   Iron-sulfur binding domain of endonuclease II
      0.062   13.5   0.1      0.092   13.0   0.1    1.3  1  BTD             Beta-trefoil DNA-binding domain
        0.1   12.6   0.1       0.37   10.7   0.0    1.8  2  DUF2400         Protein of unknown function (DUF2400)
       0.16   11.3   0.0       0.22   10.8   0.0    1.2  1  LysR_substrate  LysR substrate binding domain


Domain annotation for each model (and alignments):
>> HhH-GPD  HhH-GPD superfamily base excision DNA repair protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.9   0.0     4e-22     9e-19       2     104 ..      41     171 ..      40     175 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.9 bits;  conditional E-value: 4e-22
                 HHHHHTTS-HHHHHHHHHHHHHHHSHCSHHHHHHSHHHHHHHHHTTSTTHHHHHHHHHHHHHHHH.................................S CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................................x RF
     HhH-GPD   2 sailsqqtsderanriierlferfgfptpedladadeekLrelirelGfyrrKakyikelArilv.................................g 67 
                 +++ls+q +d+ +n++++ lf+     tpe+ a+++ e+L+e+i+++G++++Ka++i++l+++l+                                 g
  AHX11191.1  41 AVLLSAQSTDVGVNKATKVLFQIA--DTPEQYAKMSTEELKEYIKTIGLHNNKARNIIALSKKLIadnqadipndfeylqslpgigrksanvilstlfG 137
                 689********************5..5*********************************************************************985 PP

                 -SSS--TTSHHHHHHHHHHTTSSSSTTHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
     HhH-GPD  68 kpdvlivvDvhvrrilkrlrsikekktkkkvekklee 104
                    + i+vD+hv r+ +r++++++k +   +e +l +
  AHX11191.1 138 A--KRIAVDTHVFRVSNRIGLVETK-NVLATEMELLK 171
                 3..57*****************996.55555554445 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   6.2e-10   1.4e-06       4      29 ..     108     133 ..     107     134 .. 0.94

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 6.2e-10
                 HHHTSSHHHHHTSTT-SHHHHHHHHH CS
         HHH   4 glipasreeLlalPGVGpktAeaIls 29 
                 ++ip+++e L++lPG+G+k A++Ils
  AHX11191.1 108 ADIPNDFEYLQSLPGIGRKSANVILS 133
                 689**********************8 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.059   1.3e+02      10      44 ..      51      86 ..      46     101 .. 0.73
   2 !   14.8   0.0   1.4e-05     0.032       1      23 [.     114     136 ..     114     143 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.059
                --HHHHHHHHTTT--SHHHHHHS-HHHHHT.STTS- CS
       HHH_5 10 iGpktAlallsaGiesvedlaaadveeLak.ipGiG 44
                +G   A ++l +  +++e+ a++++eeL + i+ iG
  AHX11191.1 51 VGVNKATKVLFQIADTPEQYAKMSTEELKEyIKTIG 86
                67778888888844599********99988666554 PP

  == domain 2  score: 14.8 bits;  conditional E-value: 1.4e-05
                 -HHHHTSTT--HHHHHHHHTTT- CS
       HHH_5   1 feeLlsvsGiGpktAlallsaGi 23 
                 fe+L+s++GiG+k A  +ls+ +
  AHX11191.1 114 FEYLQSLPGIGRKSANVILSTLF 136
                 89******************965 PP

>> IL11  Interleukin 11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   4.4e-05     0.098      15      53 ..      89     126 ..      77     136 .. 0.87
   2 ?   -1.1   0.0      0.58   1.3e+03     116     143 ..     162     188 ..     141     190 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 4.4e-05
        IL11  15 vnqtrsLlkltkellkdhelkfpsdvehrlksLPalsns 53 
                  n++r++  l+k+l++d+++ +p+d+e+ l+sLP +  +
  AHX11191.1  89 NNKARNIIALSKKLIADNQADIPNDFEY-LQSLPGIGRK 126
                 5899***********************8.9****99766 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.58
        IL11 116 mskleaprvpvvspslppssatawevlq 143
                 +   e++ +++v+ s++p+ a +w vl+
  AHX11191.1 162 VLATEMELLKIVPESFLPQ-AHHWLVLH 188
                 4556777788889999999.99998875 PP

>> EndIII_4Fe-2S  Iron-sulfur binding domain of endonuclease III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   4.3   3.5e-05     0.079       1      17 []     193     209 ..     193     209 .. 0.99

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.5e-05
  EndIII_4Fe-2S   1 CTARkPkCeaCPLaDlC 17 
                    C+A+ PkC  C ++D C
     AHX11191.1 193 CKAKQPKCRVCIINDVC 209
                    ***************** PP

>> BTD  Beta-trefoil DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   4.1e-05     0.092      93     147 ..      41      96 ..       7     101 .. 0.83

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.1e-05
         BTD  93 kvlLdasasdepvsqLhkcafqlkdtellYlclsqdkiiqfqatel.pkdpnrevl 147
                  vlL+a+++d  v++  k+ fq+ dt  +Y ++s+++  ++ +t   ++++ r+++
  AHX11191.1  41 AVLLSAQSTDVGVNKATKVLFQIADTPEQYAKMSTEELKEYIKTIGlHNNKARNII 96 
                 58999*******************************99888777654666666665 PP

>> DUF2400  Protein of unknown function (DUF2400)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.63   1.4e+03      46      83 ..      65      84 ..      28     120 .. 0.52
   2 ?   10.7   0.0   0.00017      0.37     173     195 ..     141     163 ..     138     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.63
     DUF2400 46 kspydfvleeeeekdlkelekfkyRffnsedllallka 83
                ++p+++ +                  +++e+l++++k+
  AHX11191.1 65 DTPEQYAK------------------MSTEELKEYIKT 84
                33333333..................222222222222 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00017
     DUF2400 173 iPlDvHvarvarklgllkrkqad 195
                 i +D+Hv+rv++++gl+++k+  
  AHX11191.1 141 IAVDTHVFRVSNRIGLVETKNVL 163
                 679**************988754 PP

>> LysR_substrate  LysR substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0    0.0001      0.22      13      48 ..       4      39 ..       1      53 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.0001
                    ECCCHHHHHHHHHHHHHHHSTTEEEEEEEESHHHHH CS
  LysR_substrate 13 pptlaryllppllarfraryPevelelvegdseell 48
                      +++ + + ++l+rf+++ P+ ++el+ ++  +l+
      AHX11191.1  4 MMSFSKSQVIEILKRFQEARPDPKIELQYKNKFTLV 39
                    5689999*********************99976665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (220 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       738  (0.0411624); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1859.15
//
Query:       AHX11192.1  [L=254]
Description: CDP-alcohol phosphatidyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-13   51.6   1.0    1.2e-13   51.6   1.0    3.2  2  CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
    7.1e-10   38.6   6.9    7.1e-10   38.6   6.9    3.3  4  CDP-OH_P_tran_2  CDP-alcohol phosphatidyltransferase 2


Domain annotation for each model (and alignments):
>> CDP-OH_P_transf  CDP-alcohol phosphatidyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.6   1.0   1.3e-17   1.2e-13       2      66 .]      12      75 ..      11      75 .. 0.92
   2 ?   -8.1  11.4         2   1.8e+04      23      40 ..     166     183 ..      84     243 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.6 bits;  conditional E-value: 1.3e-17
                     -HHHHHHHHHHHHHHHHHGGGS-H..HHHHHHHHHHHHHTTHHHHHHHHTT---HHHHHHHHHHH CS
  CDP-OH_P_transf  2 lPnaiTllrlllsvlailllltyyplvlailllliasltDalDGklARrlnqvstlGkllDslaD 66
                      Pn+iT+l+l+ ++++i  +     + la++ + i+++ D++DG++AR l+++s++G+ lDslaD
       AHX11192.1 12 FPNLITFLGLCVGLTSI-RFSLGALWELALAAITISAIIDGIDGRIARMLESSSRFGAELDSLAD 75
                     5***************9.5767777999999999****************99888*********9 PP

  == domain 2  score: -8.1 bits;  conditional E-value: 2
                      S-H..HHHHHHHHHHHHH CS
  CDP-OH_P_transf  23 tyyplvlailllliaslt 40 
                      ++++++l + ll+i++lt
       AHX11192.1 166 VINHYFLVVYLLVISVLT 183
                      234455555555555543 PP

>> CDP-OH_P_tran_2  CDP-alcohol phosphatidyltransferase 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.2       1.3   1.1e+04       8      14 ..     105     111 ..     103     113 .. 0.50
   2 ?   -1.3   0.2      0.24   2.2e+03       3      11 ..     147     155 ..     146     156 .. 0.82
   3 ?   -2.2   1.5      0.46   4.2e+03       3      13 ..     173     183 ..     171     185 .. 0.59
   4 !   38.6   6.9   7.9e-14   7.1e-10       1      37 []     200     236 ..     200     236 .. 0.97

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 1.3
  CDP-OH_P_tran_2   8 llvglfa 14 
                      ++v+ +a
       AHX11192.1 105 IFVVCMA 111
                      4444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.24
  CDP-OH_P_tran_2   3 vlPllllvg 11 
                      vlP+++ +g
       AHX11192.1 147 VLPVIVTFG 155
                      899999876 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.46
  CDP-OH_P_tran_2   3 vlPllllvglf 13 
                      v+ ll++ +l 
       AHX11192.1 173 VVYLLVISVLT 183
                      55666666665 PP

  == domain 4  score: 38.6 bits;  conditional E-value: 7.9e-14
  CDP-OH_P_tran_2   1 elvlPllllvglfaAlLityPWltLsvlgilYLlslP 37 
                      +l ++l++++++ a+++i +PW+t+++l+++Y+ls+P
       AHX11192.1 200 YLESILMFFFAVTAVAFILKPWITIPILSLCYVLSIP 236
                      57899*******************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       805  (0.0448993); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2176.61
//
Query:       AHX11193.1  [L=225]
Description: phosphatidylserine decarboxylase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.8e-31  108.2   0.5    3.1e-30  105.2   0.5    1.9  1  PS_Dcarbxylase  Phosphatidylserine decarboxylase
  ------ inclusion threshold ------
      0.027   13.7   0.0      0.038   13.2   0.0    1.3  1  LSDAT_prok      SLOG in TRPM, prokaryote


Domain annotation for each model (and alignments):
>> PS_Dcarbxylase  Phosphatidylserine decarboxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.2   0.5   3.4e-34   3.1e-30       3     199 ..      40     209 ..      38     210 .. 0.91

  Alignments for each domain:
  == domain 1  score: 105.2 bits;  conditional E-value: 3.4e-34
  PS_Dcarbxylase   3 effvrklkdgaRpidddpgaivsPaDgrilqigeieegsviqvKgityslrdLlgeasessadsfkngyfvviyLspgdyHryhaPvsgkveerr 97 
                     ++++++++d++R ++  ++ i+sPaDg+++ i+     +      i+                  +++  ++i+Lsp ++H++++P++g+v++ +
      AHX11193.1  40 ALVIYFFRDPQRAVPVCKEFILSPADGIVCRIESTVPPKSSG---IE------------------DEMNKISIFLSPLNVHVNRIPINGVVRNLH 113
                     7899**********999999************5555532222...22..................36779************************* PP

  PS_Dcarbxylase  98 hipGellsvnpsalkelrglftlneRvvlvie.wkG.kvavvpvGatnvgsivlnvlkgdelkkGeelGyFqfGStvvlvfeagkfieslvekgq 190
                     +ipG+ l ++  + +++      neR+ +vie + G k++vv+  ++++++iv++++k+++++ G+++G+++fGS+v ++++++  ++ lv+++q
      AHX11193.1 114 YIPGKKLRADYDSSEDE------NERQEVVIElSDGrKIVVVQQTGFLARRIVCDLKKDQQVSAGKRFGIIKFGSRVTVYLPKD--MKILVTEQQ 200
                     *******9999999999......*********878977********************************************99..99******* PP

  PS_Dcarbxylase 191 kvkmGeklg 199
                      v +Ge+++
      AHX11193.1 201 TVIAGETVL 209
                     ******986 PP

>> LSDAT_prok  SLOG in TRPM, prokaryote
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.3e-06     0.038     133     173 ..     129     169 ..     126     202 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.3e-06
  LSDAT_prok 133 geitlkdiresvkagrpilvvaGsgrladeiaaalrgdsee 173
                 +e+ +++++ +++ gr+i+vv+ +g la +i+  l++d++ 
  AHX11193.1 129 DENERQEVVIELSDGRKIVVVQQTGFLARRIVCDLKKDQQV 169
                 67789**************************9988777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       575  (0.0320709); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1721.46
//
Query:       AHX11194.1  [L=139]
Description: putative rRNA maturation factor YbeY [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-34  116.7   0.6    6.4e-34  116.5   0.6    1.0  1  UPF0054        Uncharacterized protein family UPF0054
  ------ inclusion threshold ------
       0.03   14.0   0.0      0.034   13.9   0.0    1.2  1  DUF3152        Protein of unknown function (DUF3152)
       0.12   12.2   1.2       0.18   11.6   1.1    1.4  1  Peptidase_M10  Matrixin


Domain annotation for each model (and alignments):
>> UPF0054  Uncharacterized protein family UPF0054
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.5   0.6   1.1e-37   6.4e-34       2     128 .]       8     135 ..       7     135 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.5 bits;  conditional E-value: 1.1e-37
     UPF0054   2 eieedleklikkvleealkkekleevsvllvdneeirelnkeyrgkdkpTDVLSFpleeeeeeee...lGDivisvekakeqaeeyghslerelafllv 97 
                 +i +d +kl+++v++++l+ ek  e s++l+d++ ir+ln++yrgkd++T+VLSF + +e +      +G++v+s++++  +a ey+ ++e++++++lv
  AHX11194.1   8 KIAKDPKKLLEAVISQTLDGEKA-EFSIVLTDDDFIRTLNRNYRGKDSATNVLSFNYTNEANC-MgmiIGEVVLSFDRILIEALEYQIEFEEHFKHMLV 104
                 567889999*********85544.*******************************99998888.2356******************************* PP

     UPF0054  98 HgllHllGYDHeeeeeekeMeekeeeileel 128
                 Hg+lH+lGY H ++ee+ +Me+ke+ ile+l
  AHX11194.1 105 HGILHILGYSHCTDEEALVMEKKERGILEKL 135
                 ****************************986 PP

>> DUF3152  Protein of unknown function (DUF3152)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   5.6e-06     0.034      95     165 ..      53     120 ..      10     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 5.6e-06
     DUF3152  95 ettreaCgndieletsCkkaaedrvlinearWvrGavpfegdigsyrqylinhevGhaiGyaaheaCekdG 165
                 + + ++ +++++ e+ C+      v+++  r +  a+ ++ + + + ++++ h + h +Gy   ++C+ + 
  AHX11194.1  53 DSATNVLSFNYTNEANCMGMIIGEVVLSFDRILIEALEYQIEFEEHFKHMLVHGILHILGY---SHCTDEE 120
                 4455566899999************************************************...4565554 PP

>> Peptidase_M10  Matrixin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   1.1     3e-05      0.18     105     134 ..      95     124 ..      34     134 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3e-05
                    SSEEHHHHHHHHHHHHTTBESXSSTTSTTS CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M10 105 qgvslflVaaHEiGHalGLeHssdkdalmy 134
                     +  + ++ +H i H+lG +H +d++al++
     AHX11194.1  95 FEEHFKHMLVHGILHILGYSHCTDEEALVM 124
                    556678899*****************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1144.20
//
Query:       AHX11195.1  [L=291]
Description: succinate-CoA ligase, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      9e-32  109.6   0.7      9e-32  109.6   0.7    2.2  2  CoA_binding   CoA binding domain
    7.8e-21   74.5   0.9    1.2e-20   73.8   0.9    1.3  1  Ligase_CoA    CoA-ligase
    1.1e-11   44.7   0.3    1.1e-11   44.7   0.3    1.5  2  Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain


Domain annotation for each model (and alignments):
>> CoA_binding  CoA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  109.6   0.7   1.5e-35     9e-32       1      96 []       6      99 ..       6      99 .. 0.99
   2 ?   -0.5   0.1      0.33     2e+03      34      63 ..     176     199 ..     144     237 .. 0.55

  Alignments for each domain:
  == domain 1  score: 109.6 bits;  conditional E-value: 1.5e-35
                 CTTEEEEEETTTSHHHHHHHHHHHHHHECEEEEEEC-TTTTTCEETTEEEESCHHHHHHHCTTTEEEEES-HHHHHHHHHHHHHTT-SEEEEESST CS
  CoA_binding  1 dkdtkviviGagglgiaglyhfkeklkygikavfgvnprkvgtevlglpvyksvdeleektevdvavitvPaesaqeavdelveagikgiviiteg 96
                 +k+tkvi++G++g   +g++h+++ + yg+k+v+gv+p+k+g ++lglpv+++v  ++++t+++++vi+vPa++a++a++e+++a+i++iv+iteg
   AHX11195.1  6 NKNTKVICQGFTGH--QGTFHSEQAIAYGTKMVGGVTPGKGGATHLGLPVFDTVYHAKKETDANATVIYVPAPFAADAILEAIDAEIELIVCITEG 99
                 699********999..******************************************************************************97 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.33
                  EEC-TTTTTCEETTEEEESCHHHHHHHCTT CS
  CoA_binding  34 fgvnprkvgtevlglpvyksvdeleektev 63 
                  +g++    g+ v+gl   + +++  ++  +
   AHX11195.1 176 IGIG----GDSVHGLSFIDCIQMFLDD--P 199
                  4443....3455555555555555555..3 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.9   2.1e-24   1.2e-20       1     152 [.     151     272 ..     151     273 .. 0.96

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 2.1e-24
                 EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHH CS
  Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkai 99 
                 ++++GtL+yea+ ++++               g +q+++i++G+d+           + ++i++++ ++ dpe+++i++ +++G g++e++aae+lka 
  AHX11195.1 151 VSRSGTLTYEAVAQTTQM--------------GLGQSTCIGIGGDSVH---------GLSFIDCIQMFLDDPETEAIVMIGEIG-GSAEEKAAEMLKAS 225
                 689***************..............***************6.........***************************.*************9 PP

                 HHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
  Ligase_CoA 100 keakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                 k  k      p v ++aG +a+p++++++a+a+ + + e a+sk    +aa+ 
  AHX11195.1 226 KVKK------PTVGFIAGVTAPPGKRMGHAGAIVSNSDESAESKMRVMKAAGI 272
                 9888......****************************999999998888875 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.2   6.9e+03      52      66 ..      87     101 ..      83     106 .. 0.84
   2 !   44.7   0.3   1.8e-15   1.1e-11       1     127 [.     145     277 ..     145     281 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.2
  Succ_CoA_lig  52 dpetkvillylEsir 66 
                   d e+++i++  E+i 
    AHX11195.1  87 DAEIELIVCITEGIP 101
                   789999999999985 PP

  == domain 2  score: 44.7 bits;  conditional E-value: 1.8e-15
  Succ_CoA_lig   1 pGkialisqSGalalalldwaasrglgfskvvslGnea..dvdvadlleylaedpetkvillylEsird.grkflsaarraarkkpvvvlksGrsea 94 
                   +Gki+++s SG+l  + ++++++ glg s+++ +G  +   +++ d+++++ +dpet++i++  E  +   +k ++++++ + kkp v + +G ++ 
    AHX11195.1 145 RGKIGIVSRSGTLTYEAVAQTTQMGLGQSTCIGIGGDSvhGLSFIDCIQMFLDDPETEAIVMIGEIGGSaEEKAAEMLKASKVKKPTVGFIAGVTAP 241
                   69*********************************865225899*********************8777357888888888888*********9776 PP

  Succ_CoA_lig  95 garaaashtgalag.sdavvda...afrqaGvlrvds 127
                     +  + h ga+++ sd+  ++   +++ aG++ +++
    AHX11195.1 242 PGKR-MGHAGAIVSnSDESAESkmrVMKAAGIVIAET 277
                   5554.45666665415555543222677888887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2181.22
//
Query:       AHX11196.1  [L=392]
Description: succinyl-CoA ligase [ADP-forming] subunit beta [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.5e-75  251.7   0.6    1.1e-74  250.3   0.3    1.7  2  ATP-grasp_2  ATP-grasp domain
    2.5e-22   79.3   1.3    4.9e-22   78.4   1.3    1.5  1  Ligase_CoA   CoA-ligase
    1.1e-08   34.8   0.2      3e-08   33.4   0.1    1.7  2  ATP-grasp_5  ATP-grasp domain
  ------ inclusion threshold ------
      0.086   12.9   1.4       0.84    9.8   0.2    3.0  3  DUF1983      Domain of unknown function (DUF1983)


Domain annotation for each model (and alignments):
>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  250.3   0.3   2.5e-78   1.1e-74       1     201 [.       2     205 ..       2     206 .. 0.96
   2 ?   -1.7   0.0      0.38   1.7e+03     153     187 ..     354     388 ..     344     390 .. 0.78

  Alignments for each domain:
  == domain 1  score: 250.3 bits;  conditional E-value: 2.5e-78
                  BE-HHHHHHHHHCTT----SEEEE...SSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTSEEE-TTS-TT-EEE--E CS
  ATP-grasp_2   1 nlhEyqakeilakygvkvpegeva...esaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgkelvtkqtgkeGkkvekv 95 
                  n+hEyqakeil++yg+++p g+++   +  +e+ e +k+lg+++++vKaQ++aGGRGKagGv + +s++ea ++++++lg++lvt+qt+++G++v kv
   AHX11196.1   2 NIHEYQAKEILRSYGISTPAGFLVpenTADKEVIENLKRLGGSVFAVKAQIHAGGRGKAGGVAISRSADEALATTRRMLGMNLVTHQTSPSGQRVRKV 99 
                  79*******************998322345678888999*********************************************************** PP

                  EEEE---ECEEEEEEEEEETTTTEEEEEEESSTTS-HHHHHHH-GGGEEEEEEBTTTB--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHHHHTTEE CS
  ATP-grasp_2  96 lveealdikkElYlsivlDraskkvvviaSseGGvdiEevaakkPekiikvaidpakglkeeqareiakklglekelvkkaakiikklyklfveldat 193
                  ++e    i +E+YlsivlDras+k+ ++aS+eGG++iEeva++ Peki+k+ +dp+ g++++++r+i ++lgl++++vk +a i+kkly+lfv++da+
   AHX11196.1 100 YIEGGQSIMREYYLSIVLDRASSKIAIVASAEGGMEIEEVAKSDPEKIKKTFVDPSIGISDFHVRKIGFELGLSATQVKALAPIVKKLYTLFVAKDAS 197
                  ************************************************************************************************** PP

                  EEEEEEEE CS
  ATP-grasp_2 194 lvEiNPLv 201
                  ++EiNPL+
   AHX11196.1 198 QIEINPLI 205
                  *******8 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.38
                  B--HHHHHHHHHHCT--CHHHHHHHHHHHHHHHHH CS
  ATP-grasp_2 153 glkeeqareiakklglekelvkkaakiikklyklf 187
                  g +++   ei+k+ gl+ ++++++ ++ +k+++l+
   AHX11196.1 354 GTNHAAGMEIIKNSGLNITTASELGDAAQKIVNLI 388
                  66677778999999999988888888888887775 PP

>> Ligase_CoA  CoA-ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.4   1.3   1.1e-25   4.9e-22       1     152 [.     265     384 ..     265     385 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.4 bits;  conditional E-value: 1.1e-25
                 EESSHHHHHHHHHHHHHT..............T--BSEEEE-TSS--..........HHHHHHHHHHHHS-TT-SEEEEEEEESSSEHHHHHHHHHHHH CS
  Ligase_CoA   1 lvnGGtLayeamdlikealgdvasnkklknvlgseqheiidlGddaftkGrpHPmiDptkriealkklaadpevkvilldivlGygahedpaaellkai 99 
                 +vnG++La+++md+ik                gs +++++d+G++a            +++++a++++ ad+ vk+i+++i++G+++++ +a+++++a+
  AHX11196.1 265 MVNGAGLAMATMDIIKYY--------------GSSPANFLDVGGGAN----------LEQVTNAFRIISADKCVKAIFVNIFGGIMRCDIIAEGIVAAT 339
                 79****************..............***************..........8***************************************** PP

                 HHTT...--S-EEEEEECTTHH.....HHHHHHHTTTSSEEE-SSHHHHHHHH CS
  Ligase_CoA 100 keakaegrelpvvarvaGteadpqelseqakaleeagveiasskaqalraaka 152
                 k++     +lp+v+r+ Gt+       ++ ++++++g++i+++++  ++a+k 
  AHX11196.1 340 KDVG---LTLPLVVRLSGTNHA-----AGMEIIKNSGLNITTASELGDAAQKI 384
                 ***7...***************.....****************9999988875 PP

>> ATP-grasp_5  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.4   0.1   6.7e-12     3e-08      11     221 ..       4     220 ..       1     221 [. 0.82
   2 ?   -1.6   0.0      0.33   1.5e+03      69      89 ..     369     389 ..     338     390 .. 0.86

  Alignments for each domain:
  == domain 1  score: 33.4 bits;  conditional E-value: 6.7e-12
  ATP-grasp_5  11 teaeakelleaygipvvetrl...assaeeaveaaeeigyp.vvlKivspdilhKtdvgGvrlnlkdaeevraaaeeilervkeks...peariegvl 101
                   e++ake+l+ ygi+++   l    +  +e++e  +++g    ++K ++ +   + ++gGv++  + +e+++++ + +  ++ +++    ++r+++v 
   AHX11196.1   4 HEYQAKEILRSYGISTPAGFLvpeNTADKEVIENLKRLGGSvFAVKAQI-HAGGRGKAGGVAISRSADEALATTRRMLGMNLVTHQtspSGQRVRKVY 100
                  799***************9994444455677777788888835777776.577899*******76666666665555555555544344468999999 PP

  ATP-grasp_5 102 Vqemakr.ggrElivgvteDpvFGpvilfGlGGtavevlkdvavalpplnstlareliertkaskllkgvrgekkadlaaleellvrlsqLvvdlpeI 198
                  ++  +   +++ l + + + ++   +++  +GG+++e +++   +    +  +    i+  ++ k+  +   + + +++al+ ++ +l  L v  +  
   AHX11196.1 101 IEGGQSImREYYLSIVLDRASSKIAIVASAEGGMEIEEVAKSDPEKIKKTFVDPSIGISDFHVRKIGFELGLS-ATQVKALAPIVKKLYTLFVA-KDA 196
                  999988556666666666666667789999***************999*********************9999.9*****************98.899 PP

  ATP-grasp_5 199 reldinPllveeeg.vvalDarir 221
                  ++++inPl+ ++eg ++alDa+i+
   AHX11196.1 197 SQIEINPLIENDEGeFIALDAKIN 220
                  ************999******996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.33
  ATP-grasp_5  69 lnlkdaeevraaaeeilervk 89 
                  ln+++a+e+ +aa++i++ ++
   AHX11196.1 369 LNITTASELGDAAQKIVNLIR 389
                  899999999999999998765 PP

>> DUF1983  Domain of unknown function (DUF1983)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.2   0.00019      0.84       7      51 ..      34      78 ..      29     108 .. 0.75
   2 ?   -1.0   0.0      0.43   1.9e+03      52      76 ..     171     195 ..     166     198 .. 0.86
   3 ?   -0.4   0.0      0.28   1.3e+03      26      49 ..     351     375 ..     343     386 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00019
     DUF1983  7 avadldgklsAlytikaqvkanGqkylAGiglgaesdngqvtsqv 51
                ++ +l+     ++ +kaq++a+G+   +G +++  +d+  +t++ 
  AHX11196.1 34 VIENLKRLGGSVFAVKAQIHAGGRGKAGGVAISRSADEALATTRR 78
                66667766778999********************99988877765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.43
     DUF1983  52 lvnAdrFavvnpangkvtppfvvqn 76 
                 + +A ++  ++p  +k+++ fv+++
  AHX11196.1 171 GLSATQVKALAPIVKKLYTLFVAKD 195
                 67899999999999999**999985 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.28
     DUF1983  26 kanGqkylAGiglgaesdngq.vts 49 
                 +  G+++ AG+ +  +s  +  + s
  AHX11196.1 351 RLSGTNHAAGMEIIKNSGLNItTAS 375
                 5579999****99777664442444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (392 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      427  (0.0238162); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2918.97
//
Query:       AHX11197.1  [L=48]
Description: hypothetical protein NHE_0233 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.22s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 373.77
//
Query:       AHX11198.1  [L=251]
Description: triose-phosphate isomerase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-62  210.2   0.0    3.6e-62  209.9   0.0    1.1  1  TIM       Triosephosphate isomerase


Domain annotation for each model (and alignments):
>> TIM  Triosephosphate isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.9   0.0     2e-66   3.6e-62       2     243 .]      18     245 ..      17     245 .. 0.92

  Alignments for each domain:
  == domain 1  score: 209.9 bits;  conditional E-value: 2e-66
                 EEEEE-TBTS-HHHHHHHHHHHHHHCHGCTSEEEEE--GGGHHHHHHHHTTSSEC..EEES--BSSSSBS-TT--BHHHHHHTT-SEEEES-HHHHHHS CS
         TIM   2 liagNwKmnktleeakellkklkaklkeekvevviappflylekvkklleesklk..lgaqnvsaeksGafTGevsaemlkdlgvkyviiGHsErrqlf 98 
                 ++++NwKm+++++   +++k++     + +v vviapp++yl ++ +l++++ l   lgaq+++  ++ a TG+ sa+ml+++g++yv++GHsErr l+
  AHX11198.1  18 FVIANWKMKGNQQLCDTFVKRFIDFSFNPRVAVVIAPPAVYLWHMGNLISTTDLPlrLGAQDCAVGDNAANTGDLSARMLREVGCSYVLVGHSERRSLH 116
                 79*******************77677777*********************9987666****************************************** PP

                 T--HHHHHHHHHHHHHTT-EEEEEE---HHHHHTT.HHHHHHHHHHHHTTTS-CCCGGCEEEEE--GGGSSSS----HHHHHHHHHHHHHHHHHHSTHH CS
         TIM  99 kEtdelvakKvkaalksglkpilCvGEtleereagkteevvkeqlkeilkkldeealknvviAYePvWAiGtgktatpeqaqevhaairkelaekvske 197
                  E+++l+  K+ +al+s + p++CvG + +e + +     +++q +e++   +     ++++AYePv+AiGtg + + e++ e++  i++ +       
  AHX11198.1 117 CESNKLIGMKAGSALHSRVMPVICVGQSTREIRRE----ELVKQCRESIPINSR----DFIVAYEPVYAIGTGLVPSVEEILEAVLLIKDAV------- 200
                 **************************999887665....455566555554443....69****************************9996....... PP

                 HHTTSEEEEESS--TTTHHHHHTSTT--EEEESGGGCSHHHHHHHH CS
         TIM 198 vaekirilYGGsvnkenakellkqkdidGlLvGgaslkaesFlkii 243
                   ++i+ilYGGsv+++n++e+l+ ++ dGlLvGgasl++++F++i+
  AHX11198.1 201 -GDHIPILYGGSVSSSNCSEILSVEHLDGLLVGGASLDVDNFIRIC 245
                 .6779**************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       351  (0.0195772); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1834.28
//
Query:       AHX11199.1  [L=281]
Description: rhodanese-like domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-26   91.0   0.0    8.8e-26   90.1   0.0    1.5  1  UPF0176_N    UPF0176 acylphosphatase like domain
    3.5e-07   30.7   0.0    8.4e-07   29.5   0.0    1.6  1  Rhodanese    Rhodanese-like domain
    1.3e-05   25.5   1.7    3.3e-05   24.2   1.7    1.7  1  Rhodanese_C  Rhodanase C-terminal
  ------ inclusion threshold ------
      0.079   13.0   1.0       0.17   11.9   0.2    1.9  2  DUF3867      Protein of unknown function (DUF3867)
       0.14   12.3   0.0       0.26   11.5   0.0    1.4  1  Lsr2         Lsr2


Domain annotation for each model (and alignments):
>> UPF0176_N  UPF0176 acylphosphatase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.1   0.0   2.5e-29   8.8e-26       2      92 .]       5      95 ..       4      95 .. 0.98

  Alignments for each domain:
  == domain 1  score: 90.1 bits;  conditional E-value: 2.5e-29
   UPF0176_N  2 rvlsfYkFvpledpealaeelrelleelgllGrilvAeEGiNgtlavpeealeaflaalrsdeelsdlelklslsseppFerlkvkvkkeI 92
                ++++fY+Fv+le++e++++el+e++ +++++G+i++AeEGiN+++a+++ +++ fl+++++d++++dle+k+sl + +pF+++kv++k+e+
  AHX11199.1  5 TLITFYHFVDLENYEDMKDELLEYCLRNNIRGTIILAEEGINASIAGENWSIRGFLSFIQTDDRFRDLEWKESLVDFQPFQEMKVRLKREV 95
                789**************************************************************************************97 PP

>> Rhodanese  Rhodanese-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.5   0.0   2.4e-10   8.4e-07      31     103 ..     151     212 ..     116     215 .. 0.75

  Alignments for each domain:
  == domain 1  score: 29.5 bits;  conditional E-value: 2.4e-10
   Rhodanese  31 pgAvnvskdtlsrakkseapllelpeellel.gidnkktvvvycdgggraaaaaallkklGyknvsvldGGfka 103
                 p            ++ + +++ +++++++++ +i+ +++v  yc gg r + ++  +kk G+knv++l+GG+ +
  AHX11199.1 151 P------------ETTNFREFRDWVQKWINEnNISMDQKVAMYCTGGVRCEKSTSYMKKIGFKNVFHLKGGILN 212
                 3............55566999****************************8888888888************965 PP

>> Rhodanese_C  Rhodanase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   1.7   9.2e-09   3.3e-05       2      54 ..     226     276 ..     225     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 9.2e-09
  Rhodanese_C   2 GklfVFDkRlalkse...vvgkCieCgkpvdelrkrnCanedCnelvlvCeeCaek 54 
                  G++fVFD+R+a++++   v  +C +C+  vd+   +n       +  ++C++C+++
   AHX11199.1 226 GNCFVFDDRVAVNENlkpVELECLVCNRVVDTDDLKNIP-----RGKVMCSKCSHQ 276
                  9***********77788899********99965566664.....556777777665 PP

>> DUF3867  Protein of unknown function (DUF3867)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       1.3   4.5e+03      40      56 ..      19      35 ..      14      41 .. 0.78
   2 ?   11.9   0.2   4.6e-05      0.17      19      62 ..     136     179 ..     124     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 1.3
     DUF3867 40 sdfskkiseYmeennis 56
                +d+  ++ eY   nni 
  AHX11199.1 19 EDMKDELLEYCLRNNIR 35
                57788888999999985 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 4.6e-05
     DUF3867  19 dkfeeyiyelyyslaeGkltlsdfskkiseYmeennisqekfln 62 
                 + +e  i++  ys++  + ++ +f   ++++++ennis ++ + 
  AHX11199.1 136 NLYETKIGKFKYSIDPETTNFREFRDWVQKWINENNISMDQKVA 179
                 568999********************************987555 PP

>> Lsr2  Lsr2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   7.1e-05      0.26      11      54 ..     127     170 ..     122     197 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 7.1e-05
        Lsr2  11 DDldgseadetvefgldgveYeiDLseenaeklrdaLapyieaa 54 
                 DD+   +  + +e ++   +Y iD +++n++++rd ++++i+  
  AHX11199.1 127 DDVKTIDTRNLYETKIGKFKYSIDPETTNFREFRDWVQKWINEN 170
                 7777777777888889999**********************875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      428  (0.0238719); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2184.27
//
Query:       AHX11200.1  [L=482]
Description: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, A subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.5e-141  470.4   0.0   7.3e-141  470.2   0.0    1.0  1  Amidase   Amidase


Domain annotation for each model (and alignments):
>> Amidase  Amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.2   0.0  4.1e-145  7.3e-141       1     451 []      25     470 ..      25     470 .. 0.98

  Alignments for each domain:
  == domain 1  score: 470.2 bits;  conditional E-value: 4.1e-145
                 HHHHHHHHHHHHHHHHH--EEEEEHCCCCHHHHT---TTT......TTTT-EEEEETTB--TTSB--TTSGGGTT-B-SS--HHHHHHHHTT-EEEEEE CS
     Amidase   1 elveaflkrieavneklnalvtvfieealaqAakldkkrargkekgpLhGvPisvKDnidvkgvpttaGskalenypaekDatvverLkkaGavilgkT 99 
                 elvea l++ie+ n++ nal+ v++eea+++A+ +d+++++ ++   L+G+P ++KD +++kg++tta+skal+++++++++tv+++L +aGav+lgk+
  AHX11200.1  25 ELVEAHLRQIEQRNSESNALILVTPEEARRRAKLADDRIKKREDINMLTGIPCVIKDMYCTKGFRTTAASKALKDFVPTYESTVTDKLMDAGAVMLGKA 123
                 79************************************************************************************************* PP

                 --SGGG-SSSSTT-TT---BBTTCTCC....B--SSSHHHHHHHHTTSSSCEEEEESSSTTHHHHHHCTSEEEE--TTSC--TTB--SSTTT-EEEEEE CS
     Amidase 100 nmdefamgsstensvfgptrNPwdksr....tpGGSSGGsAAavAaglvplaiGtDtGGSiRiPAsfcglvGlKPtygrvSragvvalessldvvGpla 194
                 nmdefamgs   +s+fg+++NP+  ++    +pGGSSGGsAAavA + +p+++G+DtGGS+R+PAs+cglvGl+Ptygr Sr+g+++l++sld++G+++
  AHX11200.1 124 NMDEFAMGSANIYSYFGAVKNPLRGKKtsalVPGGSSGGSAAAVAEHYAPFSLGSDTGGSVRQPASYCGLVGLRPTYGRCSRWGMIPLANSLDQAGIFT 222
                 ***********************987767789******************************************************************* PP

                 SSHHHHHHHHHHHBS--TT-TTS----HHHHHHHHCTT---TT-EEEEEGGGCSS---CCHHHHHHHHHHHHHCTT-EEEEEE-CCGGGHHHHHHHHHH CS
     Amidase 195 rsvedlalllrvilgedpkdstssvipeesedlaeelkkslkglriGvvkedgvasldpevqravekalkaLeeaGhevvevelpsleealslyylilv 293
                 r+ved a++++vi+g+dpkdst++++    e ++  +  + +g++iG++ke +v+ ldp++ r+ e+ +++L+++G+e+ ev+lp +e+ l +yy i +
  AHX11200.1 223 RNVEDNAAVFEVISGYDPKDSTCAKL----EPFKYDKNPDIRGMKIGIPKECKVEGLDPQIIRLWEEIADKLRQLGAEITEVRLPCMEYSLMVYYVICC 317
                 ************************95....578888889999********************************************************* PP

                 HHHHHHTTT-SSSSS..---SS-SCCCCCCCHHHHCCS-HHHHHHHHHHHHHCSCCCCCCCHHHHHHHHHHHHHHHHHHCCCBSEEEEESSSSS--BCC CS
     Amidase 294 aeassnlarylgvry..erlsetkvlsellpksraellgeevkrrielgnyalsaeasskyylkaqkvrrllrrefakafeelDvllsPtaptpaprlg 390
                 ae ssnl ry+gvry  ++++++++++e+++k r++ +g+evk r+ +g++ ls++ +s+yy  a k +  + +++  +fe++D++l Ptap+ a++++
  AHX11200.1 318 AEVSSNLCRYDGVRYcpNPAIKAESIEEMYEKYRSDVFGKEVKLRLLMGTHILSSNGYSDYYASAKKLQNTIVQQYSDIFEKVDIILNPTAPSDAFPID 416
                 *************************************************************************************************** PP

                 CCCHHHCSHHHHHGCCTTT...HHHHHTT--EEEEECCCCT.TECEEEEEEESTT-HHHHH CS
     Amidase 391 ekdktidsytvlynlldftavvvpvnlaglpalsvpagksedglPvGvqvigkafqeetlL 451
                  k     +++++y  + ft   vp ++a+lp++svpag s d++P+G+ +++++f+e+tlL
  AHX11200.1 417 GK----LEPLEMYMNDIFT---VPTSVAKLPSISVPAGLSSDDMPLGMHFTANYFSENTLL 470
                 99....57***********...*************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (482 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 3755.39
//
Query:       AHX11201.1  [L=59]
Description: ribosomal protein L33 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-11   44.4   0.5      2e-11   44.2   0.5    1.2  1  Ribosomal_L33  Ribosomal protein L33


Domain annotation for each model (and alignments):
>> Ribosomal_L33  Ribosomal protein L33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.5   1.1e-15     2e-11       4      47 .]      13      56 ..       5      56 .. 0.90

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 1.1e-15
                   EEEET...........EEEEETT..--S--EEEEEETTTTEEEEEEEE- CS
  Ribosomal_L33  4 tLeCtecksrn.....YtttknkkntperLelkKYcprcrkhtlhkEtK 47
                   +L+++     +     Y +++n kn++e+ +++KY+p++rkh+l+kE+K
     AHX11201.1 13 KLVSS-----AdtgffYLVYRNLKNKQEKYSFMKYDPVIRKHVLFKEAK 56
                   67788.....445677*******************************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      289  (0.0161191); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 457.14
//
Query:       AHX11202.1  [L=164]
Description: cytochrome c oxidase assembly CtaG/Cox11 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-53  181.1   0.8    1.5e-53  180.9   0.8    1.0  1  CtaG_Cox11  Cytochrome c oxidase assembly protein CtaG/Cox11


Domain annotation for each model (and alignments):
>> CtaG_Cox11  Cytochrome c oxidase assembly protein CtaG/Cox11
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  180.9   0.8   8.4e-58   1.5e-53       1     151 []       8     154 ..       8     154 .. 0.95

  Alignments for each domain:
  == domain 1  score: 180.9 bits;  conditional E-value: 8.4e-58
  CtaG_Cox11   1 avPlyrvfCeatGlggktekaaaeksaavkvdeertevtveFdadvseklpwefkpeqrslevkpGetalafytaknksdkpiigqavysvaPeeaaky 99 
                 +vPly++fC+atG++g++++ +++ +    +  +r  +tv+F+adv+++lp++f+ +++ + vkpG+ al+fyt++n +d+pi ++avy+v+P +aaky
  AHX11202.1   8 SVPLYSLFCKATGYAGTVKRVERSFN---LAVGTR-DITVRFNADVDKDLPIRFRVKDDPVMVKPGQNALVFYTVQNLTDQPIEAIAVYNVTPYKAAKY 102
                 59*****************9886433...356889.5************************************************************** PP

  CtaG_Cox11 100 fnKieCFCFeeqkLkpgeevdlpvlFfidpelaedpelkkvkeitLsYtffe 151
                 fnK+ CFCFe+q L p++++ +pv Ffidpe+++dpe++++++ tLsYtff+
  AHX11202.1 103 FNKVACFCFERQVLPPNKTIVMPVSFFIDPEIEKDPEMNDIRTFTLSYTFFR 154
                 ***************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       463  (0.0258241); expected 358.6 (0.02)
Passed bias filter:                      385  (0.0214736); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1250.99
//
Query:       AHX11203.1  [L=38]
Description: hypothetical protein NHE_0241 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       370  (0.020637); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 282.21
//
Query:       AHX11204.1  [L=536]
Description: chromosomal replication initiator protein DnaA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-83  279.3   0.3      4e-83  278.6   0.3    1.4  1  Bac_DnaA      Bacterial dnaA  protein
    7.9e-27   93.1   0.4    2.4e-26   91.6   0.1    2.0  2  Bac_DnaA_C    Bacterial dnaA protein helix-turn-helix
    1.1e-16   60.3   0.6    3.5e-16   58.7   0.6    1.9  1  DnaA_N        DnaA N-terminal domain
    6.1e-08   32.6   0.0    1.3e-07   31.5   0.0    1.5  1  IstB_IS21     IstB-like ATP binding protein
    8.8e-07   29.4   0.5    3.9e-06   27.3   0.0    2.2  2  AAA           ATPase family associated with various cellular 
    1.4e-05   24.2   2.1       0.03   13.2   0.5    2.3  2  AFG1_ATPase   AFG1-like ATPase
    0.00041   20.3   0.2     0.0013   18.7   0.2    1.7  1  ATPase_2      ATPase domain predominantly from Archaea
     0.0069   16.8   0.3       0.07   13.5   0.5    2.5  2  RNA_helicase  RNA helicase
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.043   13.8   0.0    1.5  1  ResIII        Type III restriction enzyme, res subunit
      0.028   14.8   0.1       0.22   11.8   0.0    2.2  2  AAA_19        AAA domain
      0.051   13.9   0.3        4.2    7.6   0.0    2.5  2  AAA_22        AAA domain
      0.062   13.6   1.4       0.13   12.6   0.7    1.9  2  DUF5616       Domain of unknown function (DUF5616)
      0.081   12.8   0.0       0.16   11.9   0.0    1.6  1  NACHT         NACHT domain


Domain annotation for each model (and alignments):
>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.6   0.3   2.9e-86     4e-83       3     217 ..     199     418 ..     197     420 .. 0.95

  Alignments for each domain:
  == domain 1  score: 278.6 bits;  conditional E-value: 2.9e-86
                 SS-SGGG----TTTHHHHHHHHHHHHSTTT....S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT- CS
    Bac_DnaA   3 krytFetFviGasnrlAlaaalkvaeapgk...kynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkv 98 
                  + tF++Fv+G+ n+lA++a+++vaea++      nPlf+yg+vGlGktHL++ai ++++e+ ++ rv+Yl+ae+F+ + ++alr+k++ +fk+ +r+v
  AHX11204.1 199 WNRTFDNFVVGKPNELAFTASKRVAEAAELpipGSNPLFLYGGVGLGKTHLMHAIVWHIKEHYKNRRVIYLSAEKFMYKYITALRNKDMMSFKQIFRSV 297
                 5679**********************977544489**************************************************************** PP

                 SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT--..--TTHHHHHH CS
    Bac_DnaA  99 DvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaekle..vpeevlefia 195
                 DvL++DD+qf++gk++tqee+fhtfnal+e++kq+v+s+DrsP++l+ +e+r++sr+++Glv+di+ + +e+r++il+ k+e+      vp++v+ef+a
  AHX11204.1 298 DVLMVDDVQFISGKDSTQEEFFHTFNALIEQNKQLVISADRSPSDLQGVEERIQSRLSWGLVADINHTTFELRVGILESKLEQMTSRvvVPKKVIEFMA 396
                 **********************************************************************************7665555********** PP

                 HH--S-HHHHHHHHHHHHHHHH CS
    Bac_DnaA 196 ervtdnvRelegalnrlkayas 217
                 +++ +nvRelegaln++ a+a+
  AHX11204.1 397 RNIVSNVRELEGALNKVIAHAD 418
                 ******************9987 PP

>> Bac_DnaA_C  Bacterial dnaA protein helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.4   4.7e+03      24      43 ..     381     400 ..     365     405 .. 0.74
   2 !   91.6   0.1   1.7e-29   2.4e-26       2      69 .]     447     514 ..     446     514 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.4
                 --CSSHHHHHHHHHHHHHTS CS
  Bac_DnaA_C  24 RkkeiveaRqiamylarelt 43 
                  ++++v +++++ ++ar+++
  AHX11204.1 381 MTSRVVVPKKVIEFMARNIV 400
                 57889999999999999886 PP

  == domain 2  score: 91.6 bits;  conditional E-value: 1.7e-29
                 .HHHHTHHHHTT--HHHHHS----CSSHHHHHHHHHHHHHTS---HHHHHHHHT-STTHHHHHHHHHH CS
  Bac_DnaA_C   2 ekIieaVaeyfgvsvedlkskkRkkeiveaRqiamylareltdlslpeIGkefggrdHsTVihaikki 69 
                 ++I+ +V+eyf+++++dlks++R k++++aRq++myl++ lt+ sl +IGk++ggrdH+TViha+kki
  AHX11204.1 447 DNILLKVSEYFNIKISDLKSQRRVKDVSYARQVCMYLSKLLTQRSLLDIGKFLGGRDHATVIHAVKKI 514
                 78999**************************************************************8 PP

>> DnaA_N  DnaA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.7   0.6   2.6e-19   3.5e-16       2      62 ..      78     138 ..      77     139 .. 0.95

  Alignments for each domain:
  == domain 1  score: 58.7 bits;  conditional E-value: 2.6e-19
      DnaA_N   2 elWsavlerLkkelgeqsfdtWikplklfalknngltlivpneFardwiesnYldriaell 62 
                 e W+++  +L+k +ge+ +++W+k l++++++n++l+l+vp+ F+r+wi  nY+d i e +
  AHX11204.1  78 EKWERITGKLRKFYGEKIYRSWLKFLTFVKVENTQLVLSVPTGFIREWIMVNYSDNILEFF 138
                 68*****************************7777**********************9987 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   0.0   9.5e-11   1.3e-07      48     151 ..     234     340 ..     194     348 .. 0.86

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 9.5e-11
   IstB_IS21  48 enivllGpsGvGKshlaialgveavr..aglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllpldqaeaellfeviekryerr.si 143
                 + + l G+ G GK+hl  a+  +  +  ++ +v+++++e+++ +  +a r+  + +  + +  vd+l++Dd+ +   ++  +e++f+  ++  e++  +
  AHX11204.1 234 NPLFLYGGVGLGKTHLMHAIVWHIKEhyKNRRVIYLSAEKFMYKYITALRNKDMMSFKQIFRSVDVLMVDDVQFISGKDSTQEEFFHTFNALIEQNkQL 332
                 567899*************998766655899************************************************************99975156 PP

   IstB_IS21 144 iitsnlpf 151
                 +i+++ + 
  AHX11204.1 333 VISADRSP 340
                 77777665 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.3   0.0   2.9e-09   3.9e-06       2      92 ..     237     328 ..     236     353 .. 0.80
   2 ?   -1.0   0.1       1.7   2.3e+03      27      92 ..     392     453 ..     374     492 .. 0.68

  Alignments for each domain:
  == domain 1  score: 27.3 bits;  conditional E-value: 2.9e-09
                 EEESSTTSSHHHHHHHHHHHHT.....HEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
         AAA   2 llyGppGtGKTllakavakelg.....vefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                  lyG  G GKT l++a++ +++     ++++ +s+ +++ ky+ +  +k  + fk++ ++    +l++D++  + +++  s++ee   + n+L+++
  AHX11204.1 237 FLYGGVGLGKTHLMHAIVWHIKehyknRRVIYLSAEKFMYKYITALRNKDMMSFKQIFRSV--DVLMVDDVQFISGKD--STQEEFFHTFNALIEQ 328
                 69******************954444599***************************99886..***********9999..3333333334444433 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
                 EEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHH CS
         AAA  27 leisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlte 92 
                 +e+ + +++ + v e e  +++++++a      s++ +D    l  +   ++++++ ++ n Ll++
  AHX11204.1 392 IEFMARNIV-SNVRELEGALNKVIAHADITG--SVITVDSTKDLLADI-LRTNSVAVTLDNILLKV 453
                 555555555.446777777777777766655..777777666665554.34444555555555554 PP

>> AFG1_ATPase  AFG1-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.5   2.1e-05      0.03      64      96 ..     235     268 ..     215     288 .. 0.71
   2 !   10.7   0.1   0.00012      0.17     277     334 ..     288     344 ..     269     355 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2.1e-05
  AFG1_ATPase  64 glYlwGgvGrGKtylmdlf.feslpvekkrrvhf 96 
                   l+l+GgvG GKt+lm    ++  +  k+rrv +
   AHX11204.1 235 PLFLYGGVGLGKTHLMHAIvWHIKEHYKNRRVIY 268
                  69**************765155555556666654 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00012
  AFG1_ATPase 277 sdYlalaerfhtvlledVpvltkakedaarRfiaLvDelYdadvklvvsaevaleely 334
                  + + ++ + +  ++++dV+ +  +k++++  f     +l +++ +lv+sa+  +++l 
   AHX11204.1 288 MSFKQIFRSVDVLMVDDVQFIS-GKDSTQEEFFHTFNALIEQNKQLVISADRSPSDLQ 344
                  344455566677899******9.99*****************************9985 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.2   9.2e-07    0.0013      20     125 ..     233     337 ..     227     344 .. 0.63

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 9.2e-07
    ATPase_2  20 neiyfiYGpegsGKtaLlkeiienledkdk.yviyyialreesiskldefieeeeekkklekal..giavpkaeleeilkeksklvfkaielllekikk 115
                 ++++f+YG  g GKt L+  i+   +++ k +++ y + ++   ++++   ++++   ++++ +   +++  + ++ i  + +   ++ +   ++++ +
  AHX11204.1 233 SNPLFLYGGVGLGKTHLMHAIVWHIKEHYKnRRVIYLSAEKFMYKYITAL-RNKDMM-SFKQIFrsVDVLMVDDVQFI--SGKDSTQEEFFHTFNALIE 327
                 5899******************9985544435555555555555555554.444333.34444444233333333323..3333334666677777777 PP

    ATPase_2 116 kgkkiiiiiD 125
                 + k+++i +D
  AHX11204.1 328 QNKQLVISAD 337
                 7788887776 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.5     5e-05      0.07       2      82 ..     237     331 ..     236     340 .. 0.69
   2 ?   -1.0   0.0       1.7   2.3e+03      77     102 ..     362     387 ..     345     388 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 5e-05
  RNA_helicase   2 wlyGpsgeGKStlakeLakallkkl...........klkkkdsvysrnpeddfw.dgYtgqevvvidDfgqvkdee.nps.dlaelirlvsstpy 82 
                   +lyG  g GK++l++ ++ ++ +++           k+  k  +  rn++   + + +++ +v+++dD+  ++ +  +++  +++++ l++ ++ 
    AHX11204.1 237 FLYGGVGLGKTHLMHAIVWHIKEHYknrrviylsaeKFMYKYITALRNKDMMSFkQIFRSVDVLMVDDVQFISGKDsTQEeFFHTFNALIEQNKQ 331
                   89********************9998888888886544443333336666655524555888888888877774443444377777777777765 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.7
  RNA_helicase  77 vsstpyplnmasleekgtlftSkvvi 102
                   ++ t+++l +  le+k  ++tS+vv+
    AHX11204.1 362 INHTTFELRVGILESKLEQMTSRVVV 387
                   78899999999***********9996 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.1e-05     0.043      29      78 ..     238     294 ..     211     355 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.1e-05
                 EEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHH.......HHGGGGT CS
      ResIII  29 ikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtl.......eefkkfl 78 
                 +    G GKT ++ ++++++++++k+++++ l  +k +++            fk+++
  AHX11204.1 238 LYGGVGLGKTHLMHAIVWHIKEHYKNRRVIYLSAEKFMYKYITalrnkdmMSFKQIF 294
                 55567*************************999998666655443332223444433 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00016      0.22      10      45 ..     233     266 ..     223     273 .. 0.80
   2 ?   -0.3   0.1      0.88   1.2e+03      95     115 ..     289     309 ..     270     339 .. 0.62

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00016
      AAA_19  10 ekvllvtaGpGtGKTrvlkhivallvelggvkpeei 45 
                 +++l++ +G G GKT+++++iv +++e  +   +++
  AHX11204.1 233 SNPLFLYGGVGLGKTHLMHAIVWHIKEHYKN--RRV 266
                 67899*****************999988754..444 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.88
      AAA_19  95 eeekklqeeellivDEfqdvd 115
                 + ++ +++ ++l+vD +q ++
  AHX11204.1 289 SFKQIFRSVDVLMVDDVQFIS 309
                 34566666669****999775 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.0    0.0031       4.2       8      48 ..     236     272 ..     232     298 .. 0.73
   2 ?    4.2   0.1     0.034        48      91     113 ..     291     323 ..     270     337 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0031
      AAA_22   8 lvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlp 48 
                 l+++G +G GKT+l+  ++   +e++k    +++v++  + 
  AHX11204.1 236 LFLYGGVGLGKTHLMHAIVWHIKEHYK----NRRVIYLSAE 272
                 789**************9998887776....5555544443 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.034
      AAA_22  91 v.....ielliiDEaqhlr.s....eealeeLr 113
                 +     + +l++D++q+++ +    ee + ++ 
  AHX11204.1 291 KqifrsVDVLMVDDVQFISgKdstqEEFFHTFN 323
                 04455679**********662423344444443 PP

>> DUF5616  Domain of unknown function (DUF5616)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       4.8   6.6e+03      25      33 ..     328     336 ..     288     351 .. 0.61
   2 ?   12.6   0.7   9.2e-05      0.13      72     137 ..     392     459 ..     373     462 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 4.8
     DUF5616  25 sgevlllcd 33 
                 +++ l+++ 
  AHX11204.1 328 QNKQLVISA 336
                 122233333 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 9.2e-05
     DUF5616  72 vifllDkpvSnSgelaklireileeaglegevelvknvDkeLk...eseeivatsDsvildkvksvldl 137
                 ++f+  + vSn  el++++++++++a+++g+v +v+++   L+   +++++ +t D ++l kv++++++
  AHX11204.1 392 IEFMARNIVSNVRELEGALNKVIAHADITGSVITVDSTKDLLAdilRTNSVAVTLDNILL-KVSEYFNI 459
                 346666679*****************************9999966677779999998766.57777776 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.16       2      40 ..     235     269 ..     234     349 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                 CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEE CS
       NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFfl 40 
                 +++l G  G GKT+L++ ++  ++e + ++     v++l
  AHX11204.1 235 PLFLYGGVGLGKTHLMHAIVWHIKEHYKNRR----VIYL 269
                 57899******************99986653....4444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (536 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       903  (0.0503653); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.41
# Mc/sec: 3883.06
//
Query:       AHX11205.1  [L=341]
Description: aspartate-semialdehyde dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.4e-42  143.9   0.0    6.9e-42  143.6   0.0    1.1  1  Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation dom
    6.9e-23   81.4   0.0    1.1e-22   80.7   0.0    1.4  1  Semialdhyde_dh   Semialdehyde dehydrogenase, NAD binding doma
    0.00026   20.6   0.2    0.00058   19.5   0.0    1.6  2  Gp_dh_C          Glyceraldehyde 3-phosphate dehydrogenase, C-
  ------ inclusion threshold ------
      0.062   12.8   0.1       0.11   12.1   0.1    1.3  1  NmrA             NmrA-like family
        0.1   12.0   0.0       0.14   11.6   0.0    1.2  1  Epimerase        NAD dependent epimerase/dehydratase family
       0.15   12.2   0.3       0.42   10.7   0.1    1.9  2  DapB_N           Dihydrodipicolinate reductase, N-terminus


Domain annotation for each model (and alignments):
>> Semialdhyde_dhC  Semialdehyde dehydrogenase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  143.6   0.0   2.3e-45   6.9e-42       1     184 []     140     314 ..     140     314 .. 0.94

  Alignments for each domain:
  == domain 1  score: 143.6 bits;  conditional E-value: 2.3e-45
                      HHHHHHCTT.EEEEEEEEEEEGGGCHHHHHHHHHHHHHHHHHSTTS.CTTTSSHHTTSEESTCSTBTTTTCHCBHHHHHHHHHHHHHCTESC.S CS
  Semialdhyde_dhC   1 LkPLldalgelervivatyqavSGaGkkgvreLlkqvaelqrsdeakpgvfgvpiagNlipyidkeedkgepetreelkavaetkkilefte.k 93 
                      LkPL+  l++l+r+ v+tyq+vSG G +g++eL+++++ + +  +   +vf ++i++N+ip+i+++++ g   ++eelk ++et+kile+++ +
       AHX11205.1 140 LKPLHS-LAKLSRIWVSTYQSVSGVGESGMDELYENTKRRFAFTQQGSNVFPRNIEFNCIPQIGEFDKSG--FSDEELKLINETQKILEDKSiE 230
                      8*****.8***********************************************************999..9*******************99 PP

                      EEEEEEEESBSSEEEEEEEEEESSSHHHHHHHHHHHHCSTTEEEEESSHCHHSSHHHHTTCSSSEEEEEEEEETTCTTEEEEEEEEETTTT CS
  Semialdhyde_dhC  94 vsatcvrVPvlrGhseavtiklklkdveveeveellaaapevkvvvneeedrPtpaavaggtnsvsVGRirkdemgdeglklvvvgDNllk 184
                      v +tcvrVPv+ Gh e++t++lk +dv  e+v+e l++a++v+   n   ++  + +v+g  ++v+V Rir  +  ++ + ++vv+DNl+k
       AHX11205.1 231 VFPTCVRVPVFVGHAESITVELK-EDVYEEDVYEILSDAEGVVFSRN---QYKCQPEVVG-YDDVFVSRIRFHS--PRMISMWVVADNLRK 314
                      9*********************7.9**************55555544...6777778998.7***********9..777**********97 PP

>> Semialdhyde_dh  Semialdehyde dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.7   0.0   3.8e-26   1.1e-22       1     119 [.       4     118 ..       4     120 .. 0.94

  Alignments for each domain:
  == domain 1  score: 80.7 bits;  conditional E-value: 3.8e-26
                     EEEEETTTSHHHHHHHHHHHC.TSSEEEEEEEESTTTTTSBHHHHSGGGTTTECEBEEEGGGGGCTT-SEEEE-SCHHHHHHHHHHHHHTTSEEE CS
  Semialdhyde_dh   1 kvaivGatGyvGqellrlLee.hpevelvvllsssrsaGkklaeavkaleegkdlkvedvdeeelkevdivflalpagvskelapklaeagvkvi 94 
                     +va+vGatG +G+el+++L +     e + +l+s++s G+++++       ++ + ++dv+e ++++  ++f+ +++g+s++l +++a+ g+ v 
      AHX11205.1   4 RVAVVGATGVIGKELVKILVDkGYRKENISFLASKNSVGTRISFGE-----NESVMINDVNEHDFSKDRVAFFVAGSGISRNLGRSVASIGCLVL 93 
                     7********************66668899999*************4.....59999999************************************ PP

                     ESSSTTTTSTTSEBE-HHHHGGGGG CS
  Semialdhyde_dh  95 DlssdfRlkddavyvlpevnreaik 119
                     D ss fR+++d+++v+pevn++ ++
      AHX11205.1  94 DGSSCFRMEEDVPLVIPEVNPHVLN 118
                     *********************9876 PP

>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.6   4.9e+03      60      71 ..     104     115 ..     102     143 .. 0.59
   2 !   19.5   0.0   1.9e-07   0.00058      63     111 ..     222     270 ..     217     307 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.6
                 HHHHHSGGGTTT CS
     Gp_dh_C  60 avglVlpelkgk 71 
                 +v lV+pe++  
  AHX11205.1 104 DVPLVIPEVNPH 115
                 677788877644 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 1.9e-07
                 HHSGGGTTTEEEEEEEESSSSEEEEEEEEEESSTS-HHHHHHHHHHHHH CS
     Gp_dh_C  63 lVlpelkgkldglAvrVPtpnvsvvdlvvelekevtveevnaalkeaae 111
                 ++l + ++++  + vrVP+  +++ +++vel+++v  e+v ++l++a  
  AHX11205.1 222 KILEDKSIEVFPTCVRVPVFVGHAESITVELKEDVYEEDVYEILSDAEG 270
                 56666666666789*******************************9975 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   3.6e-05      0.11       1      24 [.       5      28 ..       5      33 .. 0.94

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.6e-05
                EEESSTTSHHHHHHHHHHHHHT-E CS
        NmrA  1 IlviGaTGrqGksvvrallkaghk 24
                ++v+GaTG +Gk +v++l+++g++
  AHX11205.1  5 VAVVGATGVIGKELVKILVDKGYR 28
                79******************9996 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   4.7e-05      0.14       2      27 ..       6      31 ..       5      71 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.7e-05
                EEETTTSHHHHHHHHHHHHCTSEEEE CS
   Epimerase  2 lVtGatGfiGsalvkallekgyevig 27
                 V+GatG iG+ lvk l +kgy+  +
  AHX11205.1  6 AVVGATGVIGKELVKILVDKGYRKEN 31
                69*******************86444 PP

>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00014      0.42       2      22 ..       4      24 ..       3      68 .. 0.75
   2 ?   -2.2   0.0       1.4   4.1e+03     100     114 ..     208     222 ..     207     228 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00014
                EEEEETTTSHHHHHHHHHHHH CS
      DapB_N  2 kvavvGasGrmGkevvkavee 22
                +vavvGa+G +Gke+vk + +
  AHX11205.1  4 RVAVVGATGVIGKELVKILVD 24
                8***************98755 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.4
                 S--HHHHHHHHHHTT CS
      DapB_N 100 Glseeelaeleelak 114
                 G+s+eel+ ++e+ k
  AHX11205.1 208 GFSDEELKLINETQK 222
                 99******9999654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (341 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2575.64
//
Query:       AHX11206.1  [L=259]
Description: hypothetical protein NHE_0244 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.8   2.4        2.4    8.5   0.6    2.1  2  MgtE      Divalent cation transporter


Domain annotation for each model (and alignments):
>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.2    0.0026        46      32      99 ..      26     100 ..       9     108 .. 0.64
   2 ?    8.5   0.6   0.00014       2.4      44     108 ..     141     209 ..      81     211 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.0026
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-............CTSHHHHHHHHHHHHHHHHHH..HHHHHHHHHHTT CS
        MgtE  32 lkkvllkelrvvlllgvilgllifllalllgw...........slllalvvglalvlvllaaallilgvllplllwklg 99 
                  + + ++++  ++ l++il++++ ++ ++ g            +  ++ ++  +l+l+ l+  ++  g    ll++ ++
  AHX11206.1  26 RALLAVRNISNGIALLLILMQVATVVYYC-GAvnaklirgndcEYGIFSFIKDSLILITLLHFTF--GLSK-LLIKGVK 100
                 46677889999999999999999987554.33466777777776666666666666666665555..3333.4555555 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.00014
                 HHHHHHHHHHHHHHHHHHT-.........CTSHHHHHHHHHHHHHHHHHH..HHHHHHHHHHTTS-GGGSHHH CS
        MgtE  44 lllgvilgllifllalllgw........slllalvvglalvlvllaaallilgvllplllwklglDPdnaaiP 108
                 +++  i gl+++ ++++  w        +++++ ++    ++++++a + +l ++l+ l +  ++DP n+++P
  AHX11206.1 141 IVKVHIGGLIVLCITFFCDWmsdhmtpaKQHISEII----AITCVLAGMPFLSFYLCKLERMQNIDPSNCIAP 209
                 233333334444444444444333433333333333....33333444446799999999999*******998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (259 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2020.97
//
Query:       AHX11207.1  [L=50]
Description: hypothetical protein NHE_0245 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 382.60
//
Query:       AHX11208.1  [L=243]
Description: RNA 2'-O ribose methyltransferase substrate binding family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-32  113.0   0.0    1.8e-32  112.5   0.0    1.3  1  SpoU_methylase   SpoU rRNA Methylase family
    1.8e-06   28.1   0.0    2.9e-06   27.4   0.0    1.4  1  SpoU_sub_bind    RNA 2'-O ribose methyltransferase substrate 
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.67    9.8   0.0    1.9  2  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase


Domain annotation for each model (and alignments):
>> SpoU_methylase  SpoU rRNA Methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.5   0.0     3e-36   1.8e-32       2     142 .]      95     237 ..      94     237 .. 0.92

  Alignments for each domain:
  == domain 1  score: 112.5 bits;  conditional E-value: 3e-36
                     EEEEEES-SSHHHHHHHHHHHHHTT-SEEEEESGSSCTCGSHHHHHHCTTHHHHHHEEEESSHHHHHHHHCCCTEEEEEEST.T-SEGCCSHHHT CS
  SpoU_methylase   2 livvlveiedpgNlGaiaRtakafgaselvlvkprsadllnpeakraaagalevlelkvvdsleealkelkeegfalvatsl.kgkslseidlke 95 
                     l+++l++i+dp N+G+i+R+ kafg++ l++ + r+    ++ +++aa+ga e ++++ v++l +a+k l+++g+ ++a+++  ++++++  l++
      AHX11208.1  95 LVIILDNITDPFNVGNIIRSSKAFGVDFLIMRE-RHSPDETSIIAKAASGAFESIPICSVSNLGNAIKTLQDSGYFCYALDGdTQSKITNEVLPD 188
                     79************************8888866.66556677799*************************************8888999999*** PP

                     TEEEEEEBTTTBS-HHHHCTSSEEEE---..-TTSSS--HHHHHHHHHH CS
  SpoU_methylase  96 kvalvfGnEdkGlsnelleladrlvkIpm..sgeveSLNvavAvailly 142
                     k+++++G+E+kG+s+ l +++d+++ Ipm   ++++S+Nv+ A+ai+++
      AHX11208.1 189 KTVFILGSEGKGVSPILKSRCDQVLAIPMhaCESFDSINVSSAAAIAMF 237
                     *****************************444789***********985 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.0   4.9e-10   2.9e-06       2      74 ..       8      79 ..       7      81 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 4.9e-10
  SpoU_sub_bind  2 iyGlhaVleaLksg.rriekllvtegradkrleellklakkrgikvelvdkekLdklsg.tanHQGvvaevkple 74
                   i+G+ha ++a  ++ rri +l+++ +r  k++ +ll+  +++   + ++d +++ k++g +a HQG++ ++++l+
     AHX11208.1  8 IFGKHAAIAAANNPnRRIFSLFISTER-RKEYCQLLNPSAMK--NISFCDNRRIAKICGkDALHQGIAVVAEKLT 79
                   9************8466*********4.44446777777777..789**********************999986 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.19   1.1e+03      18      41 ..      97     121 ..      84     138 .. 0.74
   2 ?    9.8   0.0   0.00011      0.67     130     177 ..     188     236 ..     173     240 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.19
                      EE-----H.HHHHHHHHHHHHTT-S CS
  Methyltrn_RNA_4  18 vvatsvtn.lDlhDiaRsartygvk 41 
                      ++  ++t  +++  i Rs++++gv+
       AHX11208.1  97 IILDNITDpFNVGNIIRSSKAFGVD 121
                      4555666447889999999999997 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00011
                      -S-EEEEE--TT---HHHHTT-SEEB-.-TTTTSS-----HHHHHHHHH CS
  Methyltrn_RNA_4 130 ekpvlllfGtgwGlaeevlekadyiLe.pirgaseynHLsvrsAvaiil 177
                      +k+v++l   g G+++ + +++d +L  p+++ ++++ + v sA+ai +
       AHX11208.1 188 DKTVFILGSEGKGVSPILKSRCDQVLAiPMHACESFDSINVSSAAAIAM 236
                      44455555569**************9769******************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1909.27
//
Query:       AHX11209.1  [L=103]
Description: ribosomal protein S10 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.5e-30  102.7   0.0    1.1e-29  102.6   0.0    1.0  1  Ribosomal_S10  Ribosomal protein S10p/S20e


Domain annotation for each model (and alignments):
>> Ribosomal_S10  Ribosomal protein S10p/S20e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0     6e-34   1.1e-29       1      97 [.       5      98 ..       5      99 .. 0.99

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 6e-34
                   EEEEEESSHHHHHHHHHHHHHHTTSSS-EE---EEEEEEEEEEEEE--SS--S--EEEEEEEEEEEEEEEE.E-HHHHHHHS-...S---SS-EEEE CS
  Ribosomal_S10  1 rirlkSydsklLekavkkivraakelgikvkgpvplPtkrkrvtvlksphvdkksreqfeirthkRlidisdatketidtllkllqlnlpegVsvev 97
                   ri+l+S+ds  L +++k+iv aak+ g+ v+gp+plPt+  r+tv +sphvdkksreqf++ ++k l+++s+ +++ ++t+++   ++lp+gV+v+v
     AHX11209.1  5 RIKLRSFDSGILHRSAKEIVMAAKRNGALVSGPIPLPTRMSRYTVNRSPHVDKKSREQFQLGVYKCLLELSSFNAHLLSTFTN---FQLPAGVDVSV 98
                   8**********************************************************************************...*********98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 881.29
//
Query:       AHX11210.1  [L=210]
Description: 50S ribosomal protein L3 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-15   55.3   3.6      1e-12   47.8   1.3    2.1  2  Ribosomal_L3  Ribosomal protein L3


Domain annotation for each model (and alignments):
>> Ribosomal_L3  Ribosomal protein L3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.8   1.3   5.6e-17     1e-12     204     279 ..      88     168 ..      47     174 .. 0.83
   2 !    8.5   0.1   4.8e-05      0.85     313     346 ..     172     205 ..     164     207 .. 0.87

  Alignments for each domain:
  == domain 1  score: 47.8 bits;  conditional E-value: 5.6e-17
                   C..EEECCCCS-TTSEEEEEEEE---EEE-HHHHCT----STTTSSS..SSS-S-SS-.SSSSS--TTS--SEEESCCEEE CS
  Ribosomal_L3 204 k..tvavaavFrqgeliDvigvtkGkGfeGvvkRWgvkklprkthrg..lRkvaaiga.wdparVsstvaraGqkGyhhRt 279
                   +  +    ++Fr+g+++Dv+g  +GkGf Gv+kR  + +l++ ++ +  +R  ++ g   dp++V  + ++aG++G  + t
    AHX11210.1  88 EplKSLTVEHFRPGQYVDVVGTSIGKGFAGVMKRHNFAGLRASHGVSisHRSGGSTGQcQDPGKVFKGKKMAGHMGAARVT 168
                   444556679************************************9999******996369***************87655 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 4.8e-05
                   TCTTCB..TSCEEEEES--SSSTTEEEEEEE-SS CS
  Ribosomal_L3 313 GfvhyGevkndfilvkGsvpGpkkrlvklrksll 346
                    fv+   v+  +i v+GsvpG k+  v l+++l 
    AHX11210.1 172 LFVQLVDVESGLIGVRGSVPGCKNSYVLLKDALK 205
                   5888889999********************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      333  (0.0185733); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1548.70
//
Query:       AHX11211.1  [L=214]
Description: 50S ribosomal protein L4 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.2e-57  193.3   0.1    3.5e-57  193.2   0.1    1.0  1  Ribosomal_L4  Ribosomal protein L4/L1 family


Domain annotation for each model (and alignments):
>> Ribosomal_L4  Ribosomal protein L4/L1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  193.2   0.1     2e-61   3.5e-57       3     191 ..      22     210 ..      20     211 .. 0.97

  Alignments for each domain:
  == domain 1  score: 193.2 bits;  conditional E-value: 2e-61
                   E-HHHHSS---HHHHHHHHHHHHHSS-EE------TTTSS---S-SS-SSSSSS---S-TTSTTSTT---SS---S.EEHHHHHHHHHHHHHHHHHH CS
  Ribosomal_L4   3 LspkvFaapirrdlihravvaylanrrqgtastkarsevsgsgrklwkQKGtGrARvgsirspiargGgvahgpkperdystklnkKvrrlAlrsaL 99 
                   +  ++F+ap+r+dl+ +++ ++la+rr+gt++tk+ sevsg++rk+++QKGtGrAR+gs+rsp++r Ggv++gp + r++  ++nkKvr+lAlrsaL
    AHX11211.1  22 VGSALFEAPFRPDLMSQVINWQLAKRRAGTHKTKGISEVSGTTRKPYRQKGTGRARQGSLRSPQFRTGGVIFGPVV-RQHGFSVNKKVRNLALRSAL 117
                   66789**********************************************************************9.******************** PP

                   HHHHHTT-EEEES---.-SS--HHHHHHHHHHTT-..TTSSEEEEESSSSCHHHHHHTT-TTEEEEESTT--CHHHHHSSEEEEEHHHHHHHHH CS
  Ribosomal_L4 100 sakakqglllvvdnlepleesktkelvellkklgl..ksksvLivvsekdenlvlaarnlpgvevieveslnvydllkadkvvitksaveklee 191
                   s ++++g+l+++ + + ++e+k++el++ +++     + k++Liv+++ ++ l++aa nl+ v+v+ + s nvydl+  d v+++k+ ++ l e
    AHX11211.1 118 SLRFSEGRLFALRDSN-FPEPKASELAQWVSAHAElaRGKKLLIVIDQRNDALLRAASNLHWVKVLWASSANVYDLVLSDFVLLEKASIDVLLE 210
                   *************999.***************7777899************************************************9998755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (214 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1599.64
//
Query:       AHX11212.1  [L=96]
Description: ribosomal L23 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.9e-13   49.0   0.0    6.9e-13   48.8   0.0    1.0  1  Ribosomal_L23  Ribosomal protein L23


Domain annotation for each model (and alignments):
>> Ribosomal_L23  Ribosomal protein L23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.0   3.8e-17   6.9e-13       7      82 ..      12      89 ..       6      93 .. 0.92

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 3.8e-17
                   --SHHHHHHHTT.E.EEEEE-SS-THHHHHHHHHHHH.T--EEEEEEEEE--EBESSSSSEEBE--EEEEEEEESSS- CS
  Ribosomal_L23  7 vitEkstklaek.nkyvFeVakdanKleikkaveklF.gVkVekVntlnvkgkkkrvgrkvgrrksyKkaiVtLkege 82
                   v+tEks  l+++  k+ F  + ++ K +i++ + + F ++kV ++n+++vkgk kr++ k grr++ Kk + t++ g 
     AHX11212.1 12 VLTEKSCILKDSfGKISFFAPVSVDKKQIRSVFVERFrELKVLAINSIVVKGKFKRFKGKFGRRSDRKKFVLTVEGGA 89
                   78********9988******************9999989********************************9997665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (96 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      317  (0.0176809); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.27s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 742.26
//
Query:       AHX11213.1  [L=280]
Description: ribosomal protein L2 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-54  183.3   2.4    3.2e-54  182.5   2.4    1.4  1  Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
    4.8e-26   90.5   0.4      4e-24   84.4   0.3    2.6  3  Ribosomal_L2    Ribosomal Proteins L2, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L2_C  Ribosomal Proteins L2, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.5   2.4   3.5e-58   3.2e-54       2     126 .]     132     256 ..     131     256 .. 0.99

  Alignments for each domain:
  == domain 1  score: 182.5 bits;  conditional E-value: 3.5e-58
                     SSS-EBSSSS-TTB-BBSE-SSTTS--SSS-SSSB-EEBB-B.SSEEEEEETTS-EEEEETTSBEBES-BS-TTCTT----STTHHHHTTBS--- CS
  Ribosomal_L2_C   2 vGnvlplknipeGtivhnielkpgkggklarsaGtyaqvvakegkkvtvklpSgevrkvssecrAtiGvvsngehkekklgkAgrkrwlgrrpkv 96 
                     +G++++l+++p+G +vhnielkpg gg++arsaG +a vva++g+++ v lpSge+r++ s+c AtiGvvsn+++k+ klgkAgr+rwlg+rp+v
      AHX11213.1 132 PGSCMKLEKVPLGAMVHNIELKPGAGGQIARSAGVSACVVARDGNYTLVTLPSGEKRLILSACHATIGVVSNSDKKNVKLGKAGRSRWLGIRPSV 226
                     7********************************************************************************************** PP

                     -SSSS-TTTSSS--SSSS--SSSSTEETTC CS
  Ribosomal_L2_C  97 rGvamnpvdHphGGGeGktksrkapvspwg 126
                     rGvamnpvdHp GGG+Gkt++ ++pvspwg
      AHX11213.1 227 RGVAMNPVDHPLGGGSGKTSGGRHPVSPWG 256
                     *********************77******8 PP

>> Ribosomal_L2  Ribosomal Proteins L2, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.4   0.3   4.5e-28     4e-24       1      75 [.      42     122 ..      42     124 .. 0.92
   2 ?    1.5   0.0     0.032   2.9e+02      46      68 ..     162     185 ..     139     187 .. 0.77
   3 ?    2.8   0.0     0.013   1.2e+02      46      71 ..     173     198 ..     171     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 84.4 bits;  conditional E-value: 4.5e-28
                   TB-TT--BSSTT--------EE-B--S---SS.....--EEEEEEE--TT-SS-EEEEE.ETTTEEEEEE--SS--SS-EE CS
  Ribosomal_L2   1 GrnnsgritvrhrggGhkkkyrlidfkrnkek.....vkgkVveieyDpgRsApiAlvk.yedgekryiiapeglkvGdtv 75 
                   Grnn gritvrh+gg hk +yrl+df+r  ++      k+ V+++eyDp+R+A+iAl+  +edg  +yiiape++k Gd++
    AHX11213.1  42 GRNNAGRITVRHKGGRHKVRYRLVDFRRLSGSsaspfSKAIVERVEYDPNRTAFIALIRgVEDGVLSYIIAPEKVKKGDVI 122
                   9*************************995555699*999*******************93466****************99 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.032
                   -SS-E.EEEEETTTEEEEEE--SS CS
  Ribosomal_L2  46 RsApi.Alvkyedgekryiiapeg 68 
                   RsA + A+v+  dg+++++ +p g
    AHX11213.1 162 RSAGVsACVVARDGNYTLVTLPSG 185
                   666665788888899999888876 PP

  == domain 3  score: 2.8 bits;  conditional E-value: 0.013
                   -SS-EEEEEETTTEEEEEE--SS--S CS
  Ribosomal_L2  46 RsApiAlvkyedgekryiiapeglkv 71 
                   R ++  lv + +gekr+i+ +    +
    AHX11213.1 173 RDGNYTLVTLPSGEKRLILSACHATI 198
                   5566679***********98766555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       216  (0.0120475); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 2009.99
//
Query:       AHX11214.1  [L=63]
Description: ribosomal protein S19 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.3e-27   93.1   0.4    8.3e-27   92.9   0.4    1.1  1  Ribosomal_S19  Ribosomal protein S19


Domain annotation for each model (and alignments):
>> Ribosomal_S19  Ribosomal protein S19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.9   0.4   4.6e-31   8.3e-27      28      81 .]       1      54 [.       1      54 [. 0.98

  Alignments for each domain:
  == domain 1  score: 92.9 bits;  conditional E-value: 4.6e-31
                   -EEES-TT-B--GGGTT-EEEEE-SSSEEEEE--CCCTTSBCGGGT-SS----S CS
  Ribosomal_S19 28 vikthsRdstIlPemvgltvgVynGktfvpveikeemvGhkLgEFspTrkpvkh 81
                   +ik+ sR+s+IlP +vg+t+gVynGk fvpv+++e+mvGhk+gEFspTr++ +h
     AHX11214.1  1 MIKIRSRRSVILPAFVGCTFGVYNGKAFVPVKVNENMVGHKFGEFSPTRTFNGH 54
                   599************************************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       264  (0.0147247); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 485.63
//
Query:       AHX11215.1  [L=113]
Description: ribosomal protein L22 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-25   87.0   0.4      9e-25   86.9   0.4    1.0  1  Ribosomal_L22  Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.9   0.4     5e-29     9e-25       2     102 ..       4     105 ..       3     106 .. 0.96

  Alignments for each domain:
  == domain 1  score: 86.9 bits;  conditional E-value: 5e-29
                    EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHT-SSTTHHHHHHHHHHHHHHHH..HT.-GGGEEEEEEEEEEEEEEEEEEEESTTEEEEEEEEEE CS
  Ribosomal_L22   2 kgsnlrvsfkklrevarlIrgmkveeAlkyLkfskkkaakfvlklLknaeanaelkgl.dvdslvIeeiqvnkgpklkrrtyrArGrinpirkspc 96 
                    + +n++ s++k++ va+lIrg++v+ A   L fskk aa+ + k+L + ++na+++   d+d l+I+ei v+kg  lkr+  rArGr   +rk+++
     AHX11215.1   4 TYKNIKSSVQKINLVADLIRGKSVSLARSRLLFSKKVAARAISKVLMSSVSNAQNNFSvDPDVLYIKEISVGKGMSLKRFSARARGRSASVRKHYS 99 
                    579***************************************************77669************************************* PP

                    EEEEEE CS
  Ribosomal_L22  97 hievvl 102
                    +++++l
     AHX11215.1 100 NVSILL 105
                    **9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (113 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 890.95
//
Query:       AHX11216.1  [L=211]
Description: ribosomal protein S3 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.2e-36  123.7   0.3    5.1e-36  123.1   0.3    1.3  1  Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
    2.3e-10   40.1   0.0    5.9e-10   38.8   0.0    1.7  1  KH_2            KH domain


Domain annotation for each model (and alignments):
>> Ribosomal_S3_C  Ribosomal protein S3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.1   0.3   5.6e-40   5.1e-36       1      83 []     120     203 ..     120     203 .. 0.98

  Alignments for each domain:
  == domain 1  score: 123.1 bits;  conditional E-value: 5.6e-40
                     HHHHHHTT--HHHHHHHHHHHHHHC.C-SEEEEEEEC-SS.TTT--EEEEEEC----TCHHHH-EEEEEEEEETTEEEEEEEEE CS
  Ribosomal_S3_C   1 iaeqlekrvsfRramkkairramka.gakGikiqvsGrLggaeiarsekykeGrvplhtlradidyavaeaktkyGiiGvkVwI 83 
                     ia qlekr sfRr++kkai ++m++ +++Gik+ +sGrL+gaeiar+e +keG+vplhtlradidy +aea+t yG+iGvkVwI
      AHX11216.1 120 IAFQLEKRSSFRRVIKKAIATVMREsDVRGIKVACSGRLSGAEIARTEVFKEGSVPLHTLRADIDYWIAEANTSYGVIGVKVWI 203
                     899********************8559********************************************************9 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.0   6.5e-14   5.9e-10       4      77 ..      41     110 ..      38     111 .. 0.89

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 6.5e-14
                 HHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEEEETTTG CS
        KH_2   4 eslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklnivkVkkpe 77 
                  ++  e++  gvs+v I+r+   + ++++ ++pg+ IGk+G++++ ++++l k+++       +ln+v+Vkkp 
  AHX11216.1  41 RYFSTEFAHVGVSRVLIKRKGSVCDVTLHCAKPGLMIGKKGADLEILKSKLAKKFG----FVPNLNVVEVKKPN 110
                 56777899999********99**********************************4....44468889999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (211 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 1761.05
//
Query:       AHX11217.1  [L=139]
Description: ribosomal protein L16 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.8e-36  123.2   0.0    7.6e-36  123.0   0.0    1.0  1  Ribosomal_L16  Ribosomal protein L16p/L10e


Domain annotation for each model (and alignments):
>> Ribosomal_L16  Ribosomal protein L16p/L10e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   4.2e-40   7.6e-36       1     132 []       4     132 ..       4     132 .. 0.95

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 4.2e-40
                    HXSSXXBSSSX.XSSTSXXXSXXXXXESXEEEEESSXEEEEHHHHHHHHHHHCTCCCCTSXCEEXXSXXXXEEEEE-SS-TTTSSSSXEEEEEEEE CS
  Ribosomal_L16   1 pkrkkyrKsrk.ryirgvstkgtklefgdygLvalekgqltaealeaariainrylkkkrgkklwirvfphhpvtkkagedRmgkGkGkpegwvar 95 
                    pk++k++K rk r+   +s++g+ l+fgd+gL+a  +++l+ +++e+ar++i+r ++  r +klwi+vfp +p+t+k++++Rmg GkG+++ ++ +
     AHX11217.1   4 PKKVKHKKFRKvRF-SPASSRGSGLAFGDFGLKAVGSARLNGKQIESARRVITRIIS--RAGKLWINVFPGIPLTRKPTDVRMGGGKGSVDSYIFP 96 
                    67777777777557.7788**************************************..************************************* PP

                    EXSSCEEEEETTXXXSHHHHHHHHHHHHTSSSXEEEE CS
  Ribosomal_L16  96 vkigqiifeikagvneeiakealrraasKlpiktkiv 132
                    v++g+++fe+ +gv++ +a+ al +a++Klp++tk++
     AHX11217.1  97 VSPGRVLFEL-SGVDKTVARLALCKASAKLPFSTKFI 132
                    **********.99**********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      219  (0.0122148); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 1224.81
//
Query:       AHX11218.1  [L=63]
Description: ribosomal protein L29 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-13   48.9   0.0    5.5e-13   48.7   0.0    1.1  1  Ribosomal_L29  Ribosomal L29 protein
  ------ inclusion threshold ------
       0.09   12.2   0.0      0.093   12.2   0.0    1.0  1  Orthopox_A5L   Orthopoxvirus A5L protein-like


Domain annotation for each model (and alignments):
>> Ribosomal_L29  Ribosomal L29 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.7   0.0   6.1e-17   5.5e-13       2      56 ..       5      59 ..       4      60 .. 0.94

  Alignments for each domain:
  == domain 1  score: 48.7 bits;  conditional E-value: 6.1e-17
                   HHHHS-HHHHHHHHHHHHHHHHHHHHHHHHTSSS-CHHHHHHHHHHHHHHHHHHH CS
  Ribosomal_L29  2 elrelsdeeLkeklkelkkeLfnLrfqkatgqlenpsrirkvRkdIARikTvlre 56
                   +lr++s++eL+  l++++ eLfnL ++ +  + +  s  r +R+ +ARi+T+l+e
     AHX11218.1  5 DLRNMSVAELRGLLSSMRSELFNLSLKPRGLSGNARSSRRYIRRGVARILTCLKE 59
                   9****************************556699******************98 PP

>> Orthopox_A5L  Orthopoxvirus A5L protein-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     1e-05     0.093     214     268 ..       8      62 ..       2      63 .] 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
  Orthopox_A5L 214 eldnmalkdlmssvekdmrqlqaetedlvtdvydareytrraidqlldlvkgfer 268
                   ++    l+ l+ss++ ++ +l  +   l  +   +r y rr + ++l  +k  +r
    AHX11218.1   8 NMSVAELRGLLSSMRSELFNLSLKPRGLSGNARSSRRYIRRGVARILTCLKENKR 62 
                   3343457889***************************************998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (63 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 554.53
//
Query:       AHX11219.1  [L=119]
Description: ribosomal protein L14 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.1e-37  126.4   1.8    6.8e-37  126.3   1.8    1.0  1  Ribosomal_L14  Ribosomal protein L14p/L23e
  ------ inclusion threshold ------
       0.14   11.7   0.1       0.14   11.7   0.1    1.1  1  DUF2464        Multivesicular body subunit 12


Domain annotation for each model (and alignments):
>> Ribosomal_L14  Ribosomal protein L14p/L23e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.3   1.8   7.6e-41   6.8e-37       1     121 [.       1     117 [.       1     118 [. 0.96

  Alignments for each domain:
  == domain 1  score: 126.3 bits;  conditional E-value: 7.6e-41
                    ..CSS-EEE--SSSSBSEEEEEEETT-.---EE-SSSEEEEEESSS-T...TTSSCEEEEEEEE-SS-EE-TTS-EEEESS-EEEEB-TTS-BSS- CS
  Ribosomal_L14   1 miqlktrlkvaDNsgakevecikvlggkkrkaasvGdiivvsvkkakpkgkvkkgdvvkavvvrtkkevrrkdGsvirfddnaaVllnkkgeplGt 96 
                    mi+++t+l+vaDNsgak+v ci + g++  ++as+Gd+ivvsvkk +p+gkv  g++++avvvr+kk   r   sv+ f dna+Vlln+++e++Gt
     AHX11219.1   1 MIKKETILDVADNSGAKKVLCIGISGSR--RTASIGDVIVVSVKKCAPSGKVSAGSIYRAVVVRVKK---RLPSSVVVFSDNAVVLLNQQNEMIGT 91 
                    9***********************9997..***********************************97...77899********************* PP

                    .B-SBEEHHHHHH..-HHHHHTBSBE CS
  Ribosomal_L14  97 rifgpvarelrek.kflkivslApev 121
                    r+fgp  + lr++  f+ki sl++ev
     AHX11219.1  92 RVFGPTDSLLRKNrGFAKISSLSQEV 117
                    **********98758*********98 PP

>> DUF2464  Multivesicular body subunit 12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   1.6e-05      0.14      86     140 ..       9      62 ..       2     107 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
     DUF2464  86 DskekalrKkqlcvklsprgsaetAVtDiillskskkapegytlaGeingllicy 140
                 D   ++  Kk lc+ +s  +++   + D+i++s +k ap g   aG i   +++ 
  AHX11219.1   9 DVADNSGAKKVLCIGISGSRRT-ASIGDVIVVSVKKCAPSGKVSAGSIYRAVVVR 62 
                 666667779******9988776.56**********************98776654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 937.96
//
Query:       AHX11220.1  [L=103]
Description: ribosomal protein L24 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-08   34.1   0.1      4e-08   33.5   0.1    1.4  1  ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L
    0.00015   21.6   1.4    0.00027   20.8   1.2    1.6  1  KOW            KOW motif
  ------ inclusion threshold ------
      0.088   12.5   0.3      0.086   12.5   0.3    1.1  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin


Domain annotation for each model (and alignments):
>> ribosomal_L24  Ribosomal proteins 50S L24/mitochondrial 39S L24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.1   6.8e-12     4e-08       6      63 ..      49     101 ..      45     103 .] 0.83

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 6.8e-12
  ribosomal_L24   6 khvkpsqqneqGgiiekEapIhvSnVmlvdpkcgkptrvgfrlkedgkkvRvskksge 63 
                    ++vk+sq++    + +k +pI +SnV+lv       ++vgf+lk dg k R+ kk+ge
     AHX11220.1  49 RFVKKSQAG--KRFETKACPISASNVALVSGA--VFSKVGFKLK-DGVKRRFLKKTGE 101
                    778886643..4788999***********854..56*****887.************8 PP

>> KOW  KOW motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   1.2   4.5e-08   0.00027       2      23 ..       7      28 ..       6      43 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 4.5e-08
                TSEEEESSSTTTTCEEEEEEEE CS
         KOW  2 GdhVkVvsGphkGktGkVvkvd 23
                Gd Vk++sG   Gk G+V kv+
  AHX11220.1  7 GDQVKIISGSETGKSGVVQKVI 28
                9*******************97 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.3   1.4e-05     0.086      11      52 ..       4      48 ..       1      85 [. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.4e-05
                 EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS...SEEEEEEESEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxx RF
  ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskqsnsd...daiiyvgiGer 52
                 iv G ++ i++++++Gk+ ++q+++  s++    +++i+ gi  r
   AHX11220.1  4 IVTGDQVKIISGSETGKSGVVQKVITSSSAGvlkQYVIVSGINLR 48
                 899*********************999855477458888777655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 829.07
//
Query:       AHX11221.1  [L=177]
Description: ribosomal L5 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-32  111.2   0.0    3.1e-32  110.6   0.0    1.3  1  Ribosomal_L5_C  ribosomal L5P family C-terminus
    3.4e-21   75.3   0.0    5.9e-21   74.6   0.0    1.4  1  Ribosomal_L5    Ribosomal protein L5


Domain annotation for each model (and alignments):
>> Ribosomal_L5_C  ribosomal L5P family C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.6   0.0   3.4e-36   3.1e-32       1      94 []      82     175 ..      82     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 110.6 bits;  conditional E-value: 3.4e-36
  Ribosomal_L5_C   1 piGvkvtLrgekmyefldkllevvlprlrdFkGiskssfdgrGnvsfGikeqiifpeieydkdkgifGmditivttaktdeearallkelgipf 94 
                     p+G++vtLr+++m +f+++ll v+lp  +dF G++ ++fdgrGn++fG+ke+i+fpei++dk  ++ Gm++++vtta+td  ar ll+ +g+pf
      AHX11221.1  82 PVGCRVTLRKRNMLDFINRLLYVALPDQKDFTGFTMQNFDGRGNMAFGMKEHIVFPEIDFDKAYRVIGMNVVVVTTAPTDALARVLLSCYGFPF 175
                     79*******************************************************************************************9 PP

>> Ribosomal_L5  Ribosomal protein L5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.0   6.6e-25   5.9e-21       2      57 .]      23      78 ..      22      78 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 6.6e-25
                  CTTS-EEEEEEEEEE-SSSSSCHHHHHCCHHHHCCCHSS--EECC--TTCTTTCSC CS
  Ribosomal_L5  2 vMqvPrleKivinmgvGeagedkkllekaakeLaeItGQkPvvtkakksianFkiR 57
                  +M+ PrleK+++++g+G a++d kll++a+++L+ I+GQ++vvt akksi++Fk+R
    AHX11221.1 23 IMKAPRLEKVCLSVGLGAASSDDKLLKSAVDDLSLIAGQRAVVTVAKKSISSFKLR 78
                  8******************************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       285  (0.015896); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1366.46
//
Query:       AHX11222.1  [L=101]
Description: ribosomal S14p/S29e family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.6e-26   90.1   0.5    5.6e-26   90.1   0.5    1.9  2  Ribosomal_S14  Ribosomal protein S14p/S29e


Domain annotation for each model (and alignments):
>> Ribosomal_S14  Ribosomal protein S14p/S29e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.5     0.072   1.3e+03      34      45 ..      23      34 ..      11      37 .. 0.72
   2 !   90.1   0.5   3.1e-30   5.6e-26       2      54 .]      48     100 ..      47     100 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.072
                   EHHHHHHHTTT. CS
  Ribosomal_S14 34 sRicfRelAlkg 45
                    R+ +R++ ++ 
     AHX11222.1 23 KRQSIRKMRNDK 34
                   688888887765 PP

  == domain 2  score: 90.1 bits;  conditional E-value: 3.1e-30
                    ------SS..CTTT---SSS--SSSEE-GGG-EHHHHHHHTTT...TT-EE-- CS
  Ribosomal_S14   2 laklprnssptrirnrCrvtGrprGvirkfgLsRicfRelAlkgelpGvkKaS 54 
                    l++lpr++sp+r +nrC++tGrprG++rkfg+sRi++R lA+ g lpGv+K+S
     AHX11222.1  48 LNSLPRDTSPVRSKNRCAITGRPRGYYRKFGISRIQLRVLANWGRLPGVVKSS 100
                    89*************************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (101 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.26s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 791.11
//
Query:       AHX11223.1  [L=131]
Description: ribosomal S8 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-35  120.4   0.0    5.1e-35  120.2   0.0    1.0  1  Ribosomal_S8  Ribosomal protein S8


Domain annotation for each model (and alignments):
>> Ribosomal_S8  Ribosomal protein S8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.2   0.0   2.8e-39   5.1e-35       3     127 .]       6     131 .]       4     131 .] 0.95

  Alignments for each domain:
  == domain 1  score: 120.2 bits;  conditional E-value: 2.8e-39
                   HHHHHHHHHHHHHTT-SEEEEE--HHHHHHHHHHHHCTSEEEEEEE..CCCCCCEEEEE-BSSS-SBSSSEEEE-SBTTC--EE-CCC---CGGGTS CS
  Ribosomal_S8   3 iadmltrirNaekakkeevevpasklkeeilkvLkeeGyikdfeve..eekkkkikielkynkkkksvikklkrvskpgrrvYakvkelpkvlnglG 97 
                   iad+++rirNa++a+ +ev + +s+l  +++++L++eGyi+++ev   + + k i + lky   + +vi+k+k +s+pg+r+Y+++k++pk+++glG
    AHX11223.1   6 IADAVARIRNAQSARLREVVIYYSRLLVDVASLLEDEGYISSYEVFeiRPSVKRIVLRLKYYA-NAPVINKIKLFSRPGKRMYSSAKNIPKFYGGLG 101
                   9********************************************753333667********9.79******************************* PP

                   EEEEEETTEEEEHHHHHHCT--EEEEEEEE CS
  Ribosomal_S8  98 iaivsTskGvmtdkeArkkkvGGevlayvw 127
                   i+++sTskGv+   +A + + GGe+l  v+
    AHX11223.1 102 ITVLSTSKGVLPSYKAMSFNCGGELLFGVY 131
                   **************************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (131 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1025.71
//
Query:       AHX11224.1  [L=176]
Description: ribosomal L6 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-07   30.3   0.0    4.3e-06   27.3   0.0    2.0  2  Ribosomal_L6  Ribosomal protein L6


Domain annotation for each model (and alignments):
>> Ribosomal_L6  Ribosomal protein L6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.0     0.052   9.2e+02      27      69 ..      37      74 ..      33      80 .. 0.63
   2 !   27.3   0.0   2.4e-10   4.3e-06       2      73 ..      90     161 ..      89     162 .. 0.97

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.052
                  E-CTTSEEEEEECSTEEEEEEC.SESCHHHHHHHHHHHHHHHHH CS
  Ribosomal_L6 27 eipegvtvevkvegnkvtvivv.sgidkekvAligtvrslinnm 69
                   +p+g+t e++     ++  ++ +++  + v l+g+ rsl nn 
    AHX11224.1 37 VLPSGITCEID-----GNCMRLkTEDTSASV-LLGLHRSLLNNV 74
                  56778888877.....444444234444555.788888888875 PP

  == domain 2  score: 27.3 bits;  conditional E-value: 2.4e-10
                   STTEEEEEETTTEEEEEESSEEEEEE-CTTSEEEEEECSTEEEEEECSESCHHHH....HHHHHHHHHHHHHHHHH CS
  Ribosomal_L6   2 PvgvrvsikggqlvlvlGpkgeltreipegvtvevkvegnkvtvivvsgidkekv....AligtvrslinnmikGV 73 
                   +vg+++++ g +l+l lG+ + +++ i+++v ++      k+t+  ++ +dk+      +++ + r+  ++++kG+
    AHX11224.1  90 GVGYKAEVRGRYLILWLGYTHNIKYFISSAVSITSL----KPTELLIESSDKHILglvvSDLCSLRKYDPYKGKGI 161
                   89********************************88....*************99999*****************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1434.15
//
Query:       AHX11225.1  [L=117]
Description: ribosomal L18p/L5e family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-16   60.7   0.0      2e-16   60.4   0.0    1.1  1  Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. a


Domain annotation for each model (and alignments):
>> Ribosomal_L18p  Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   0.0   1.1e-20     2e-16       5     111 ..       6     113 ..       2     117 .] 0.76

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 1.1e-20
                     HHHCHHHHHHTTT--TTSSS-EEEEEE-SS-EEEEEE-TTT--EEEEECS-SCCCT.S-SSSCHHHHHHHHHHHHHHHCH.HCHTC-EE--TTSS CS
  Ribosomal_L18p   5 earkrRhkRirkklsgtaerprlvvfrsnrhiyaQviddvkgktlasastlekelk.lkstknkeaakkvgeliAerake.kgiekvvfDrggyk 97 
                     ++++rR  R + + +g+    rlvv r nr++++Q+idd++ +tl ++stl k +  +    n++ +  ++e + ++  e    +kvvfD g++ 
      AHX11225.1   6 DRQRRRVSRSHYRKRGKL-PFRLVVSRKNRNFHVQLIDDIEANTLYHVSTLSKGFCrKGGVLNSAVVGDLAEYFVKHIPEsLSGSKVVFDCGASA 99 
                     555666666666666665.67*********************************99222233444444555666666544156689********* PP

                     S-CHHHHHHHHHHC CS
  Ribosomal_L18p  98 YhGrvaalAdaaRe 111
                     YhG va +A+ +Re
      AHX11225.1 100 YHGLVALFAERVRE 113
                     *************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (117 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 889.07
//
Query:       AHX11226.1  [L=172]
Description: ribosomal S5, N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-21   74.8   0.0    3.9e-21   74.3   0.0    1.3  1  Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
    1.7e-20   72.7   1.5    3.2e-20   71.9   1.5    1.5  1  Ribosomal_S5    Ribosomal protein S5, N-terminal domain


Domain annotation for each model (and alignments):
>> Ribosomal_S5_C  Ribosomal protein S5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.3   0.0   4.4e-25   3.9e-21       3      72 .]      89     158 ..      87     158 .. 0.98

  Alignments for each domain:
  == domain 1  score: 74.3 bits;  conditional E-value: 4.4e-25
                     EETTEEEEEEE--TT--EES-HHHHHHHHHHT--SEE---BS-SSHHHHHHHHHHHHHHTTTT-.-GGGG CS
  Ribosomal_S5_C   3 kfgavkvllkpaprGtGiiaggavravlelaGikDvlakslgsrnpinvvkAtfeALkklrspeevaalR 72 
                     k ga+k++++pap+GtGi+aggavr+ +e++G++D++aks+gs++   +++ +++A ++++ p+ +a++R
      AHX11226.1  89 KLGASKLFVRPAPEGTGIVAGGAVRKFCEMLGVSDIIAKSYGSSTSDITIRNAIKAFSSIYPPRYIANKR 158
                     789*****************************************************************98 PP

>> Ribosomal_S5  Ribosomal protein S5, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.9   1.5   3.5e-24   3.2e-20       3      63 ..      13      73 ..      11      75 .. 0.96

  Alignments for each domain:
  == domain 1  score: 71.9 bits;  conditional E-value: 3.5e-24
                  EEEEEEEEEEEEETTEEEEEEEEEEEEEETTTEEEEEEEEESSHHHHHHHHHHHHHHTEEE CS
  Ribosomal_S5  3 ekvlkikrvqkvtkgGrrtsfsalvvvGdgnGlvGlGvgkakevatAirkAiekAkknlvp 63
                  e v+++ rv+kvtkgGr++sf++ + vGd++G+vG++v+k +e+ +A +kA++kAk  + +
    AHX11226.1 13 ESVVDVARVSKVTKGGRQFSFRVAALVGDRKGCVGYAVAKHDEMLDARNKAVRKAKGAMRY 73
                  88******************************************************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       343  (0.019131); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1384.74
//
Query:       AHX11227.1  [L=82]
Description: putative ribosomal protein L15 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.13   12.9   0.0       0.14   12.8   0.0    1.0  1  Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27


Domain annotation for each model (and alignments):
>> Ribosomal_L27A  Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0     8e-06      0.14      46     116 ..       3      75 ..       1      78 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8e-06
                     .---EEEEHHHHHHTTTTGTTS------EEEGGGTTTTSSS....SEEEE--S---.-....-EEEESEE-HHHH CS
  Ribosomal_L27A  46 kkeykvvnlkdLdelideerleladeaeeidleelaeaglikkkdgvKvlgkgeltkk....lkvkaskfSkkAk 116
                     kk y++v+ +++ +l++++ ++ +  +  ++ e + + gl+++   vK+l++ +++ +    l+ + +k+S++Ak
      AHX11227.1   3 KKIYSIVSAERIASLVQSDLFDSG--ERHLSKEMMLKCGLVREGFPVKILASHNVSLAelglLSCEYDKASSAAK 75 
                     688999***************855..899***********************98854222246778888888877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       309  (0.0172346); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 708.07
//
Query:       AHX11228.1  [L=435]
Description: preprotein translocase, SecY subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-83  279.8  19.4    2.7e-83  279.8  19.4    1.9  2  SecY      SecY translocase


Domain annotation for each model (and alignments):
>> SecY  SecY translocase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.016   2.8e+02     210     238 ..      19      50 ..       5      56 .. 0.70
   2 !  279.8  19.4   1.5e-87   2.7e-83       1     305 [.      73     408 ..      73     409 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.016
                 HHHHHHHHH...HHHHHHTCTTHHHHHHHCCH CS
        SecY 210 vlyvlliif...Fayfyteitfnpkevaenlk 238
                 vl++l++++   F  f t  ++np +v+e + 
  AHX11228.1  19 VLFLLMVLVvyrFGTFITLPSVNPARVSEIFA 50 
                 444444444556****99999***99998765 PP

  == domain 2  score: 279.8 bits;  conditional E-value: 1.5e-87
                 BTTSSTCHHHHHHHHHHHHHHHHSSSSSSTS-SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC..............HH.HHHHHHHHHHHHHHHHH CS
        SecY   1 sifaLGImPyitasIilqLltvvipkleelkkegeegrkkinqitryltvvlalvqalgialslg..............lalllivlqltagtvllmwL 85 
                 ++faL+ImPyi +sIi+q++ +++++  +++ e    + k++ + ++l+++l+++q+++i+++l+              l   l vl+l++gt+ l+wL
  AHX11228.1  73 TLFALNIMPYIVSSIIVQVFFSMLKSEGKISSE-SISESKLSFYSKILALFLSVFQGFVIVIGLEksqafiggstefysLLRYLSVLSLVCGTFCLIWL 170
                 89******************5558888889855.56789********************9999889************97789**************** PP

                 HHHHHHHSSTTHHHHHHHHHHHHHHCCHSS-.HHHHSS....THHHHHHHHHHHHHHHHHCHHHHBEEEECBBBSTT........S.S-EEEEETTCCC CS
        SecY  86 gEqitekGiGnGisllifagivarlpkalsg.lielale..gilallllllvtllvillvvyveeaerripvqyakrgrk....ggqssylPlklnyag 177
                 g qi+ kGiGnGis++if+giva++p+ + + ++ +  +  g++++l  l+++ ++++l+v+ve++ r+ipv+y +r r+      +ss +P+kln +g
  AHX11228.1 171 GQQINTKGIGNGISMIIFTGIVAEMPSLFGNlFMGIGFSgsGLFNILGSLFLFTFIVALIVLVERSYRNIPVSYPRR-RNwgamYDSSSGIPVKLNVSG 268
                 ******************************955444333779999******************************88.444322556************ PP

                 SCHHHHHHHHHHHHHCCCCS..........TCCC.STHHHHHHHHHHHHHHHHHHHHTCTTHHHHHHHCCHHTBSSSCTTTTCHHHHHHHHHHHHHHHH CS
        SecY 178 viPiIfassllalpstiaqfl.........lall.spsvlyvvlyvlliifFayfyteitfnpkevaenlkksggfipgirpgketakyLekvlsritl 266
                 viP Ifas+l+++p t+a+f          ++++ ++++ly++ly +li+fF++fy+ ++fn+ke++e lkks++ + g rpg +t++yL++vl+rit+
  AHX11228.1 269 VIPPIFASALILFPLTLANFSsdgwlggffIKYFsAGQPLYFLLYSVLIVFFCFFYSDFVFNTKEISESLKKSEAIVAGRRPGVSTKNYLDYVLNRITV 367
                 *******************99999999888666745999************************************************************ PP

                 HHHHHHHHHHHHHHHHTTS...TT.TTHHHHHHHHHHHHHH CS
        SecY 267 iGalflaliavlpdllgasl..igafggtslLivVgvalet 305
                 iGal+l++++v+p++ ++ +  +  ++g slLi+++v+ ++
  AHX11228.1 368 IGALYLVFVCVVPEVSRNYFgfNAVVSGASLLIIINVITDL 408
                 ******************44534789************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       669  (0.0373138); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.35
# Mc/sec: 3715.31
//
Query:       AHX11229.1  [L=209]
Description: adenylate kinase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-27   95.1   0.0    5.3e-27   94.8   0.0    1.1  1  ADK             Adenylate kinase
    1.4e-12   48.2   0.0    2.6e-12   47.3   0.0    1.4  1  AAA_17          AAA domain
    1.3e-05   25.4   0.0    1.9e-05   24.8   0.0    1.2  1  AAA_33          AAA domain
    0.00044   19.9   1.5     0.0012   18.5   1.5    1.7  1  Rubredoxin_2    Rubredoxin metal binding domain
  ------ inclusion threshold ------
      0.037   14.0   2.1      0.092   12.7   2.1    1.7  1  ADK_lid         Adenylate kinase, active site lid
      0.074   13.6   0.0       0.14   12.7   0.0    1.5  1  AAA_18          AAA domain
      0.099   12.4   0.1       0.22   11.2   0.0    1.7  2  Cytidylate_kin  Cytidylate kinase
       0.13   12.3   1.1        1.8    8.7   0.0    2.6  2  zf-ACC          Acetyl-coA carboxylase zinc finger domain


Domain annotation for each model (and alignments):
>> ADK  Adenylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   0.0   2.3e-30   5.3e-27       1     150 [.       5     182 ..       5     183 .. 0.95

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 2.3e-30
                 EEESTTSSHHHHHHHHHHHHTSEEEEHHHHHHHHHHCT-HHHHHHHHHHHTTSS--HHHHHHHHHHHHHCH.GTTTEEEEESB-SSHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK   1 llGaPgaGKGtqaeklvkkyglahlstGdllRaevksgtelGkeakevmdkgelvpdevvvklvkeeleke.dkkkgfllDGfPRtveqaealeellee 98 
                 + G+Pg+GKGtq+ ++ +  ++  +  G llR    s+ +l     + ++ g+l++d+ v+++vk++l++  +  ++f+lDGfPR+++q +al ++ +e
  AHX11229.1   5 VFGPPGSGKGTQSLRICSYVTASVVDCGKLLRGIRLSQDQL-----KNLNSGDLLSDDFVIQVVKDKLSHLtKLGSNFILDGFPRSITQCSALFDMSSE 98 
                 68******************************877666554.....6689*******************997899************************ PP

                 HTSEESEEEEEE--HHHHHHHHHT................................GSHHHHHHHHHHHHHHHHHHHHHHHHTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxx................................xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
         ADK  99 ekvkldlvleldvpeevlveRltg................................DneetvkkRletykkqtkplidyykkkg 150
                  + ++ ++++++++e+++ eRl+g                                 ++e+vkkRl  y++  + ++d +k++g
  AHX11229.1  99 LEFEISCLVKFELSEKTVFERLLGrlvcnkcgdlydtsfgkclscgsltynrrhddSSAEAVKKRLLLYSAVERDIVDLFKSRG 182
                 ******************************************************966789********************9986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.3   0.0   1.2e-15   2.6e-12       1     122 [.       6     123 ..       6     131 .. 0.90

  Alignments for each domain:
  == domain 1  score: 47.3 bits;  conditional E-value: 1.2e-15
                 EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHHHHHHTTTSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHH.HSSEEEEEE-SEEEETTEEEESSHHHHHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaGdllreeakrgglakardemrklpleekkelqkeaaekiaeea.kkkgvlvdghprikeqagfldglpkevle 98 
                 +G+PGsGKgtq+ ++   +  +++  G llr    ++    + ++++ ++l  ++ + + +++k+ +     +++++dg+pr  +q  +l ++ +e   
  AHX11229.1   6 FGPPGSGKGTQSLRICSYVTASVVDCGKLLRGIRLSQD---QLKNLNSGDLLSDDFVIQVVKDKLSHLTkLGSNFILDGFPRSITQCSALFDMSSEL-- 99 
                 6******************************8754443...45899999****************997647899**************999999986.. PP

                 HH..SEEEEEE--HHHHHHHHHHH CS
      AAA_17  99 elkpdaiilleadpeeilerrlkd 122
                 e++++ ++ +e ++++++er+l +
  AHX11229.1 100 EFEISCLVKFELSEKTVFERLLGR 123
                 666699999************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   8.6e-09   1.9e-05       3     118 ..       4     123 ..       3     127 .. 0.85

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 8.6e-09
      AAA_33   3 llvGlpGsGKstlaerllkklgavllssdtlrrrlfgtdqq.sktdytr.vldr.lyqilnelarkalsagrnvildatnlsrrerarflklarrlgvp 98 
                 ++ G+pGsGK t + r++   +a +++  +l+r ++ +++q +  ++ + ++d+ ++q +++ +    + g n+ild   +s  + ++++ + ++l+++
  AHX11229.1   4 VVFGPPGSGKGTQSLRICSYVTASVVDCGKLLRGIRLSQDQlKNLNSGDlLSDDfVIQVVKDKLSHLTKLGSNFILDGFPRSITQCSALFDMSSELEFE 102
                 678***************************99977654333122233442443369**********************99999**************** PP

      AAA_33  99 vri.vvvetdeetlkeRlakR 118
                 +++ v +e +e+t  eRl  R
  AHX11229.1 103 ISClVKFELSEKTVFERLLGR 123
                 *99788***********9877 PP

>> Rubredoxin_2  Rubredoxin metal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   1.5   5.2e-07    0.0012       2      22 ..     125     145 ..     125     145 .. 0.97

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 5.2e-07
  Rubredoxin_2   2 vCsqCGfesakwfGrCpsCgs 22 
                   vC++CG  + + fG+C sCgs
    AHX11229.1 125 VCNKCGDLYDTSFGKCLSCGS 145
                   7******************97 PP

>> ADK_lid  Adenylate kinase, active site lid
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   2.1   4.1e-05     0.092       1      32 [.     123     148 ..     123     154 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 4.1e-05
                 EEE-TTT--EEETTTB--SSTTB-TTT--.-B CS
     ADK_lid   1 RrvCpkCGrsYhvvfnpPkveglCDkCGepLv 32 
                 R+vC kCG  Y   f      g+C  CG+  +
  AHX11229.1 123 RLVCNKCGDLYDTSF------GKCLSCGSLTY 148
                 9***********777......*******9544 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   6.4e-05      0.14       2     114 ..       4     124 ..       3     130 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.4e-05
      AAA_18   2 lltGtpGvGKttlakeLskrlgf....gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleegknlvidghlaeleseaakdikk 96 
                 ++ G+pG+GK t + ++ +   +    +v ++++++  +l+ ++ ++ l++ + l +d++ ++++    +      g+n ++dg++    + +a +   
  AHX11229.1   4 VVFGPPGSGKGTQSLRICS---YvtasVVDCGKLLRGIRLSQDQLKN-LNSGDLLSDDFVIQVVKDKLSHL--TKLGSNFILDGFPRSITQCSALFDMS 96 
                 689*********8777733...3343499999999999999999999.66666666666554444444443..3579999*****99999888887777 PP

      AAA_18  97 ..........vvLtaspeelleRlekRg 114
                           v  ++s+++ +eRl  R 
  AHX11229.1  97 selefeisclVKFELSEKTVFERLLGRL 124
                 8999999999999999999999999885 PP

>> Cytidylate_kin  Cytidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.9e-05      0.22       5      41 ..       7      43 ..       3     127 .. 0.76
   2 ?   -1.6   0.1      0.83   1.9e+03     146     177 ..     150     179 ..     147     198 .. 0.67

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.9e-05
                    -STTSSHHHHHHHHHHHHT-EEEEHHHHHHHHHHHHH CS
  Cytidylate_kin  5 GPagsGKssvaralaeklglkyldtgalYRalalaal 41
                    GP gsGK++ + ++ + + ++++d g+l R + l   
      AHX11229.1  7 GPPGSGKGTQSLRICSYVTASVVDCGKLLRGIRLSQD 43
                    9*****************************9887653 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.83
                     HHHHHHHHTT----HHHHHHHHHHHHHHHHCT CS
  Cytidylate_kin 146 RRlkqlkakgtsvsleellaeikeRDklDker 177
                     RR ++ +a+  +v++  ll +  eRD +D  +
      AHX11229.1 150 RRHDDSSAE--AVKKRLLLYSAVERDIVDLFK 179
                     777774444..567788888899999888433 PP

>> zf-ACC  Acetyl-coA carboxylase zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.3      0.14   3.2e+02       4       8 ..     126     130 ..     125     132 .. 0.64
   2 ?    8.7   0.0    0.0008       1.8       3      15 ..     139     151 ..     137     156 .. 0.88

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.14
      zf-ACC   4 CpsCg 8  
                 C++Cg
  AHX11229.1 126 CNKCG 130
                 66666 PP

  == domain 2  score: 8.7 bits;  conditional E-value: 0.0008
      zf-ACC   3 KCpsCgemlykke 15 
                 KC sCg+++y++ 
  AHX11229.1 139 KCLSCGSLTYNRR 151
                 9*********985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       670  (0.0373696); expected 358.6 (0.02)
Passed bias filter:                      551  (0.0307323); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1589.45
//
Query:       AHX11230.1  [L=123]
Description: 30S ribosomal protein S13 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-27   95.0   0.4    6.2e-25   88.1   0.4    2.0  1  Ribosomal_S13  Ribosomal protein S13/S18


Domain annotation for each model (and alignments):
>> Ribosomal_S13  Ribosomal protein S13/S18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.1   0.4   3.5e-29   6.2e-25       1     128 []       2     108 ..       2     108 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.1 bits;  conditional E-value: 3.5e-29
  Ribosomal_S13   1 RilgtdidgkkkveialtaikGiGrrkakiilkkadvdedkrigelteeeiekieeivenkaqykipnwinrqkdikdGkdshvvendlrrklred 96 
                    R lg++++++k v++alt+i+G+G  ++++i+++  v+e++++++l++ +++ i+++++n                     +   e+dlr++++ +
     AHX11230.1   2 RFLGVNLPDNKAVVVALTYIYGVGFPTSRKICAASSVSESAKLSDLQQGQLNAIMTYIKN---------------------EIPFEGDLRKSVAFS 76 
                    7899********************************************************.....................56789********** PP

  Ribosomal_S13  97 ieRlkkirsyrGlRHkrGlkvRGQrTkttgRt 128
                    i+ l++i++yr  RH++ l+vRGQrT+t++Rt
     AHX11230.1  77 IKHLMDIKCYRATRHRKNLPVRGQRTRTNART 108
                    *******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (123 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       492  (0.0274416); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1034.52
//
Query:       AHX11231.1  [L=332]
Description: DNA-directed RNA polymerase, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-21   75.5   1.3    3.4e-21   74.8   1.3    1.3  1  RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C termin
    1.4e-18   66.1   0.0    2.1e-18   65.5   0.0    1.3  1  RNA_pol_L      RNA polymerase Rpb3/Rpb11 dimerisation domain
    9.3e-17   61.4   0.0      2e-16   60.3   0.0    1.5  1  RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
  ------ inclusion threshold ------
       0.36   11.5   1.6        1.7    9.3   0.0    2.9  4  HHH_5          Helix-hairpin-helix domain


Domain annotation for each model (and alignments):
>> RNA_pol_A_CTD  Bacterial RNA polymerase, alpha chain C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   1.3   7.6e-25   3.4e-21       4      65 ..     258     319 ..     255     321 .. 0.95

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 7.6e-25
                    .XXXXXXX--BHHHHT--HHHHHHHHHTT--BHHHHHHS-HHHHTTSSS-SSHHHHHHHHHH CS
  RNA_pol_A_CTD   4 eeeelkklsisIeeLeLSvRslNcLkragiktvgeLvklseeeLlkikNlGkKSleEIkekL 65 
                     ++ +++ls +++ L LS+Rs++cL +++i ++++Lv+++e++Llk +N+G++Sl+E+k+ L
     AHX11231.1 258 ANDTNDLLSAKVDRLYLSARSRKCLSNENIVYIRDLVSKTEADLLKAPNFGRRSLDEVKKEL 319
                    677899*****************************************************998 PP

>> RNA_pol_L  RNA polymerase Rpb3/Rpb11 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   4.8e-22   2.1e-18       1      67 [.      36     231 ..      36     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 4.8e-22
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................................................... RF
   RNA_pol_L   1 efllrgvdhtlgNaLRrillsevpgvaiea..................................................................... 30 
                 e+l  g+++t+gNa+Rr+lls++ +vai a                                                                     
  AHX11231.1  36 EPLYTGFGLTIGNAMRRVLLSSLGSVAISAigikglthefscvpgvredfsdlalnlkkvvlrsvsgvkegclylsvsgagpvlsgmispsddfevvnt 134
                 79999****************************************************************************999999999999999999 PP

                 .................................................xxxxxx...........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
   RNA_pol_L  31 .................................................pvvkvn...........tdkdklilevetdgslkPeealkeAlkiLke 67 
                                                                  pv+ vn             +d+lil+vet+g+++P++a++eA ++L  
  AHX11231.1 135 dlllcnvaegaslemkikvswgfgyvssvsvkrdeydlegfvpidttynPVRAVNfavkptgvggfVGYDRLILSVETNGAIDPKDAVLEASRVLAT 231
                 9999999999999999999999999999999999999999988888888777777888899999*99**************************9975 PP

>> RNA_pol_A_bac  RNA polymerase Rpb3/RpoA insert domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.3   0.0   4.5e-20     2e-16      15     108 ..      71     161 ..      61     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 60.3 bits;  conditional E-value: 4.5e-20
                    HHCHHHCSTCBSSCHHHHHHHHCTT-.ETSSSSTTCSEEEEEEEEESSECEEGGGCBESSSSCEESSTTSEEEEEETT-EEEEEEEEEEESSEEC CS
  RNA_pol_A_bac  15 vaHrlgliplvsedvleillnlkelv.eeeeegeeeksvelkLnvkgpgevtagdlkledadveivnpdilIakLrkgqeleleakvkkGiGkeh 108
                    + H+++ +p+v+ed  ++ lnlk++v ++ +  +e +   l+L+v+g g v +g++   ++d+e+vn d+l++++++g++le+++kv  G+G+++
     AHX11231.1  71 LTHEFSCVPGVREDFSDLALNLKKVVlRSVSGVKEGC---LYLSVSGAGPVLSGMISP-SDDFEVVNTDLLLCNVAEGASLEMKIKVSWGFGYVS 161
                    89***********************975567888888...******************.9*********************************97 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       2.3     1e+04      10      27 ..      46      62 ..      46      81 .. 0.57
   2 ?   -2.0   0.0       1.3   5.9e+03       5      15 ..     110     120 ..     108     125 .. 0.81
   3 ?   -1.6   0.1      0.95   4.2e+03      24      37 ..     259     272 ..     248     274 .. 0.57
   4 ?    9.3   0.0   0.00038       1.7      16      55 ..     279     319 ..     275     319 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 2.3
                --HHHHHHHHTTT--SHH CS
       HHH_5 10 iGpktAlallsaGiesve 27
                iG ++ + lls   +sv+
  AHX11231.1 46 IGNAMRRVLLSS-LGSVA 62
                566666666666.44443 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                 HTSTT--HHHH CS
       HHH_5   5 lsvsGiGpktA 15 
                 lsvsG Gp++ 
  AHX11231.1 110 LSVSGAGPVLS 120
                 79*****9875 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.95
                 -SHHHHHHS-HHHH CS
       HHH_5  24 esvedlaaadveeL 37 
                 +   dl++a v++L
  AHX11231.1 259 NDTNDLLSAKVDRL 272
                 34456666666655 PP

  == domain 4  score: 9.3 bits;  conditional E-value: 0.00038
                 HHHHTT.T--SHHHHHHS-HHHHHTSTTS-HHHHHHHHHHH CS
       HHH_5  16 lallsa.GiesvedlaaadveeLakipGiGkktAeriilel 55 
                 ++ ls+  i  + dl+++++++L k+p +G +  + ++ el
  AHX11231.1 279 RKCLSNeNIVYIRDLVSKTEADLLKAPNFGRRSLDEVKKEL 319
                 6777775588899*******************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       353  (0.0196888); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2773.05
//
Query:       AHX11232.1  [L=116]
Description: ribosomal protein L17 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.4e-30  106.0   0.0    1.7e-30  105.7   0.0    1.1  1  Ribosomal_L17  Ribosomal protein L17


Domain annotation for each model (and alignments):
>> Ribosomal_L17  Ribosomal protein L17
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.7   0.0   9.5e-35   1.7e-30       1      94 []      20     116 .]      20     116 .] 0.96

  Alignments for each domain:
  == domain 1  score: 105.7 bits;  conditional E-value: 9.5e-35
                    HHHHHHHHHHHHSEEEEEHHHHHHHHHHHHHHHHHHHH-SHHHHHHHHHHS-...HHHHHHHTHHHHTSS--S--EEEEEEEE-TTTH-EEEEEEE CS
  Ribosomal_L17   1 LlrnlvtsLleherIetTlakAkelrklaeklitlakkgelaarrkalayla...lvkkLfeelapryadrngGYtRilklgprrgDaaemailel 93 
                    L+ nl  +L++h+ I tTlakAk+lr+++ekl+t+a++++l++rr +++ ++   +v+kL++e+a++y dr+gGY+Ri+k g r gDaa+ma++e+
     AHX11232.1  20 LMCNLSIALITHGCISTTLAKAKALRPFIEKLVTKARSSSLSSRRLLISRIKnevAVSKLIDEVAKKYLDRPGGYCRIMKNGYRAGDAAPMAVIEF 115
                    6789******************************************9999954558***************************************9 PP

                    - CS
  Ribosomal_L17  94 V 94 
                    V
     AHX11232.1 116 V 116
                    8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (116 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1007.21
//
Query:       AHX11233.1  [L=107]
Description: merR HTH regulatory family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-21   75.0   0.9      5e-21   74.6   0.2    1.5  2  MerR_1           MerR HTH family regulatory protein
      5e-05   23.0   0.0    9.4e-05   22.1   0.0    1.5  1  MerR             MerR family regulatory protein
  ------ inclusion threshold ------
      0.027   14.3   0.1      0.033   14.1   0.1    1.1  1  Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
       0.03   14.4   0.1        7.6    6.7   0.0    2.1  2  ImpA_N           ImpA, N-terminal, type VI secretion system
      0.058   13.6   0.2       0.46   10.7   0.0    2.0  2  Ribonuc_2-5A     Ribonuclease 2-5A
       0.08   13.2   0.2       0.12   12.6   0.2    1.2  1  Ribosomal_L22    Ribosomal protein L22p/L17e


Domain annotation for each model (and alignments):
>> MerR_1  MerR HTH family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.6   0.2   1.7e-24     5e-21       1      68 [.      11      80 ..      11      81 .. 0.94
   2 ?   -2.2   0.0       1.6   4.7e+03      43      54 ..      91     102 ..      88     104 .. 0.65

  Alignments for each domain:
  == domain 1  score: 74.6 bits;  conditional E-value: 1.7e-24
                EEHHHHHHHHTS-HHHHHHHHHHTT..-S-EE-TTS-EEEEHHHHHHHHHHHHHHH.TT--GGG---XXXX CS
      MerR_1  1 ysigevakilgvtthtlrywekegl..lkpkrteggrryYtdedierLklikyLlk.rGltlkgikkllns 68
                ysi+e+a i+g++ ++lrywe++++  l+pkr + g r+Yt++di+++++i++Ll+ +G+t+kg++ +l+s
  AHX11233.1 11 YSIKEAAGIVGLKEYVLRYWETQFPklLNPKR-QSGKRLYTRSDINTIRKIQELLHvKGMTIKGAAMALES 80
                9*************************888888.6777****************************999976 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.6
                 HHHHHHHHHHHH CS
      MerR_1  43 ierLklikyLlk 54 
                 ie+Lk  + +lk
  AHX11233.1  91 IEQLKSLRDFLK 102
                 666776666665 PP

>> MerR  MerR family regulatory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.0   3.2e-08   9.4e-05       1      38 []      12      49 ..      12      49 .. 0.86

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 3.2e-08
                EHHHHHHHHTTTHHHHHHHHHT.T.SSTSEEETTTSSEEE CS
        MerR  1 tIgevAeltGvsprtLRyYEre.G.LipppeRtegGyRlY 38
                +I+e+A ++G+    LRy+E +   L+  p R ++G RlY
  AHX11233.1 12 SIKEAAGIVGLKEYVLRYWETQfPkLL-NPKR-QSGKRLY 49
                7*********************97355.5555.78***99 PP

>> Methyltrn_RNA_4  SAM-dependent RNA methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.1   1.1e-05     0.033      43     128 ..      10      93 ..       3     100 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.1e-05
                      EEEE---HHHHHHHHHHHHHHHTSGGGGT-SSSHHHHTTEEEESSHHHHHHHHHHHHSS--EEEE--SS--SS-B-HHHHHHHHHH CS
  Methyltrn_RNA_4  43 yyvvtpleaqrelverilehWtegagaeynpdRkealslvkvvesleealeeiekeegkkplvvatsArkkentvsyeelrellee 128
                      yy +++ +    l e +l++W++++ + +np+R++  +++ + ++++ ++++i++  + k +++   A + e++ +y+e+++++e+
       AHX11233.1  10 YYSIKEAAGIVGLKEYVLRYWETQFPKLLNPKRQSG-KRLYTRSDIN-TIRKIQELLHVKGMTIKGAAMALESRSKYQEAESVIEQ 93 
                      7777777788889999*****************986.5666777776.5788999999*******************999999854 PP

>> ImpA_N  ImpA, N-terminal, type VI secretion system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0026       7.6      82     103 ..      17      40 ..      10      56 .. 0.76
   2 ?    6.3   0.0    0.0032       9.6      48      97 ..      58     107 .]      50     107 .] 0.93

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0026
      ImpA_N  82 eglellaelleryWdelhPal..d 103
                 +g+  l+e + ryW++ +P+l   
  AHX11233.1  17 AGIVGLKEYVLRYWETQFPKLlnP 40 
                 677789999***********9742 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0032
      ImpA_N  48 elaeelleerskDLrvavwlteallrleglaglaeglellaelleryWde 97 
                 ++++ell  ++  ++ a++ +e++ + ++++++ e l+ l+++l+++ de
  AHX11233.1  58 RKIQELLHVKGMTIKGAAMALESRSKYQEAESVIEQLKSLRDFLKKFSDE 107
                 789999999*************************************9985 PP

>> Ribonuc_2-5A  Ribonuclease 2-5A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00016      0.46      89     106 ..      21      38 ..       5      53 .. 0.78
   2 ?    1.6   0.0     0.098   2.9e+02      51      76 ..      78     104 ..      45     107 .] 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00016
  Ribonuc_2-5A  89 elpegflsYftkrFPkLl 106
                    l+e +l+Y++++FPkLl
    AHX11233.1  21 GLKEYVLRYWETQFPKLL 38 
                   3688999**********9 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.098
  Ribonuc_2-5A  51 lgkyrkYkg.dsvrdLLRaiRNkkeHy 76 
                   l+++ kY++ +sv + L+ +R+  + +
    AHX11233.1  78 LESRSKYQEaESVIEQLKSLRDFLKKF 104
                   556667764267888888888876655 PP

>> Ribosomal_L22  Ribosomal protein L22p/L17e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.2     4e-05      0.12      11      51 ..      58      98 ..      51     104 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4e-05
                   HHHHHHHHHHTTSBHHHHHHHHHT.-SSTTHHHHHHHHHHHH CS
  Ribosomal_L22 11 kklrevarlIrgmkveeAlkyLkf.skkkaakfvlklLknae 51
                   +k++e+++ ++gm+++ A   L+  sk + a+ v++ Lk+ +
     AHX11233.1 58 RKIQELLH-VKGMTIKGAAMALESrSKYQEAESVIEQLKSLR 98
                   56666665.9**************9**************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 828.80
//
Query:       AHX11234.1  [L=165]
Description: phosphatidylglycerophosphatase A family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-39  132.7   6.7    1.1e-38  132.5   6.7    1.0  1  PgpA      Phosphatidylglycerophosphatase A


Domain annotation for each model (and alignments):
>> PgpA  Phosphatidylglycerophosphatase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   6.7     6e-43   1.1e-38       4     142 ..      12     160 ..       9     161 .. 0.88

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 6e-43
                 HHHHHHTT......--HHHHHHHHHHHTT.HHHHH..HHHHHHHHHHHHHHHHHHHHHT-S-HHT-TT--HHHHTTHHHHH................TT CS
        PgpA   4 latlfgsGllpvaPgtvgslaalllallllllesls.lllllilllflvGiwackktekelgekDpgeiviDEvvgqwiallllpa........tllal 93 
                 +at+fg+G +   Pgtv s a +ll+ l+ +l  +  ++l++ +llf++G++ c+k+e  ++++Dpg++viDE+v+q i +l++++         +l+l
  AHX11234.1  12 IATCFGIGNFTTFPGTVASAAVFLLFPLIVFLDLPLaSILIASVLLFALGTYSCHKYEMLYSVRDPGNVVIDEFVAQTILILFTNYifrgysntMILVL 110
                 89*************************997666664244489999************************************999555555555444444 PP

                 .HHHHHHHHHHHHS--THHHHTSSS.-S---TTHHHHHHHHHHHHHHHHH CS
        PgpA  94 .llafilFrlfDivKpgpigwldrklkgglgvmlDDllAgiaaalvlali 142
                  +l+f+lFr+fDivKp+pi+ ++r++ gg+gvm+DDllA+ia+++vl li
  AHX11234.1 111 cILSFLLFRFFDIVKPWPISVVQRSMRGGFGVMFDDLLAAIASLIVLLLI 160
                 599*******************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (165 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       840  (0.0468515); expected 358.6 (0.02)
Passed bias filter:                      340  (0.0189637); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1258.38
//
Query:       AHX11235.1  [L=188]
Description: translation initiation factor IF-3 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-24   84.4   0.5    7.6e-24   83.5   0.5    1.5  1  IF3_C     Translation initiation factor IF-3, C-terminal doma
    4.4e-22   78.1   0.9    9.6e-22   77.0   0.9    1.6  1  IF3_N     Translation initiation factor IF-3, N-terminal doma
  ------ inclusion threshold ------
        0.1   12.4   1.2       0.16   11.8   0.1    1.9  2  PPI_Ypi1  Protein phosphatase inhibitor


Domain annotation for each model (and alignments):
>> IF3_C  Translation initiation factor IF-3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.5   1.3e-27   7.6e-24       2      86 .]     101     186 ..     100     186 .. 0.97

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 1.3e-27
                 -EEEEEEESS--HHHHHHHHHHHHHHHHHT-EEEEEEE--S-TTSHHHHHHHHHHHHHHHTT.TTEEEEEEEEE-SSEEEEEEEES CS
       IF3_C   2 evKEiklrpkidehDlevKlknarkFLeegdkvKvtlrfrGReiahkelgkevleriaeele.evakvekkpklegrqmimvlapk 86 
                 ++KEi+lr  i  +Dl++Klk++r+FL ++d+vKv +r+rGRe+ +k+l+ ++l+++++e+  e+ak+ek+  ++++++++vlap+
  AHX11235.1 101 TIKEIQLRQCIGAGDLNTKLKKIREFLLDEDRVKVVVRLRGREMINKNLALNLLNKVITEIGsEIAKLEKEVVQNNNNFFIVLAPN 186
                 59********************************************************999658********************96 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.0   0.9   1.6e-25   9.6e-22       8      66 ..      31      89 ..      28      97 .. 0.95

  Alignments for each domain:
  == domain 1  score: 77.0 bits;  conditional E-value: 1.6e-25
                SEEEEE-SSS-EEEEEEHHHHHHHHHHHTSEEEEEESSSSS-EEEEE-HHHHHHHHHHH CS
       IF3_N  8 revrlvdedGeqlGvistreAlrlaeekgldLVevspnaepPVcrimdygkfrYeqkkk 66
                +evr++d+d + +Gv++++ Al+la+e++ldLVevs +  pP+c+i+dygk++Ye kk 
  AHX11235.1 31 NEVRVIDADDKFVGVMKIAAALQLAKERNLDLVEVSSTVVPPICKILDYGKYKYEIKKD 89
                69*******99********************************************9985 PP

>> PPI_Ypi1  Protein phosphatase inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.7e-05      0.16      10      30 ..      12      32 ..       6      34 .. 0.88
   2 ?   -3.9   0.2       2.1   1.3e+04      33      38 ..      93      98 ..      88     102 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.7e-05
    PPI_Ypi1 10 kkkkkkskrrVrWeedvvDNE 30
                ++++ ++++r+ W+ ++vDNE
  AHX11235.1 12 ESRRASDDKRIVWRPGTVDNE 32
                6788899*************9 PP

  == domain 2  score: -3.9 bits;  conditional E-value: 2.1
    PPI_Ypi1 33 nkkksK 38
                 +kk K
  AHX11235.1 93 KRKKQK 98
                333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1484.37
//
Query:       AHX11236.1  [L=623]
Description: threonine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.3e-41  142.5   0.0    2.6e-41  141.6   0.0    1.4  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    8.6e-13   48.3   0.5      2e-12   47.1   0.2    1.8  2  HGTP_anticodon  Anticodon binding domain
    2.2e-12   46.9   0.0    4.4e-12   45.9   0.0    1.5  1  tRNA_SAD        Threonyl and Alanyl tRNA synthetase second ad
  ------ inclusion threshold ------
       0.12   11.2   0.0       0.18   10.6   0.0    1.1  1  PPV_E1_C        Papillomavirus helicase


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.6   0.0   5.8e-45   2.6e-41       5     179 .]     309     517 ..     302     517 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.6 bits;  conditional E-value: 5.8e-45
                   ETTSEEEEE-SSSHHHHHHHHHHHEEEBGG.SSEEEEEEEEEEBTTTS.TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   5 drndreyiLkPtneetfvelirdevlrskr.LPlklyqiqtkyRdEks.dsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglefr 99 
                   d  d e+ LkP+n+++++e++++  ++s+r LPl+l++++ ++R+E+s +++GL+Rvr+F q+d+++f++++++  +      + ++i+ +lg+++ 
    AHX11236.1 309 DSVDGEFSLKPMNCPAHIEVFKQS-IKSYRdLPLRLAEFGMCHRNEASgALHGLMRVRGFVQDDAHIFCTPEQICPETVAFCALLKEIYTQLGFSKT 404
                   566889****************99.***777*****************9**********************************************99 PP

                   EEEEEGTTSC.................................BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEE CS
                   xxxxxxxxxx.................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 100 aiielmsaks.................................adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimic 163
                    i+ + + +                                  a+y++k ef +++  l++++++gt q + + l+ rlgat++d ++r+++++m++
    AHX11236.1 405 EIRFSDRPEVrlgddttwdkaenalksameeagleyginpgegAFYGPKIEFVLTDA-LNRKWQCGTLQVD-FILPGRLGATYVDAEGRKQHPVMLH 499
                   9998844333566788999999********************************999.*************.************************* PP

                   EE.EE.HHHHHHHHHHHH CS
                   xx.xx.xxxxxxxxxxxx RF
  tRNA-synt_2b 164 aa.ig.veRllsaileqn 179
                   +a +g  eR++++++e++
    AHX11236.1 500 RAvLGtFERFIGILIEHY 517
                   *****99********986 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       1.9   8.3e+03      39      55 ..     107     123 ..      99     124 .. 0.79
   2 !   47.1   0.2   4.5e-16     2e-12       1      91 [.     529     616 ..     529     619 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 1.9
                     STHHHHHHHHHHTT-SE CS
  HGTP_anticodon  39 esigkkireadllgipf 55 
                     e+i kki+e  ++ +p+
      AHX11236.1 107 ENIEKKISEIVRKDYPI 123
                     78999999998888887 PP

  == domain 2  score: 47.1 bits;  conditional E-value: 4.5e-16
                     SEEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHH CS
  HGTP_anticodon   1 qvvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelvekl 91 
                     qv+v++++e   ++++ a k+ e L+ ++ir+ +d sn++i +kir++ +  +p+  ++G+ e++++ v+vr++ + + e+ s+d+++ ++
      AHX11236.1 529 QVCVLTITE---KVQDHAAKIVELLLGKNIRTTFDFSNQRIDYKIRHHTTRRVPILWIIGKIEAQSNAVSVRRLGSLRSENKSVDDALYEV 616
                     89*******...9****************************************************************99999999987666 PP

>> tRNA_SAD  Threonyl and Alanyl tRNA synthetase second additional domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   9.8e-16   4.4e-12       1      44 []     158     207 ..     158     207 .. 0.98

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 9.8e-16
                 EEEEEETT.EEEEESS---SBGGGC-SEEEE.......CCECCCTCEEEEE CS
    tRNA_SAD   1 vrvvsiGdisvelCgGtHvpnTgeIgafkil.......seesiakglrRIy 44 
                 ++v+++   +v+lC+G+H p+Tg +++fk+l        ++++++ ++RIy
  AHX11236.1 158 ISVYKQDG-FVDLCRGPHAPSTGWLKHFKLLkvsgaywLGDAKNDSMQRIY 207
                 68****97.*****************************************9 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.0   4.1e-05      0.18     288     365 ..     511     592 ..     503     600 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 4.1e-05
    PPV_E1_C 288 GkvlsfvnskshfWlqPLaeakvall....DDatkacwkyiDtylrnalDGnevsiDlkhkapvqlkcPPllitsnidvkad 365
                 G ++ + n k  +Wl+P++ + +++     D a+k +   + +++r ++D  +  iD k +  +  ++P l i   i+ +++
  AHX11236.1 511 GILIEHYNGKFPLWLAPVQVCVLTITekvqDHAAKIVELLLGKNIRTTFDFSNQRIDYKIRHHTTRRVPILWIIGKIEAQSN 592
                 7889999**************998752222667777778899*******************************999998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (623 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      509  (0.0283898); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.38
# Mc/sec: 4970.71
//
Query:       AHX11237.1  [L=316]
Description: hypothetical protein NHE_0278 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      507  (0.0282782); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2438.84
//
Query:       AHX11238.1  [L=111]
Description: 2Fe-2S iron-sulfur cluster binding domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.9e-13   48.8   0.2    5.9e-13   48.6   0.2    1.1  1  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.066   12.8   0.2       0.12   11.9   0.2    1.4  1  MCR       Magnetochrome domain


Domain annotation for each model (and alignments):
>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.6   0.2   6.5e-17   5.9e-13       3      77 ..      12      92 ..      10      93 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.6 bits;  conditional E-value: 6.5e-17
                TTTEEEEEEEETTTHBHHHHHHHTTTTTSTTSSSSSS.SSTTEEEEEESCE.CTT.SSSSTHHHHHTTEE.....EEGGGSEE CS
        Fer2  3 idgkevevevadgettlldaaeenggidipysCgggg.CgtClvevlegev.qsd.etelegeeldegkl.....rlaCqtiv 77
                +dg e+ + +++get +l +a +n +id++ +C+g+  C+tC+v v++++  + +  +  e+++ld ++      rl Cq+ +
  AHX11238.1 12 PDGVEHHCFAQEGET-ILTVAHRN-NIDLEGACEGSLaCSTCHVIVDAEWFeKLEpISGEEDDMLDLAFGlastsRLGCQITM 92
                68999999999****.77777778.8*********99*******9888777744468999999998888899********987 PP

>> MCR  Magnetochrome domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   1.4e-05      0.12      19      29 ..      47      57 ..      45      58 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 1.4e-05
                -GGGT--BSST CS
         MCR 19 nCtkCHqIiga 29
                +C++CH+I+ a
  AHX11238.1 47 ACSTCHVIVDA 57
                8*******965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      279  (0.0155614); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.39
# Mc/sec: 856.74
//
Query:       AHX11239.1  [L=599]
Description: hsp70 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.2e-140  467.8   2.2   6.7e-140  467.1   2.2    1.3  1  HSP70          Hsp70 protein
    6.3e-18   64.7   0.9    2.2e-14   53.0   0.0    3.1  4  MreB_Mbl       MreB/Mbl protein
      0.004   16.7   0.1       0.69    9.3   0.0    2.3  2  BcrAD_BadFG    BadF/BadG/BcrA/BcrD ATPase family
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.33   11.1   0.1    1.7  1  SLBP_RNA_bind  Histone RNA hairpin-binding protein RNA-bindin
       0.16   11.6   0.0       0.29   10.8   0.0    1.3  1  UL16           Viral unique long protein 16


Domain annotation for each model (and alignments):
>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  467.1   2.2  1.9e-143  6.7e-140       1     596 [.      17     583 ..      17     586 .. 0.92

  Alignments for each domain:
  == domain 1  score: 467.1 bits;  conditional E-value: 1.9e-143
                 EEEEEEXSSEEEEEEEETTEEEEEXXTTSXSSEESEEEEXTTSEEETHHHHHCTTTTGGGEEEXGGGTTTXBTTSHHHHHHHTTXSSEEEEETTSBEEE CS
       HSP70   1 viGiDLGttnsvvavmeggkievianeegnrttPsvvaFtkkerlvGeaAkrqavtnpkntvfsvKrliGrkfsdpevqkeikelpykvvkkengkavv 99 
                 ++GiD Gttns+++v++++k  vi  e g+   Ps++a ++k+ +vG++Ak+      kn + s+Kr+i +k +   v  +    +++++++ +++++ 
  AHX11239.1  17 IVGIDFGTTNSLISVFQDEKCVVIPQESGKNFLPSLIAVQDKNIIVGKEAKK-----YKNYIPSIKRIIATKEN--LVIPN----ACTINTQ-TQDPQS 103
                 69************************************************97.....5899********99433..33333....4445444.333332 PP

                 EEEETTEEEEHHHHHHHHHHHHHHHHHHHHTSBEEEEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXE CS
       HSP70 100 eveaagekftpeqisamvLkklketaeaylgkkvtdavitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtf 198
                 + +       +   ++++ + lk+ ae+ylg+ v +av+tvPaYf+++ R a+kdA++i GLnv+R++ epTAaal YG+d+k +e + +vyDlGggtf
  AHX11239.1 104 NYA------LTIGYASKIFSSLKKSAEKYLGHAVRNAVVTVPAYFDNTSRSAIKDAATISGLNVIRLLSEPTAAALFYGIDEKREEGKYVVYDLGGGTF 196
                 222......2344578999******************************************************************************** PP

                 EEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHHHHHHHHHHHSXXGGGSHHHHHHHHHHHHHHHHHTTTSSCSEEEEEEEEEETTTEEEEEEEEHHH CS
       HSP70 199 dvSilelekGvfevkaTagDthlGGedfDealvehlveefkkkegidlskdkkalqrlkeaaekaKkeLSsskqteinleietvdedgkdlseklsRak 297
                 d+Sile+++G+f+v    gD hlGG+dfD +l+ehl+++    +++ ls ++k+  + ++ ++++K eL +   ++  + + + +e  +d  ++++ + 
  AHX11239.1 197 DISILEFHRGIFKVSCSDGDDHLGGDDFDLRLMEHLIQK----HELHLSGEEKV--HFLDFCKEIKEELAH---EDRIVRYFSYQE--NDACIDVTLED 284
                 ************************************975....45667777665..689************...344566777777..4667777779* PP

                 HHHHHHHHHHHTHHHHHHHHHHCTEEGGGCSEEEEESGGGGSHHHHHHHHHHTTCH.HBSSSHTTTHHHHHHHHHHHHHCTCGCSHCCEEEEBESS-EE CS
       HSP70 298 feelvedllertlepvekalkdaklkkeeidevvlvGGstRiPkvqelvkelfgke.psktvnpDeavaiGAAvqagvlsgeeevkdllllDvtpLslg 395
                 fe+ +e+ ++rt+  +++al+ +++ + e+d v+lvGGst+i  ++ +++elfgke   +++np  +v +GAA+ +  l+g  + ++++llDv pLslg
  AHX11239.1 285 FEKTIEKDIDRTIAILKRALRSSDIPVAEVDGVLLVGGSTKIGLIHRKISELFGKEkIISGINPETIVVMGAALFGSFLNG-RNPEKIVLLDVLPLSLG 382
                 ******************************************************7625799********************.88999************ PP

                 EEETTTEEEEEESTTCBSSEEEEEEEEESSTTSSSEEEEEEESSSSBGGGSEEEEEEEEECESSCSTTCSEEEEEEEEETTSCEEEEEEETTTCCEEEE CS
       HSP70 396 ietlggvmtkliernttiptkksqvfstaadnqtaveievlqgerelvkdnkllgsfeldgippaprGvpqieVtfdidanGiltvsakdketgkeeei 494
                 ietl+g ++++i +   ip ++sqv + a d+qt+++i+vlqgerel+kdn++l++f+l+++p +p+G+ +ieVtf+id++Gil+vsak+  tgk +ei
  AHX11239.1 383 IETLDGTIERIIMKDSPIPIRQSQVLTNAVDGQTSFKIHVLQGERELAKDNRSLAEFTLNELPSLPAGKARIEVTFSIDEDGILKVSAKELITGKIQEI 481
                 *************************************************************************************************** PP

                 EEECCSSSBHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGSTHHHHHHHHHHHHHHHCHTTSSCHHHHHHHHHHHHHHHHHH CS
       HSP70 495 tieaseglseeeiekmvkdaeesaeedkkkkeaieakneaeelvyslekkleeeaekvseaekekvesaieeLkeeleeeekeeieakteelkkvveki 593
                 +++ + gl+ +  ++m++d+ ++ eed ++++ iea+ +a+++++ ++++++e+++ +  +e+ek+ + ++ +++++e+ ++ +i++ teel+k+v ++
  AHX11239.1 482 EVNPHYGLNRDIADQMIRDSFANLEEDVAQRSVIEAQCHADRVLKVVRRAIKENGNLLIGNEAEKIAEYTKTVEASMEKCDSIKIRESTEELEKIVDPF 580
                 ***********************************************************************************************9998 PP

                 HHH CS
       HSP70 594 aek 596
                  ++
  AHX11239.1 581 LKR 583
                 876 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0   0.00036       1.3       4      48 ..      18      68 ..      15      91 .. 0.79
   2 !   53.0   0.0   6.1e-18   2.2e-14      83     317 ..     121     358 ..     105     365 .. 0.82
   3 ?   -2.4   0.2      0.44   1.6e+03     217     240 ..     463     486 ..     451     533 .. 0.59
   4 ?   -0.2   0.1     0.097   3.5e+02      72     118 ..     492     538 ..     487     558 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00036
                EEEEE-SSEEEE..EETTTEEEEEE.......ES-EEEETTT--EEEESHHHHT CS
    MreB_Mbl  4 lgiDLGtantlv..yvkgkgivlne.......psvvAikkktkkvlavGeeAkk 48
                +giD Gt+n l+  ++ +k +v+ +       ps++A++ k    + vG+eAkk
  AHX11239.1 18 VGIDFGTTNSLIsvFQDEKCVVIPQesgknflPSLIAVQDK---NIIVGKEAKK 68
                79*******99755889999999764555566788888765...4779999998 PP

  == domain 2  score: 53.0 bits;  conditional E-value: 6.1e-18
                 HHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EEEE.EE-SS-EEEEEEETTEEEEEEEE.....S- CS
    MreB_Mbl  83 kkvkkkkslskprvvicvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnmvv.diGggttevavislggivtsksv.....rv 175
                 k ++k    +  + v++vP   ++ +r A+k+aa+  G + + l++ep aAA+  g++ ++ +g+ vv d+Gggt +++++ +   + + s      ++
  AHX11239.1 121 KSAEKYLGHAVRNAVVTVPAYFDNTSRSAIKDAATISGLNVIRLLSEPTAAALFYGIDEKREEGKYVVyDLGGGTFDISILEFHRGIFKVSCsdgddHL 219
                 444444445667899*************************************************97766************987555555542333479 PP

                 SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHHEEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHH CS
    MreB_Mbl 176 aGdeldeaiikyirkkynlliGertaekikieigsavkeeeeekmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivd 274
                 +Gd++d  +++++ +k++l +  ++  +  ++  + +kee +++ +i      +     + v+ e+ ++++++ + + +  +k++L++     a     
  AHX11239.1 220 GGDDFDLRLMEHLIQKHELHLSGEEKVHF-LDFCKEIKEELAHEDRIVRYFSYQENDACIDVTLEDFEKTIEKDIDRTIAILKRALRSSDIPVAE---V 314
                 *******************9965543333.45677777777777777777778888999***************************988766543...3 PP

                 H-EEEESGGGGSBTHHHHHHHHHSS-.EEE-SSTTTHHHHHHHH CS
    MreB_Mbl 275 rgivltGGgallkgldkllseetglp.vkvaedpltcvakGtgk 317
                  g++l+GG++++  +++ +se +g + ++ + +p t v+ G++ 
  AHX11239.1 315 DGVLLVGGSTKIGLIHRKISELFGKEkIISGINPETIVVMGAAL 358
                 7*********************98761555679******99875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 0.44
                 HHEEEEEEEETTTTCEEEEEEEHH CS
    MreB_Mbl 217 eekmeikGrdlvtglpkevevsse 240
                 +  ++++ ++l+tg  +e+ev+ +
  AHX11239.1 463 DGILKVSAKELITGKIQEIEVNPH 486
                 555666667777777777666643 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 0.097
                 HHHHHHHHHHHHHHHTSS-SS--EEEEEE-SS--HHHHHHHHHHHHH CS
    MreB_Mbl  72 evaeellkyfikkvkkkkslskprvvicvPsgiteverrAvkeaakk 118
                 ++a+++++  + +++++ + ++     c    + +v rrA+ke  + 
  AHX11239.1 492 DIADQMIRDSFANLEEDVAQRSVIEAQCHADRVLKVVRRAIKENGNL 538
                 67888999999988888777777777888999999999999987654 PP

>> BcrAD_BadFG  BadF/BadG/BcrA/BcrD ATPase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.2   0.0    0.0035        13       1      30 [.      18     113 ..      18     158 .. 0.66
   2 !    9.3   0.0   0.00019      0.69     194     267 .]     289     360 ..     273     360 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0035
                  EEEEE-SSEEEEEEEETTTEEEEEEEE--..................................................................T CS
  BcrAD_BadFG   1 vGiDgGsTttkavlmdekgevlgrgitns..................................................................a 30 
                  vGiD G+T     ++++++ v+    ++                                                                   +
   AHX11239.1  18 VGIDFGTTNSLISVFQDEKCVVIPQESGKnflpsliavqdkniivgkeakkyknyipsikriiatkenlvipnactintqtqdpqsnyaltigyaS 113
                  8*****************997766666655666666666666665555555555555555555555555555555555555555555555555553 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00019
                  HHHHHHHHHHHHHHHHHHTT---SS...EEEESGGGG-HHHHHHH.....HHHH-S-EE--GGGGGHHHHHHHHHH CS
  BcrAD_BadFG 194 Ilaglhraialrvialisrsggvtde..vtltGGvakneaavkelrklvkenygevkininpdsiytgalGAalfA 267
                  I +++ r ia +  al+s+   v +   v+l+GG  k       +   ++e +g++ki   + ++   ++GAalf+
   AHX11239.1 289 IEKDIDRTIAILKRALRSSDIPVAEVdgVLLVGGSTKI----GLIHRKISELFGKEKIISGINPETIVVMGAALFG 360
                  5556666666666666666666655588**********....4456778*************************96 PP

>> SLBP_RNA_bind  Histone RNA hairpin-binding protein RNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   9.2e-05      0.33      10      35 ..      57      82 ..      51      98 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.2e-05
  SLBP_RNA_bind 10 qkqIdlGKntegYerYlkavpkekrk 35
                    k+I +GK+ ++Y++Y+  +++   +
     AHX11239.1 57 DKNIIVGKEAKKYKNYIPSIKRIIAT 82
                   69***************999976555 PP

>> UL16  Viral unique long protein 16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0     8e-05      0.29      41     100 ..     257     316 ..     237     334 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 8e-05
        UL16  41 envtedeiigvaftwqhnesvvdlwlyqndtvirnfsdittnilqdglkmrtvpvtklyt 100
                 e+++ ++ i   f++q n++ +d+ l + +  i +  d t  il+  l+   +pv+++  
  AHX11239.1 257 EELAHEDRIVRYFSYQENDACIDVTLEDFEKTIEKDIDRTIAILKRALRSSDIPVAEVDG 316
                 555555556678*******************************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (599 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.65u 0.29s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 4018.26
//
Query:       AHX11240.1  [L=152]
Description: dnaJ domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.6e-05   23.8   0.3      8e-05   22.7   0.3    1.6  1  DnaJ           DnaJ domain
     0.0013   19.2   3.5     0.0013   19.2   3.5    2.0  2  HSCB_C         HSCB C-terminal oligomerisation domain
  ------ inclusion threshold ------
       0.12   12.1   0.9        1.1    9.0   0.1    2.2  2  Endonuc-PvuII  Restriction endonuclease PvuII
        2.6    8.6   5.0         13    6.3   0.3    2.7  3  COX16          Cytochrome c oxidase assembly protein COX16


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3   1.8e-08     8e-05       1      61 [.       7      64 ..       7      65 .. 0.89

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 1.8e-08
                HHHHHHTSSTT..G-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHH CS
        DnaJ  1 dyYeiLgvskd..asedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkq 61
                +y+eiLg+++    s  e+ ++Y +l +k+     ++d ++++k  +in+Ay +L+dp +R+q
  AHX11240.1  7 NYFEILGLKQRfkLSPGELENEYLRLQKKL-----REDDQSDNKISQINKAYFFLKDPVNRAQ 64
                79********95558999************.....356668999*****************97 PP

>> HSCB_C  HSCB C-terminal oligomerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.1      0.94   4.2e+03      47      52 ..      33      38 ..      23      58 .. 0.47
   2 !   19.2   3.5   2.9e-07    0.0013       2      75 ..      80     146 ..      79     147 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.94
                HHHHHT CS
      HSCB_C 47 eeafek 52
                ++ +++
  AHX11240.1 33 QKKLRE 38
                333311 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 2.9e-07
                 -HHHHHHHHHHHHHHHCGGGSSSHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHH CS
      HSCB_C   2 dpefLmevMelrEeleeaeeaadkeeleelkaeveerieeleaeleeafekkdleaaadllrrlrYlekikeei 75 
                 ++e+L ++ el E+l+e  e  +     e   +vee+ +  ++ +e+afek+++  a  + + l+Y++k++++i
  AHX11240.1  80 PMELLSKIIELEEKLAEK-E--S----PETVTAVEEMYKVHLELMETAFEKEEYGIADSHRVALKYITKLRNRI 146
                 6899***********999.3..3....3567788999999999999999999********************98 PP

>> Endonuc-PvuII  Restriction endonuclease PvuII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00024       1.1     101     137 ..       9      45 ..       5      57 .. 0.82
   2 ?    1.8   0.1     0.041   1.8e+02     106     130 ..     106     130 ..      81     146 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00024
  Endonuc-PvuII 101 yknielkeiyrlkpesleskfsewekkvrdeggkdin 137
                    ++ + lk+ ++l+p +le+ + + +kk+r++ + d  
     AHX11240.1   9 FEILGLKQRFKLSPGELENEYLRLQKKLREDDQSDNK 45 
                    667789***********************87766544 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.041
  Endonuc-PvuII 106 lkeiyrlkpesleskfsewekkvrd 130
                    ++e+y+++ e +e+ f++ e  + d
     AHX11240.1 106 VEEMYKVHLELMETAFEKEEYGIAD 130
                    6789999999999999988776664 PP

>> COX16  Cytochrome c oxidase assembly protein COX16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   0.3     0.003        13      50      68 ..      19      40 ..       2      50 .. 0.72
   2 ?    3.7   0.2      0.02        91      36      65 ..      88     117 ..      74     125 .. 0.81
   3 ?   -1.5   0.0      0.85   3.8e+03      16      30 ..     134     148 ..     133     151 .. 0.81

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.003
       COX16 50 kv...dleeeyerlqakldldd 68
                k+   +le+ey rlq+kl +dd
  AHX11240.1 19 KLspgELENEYLRLQKKLREDD 40
                4455589**********66665 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.02
       COX16  36 lskeealelkkkrrkvdleeeyerlqakld 65 
                 ++ ee+l++k++++ v+  ee +++  +l 
  AHX11240.1  88 IELEEKLAEKESPETVTAVEEMYKVHLELM 117
                 677999999*******99999999876545 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.85
       COX16  16 fgLteftqlryevrd 30 
                 ++L+++t+lr+  + 
  AHX11240.1 134 VALKYITKLRNRIHA 148
                 689999**9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1100.16
//
Query:       AHX11241.1  [L=119]
Description: iron-sulfur cluster assembly accessory family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.2e-11   43.4   0.0    4.2e-11   43.0   0.0    1.1  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis
  ------ inclusion threshold ------
       0.52   10.4   2.5        1.1    9.3   0.0    2.2  2  DUF1573      Protein of unknown function (DUF1573)


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.0   4.7e-15   4.2e-11       3     111 .]       6     115 ..       4     115 .. 0.89

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 4.7e-15
                  EEE-HHHHHHHHHHHHCTTEC......EEEEEECCTSCCGGS.TT.EEEEEEEEESSTSTTTEEEEE.E....TTEEEEEEGGGHHHS.TTEEEEEEE CS
  Fe-S_biosyn   3 itlteaAaeklkkllaedkke......lrLdvddgggpyskggCsiggkyslvlvdeedeeydevle.s....nggkvyvksyslvfldeglvldfve 89 
                  it+++ A ekl++l++++ ++      + +++  +g       C  g +y++++vde+ ++ydev+e      + + ++++++++  +  g+ +d++e
   AHX11241.1   6 ITVSALALEKLSELIENRRNTgkstlgIKVALVSKG-------CG-GNEYEMEYVDEP-QKYDEVVEyVdksgATIMIFIDPKTMFKI-LGTYIDYEE 93 
                  9****************9999999*88888888888.......**.************.******99523322346789999999988.8******** PP

                  ETTEEEEEEETCCEEEEEEEEE CS
  Fe-S_biosyn  90 dlgtlgLksdngilddnvglgk 111
                  +++ +g+ ++n+  + ++g+gk
   AHX11241.1  94 TKFKSGFVFKNPGEKARCGCGK 115
                  ********************97 PP

>> DUF1573  Protein of unknown function (DUF1573)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00013       1.1      26      69 ..      24      67 ..      20      87 .. 0.87
   2 ?    0.6   0.9     0.067     6e+02      15      31 ..      92     108 ..      78     117 .. 0.75

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00013
     DUF1573 26 tNtgkaplvitnvktsCgCttpeypkepiapGesgkikvtfnak 69
                +Ntgk++l i+ +  s gC   ey++e +   ++ +  v++  k
  AHX11241.1 24 RNTGKSTLGIKVALVSKGCGGNEYEMEYVDEPQKYDEVVEYVDK 67
                7**************************99988888777777655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.067
     DUF1573  15 egekvtatFeftNtgka 31 
                 e++k +  F f+N g++
  AHX11241.1  92 EETKFKSGFVFKNPGEK 108
                 56677778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (119 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 966.72
//
Query:       AHX11242.1  [L=140]
Description: nifU-like protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-55  184.6   0.3    8.1e-55  184.4   0.3    1.0  1  NifU_N    NifU-like N terminal domain


Domain annotation for each model (and alignments):
>> NifU_N  NifU-like N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.4   0.3   4.5e-59   8.1e-55       2     126 ..       3     125 ..       2     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 184.4 bits;  conditional E-value: 4.5e-59
                 SCHHHHHHHHSSSSBSS-TTSSS--EEEEEEETTTTEEEEEEEEEETTTTEEEEEEEEEESSHHHHHHHHHHHHHHTTSBHHHHCCCCHHHHHHHHTCS CS
      NifU_N   2 ysdkvldhyknPrnvGvleeedakvgvgevgapacGDavrLqikvdeetdriedakFktfGCgsaiAssslltelvkgktleealkitnkeiaeelggl 100
                 ys+ vldhy+nPrnvG l++++++vg+g vgapacGD+++Lqi+v++e + i+dakFktfGCgsaiAsssl+te ++gktle+a+ki+n+eia+el+ l
  AHX11242.1   3 YSESVLDHYNNPRNVGALDKKKKNVGTGVVGAPACGDVMKLQIEVNDE-GCIVDAKFKTFGCGSAIASSSLATEYIIGKTLEDAEKIKNTEIASELN-L 99 
                 9**********************************************7.************************************************.* PP

                 CSSSCHCSCHHHHHHHHHHHHHHHHC CS
      NifU_N 101 pkeklhcsvlaedalkaavkkYkakk 126
                 p+ k+hcs+laeda+kaa++++k+k+
  AHX11242.1 100 PPIKMHCSMLAEDAIKAAIRDFKEKQ 125
                 ************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       363  (0.0202465); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1185.26
//
Query:       AHX11243.1  [L=402]
Description: cysteine desulfurase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-83  279.8   0.0    3.8e-83  279.5   0.0    1.0  1  Aminotran_5      Aminotransferase class-V
      1e-06   28.3   0.0    1.1e-06   28.1   0.0    1.1  1  Beta_elim_lyase  Beta-eliminating lyase
     0.0019   17.6   1.0      0.003   16.9   1.0    1.2  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
     0.0057   15.4   0.1     0.0088   14.8   0.1    1.4  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  279.5   0.0   8.5e-87   3.8e-83       1     369 [.       3     365 ..       3     366 .. 0.96

  Alignments for each domain:
  == domain 1  score: 279.5 bits;  conditional E-value: 8.5e-87
                  EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC..-TTTSEEEEETT CS
  Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslars..lkpgdeivvtea 96 
                  +++d++ tt++ ++Vl+++ ++++    n+h+ +h +g++a +ave+arekva+lina+  ++i+ftsG+te++nl+++++      +++++++++++
   AHX11243.1   3 VFFDNQSTTRTDPAVLKEMIKFFE-APCNPHSRTHIYGWQAEAAVENAREKVAQLINASP-KDIVFTSGATESNNLAIKGAVTFyhSDKKNHVITVAT 98 
                  689*******************87.899*******************************7.*******************98888899********** PP

                  SHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESE CS
  Aminotran_5  97 ehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDf 194
                  eh++ l  +++l+ + g+kv+++p++++g +dld l++ +++ t +v+i++++n++G+iqp++eig+++k++ +++++Daaqa+g+ip+dv+++++ +
   AHX11243.1  99 EHKCVLDSCRHLE-EIGIKVTYLPVQKNGIVDLDVLRESIKDSTIMVSIMAANNEIGVIQPIKEIGQICKEASVIFHTDAAQAFGKIPLDVEEMNISL 195
                  ************8.88********************************************************************************** PP

                  EEEETTTTTSSTT-EEEEEEHH.HHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_5 195 lafsghKllgPtGiGvlyvrke.llekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerl 291
                  +++sghK++gP G+G+ly+r++    +l p+  gg+       +e++       +++GT +++ + glg+a+e+  ++++++  ++ k l+ +l+  +
   AHX11243.1 196 MSISGHKIYGPMGVGALYIRRKnPRIRLTPVFNGGG-------QERG-------MRSGTVPTPLVAGLGKAAEIA-AQNMQEEYNRIKYLSTKLYGII 278
                  *******************98625668899999999.......8999.......899****************99.9999****************** PP

                  CT.STTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHH CS
  Aminotran_5 292 ks.lpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevd 369
                  k+ +p++ l+g d+++r ++ ++++f++v+ e + +++ +  I v+sG++c+    +p+++++al        +++R+S+++ynteee++
   AHX11243.1 279 KAgIPDIVLNG-DPEQRLPGNLNISFPYVEGESIIMAITD--ISVSSGSACTsaslEPSYVLRALGvgddlahSSIRFSIGRYNTEEEIE 365
                  *99******99.9*******************99777665..**********9999999999999899********************98 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   2.5e-10   1.1e-06      34     234 ..      46     275 ..      35     379 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 2.5e-10
                      HHHHHHHHHHHTT-S..EEEEES-HHHHHHHHH.....HHH--TTEEEEEETT-HHH.HSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS- CS
  Beta_elim_lyase  34 vnrLedavaelfgke..aalfvpqGtaAnsill.....killqrgeevivtepahih.fdetgaiaelagvklrdlknkeaGkmdlekleaaik 119
                      v++  ++va+l+ +    ++f+   t +n++++      ++  +++ vi   + h +  d ++ ++e+ g+k++ l+ +++G +dl+ l++ ik
       AHX11243.1  46 VENAREKVAQLINASpkDIVFTSGATESNNLAIkgavtFYHSDKKNHVITVATEHKCvLDSCRHLEEI-GIKVTYLPVQKNGIVDLDVLRESIK 138
                      5667777788777643367888889********88887788877777777777665516666777766.78899***9999************* PP

                      -S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-H CS
  Beta_elim_lyase 120 evgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrd 212
                      +       + ++s+  +nn     +  ++ ++e+ +i+k+  + +h D+A  +    ++  +v+em   +  +++s+ K    ++G g l +r+
       AHX11243.1 139 DS------TIMVSIMAANNE----IGVIQPIKEIGQICKEASVIFHTDAAQAF---GKIPLDVEEMN--ISLMSISGHKI-YGPMGvGALYIRR 216
                      *3......66*********5....66788899*****************9644...56677777775..34577777774.4567777777777 PP

                      H.........................................HHHHHHHHHHHHT---S CS
  Beta_elim_lyase 213 del.....................................edylaerveqrkylggglr 234
                      ++                                       + ++e  +  kyl  +l+
       AHX11243.1 217 KNPrirltpvfngggqergmrsgtvptplvaglgkaaeiaAQNMQEEYNRIKYLSTKLY 275
                      64456666666666666666666666666666666666554444555555555555555 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.0   6.6e-07     0.003      41     150 ..      64     182 ..      40     193 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 6.6e-07
                      EEEESSHHHHHHHHHHH....TTTTTT-EEEEESSS-THHHHH...HHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE..EEEEEB-.GGGB- CS
  DegT_DnrJ_EryC1  41 aiavssGtaAlhlaLra....lgvgpgdeVIvpsltFvatana...vlelgakpvfvDvdpdtynidpaaieaaitert..kaIlpVh.lyGqv 124
                       + +s +t+++ la++        ++++ VI++++       +     e+g k+ ++ v+ +   +d + +++ i   t    I++++   G +
       AHX11243.1  64 IVFTSGATESNNLAIKGavtfYHSDKKNHVITVATEHKCVLDScrhLEEIGIKVTYLPVQ-KNGIVDLDVLRESIKDSTimVSIMAANnEIGVI 156
                      455666788888888865554556699999999999877665511155679999999998.7789**************887888886258*** PP

                      --HHHHHHHHHHCT-EEEEE-TT-TT CS
  DegT_DnrJ_EryC1 125 admdalkaiaakhglkvieDaAhAlG 150
                        ++++ +i+++  +++  DaA+A+G
       AHX11243.1 157 QPIKEIGQICKEASVIFHTDAAQAFG 182
                      *************************9 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1     2e-06    0.0088     152     238 ..      97     180 ..      51     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2e-06
                    TTS-HHH.HHHHHH..HT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTG CS
  Pyridoxal_deC 152 dqahssv.ekaalv..lgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAya 238
                    +  h +v +++  +  +g+k+ ++p+++ng++  + l++ i++      ++ +v   +     g    +ke+g+ic++  +  H DAA a
     AHX11243.1  97 ATEHKCVlDSCRHLeeIGIKVTYLPVQKNGIVDLDVLRESIKDS-----TI-MVSIMAANNEIGVIQPIKEIGQICKEASVIFHTDAAQA 180
                    444666644444441145678899****9988888888888654.....34.577777788899999*********************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       528  (0.0294495); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3079.64
//
Query:       AHX11244.1  [L=521]
Description: rrf2 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.9e-50  170.5   2.2      6e-50  170.2   2.2    1.1  1  Aminotran_5      Aminotransferase class-V
    2.6e-20   72.6   0.1    8.6e-20   70.9   0.1    2.0  1  Rrf2             Transcriptional regulator
    4.9e-05   22.7   0.1    7.7e-05   22.1   0.1    1.4  1  Beta_elim_lyase  Beta-eliminating lyase
    0.00089   18.7   0.0     0.0014   18.0   0.0    1.3  1  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00097   18.7   0.0     0.0022   17.6   0.0    1.6  1  HrcA_DNA-bdg     Winged helix-turn-helix transcription repres
     0.0089   14.8   0.0      0.015   14.0   0.0    1.3  1  Pyridoxal_deC    Pyridoxal-dependent decarboxylase conserved 


Domain annotation for each model (and alignments):
>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.2   2.2     2e-53     6e-50       1     371 []     157     509 ..     157     509 .. 0.90

  Alignments for each domain:
  == domain 1  score: 170.2 bits;  conditional E-value: 2e-53
                  EEEBTTTS----HHHHHHHHHHHHCTCCSSSSSSSHHHHHHHHHHHHHHHHHHHHHT-STGGGEEEESSHHHHHHHHHHHCCCC-TTTSEEEEETTSH CS
  Aminotran_5   1 iyldsaAttqkpqeVldalqeyytdynanvhrsvhhlgkeatkaveearekvaelinaeseeeiiftsGtteainlvalslarslkpgdeivvteaeh 98 
                  iy+d++Att   + +++++    +  + n+ +s+h+ g+ a + vee r  +++ +n ++e++++fts++tea+n+v +s++    +  + vv +++h
   AHX11244.1 157 IYMDNNATTTPLRYAVEKAYSIIR-TAYNP-SSIHRQGQVARERVEESRRAIKKHLNLNEEYDLVFTSSGTEANNMVFHSMG----N-YRHVVCSTDH 247
                  8********999999999888855.55566.8*************************************************4....4.45566789** PP

                  GGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--..TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTTTS---HHHHTESE CS
  Aminotran_5  99 hanlvpwqelakrtgakvkvipldeegeldldeleklln..ektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavghipidvkklgvDf 194
                   + l    ++a r  +kv    +d++g ++ld+le  l+  +   l++++ ++++tG+iqp++ + ++akk++alv++Da+qav  i+  +++++ Df
   AHX11244.1 248 SSVL----RAA-RNPIKV---DVDKNGIIKLDHLERILEeaPGKTLISVSLANSETGIIQPLDLLLDIAKKHEALVHTDAVQAVSRIHCRFNETQPDF 337
                  ****....444.334444...7899*************6347789***************************************************** PP

                  EEEETTTTTSSTT-EEEEEEHHHHHTS..SS.STTSEEEEETTEEEEHCTTGGGS.SS--HHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHC CS
  Aminotran_5 195 lafsghKllgPtGiGvlyvrkellekleplllggemveevsleettfaeapskfeaGTpnvagiiglgaaleyleeigleaiekhekelaeyllerlk 292
                  +++s+hK+ g  G G+l+ +k+   +l  l lgg+       +e++       +++GT+n+a+i ++g a+ ++ +  ++++++      ++  e l+
   AHX11244.1 338 ITLSSHKMGGIIGAGALVYKKSRFAELTALILGGN-------QEKG-------LRSGTENIAAISAFGVAATFI-NASIKSMKNIRFLRDHMESEILS 420
                  ***********************************.......9999.......99*******************.88999888877777777777777 PP

                  TSTTEEEES.-B-CTCBSEEEEEETTCSHHHHHHHHHHTTEEEEEE-TTT....HHHHHHTT.S.......-EEEEE--TTS-HHHHHHH CS
  Aminotran_5 293 slpgvrlygpdkaerrasivsfnfkgvhaedvatlLdeegIavrsGhhca....qplmkrlale.......gtvRaSlyiynteeevdrl 371
                   +++  ++g ++ er +++ ++ +++++ +   +  d +g++v+ G++c+    + ++++la+        +++R+Sl+i ntee+v++l
   AHX11244.1 421 RMKSAVVVG-KESERLPNTSCIIIPEIDGATQLMHFDIHGVCVSNGSACSsgqtEASHVLLAMGfdhkmakSAIRISLGISNTEEDVNKL 509
                  788888888.799*************************************998877888888879999999****************987 PP

>> Rrf2  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9   0.1   2.9e-23   8.6e-20       1      83 []       1      83 [.       1      83 [. 0.97

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 2.9e-23
                X---HHHHHHHHHHHHHHHSSTCC-.B-HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT-TCEEESSHCCCSBHHHHHHHH CS
        Rrf2  1 MklsskteyalhallyLakeeeeep.vsseeiaerqnispsylekilakLrkaglvksvrGkgGGyrLakppeeItlldvvrav 83
                M l++k +ya+ a +++a+++ +++ ++++eia+rqnis+++le il  Lrk+g+++s  G+gGGy+Lak+p++I l ++++av
  AHX11244.1  1 M-LTAKARYAIMASVDIAMHAVSGKyIKTSEIASRQNISEKFLELILPSLRKQGILESLLGPGGGYKLAKDPDTIFLMQIIKAV 83
                5.899***************998888********************************************************97 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.1   2.6e-08   7.7e-05      44     212 ..     212     358 ..     151     438 .. 0.80

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 2.6e-08
                      HTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSB CS
  Beta_elim_lyase  44 lfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevgaheekiklisltvTn 137
                      l +    +f+ +Gt An++ +  +          +  h+   +    +  a  ++++++ +++G ++l+ le++++e  a  +   lis+  +n
       AHX11244.1 212 LNEEYDLVFTSSGTEANNMVFHSMG---------NYRHVVCSTDHSSVLRAARNPIKVDVDKNGIIKLDHLERILEE--A--PGKTLISVSLAN 292
                      44444567*************9999.........667888888888888888999**********************..7..8899*****999 PP

                      TTTTTB---HHHHHHHHHHHHHCT-EEEEEETTHHHHHHHHTS-CHHHHTTSSEEEEESSSTT--SS-.EEEEE-H CS
  Beta_elim_lyase 138 ntagGqvvsleelrevaaiakkygiplhlDgARfanaakslgeivkemfsyvDsvtmslkKdllanvG.gvlafrd 212
                          G + +l+ l    +iakk++  +h D+   + a+  + +   e     D +t+s  K +++ +G g l+ ++
       AHX11244.1 293 SE-TGIIQPLDLL---LDIAKKHEALVHTDA---VQAVSRIHCRFNET--QPDFITLSSHKMGGI-IGaGALVYKK 358
                      85.8998887766...6789**********8...57777777777775..457777777776555.5544444444 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   4.8e-07    0.0014      42     149 ..     219     323 ..     190     345 .. 0.86

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 4.8e-07
                      EEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTE.EEEEEB-GG....GB---HHHH CS
  DegT_DnrJ_EryC1  42 iavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitert.kaIlpVhly....Gqvadmdal 130
                      + +ssGt+A+ ++ + +g    + V+  +       ++vl++  +p+ vDvd +   i+ +++e+ ++e   k  + V l+    G +  +d l
       AHX11244.1 219 VFTSSGTEANNMVFHSMGNY--RHVVCST-----DHSSVLRAARNPIKVDVD-KNGIIKLDHLERILEEAPgKTLISVSLAnsetGIIQPLDLL 304
                      56899999999999998877..4554432.....3468999999********.7899************98899999999655548899***** PP

                      HHHHHHCT-EEEEE-TT-T CS
  DegT_DnrJ_EryC1 131 kaiaakhglkvieDaAhAl 149
                       +ia+kh+  v  Da +A+
       AHX11244.1 305 LDIAKKHEALVHTDAVQAV 323
                      *****************98 PP

>> HrcA_DNA-bdg  Winged helix-turn-helix transcription repressor, HrcA DNA-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   7.5e-07    0.0022      14      64 ..      16      66 ..       1      78 [. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 7.5e-07
  HrcA_DNA-bdg 14 ielyrkkkravKgeeiAevlkrneGtvRNqlqsLkalgLvegvpGPkGGYk 64
                  i ++  +++ +K+ eiA+  +  e  +  +l sL+  g++e+  GP GGYk
    AHX11244.1 16 IAMHAVSGKYIKTSEIASRQNISEKFLELILPSLRKQGILESLLGPGGGYK 66
                  444556699*****************************************8 PP

>> Pyridoxal_deC  Pyridoxal-dependent decarboxylase conserved domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.0   0.0     5e-06     0.015     148     281 ..     241     358 ..     225     365 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 5e-06
                    EEEETTS-HHHHHHHHHHT-EEEEE--BTTTBB-HHHHHHHHHHHHCTT.EEEEEEEEBS-TTT-BB--HHHHHHHHHHCT-EEEEE-TTGGGGGG CS
  Pyridoxal_deC 148 lytsdqahssvekaalvlgvklrvipldengklrgaalekaieedkekGlipffvvatlGttvlgaFddlkelgdicekydlwlHvDAAyaGsafi 243
                    +++s   hssv +aa+      + + +d+ng++  ++le+ +ee+  k l    + + l  + +g    l+ l di +k++  +H DA  a s + 
     AHX11244.1 241 VVCST-DHSSVLRAARN----PIKVDVDKNGIIKLDHLERILEEAPGKTL----ISVSLANSETGIIQPLDLLLDIAKKHEALVHTDAVQAVSRIH 327
                    46666.58888888874....57899******************998844....457899999****************************99999 PP

                    SGGGGGGGTTGGGESEEEEECCCCTS--SS-EEEEESS CS
  Pyridoxal_deC 244 cpeirhllkgieradSitvnphKlllvlldcsalivkd 281
                    c++  +        d it++ hK++++ ++++al++k+
     AHX11244.1 328 CRFNET------QPDFITLSSHKMGGI-IGAGALVYKK 358
                    988765......346677777877665.5666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (521 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       770  (0.0429472); expected 358.6 (0.02)
Passed bias filter:                      577  (0.0321825); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3973.68
//
Query:       AHX11245.1  [L=37]
Description: hypothetical protein NHE_0286 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.23s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 318.77
//
Query:       AHX11246.1  [L=542]
Description: binding--dependent transport system inner membrane component family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.9e-05   24.5  46.9    0.00025   20.8  15.4    3.6  4  BPD_transp_1    Binding-protein-dependent transport system in
  ------ inclusion threshold ------
      0.039   14.2   0.1      0.097   12.9   0.1    1.6  1  Chordopox_A13L  Chordopoxvirus A13L protein
       0.41   10.9   0.1       0.41   10.9   0.1    4.4  5  DUF3951         Protein of unknown function (DUF3951)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.5      0.32   1.9e+03      26      68 ..      11      58 ..       3      61 .. 0.56
   2 !   17.8  23.5   3.5e-07    0.0021       4     175 ..      59     242 ..      56     247 .. 0.79
   3 ?   -2.6  10.9      0.66     4e+03      21      72 ..     273     325 ..     272     334 .. 0.75
   4 !   20.8  15.4   4.2e-08   0.00025       4     176 ..     324     516 ..     321     519 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.32
  BPD_transp_1 26 vllslPsfvlaillvlvf.......vilsilghlilp.viillllsaapyv 68
                  +l+  P++ l+++    f       v++  lg ++l  +iil+ ++++ +v
    AHX11246.1 11 FLFFAPTLSLILPS---FnsyepggVFNWLLGEYVLNtLIILSGVGFLTFV 58
                  44444444444443...0344777644445778888867777777766665 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 3.5e-07
  BPD_transp_1   4 lGilaa...lnrnkkldkllrpliivllslPsfvlaillvlvf..............vilsilghlilp.viillllsaapyvrlirraalrslpkd 82 
                   +G+ aa   ++ +++++ llr+l +++l++P ++ a+  v +f               ++  +    l+ +i+++ + + pyv+++  a + s   +
    AHX11246.1  59 FGVGAAcavTFLRFPGRGLLRVLLFLPLAVPGYITALSYVQFFdfssdfslffrevfGFKHLFRIQSLYgAIFVMSVAFYPYVYMFSLARITSA-GN 154
                   5555556599************************888877666888888998899887777777556664777788888888777777666665.58 PP

  BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleai.lgydyseisnggvlalviavlllnlvadil 175
                   +v  +r +G s   ++  vv+P a p i+ gl l+++ ++ ++ ++ f+g    l+t+++ ++  ++ ++  +  g+  l++++l +++++ +l
    AHX11246.1 155 FVAISRSCGKSFLATMLEVVIPVARPAIVGGLTLVLMEVISDFGIMQFFG----LQTVVTGIYrKWFLLNDVI--GASRLILFLLTFVALMIFL 242
                   **************************************************....8877776641455555444..6666666666666666555 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.66
  BPD_transp_1  21 rpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlir 72 
                   ++++ivl+ lP f ++++++ ++ + l++  ++ l  +i++ +++a ++ +++
    AHX11246.1 273 MTVTIVLSLLPLFGIGFPIFSLIsMTLNATPDYQLFSLIIGSVQIALFASFLT 325
                   7999************9999888755556667777777777777777666654 PP

  == domain 4  score: 20.8 bits;  conditional E-value: 4.2e-08
  BPD_transp_1   4 lGilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvf............vilsilg.hlilpviillllsaapyvrlirraalrslpkd 82 
                   l il+a     ++r+kk+  +l  ++++++s+P +v+++ ++ +f            + ++il+  ++++++  +++ ++++ +  ++++++ +p++
    AHX11246.1 324 LTILIAfffvyMKRKKKIGAALFQMSNLGYSIPGLVVGMGIINFFtssssilsyftfSGFQILTaGTFTALMYSYIFRFLALGCNSIQSGIEKIPSE 420
                   556666666689*******************************99****88888777444444424555577777777777788889********** PP

  BPD_transp_1  83 lveaaralGasrwqifrkvvlPnalppiitglilafggllggavlleflgswpG..lgtllleailgydyseisnggvlalviavlllnlvadilq 176
                      ++r+ G + +    +v  P++++++++g+il f   l++  +++++   +   ++ ++ e      y+ +++ ++++++i+++++++++  ++
    AHX11246.1 421 ISWTMRLVGKNSFLDAIQVYSPMLIRYLVSGVILIFLDTLKELPATLLVRPFNFetMSIRVYELVVDERYNDAAVPALIMTAICLAVILFLIKSMY 516
                   ************************************************983331225555555555555555559999999999999999998887 PP

>> Chordopox_A13L  Chordopoxvirus A13L protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1   1.6e-05     0.097       4      30 ..     497     523 ..     495     528 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.6e-05
  Chordopox_A13L   4 dlllliiCvaivglivYgiYnrkketq 30 
                      l++ +iC a++ +++ ++Y r+ ++ 
      AHX11246.1 497 ALIMTAICLAVILFLIKSMYSRGLHNR 523
                     589******************987655 PP

>> DUF3951  Protein of unknown function (DUF3951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.6       1.3   7.9e+03      12      25 ..      45      58 ..      41      64 .. 0.71
   2 ?   10.9   0.1   6.8e-05      0.41      14      37 ..     228     252 ..     219     254 .. 0.89
   3 ?   -3.5   0.8       2.1   1.3e+04      10      20 ..     274     284 ..     272     294 .. 0.59
   4 ?    1.4   3.8     0.064   3.8e+02       5      30 ..     311     337 ..     307     341 .. 0.76
   5 ?   -0.8   0.8      0.29   1.8e+03       6      22 ..     495     511 ..     493     516 .. 0.67

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.3
     DUF3951 12 tlvilviIgfvayk 25
                tl+il  +gf+++ 
  AHX11246.1 45 TLIILSGVGFLTFV 58
                67777777888775 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 6.8e-05
     DUF3951  14 vilviIgfvayklFvkkesidi.yY 37 
                 +il+++ fva ++F +k s +  +Y
  AHX11246.1 228 LILFLLTFVALMIFLEKTSRQNaFY 252
                 699****************998787 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 2.1
     DUF3951  10 lltlvilviIg 20 
                  +t+v++++  
  AHX11246.1 274 TVTIVLSLLPL 284
                 67788777633 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.064
     DUF3951   5 tiGillltlvilviIgfvayk.lFvkk 30 
                  iG + ++l+ +++ +++a+  +++k+
  AHX11246.1 311 IIGSVQIALFASFLTILIAFFfVYMKR 337
                 589999999999999999984145555 PP

  == domain 5  score: -0.8 bits;  conditional E-value: 0.29
     DUF3951   6 iGillltlvilviIgfv 22 
                 + +l++t++ l +I f+
  AHX11246.1 495 VPALIMTAICLAVILFL 511
                 56788888777766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       737  (0.0411066); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.25s 00:00:00.80 Elapsed: 00:00:00.38
# Mc/sec: 4280.37
//
Query:       AHX11247.1  [L=195]
Description: ribosomal protein L25, Ctc-form [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-21   76.4   0.3    3.3e-21   75.4   0.3    1.4  1  Ribosomal_TL5_C  Ribosomal protein TL5, C-terminal domain
    2.2e-19   69.7   0.0    6.5e-19   68.2   0.0    1.8  2  Ribosomal_L25p   Ribosomal L25p family


Domain annotation for each model (and alignments):
>> Ribosomal_TL5_C  Ribosomal protein TL5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.4   0.3   3.7e-25   3.3e-21       3      84 ..     100     182 ..      99     184 .. 0.95

  Alignments for each domain:
  == domain 1  score: 75.4 bits;  conditional E-value: 3.7e-25
                      EEEEEEEEES..--TTTTTTSEEEESSSEEEEESSTTS--SSEEEE-TT--SSBEEETTTS--SSS-EE.SS-TTSEEEEEE- CS
  Ribosomal_TL5_C   3 tveVpvhfvgeeespgvkkggvleqvlreveveclpkdlPeeievDvsgleigdsihvsdlklpegvel.ltdpdevvvsvva 84 
                      ++eVp++f+++e+s+++k g vl++v+r+  v+c  ++lP++i vD+++ ++gdsi++sdl + +gv+   +d+d vv+++v 
       AHX11247.1 100 KFEVPLNFINKEKSEAIKLGAVLNIVRRTALVKCSSSNLPKSIPVDIEHSKVGDSIKLSDLMFADGVTPiAKDADSVVATIVG 182
                      579*****************************************************************956679*******86 PP

>> Ribosomal_L25p  Ribosomal L25p family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.0   7.2e-23   6.5e-19       2      81 .]       6      91 ..       5      91 .. 0.94
   2 ?   -1.9   0.0      0.56   5.1e+03      54      54 ..     132     132 ..     102     160 .. 0.51

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 7.2e-23
                    EEEECTS.SCCCHHHHHHTTEEEEEEEESSSCEEEEEEEHHHHHHHCH....CSEEEEEETT..CEEEEEEEEEETTTTCEEEEEE CS
  Ribosomal_L25p  2 kaekRte.gkgaarrlRregkvPavlyGggkepisisvdakelrkllkt...stlieLevdg..ekvllkdvqrhpvkdkilHvDF 81
                    + ++R   g +++r lR++g+vPav+yGgg e+isi+++ +e++k +++   +t++eL+  +  +kv+ k+++ hpv+ ++lH+DF
      AHX11247.1  6 EYSPRVAfGCRNTRILRESGFVPAVVYGGGAETISIALSVREVDKKISSlmsKTVVELSCGDvvHKVIPKAYELHPVTSAVLHLDF 91
                    5678977799*************************************87***********85689********************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.56
                     E CS
  Ribosomal_L25p  54 e 54 
                     +
      AHX11247.1 132 K 132
                     2 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      346  (0.0192983); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.19s 00:00:00.56 Elapsed: 00:00:00.33
# Mc/sec: 1772.80
//
Query:       AHX11248.1  [L=169]
Description: peptidyl-tRNA hydrolase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-35  123.1   0.0    1.2e-35  123.0   0.0    1.0  1  Pept_tRNA_hydro  Peptidyl-tRNA hydrolase
  ------ inclusion threshold ------
      0.041   13.3   0.1       0.78    9.1   0.0    2.0  2  R-HINP1I         R.HinP1I restriction endonuclease


Domain annotation for each model (and alignments):
>> Pept_tRNA_hydro  Peptidyl-tRNA hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.0   0.0   1.3e-39   1.2e-35      37     166 ..      27     153 ..       1     158 [. 0.84

  Alignments for each domain:
  == domain 1  score: 123.0 bits;  conditional E-value: 1.3e-39
                      EETTEEEEEEEESS-GGGHHHHHHHHHHHCT--..GEEEEEEETTSSTTEEEEEESS--TT-HHHHHHHHHHT-S-SEEEEEEE---ST-CGGH CS
  Pept_tRNA_hydro  37 kiegekvlllkPqtymNlsGeavkellkfykieseeilvvhDdldlplgkirlkkkgssgghnGlksiikklgtekfvRlriGIgrpekakkkv 130
                       +++ k++l+kP+t+mN+sG  +++l++fyk+++ ++lv+hDd dl +g+i++kk+gssgghnGlksi ++lg  +++R+r+G+g++e+  +++
       AHX11248.1  27 VTSSIKLYLFKPMTFMNNSGFPLARLVNFYKVHPCNVLVFHDDADLGFGRIKIKKGGSSGGHNGLKSIDSNLGR-DYWRFRFGVGKEEN--SNL 117
                      5677899*************************99**************************************98.5*********8865..56* PP

                      HHHCTSB-HHHH.HCHHHHHHHHHHCHHHHHHHTSCC CS
  Pept_tRNA_hydro 131 adyVLskfskee.ekleevlekaaealeellkeelea 166
                      a+yVLs+f++ e  +l++v+e +a+ +  ll+ ++e+
       AHX11248.1 118 AKYVLSSFTECEiGHLNKVFEFIAKNIILLLS-DIER 153
                      *********99956699999987777655554.3554 PP

>> R-HINP1I  R.HinP1I restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.01        92     165     191 ..      64      90 ..      39      98 .. 0.70
   2 ?    9.1   0.0   8.7e-05      0.78     103     140 ..     130     167 ..     112     169 .] 0.82

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.01
    R-HINP1I 165 vkisergslkigkvtiqrkggdggret 191
                 + + +  +l +g++ i++ g  gg + 
  AHX11248.1  64 LVFHDDADLGFGRIKIKKGGSSGGHNG 90 
                 4567788999******98777777654 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 8.7e-05
    R-HINP1I 103 ekeqakilnflkenkilvltdilkgrgdfaaewvlvaq 140
                     +k+++f+ +n il+l+di + +  f  +++ v +
  AHX11248.1 130 IGHLNKVFEFIAKNIILLLSDIERQKSTFLMDYMSVLN 167
                 4456899************************9998875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       272  (0.015171); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1467.62
//
Query:       AHX11249.1  [L=389]
Description: glutamate--cysteine ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   3.3e-105  351.9   2.7   4.6e-105  351.5   2.7    1.1  1  GshA      Glutamate-cysteine ligase


Domain annotation for each model (and alignments):
>> GshA  Glutamate-cysteine ligase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  351.5   2.7  2.6e-109  4.6e-105       4     366 ..       8     354 ..       6     374 .. 0.93

  Alignments for each domain:
  == domain 1  score: 351.5 bits;  conditional E-value: 2.6e-109
                 HHTSHHHHHHHHHHHHHHH---SEEEEEEEE-SS-EEEEEEESS---GGGS-GGGHHHHHHHHHHHHHHHSTT-SEEEEEE-S-SS-HHHHHHHHHHHH CS
        GshA   4 lleakakiekwfrkkwqehtapfysSvDlRnsgfKlapvDtNlfpaGfnnlnpeflplavqaaqeaiekicpeakklllipEnhtrNtfYlenvaalke 102
                 +l+ +++i +w ++k   +++ fy S D+Rn+gfK+apvD+N+fpaGf  +++e +  a++++ ++ +      k +lli+E+htrN+ Yl+nv alk+
  AHX11249.1   8 FLRYSEEIARWCQSKC--TRSLFYLSADIRNAGFKVAPVDVNMFPAGFHIISEESQMRAAHLIAKHYT-----NKIILLITESHTRNSQYLSNVLALKK 99 
                 56778999***98886..5689*******************************999988887766544.....5569********************** PP

                 HHHHTT-EEEEEE--TT--S-EEEE-SSS-EEEEEE-EEETTEE.EETTEE-SEEEEES--TT---GGGSS-SSEEES---TTGGGS-TTHHHHHHHHH CS
        GshA 103 ilekaglevrlgsleeeiteptelelssgekltleplvrkgerl.glkdfdpclillNnDlsagipeileeleqtllPpleaGWatRrKskhfkaYeev 200
                 ile ag ++ lg l ++          + ekl++++  r+g+++   ++  p+l++lNnD+ +  pe+l+++ q+ +P+  +GW++R Ks++f++Y++v
  AHX11249.1 100 ILEIAGNKLILGNLANQ----------RIEKLEMTKFHRSGNHIvIEDNVIPDLVILNNDMISEDPETLSNIIQPCIPSPLLGWYRRTKSHYFSHYQKV 188
                 ************99843..........445777888889999985677899************************************************ PP

                 HHHHHHHHT--GGGG---EEEEE---TTSSTTHHHHHHHHHHHHHHHHHHHHHHT--S---EEEEEE-GGG-EEEEEESSGGGGSS--HHHHHHHH-SS CS
        GshA 201 akefaklididpwlinplfekceevdfkekegeeklaekvdellakirekykeygikekPfvivKadaGTyGmgvmtvksaeevkelnrkqrnkmsvvk 299
                 ++ef+k +didpwl++p+ ++c+++df+ ++   kla++vde+++k+++ky++y+ik++Pfv++Ka++G yG+g+ t++++++v ++n+k+rnk++++k
  AHX11249.1 189 VEEFSKAFDIDPWLLHPYSKECNNIDFTVQATFSKLADTVDEIIEKVQKKYEQYKIKSEPFVFIKANSGSYGIGISTATNSKDVLNMNKKNRNKLKTTK 287
                 *************************************************************************************************** PP

                 SSS---EEEEEE-----EEETTEEEEEEEEEETTEEEEEEEEEES--STTTTTS--TT-EEEEE--S CS
        GshA 300 eglevseviiqEGvytfeklneavaEpvvYmidrevvggfyRvhaergadenLnapGmhfvplafee 366
                 ++++v+++i+qEG++t+e++n + +E ++Y +  e ++ + R++  +++ enLn+ Gm f++ + + 
  AHX11249.1 288 GSTSVTNIIVQEGIETIESYNSHPSEVLMYSVLGEQIAFIQRYNDRHNRRENLNSAGMLFAECTKNY 354
                 ************************************************************9876654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1140  (0.0635841); expected 358.6 (0.02)
Passed bias filter:                      567  (0.0316247); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2934.86
//
Query:       AHX11250.1  [L=195]
Description: dephospho-CoA kinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.1e-25   88.9   0.3    3.6e-25   88.7   0.3    1.1  1  CoaE          Dephospho-CoA kinase
    6.4e-05   23.5   0.2    0.00012   22.6   0.2    1.4  1  AAA_18        AAA domain
     0.0066   16.3   0.1      0.053   13.4   0.0    2.1  2  dNK           Deoxynucleoside kinase
  ------ inclusion threshold ------
      0.023   15.0   0.1         26    5.3   0.0    3.2  3  Endotoxin_C2  Delta endotoxin


Domain annotation for each model (and alignments):
>> CoaE  Dephospho-CoA kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.7   0.3   8.1e-29   3.6e-25       2     144 ..       3     147 ..       2     170 .. 0.93

  Alignments for each domain:
  == domain 1  score: 88.7 bits;  conditional E-value: 8.1e-29
                 EEEEEESTTSSHHHHHHHHHH.TT-EEEEHHHHHHHTTCCTHHHHHHHHHHHGGGCB.TTSSE-HHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHHHHH CS
        CoaE   2 ivgltGgiasGKstvanlfad.lgvpivDaDlvArqvvepgsealkkiveeFgeeildedGeLdReaLrkkvFadpeekkaLnallhPlirreikkela 99 
                 i+g+tG+iasGK+  +++++  + ++i DaD+v + + +++ ++ ++i ++    i  ++ ++dR+ L   + ++p+  +++++++hP +++++++ ++
  AHX11250.1   3 IIGVTGNIASGKTYFSSILRRtFRCKIFDADKVVHALYQNDISVTRAINDAISTGI--RESSIDRKRLLAAIIRQPSLLQKIEEIVHPNVKAKLTSFIK 99 
                 8*******************99**********************************..999**********************************9999 PP

                 H--S...SEEEEE-TTTTTTTGGGGSSEEEEEE--HHHHHHHHHHCCT CS
        CoaE 100 kles...kyvlldvPLLvEkqlekliervlvvdvelelqveRlvardg 144
                  +++   ++++ld+PLL+E   +k+++++++++ ++ ++v+Rl +r +
  AHX11250.1 100 LCKRdntRIIVLDIPLLFEIAADKICDTIIILQSSKITNVHRLRKRYN 147
                 98887889***********************************99964 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   2.8e-08   0.00012       1     114 [.       4     146 ..       4     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.8e-08
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf.............................gvnlrdvakenglllevdpe.aldeskrldedkldklldaleenss 69 
                 I++tG +++GKt ++  L++   +                             g++ +++ +++ l     ++  l++ ++++ +++++ l+ + + ++
  AHX11250.1   4 IGVTGNIASGKTYFSSILRRTFRCkifdadkvvhalyqndisvtraindaistGIRESSIDRKRLLAAIIRQPsLLQKIEEIVHPNVKAKLTSFIKLCK 102
                 89****************99877799**55555555555555544444444444444444444444444444466666666666666666666666665 PP

      AAA_18  70 aleegknlvidghlaeleseaakdikk.vvLtaspeelleRlekRg 114
                   +++  +++ +++  +e +a+k+  + ++L+ s+ +   Rl+kR 
  AHX11250.1 103 --RDNTRIIVLDIPLLFEIAADKICDTiIILQSSKITNVHRLRKRY 146
                 ..8999999999******9999987779****************95 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.0   1.2e-05     0.053       1      28 [.       4      31 ..       4      85 .. 0.89
   2 ?    1.0   0.1     0.074   3.3e+02     123     146 ..     125     148 ..     113     156 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.2e-05
                EEEEESTTSSHHHHHHHHHCCSTCEEEE CS
         dNK  1 ivveGnIgaGKstlvklLskklgvkvfe 28
                i v GnI++GK+ + ++L++++  k+f 
  AHX11250.1  4 IGVTGNIASGKTYFSSILRRTFRCKIFD 31
                6799****************99988875 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.074
                 -SEEEEEE--HHHHHHHHHHCTTC CS
         dNK 123 pdlliYLkasletclerikkRgre 146
                  d +i L+ s  t ++r++kR + 
  AHX11250.1 125 CDTIIILQSSKITNVHRLRKRYND 148
                 699999***999*******99875 PP

>> Endotoxin_C2  Delta endotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.019        86       4      24 ..      30      52 ..      28      66 .. 0.72
   2 ?    2.2   0.0     0.051   2.3e+02      36      54 ..      80      98 ..      79     102 .. 0.87
   3 ?    5.3   0.0    0.0057        26      33      54 ..     165     186 ..     164     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.019
  Endotoxin_C2  4 eaAtkaVnaLFtdnnptk..ikd 24
                    A k V+aL++++   +  i+d
    AHX11250.1 30 FDADKVVHALYQNDISVTraIND 52
                  579999*******9665556554 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.051
  Endotoxin_C2 36 alVdkvtdstkKaeLqadi 54
                  ++++++ ++++Ka+L++ i
    AHX11250.1 80 QKIEEIVHPNVKAKLTSFI 98
                  58999**********9866 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0057
  Endotoxin_C2  33 aAqalVdkvtdstkKaeLqadi 54 
                   +Aq+++  v+++++K eL +++
    AHX11250.1 165 EAQKKIRLVPSGADKRELFKYV 186
                   69****************8876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      508  (0.028334); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 1606.83
//
Query:       AHX11251.1  [L=254]
Description: ATP-NAD kinase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.2e-25   90.3   0.1    1.7e-25   89.8   0.1    1.1  1  NAD_kinase  ATP-NAD kinase


Domain annotation for each model (and alignments):
>> NAD_kinase  ATP-NAD kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.8   0.1   9.4e-30   1.7e-25      66     274 ..      22     222 ..       3     228 .. 0.86

  Alignments for each domain:
  == domain 1  score: 89.8 bits;  conditional E-value: 9.4e-30
                 EEECCC-TTTTTSSSEEEEEE-HHHHHHHHHHHHHCT-EEEEEESSS--SS-SEEGGGHHHHHHHHHH.T-SEEEEEEEEEEEEEETTE......EEEE CS
  NAD_kinase  66 dtrkaleafadagvdliivvGGDGTaldvarllqkaeiPvlgvnaGvkgfltefepeaaaelleklle.geirvekrevldavimrskgeediadivie 163
                 + +k++++ ad ++ li+++GGDG +ld  r    ++iPv g+n G++gfl  +++ + ++ll+++   +e++++   +l+a + +++g        i 
  AHX11251.1  22 YGIKKIDRYADIEASLILALGGDGFMLDTLRRRMGNNIPVYGINCGNVGFL--LNEFHSDQLLADIESaEEYNLN---ILKAELSNENG-------TIS 108
                 567889999999*******************99999**************9..5566778888888886778776...8999999****.......356 PP

                 EEESSEEEEEESSSSS-EEEEEEETTEE.EEEEEESEEEEE-TGGGGTHHHHTT--EE-TT---EEEEEESESS.S----EEE-TT-EEEEEE-..SS- CS
  NAD_kinase 164 nsvlnevviirgpgstlielelyvdtel.leadqldglivstPtGstayslsaGgplisPgvlailivpicPhs.lssrpiVvssssklrirva..srs 258
                  +++n+ +i r  g + ++l + vd+el +e+++ dg+ivst+ Gstay  +aGgp++  + ++i+++ i++++ ++ r iV+ +ss ++i v   +r+
  AHX11251.1 109 GTAINDFYILRNHG-KASKLRISVDDELlIENFVGDGVIVSTAVGSTAYNAAAGGPILALDSNCITLTTINAFIpKQCRSIVLLDSSIIEIDVLypDRR 206
                 67799998877655.6677999**99963699****************************************983667*************99999*** PP

                 -EEEEETTTEEEEE-T CS
  NAD_kinase 259 eallaldGseelelsp 274
                  +++ald +  +++++
  AHX11251.1 207 PVMAALDAQVFTNIKK 222
                 *******998888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1951.12
//
Query:       AHX11252.1  [L=45]
Description: glutaredoxin family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-05   23.2   0.0    7.4e-05   22.9   0.0    1.2  1  Glutaredoxin  Glutaredoxin


Domain annotation for each model (and alignments):
>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.0   4.1e-09   7.4e-05      43      60 .]       3      21 ..       1      21 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 4.1e-09
                  HHH.TSSSSSEEEETTEEE CS
  Glutaredoxin 43 els.gvrtvPqvfidgkhv 60
                  ++s g+rtvPq+fidgk++
    AHX11252.1  3 QKSgGRRTVPQIFIDGKCI 21
                  4445*************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       154  (0.00858944); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 370.93
//
Query:       AHX11253.1  [L=55]
Description: hypoxia induced conserved region family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-06   28.2   1.6      2e-06   27.9   1.6    1.2  1  HIG_1_N   Hypoxia induced protein conserved region


Domain annotation for each model (and alignments):
>> HIG_1_N  Hypoxia induced protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.6   1.1e-10     2e-06       9      50 ..       8      49 ..       4      50 .. 0.96

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-10
     HIG_1_N  9 ilatvgalvrglrsmkrgdskqsnrlmraRiaaQaftvlalv 50
                i+at  +l+ g+ sm + d++  n+lm +R+++Q++ v++l+
  AHX11253.1  8 IAATFFVLIAGVLSMLSLDRNYGNKLMILRVFLQFVSVALLL 49
                79*************************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 420.81
//
Query:       AHX11254.1  [L=622]
Description: RNA polymerase sigma factor rpoD [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.3e-22   77.7   0.6      7e-21   74.1   0.0    2.9  2  Sigma70_r3    Sigma-70 region 3
    2.2e-20   72.2   0.0      6e-20   70.8   0.0    1.8  1  Sigma70_r2    Sigma-70 region 2
    7.7e-16   57.4   0.1    8.7e-12   44.4   0.0    3.3  2  Sigma70_r4    Sigma-70, region 4
    2.4e-15   57.0   4.7    2.4e-15   57.0   4.7    2.4  2  Sigma70_ner   Sigma-70, non-essential region
    3.5e-14   52.6   5.8    1.4e-13   50.6   5.8    2.1  1  Sigma70_r1_1  Sigma-70 factor, region 1.1
    7.4e-10   38.7   0.9    7.4e-10   38.7   0.9    2.9  3  Sigma70_r1_2  Sigma-70 factor, region 1.2
    0.00032   20.3   1.3       0.48   10.1   0.0    3.7  3  Sigma70_r4_2  Sigma-70, region 4
    0.00041   20.0   0.2      0.063   13.0   0.0    3.0  2  HTH_41        Helix-turn-helix domain
     0.0023   17.9   0.0        1.3    9.1   0.0    3.4  3  HTH_15        Helix-turn-helix domain of alkylmercury lyase
     0.0065   16.1   0.8        6.6    6.5   0.0    4.1  5  GntR          Bacterial regulatory proteins, gntR family
  ------ inclusion threshold ------
      0.014   14.4   0.1      0.037   13.0   0.1    1.8  1  TnsD          Tn7-like transposition protein D


Domain annotation for each model (and alignments):
>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.1      0.59   9.6e+02      35      69 ..     136     173 ..     133     180 .. 0.64
   2 !   74.1   0.0   4.3e-24     7e-21       1      76 [.     446     522 ..     446     524 .. 0.95

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.59
                 HHHHHHHHHHXXX..EETTXBSSSSTTXBS.TTTXBXS CS
  Sigma70_r3  35 ekVrevleaarep..vSldlpvgeeedtel.gdlledd 69 
                 + +re++e+ ++    S++l+   e+d+ l ++l+ed 
  AHX11254.1 136 SAIREIMELGNRLeeKSVSLREVIESDSGLkSELTEDA 173
                 56889999888642267888877777776624555555 PP

  == domain 2  score: 74.1 bits;  conditional E-value: 4.3e-24
                 XHHHHHHHHHHHHHHHHSSXXXHHHHHHHHTXXHHHHHHHHHHHXXXEETTXBSSSSTT.XBSTTTXBXSSSXXHHH CS
  Sigma70_r3   1 EklnkikraqreLeqelgrePtpeEiAeeLglseekVrevleaarepvSldlpvgeeed.telgdlleddeaespee 76 
                 E+ nk+ r++r+L+   grePt+eEiA  Lg+s++kV++ l+ +++pvSl++pvg++ + +++gd++ed++a ++++
  AHX11254.1 446 ETANKVMRTRRKLYNLNGREPTVEEIASLLGISVDKVKKSLKVNQDPVSLESPVGDDNNsGSFGDFIEDKNAINQVD 522
                 899****************************************************9977369**********99987 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   3.7e-23     6e-20       1      66 [.     367     432 ..     367     436 .. 0.97

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 3.7e-23
                 HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHH CS
  Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlR 66 
                 +ve++l+lv ++a++++++g  + Dl+Qe++++l++av++fd+ rg++fs++++++ r+a+ +++ 
  AHX11254.1 367 MVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFSTYATWWCRQAITRAIA 432
                 689**********************************************************99986 PP

>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00057      0.93      16      38 ..     455     483 ..     445     487 .. 0.79
   2 !   44.4   0.0   5.3e-15   8.7e-12       1      49 [.     536     608 ..     536     609 .. 0.98

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00057
                 HH......TTT--HHHHHHHHTS-HHHHH CS
  Sigma70_r4  16 rf......geglTleEIgerlgiSrerVr 38 
                 r+      g++ T eEI+  lgiS   V+
  AHX11254.1 455 RRklynlnGREPTVEEIASLLGISVDKVK 483
                 445667778899************99888 PP

  == domain 2  score: 44.4 bits;  conditional E-value: 5.3e-15
                 HHHHS-HHHHHHHHHHH........................TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHH CS
  Sigma70_r4   1 aLasLpererevlelrf........................geglTleEIgerlgiSrerVrqiekrAlrkLR 49 
                 aL+ L++re ++l++rf                        g +lTle++g  ++++rer+rqie++ lrk+R
  AHX11254.1 536 ALSMLSPREEKILRYRFglcntvhspedehylkslkidlnkGTNLTLEQVGILYNVTRERIRQIESKSLRKMR 608
                 7999********************************************************************9 PP

>> Sigma70_ner  Sigma-70, non-essential region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.9      0.12     2e+02      32      54 ..      62      83 ..      21     124 .. 0.64
   2 !   57.0   4.7   1.5e-18   2.4e-15       1     160 [.     134     298 ..     134     299 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.12
  Sigma70_ner 32 eeeeeeeeeeeedeeeeeeeedd 54
                 e ++ee+e  +  +eeeeeeed+
   AHX11254.1 62 E-KDEEDELTDGVKEEEEEEEDE 83
                 1.222222222222222222222 PP

  == domain 2  score: 57.0 bits;  conditional E-value: 1.5e-18
  Sigma70_ner   1 yPetiaellelydrveageirLrdiidGflDeeeeeeeeeeeedeeeeeee..edddeeeseseaadeeelkeealekfeelreqyeklrk....... 89 
                  +P++i+e++el +r+e+  ++Lr++i+   D+  + e    +ed+e+ ++e  ++ d++ +e+++ + eel +++ e fe+lr++++ + +       
   AHX11254.1 134 FPSAIREIMELGNRLEEKSVSLREVIE--SDSGLKSEL---TEDAERGSDElfDSADGKLDEANQMSDEELMKRVFEIFEHLRTTIQSALErikdkqv 226
                  7**************************..884333333...233334444445666767889999999*********************999****** PP

  Sigma70_ner  90 .alkkkgr.kskkyekareelseefkefrLtpkqidrLveqlrslvervraqEreimrlcverakmprkdFik 160
                   ++ +k+   +++ye+++  l+  +++++L+pk    L  +l++  + +   E++++++   +++++r + +k
   AHX11254.1 227 vQISNKDIvLDAEYENLHSLLVSSLSQMKLNPKVLSGLFATLQAKHDLILDREKKLLTY-LSEHGVDRSKIVK 298
                  966666566**************************************************.999****998776 PP

>> Sigma70_r1_1  Sigma-70 factor, region 1.1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   5.8   8.9e-17   1.4e-13       4      77 ..      10      83 ..       7      86 .. 0.78

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 8.9e-17
                  HHHHHHHHHHHHHHSCEEHHHHHHHGCCSS.--HHHHHHHHHHHHCCT-EEE-SS-.........S-SSSXXXXX CS
  Sigma70_r1_1  4 kaavkeLikkgKkkGyLtyeEindaLpdde.ldseqiediiemLedmgIdvveeaededellleeeaedaeeede 77
                  ++ vk+Li+kg kkG++ty E+++ ++d++  +   ie+ i++Le+ gId++e++e edel +  ++e++eeede
    AHX11254.1 10 HQIVKALITKGLKKGFVTYGELSNSFSDEDfENLNCIEEAISKLEESGIDILEKDE-EDELTDGVKEEEEEEEDE 83
                  6789***********************666367799*****************888.666434444444333333 PP

>> Sigma70_r1_2  Sigma-70 factor, region 1.2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   2.2       4.3   7.1e+03      14      33 ..      59      78 ..      57      79 .. 0.75
   2 !   38.7   0.9   4.6e-13   7.4e-10       1      30 [.      93     122 ..      93     126 .. 0.94
   3 ?   -1.5   0.0       1.6   2.6e+03      15      24 ..     539     548 ..     538     548 .. 0.85

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.3
                  X--THHHHHHHHHHHHCCHH CS
  Sigma70_r1_2 14 PLLtaeEEveLAkrieaGde 33
                  + L ++EE eL   +++ +e
    AHX11254.1 59 DILEKDEEDELTDGVKEEEE 78
                  668899**999777777665 PP

  == domain 2  score: 38.7 bits;  conditional E-value: 4.6e-13
                   HHHHHHHHHHHHSX--THHHHHHHHHHHHC CS
  Sigma70_r1_2   1 DpvrlYLrEIGriPLLtaeEEveLAkriea 30 
                   DpvrlYLrE++ ++LL++e+Eve+Ak i a
    AHX11254.1  93 DPVRLYLREMSYVKLLSREDEVEIAKTILA 122
                   9*************************9976 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 1.6
                   --THHHHHHH CS
  Sigma70_r1_2  15 LLtaeEEveL 24 
                   +L++ EE+ L
    AHX11254.1 539 MLSPREEKIL 548
                   8******866 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2     2e+03       2      13 ..      44      55 ..      43      66 .. 0.91
   2 !   10.1   0.0    0.0003      0.48      28      47 ..     467     486 ..     466     487 .. 0.90
   3 !    6.6   0.1    0.0037       6.1       3      22 ..     532     551 ..     530     554 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                  HHHHHHHTTS-H CS
  Sigma70_r4_2  2 qalrealaeLpe 13
                  ++++ea+++L e
    AHX11254.1 44 NCIEEAISKLEE 55
                  79********87 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.0003
                   -HHHHHHHHT--HHHHHHHH CS
  Sigma70_r4_2  28 sykEIAellgisegtVksrl 47 
                   + +EIA+llgis+  Vk+ l
    AHX11254.1 467 TVEEIASLLGISVDKVKKSL 486
                   579**************876 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.0037
                   HHHHHHTTS-HHHHHHHHHH CS
  Sigma70_r4_2   3 alrealaeLperqreifllr 22 
                    l+eal++L++r+ +i+  r
    AHX11254.1 532 VLDEALSMLSPREEKILRYR 551
                   699*************9876 PP

>> HTH_41  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   3.9e-05     0.063      21      41 ..     212     232 ..     201     232 .. 0.90
   2 ?    3.5   0.0     0.035        58       7      29 ..     466     488 ..     463     496 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.9e-05
      HTH_41  21 GlvQkALklLeddkaislerr 41 
                  ++Q+AL+ ++d+++++++ +
  AHX11254.1 212 TTIQSALERIKDKQVVQISNK 232
                 69***************9876 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.035
      HTH_41   7 ktIeelakeleLSvGlvQkALkl 29 
                 +t+ee+a+ l++Sv  v k Lk 
  AHX11254.1 466 PTVEEIASLLGISVDKVKKSLKV 488
                 8*************999999985 PP

>> HTH_15  Helix-turn-helix domain of alkylmercury lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.35   5.8e+02      40      62 ..      83     105 ..      80     107 .. 0.87
   2 !    9.1   0.0   0.00077       1.3      32      57 ..     462     487 ..     446     492 .. 0.88
   3 ?    3.3   0.0     0.049        80      15      55 ..     559     599 ..     549     603 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.35
      HTH_15  40 eLAaatgrsveevrqaLaalpst 62 
                 e A+++g +++ vr  L  ++ +
  AHX11254.1  83 EAAGILGHTDDPVRLYLREMSYV 105
                 6799*************999865 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00077
      HTH_15  32 kGepVtveeLAaatgrsveevrqaLa 57 
                 +G+  tvee+A  +g sv++v++ L+
  AHX11254.1 462 NGREPTVEEIASLLGISVDKVKKSLK 487
                 68888******************997 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.049
      HTH_15  15 eggssaellrpLlrlLakGepVtveeLAaatgrsveevrqa 55 
                 ++ ++   l +L   L kG   t+e++    + + e++rq+
  AHX11254.1 559 HSPEDEHYLKSLKIDLNKGTNLTLEQVGILYNVTRERIRQI 599
                 666777788999999************************97 PP

>> GntR  Bacterial regulatory proteins, gntR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.5   2.4e+03      40      53 ..      45      58 ..      42      58 .. 0.83
   2 !    6.5   0.0     0.004       6.6      32      57 ..     205     230 ..     187     233 .. 0.86
   3 ?    4.2   0.0      0.02        33      25      46 ..     466     487 ..     455     488 .. 0.89
   4 ?   -2.6   0.0       2.7   4.4e+03      38      49 ..     530     541 ..     530     545 .. 0.85
   5 ?   -1.0   0.0      0.88   1.4e+03      18      43 ..     574     598 ..     570     598 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.5
                HHHHHHHHHHHTTS CS
        GntR 40 tvReALrrLeaegl 53
                 + eA+++Le+ g+
  AHX11254.1 45 CIEEAISKLEESGI 58
                588*******9885 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.004
                 HHHTS-HHHHHHHHHHHHHTTSEEEE CS
        GntR  32 aefgVsrttvReALrrLeaeglverr 57 
                 + f+  rtt++ AL r + +++v++ 
  AHX11254.1 205 EIFEHLRTTIQSALERIKDKQVVQIS 230
                 567778*****************986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.02
                 --HHHHHHHHTS-HHHHHHHHH CS
        GntR  25 PsereLaaefgVsrttvReALr 46 
                 P+++e+a+ +g+s   v ++L+
  AHX11254.1 466 PTVEEIASLLGISVDKVKKSLK 487
                 9*************99999986 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 2.7
                 HHHHHHHHHHHH CS
        GntR  38 rttvReALrrLe 49 
                 r ++ eAL++L+
  AHX11254.1 530 RKVLDEALSMLS 541
                 67899*****96 PP

  == domain 5  score: -1.0 bits;  conditional E-value: 0.88
                 S-TTSB---HHHHHHHHTS-HHHHHH CS
        GntR  18 lrpGdkLPsereLaaefgVsrttvRe 43 
                 l+ G+ L + +++   ++V+r  +R+
  AHX11254.1 574 LNKGTNL-TLEQVGILYNVTRERIRQ 598
                 6789999.9999999******99986 PP

>> TnsD  Tn7-like transposition protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   2.3e-05     0.037     156     229 ..     420     495 ..     401     569 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
        TnsD 156 C.scGfsytrsgedlseedayrisrikkfGivweerlkeLvee..eglslkeiAkelgvdiktVlryakklgllkek 229
                    c+++ tr+  d +++   + ++i +  +++ + +++L++   ++ +++eiA+ lg+++ +V++++k +++ ++ 
  AHX11254.1 420 TwWCRQAITRAIADCGSI-VRKPVHIHETANKVMRTRRKLYNLngREPTVEEIASLLGISVDKVKKSLKVNQDPVSL 495
                 44699999*******999.889999****************997777899*******************99886654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (622 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1156  (0.0644765); expected 358.6 (0.02)
Passed bias filter:                      666  (0.0371465); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.41
# Mc/sec: 4588.03
//
Query:       AHX11255.1  [L=743]
Description: sigma-54 interaction domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-42  146.0   0.1    4.7e-41  140.8   0.0    3.0  3  AAA_2            AAA domain (Cdc48 subfamily)
    7.6e-25   87.9   0.0    8.4e-12   45.7   0.0    2.9  2  AAA              ATPase family associated with various cellul
    1.5e-20   73.0   0.4    4.2e-20   71.6   0.4    1.9  1  AAA_lid_9        AAA lid domain
    2.5e-13   50.2   0.0    1.3e-08   34.9   0.0    2.9  2  AAA_5            AAA domain (dynein-related subfamily)
    2.1e-11   43.8   0.1    9.3e-08   31.9   0.1    2.5  2  Sigma54_activat  Sigma-54 interaction domain
      7e-10   38.9   3.8      2e-09   37.5   0.8    3.0  2  Clp_N            Clp amino terminal domain, pathogenicity isl
    7.6e-08   32.5   0.1     0.0093   16.0   0.0    3.4  3  AAA_14           AAA domain
    3.3e-07   30.6   0.2      0.053   13.8   0.0    4.1  2  AAA_22           AAA domain
    5.1e-07   30.2   0.2       0.12   12.7   0.0    3.5  3  AAA_16           AAA ATPase domain
      8e-07   28.6   0.0    0.00038   19.9   0.0    3.6  3  TniB             Bacterial TniB protein
    3.1e-06   27.1   0.0      6e-05   22.9   0.0    3.0  3  AAA_3            ATPase family associated with various cellul
    1.3e-05   25.2   0.3    5.6e-05   23.1   0.3    2.2  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    1.9e-05   24.7   0.0       0.15   12.0   0.0    3.1  2  NACHT            NACHT domain
    2.6e-05   23.8   0.1       0.11   12.1   0.0    3.1  2  AAA_7            P-loop containing dynein motor region
    5.6e-05   23.5   0.4       0.12   12.8   0.5    3.5  2  RNA_helicase     RNA helicase
    8.2e-05   22.6  12.2      0.032   14.2   0.2    5.2  5  ATPase_2         ATPase domain predominantly from Archaea
    0.00014   21.3   0.2        7.7    5.8   0.0    3.9  4  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00031   20.9   0.0     0.0012   18.9   0.0    2.0  1  Torsin           Torsin
    0.00067   19.4   0.2        2.5    7.8   0.0    4.1  4  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00069   19.0   0.0      0.034   13.4   0.0    2.9  2  Zeta_toxin       Zeta toxin
    0.00088   19.3   0.0        0.3   11.1   0.0    2.9  3  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
    0.00089   19.0   0.0        2.3    7.9   0.0    3.0  2  IstB_IS21        IstB-like ATP binding protein
     0.0016   18.2   0.2      0.056   13.2   0.0    2.7  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
     0.0022   18.1   0.0       0.36   11.0   0.0    2.8  2  AAA_33           AAA domain
     0.0085   15.1   0.0       0.02   13.9   0.0    1.6  1  AAA_6            Hydrolytic ATP binding site of dynein motor 
  ------ inclusion threshold ------
      0.028   13.6   0.4        5.7    6.0   0.2    3.0  2  NB-ARC           NB-ARC domain
      0.034   14.2   0.2        1.1    9.3   0.0    3.1  3  ResIII           Type III restriction enzyme, res subunit
      0.056   13.7   0.0        5.1    7.3   0.0    2.7  2  Roc              Ras of Complex, Roc, domain of DAPkinase
      0.059   13.3   0.0         12    5.8   0.0    2.7  2  RsgA_GTPase      RsgA GTPase
      0.062   13.2   0.9         12    5.7   0.0    2.9  3  NTPase_1         NTPase
      0.075   13.6   0.0         20    5.7   0.0    3.3  2  AAA_18           AAA domain
       0.22   11.1   0.1        5.6    6.5   0.0    2.9  3  AAA_25           AAA domain
        7.9    6.5   8.5       0.52   10.3   0.3    3.1  3  PP1_inhibitor    PKC-activated protein phosphatase-1 inhibito


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       6.2   3.3e+03      37      57 ..     173     193 ..     156     200 .. 0.82
   2 ?    1.4   0.0      0.56   3.1e+02      70      82 ..     267     292 ..     205     308 .. 0.58
   3 !  140.8   0.0   8.6e-44   4.7e-41       1     169 [.     488     647 ..     488     649 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.2
                 EEEGGG-------THHHHHHH CS
       AAA_2  37 radaselleeeevehlvsrli 57 
                   d++el+ + ++++l++r++
  AHX11255.1 173 CTDMNELALQGKIDKLINREK 193
                 579999999999999999876 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.56
                 S.............EEEEETGGG--- CS
       AAA_2  70 G.............ivllDEidKihp 82 
                               i+++DEi  i  
  AHX11255.1 267 IkmvineianckntILFIDEIHTIVG 292
                 34444555555555999999988876 PP

  == domain 3  score: 140.8 bits;  conditional E-value: 8.6e-44
                 -----EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS............EEEEETGGG-------- CS
       AAA_2   1 rpiisilllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG............ivllDEidKihpkessg 87 
                 +pi++ l+ g+tg+Gktelak++a+ l +    +++r+d+se++e    +h+vsrl+gappgyvg+++gG             +l+DEi+K+h+     
  AHX11255.1 488 KPIGTYLFGGETGIGKTELAKQIAKNLCM----QFVRIDMSEYME----SHSVSRLLGAPPGYVGHDKGGflvealfkhgntLILFDEIEKAHK----- 573
                 58999***********************9....************....*********************************************..... PP

                 -----HHHHHHHHHHHH--EE-------EE-TT-EEEEEE--TTHHHHTTTS-STTTTSGGG--HHHHHHTT--HHHHTT-- CS
       AAA_2  88 advSregVqrdLLqileggtltdkqgrkvdtknilfImtgafgsskisdesrskeeeeekkkeeveeelkkglipEllgRlp 169
                       ++q++LLqi++ g +td+ grk +++n+++I+t+++gss i++++     +++ +k + e++  k+++ Ell+Rl+
  AHX11255.1 574 ------DIQNILLQIMDYGCITDSTGRKSKFQNCIVICTTNVGSSFIESNHL--GFSKDCVKIDREDQFAKFFTKELLNRLD 647
                 ......******************************************9555..6999***********************9 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   1.5e-14   8.4e-12       4     126 ..     213     343 ..     210     348 .. 0.79
   2 !   39.1   0.0   1.6e-12   8.9e-10       2     112 ..     494     610 ..     493     623 .. 0.84

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 1.5e-14
                 ESSTTSSHHHHHHHHHHHH..........THEEEEEETTTCS..SSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
         AAA   4 yGppGtGKTllakavakel..........gvefleisgsell..skyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLl 90 
                 +G pG+GKT++ + +++ +          ++++++++  +ll    y g+ e++i+++++e+ + +  +ilfiDEi+ ++++   s+s+ + ++ n L 
  AHX11255.1 213 VGEPGVGKTAILEGLVHAIvngdvphklrNARVYSLKIGSLLagTRYRGDFEERIKMVINEIANCK-NTILFIDEIHTIVGAG--STSNGSIDAGNLLK 308
                 8*****************77776676666799*********96445***************87765.7**************9..77788888888888 PP

                 HHHHHTTTSSSTEEEEEEESS.....GGGSTHHHHSTTSSE CS
         AAA  91 teldgvkkkeskvivigatnr.....pdkldpallrgRfdr 126
                 ++l +       + +igat++       + d al  +Rf+r
  AHX11255.1 309 PFLTKGP-----LRCIGATTYkeysaHFEKDAALN-RRFQR 343
                 8876553.....57999998866644344455555.56655 PP

  == domain 2  score: 39.1 bits;  conditional E-value: 1.6e-12
                 EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS............STTHHHH..HHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHH CS
         AAA   2 llyGppGtGKTllakavakelgvefleisgsellsk............yvgesek..kirelfkeakekakpsilfiDEidalaksrsgseseeeervv 86 
                 l+ G  G+GKT lak++ak+l ++f++i++se +++            yvg+ +    +++lfk+    +  + +++DEi++ +k+            +
  AHX11255.1 494 LFGGETGIGKTELAKQIAKNLCMQFVRIDMSEYMEShsvsrllgappgYVGHDKGgfLVEALFKH---GN--TLILFDEIEKAHKDI-----------Q 576
                 7889******************************667***********88887762256777744...44..99*********8877...........* PP

                 HHHHHHHHHTTTS........SSTEEEEEEESSG CS
         AAA  87 nqLlteldgvkkk........eskvivigatnrp 112
                 n Ll+ +d              +++ivi++tn  
  AHX11255.1 577 NILLQIMDYGCITdstgrkskFQNCIVICTTNVG 610
                 ********8777777888888566*******975 PP

>> AAA_lid_9  AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.6   0.4   7.7e-23   4.2e-20       2      70 ..     351     419 ..     350     470 .. 0.85

  Alignments for each domain:
  == domain 1  score: 71.6 bits;  conditional E-value: 7.7e-23
   AAA_lid_9   2 eeetieiLrglkekyekhHgvkisdealeaavklSkrYisdrflPdkAIDllDeaaarvrlkkeskpee 70 
                  ++t++i+ g k +ye++H+v++++  l+++v+l++rYi++r +PdkAIDl+D  +a+ + ++++ +++
  AHX11255.1 351 LQNTLSIIDGAKAYYEDFHRVRYTKTSLNEIVNLAHRYIPGRAFPDKAIDLMDDLGASYNADSSKVNKR 419
                 679******************************************************999888765554 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00032      0.18       5      76 ..     213     289 ..     210     293 .. 0.77
   2 !   34.9   0.0   2.4e-11   1.3e-08       5     123 ..     496     610 ..     493     619 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00032
                 E--SSSSHHHHHHHGGGGB.S--EEEEE--TT...--HHHHH--B--.........--------.G-SEEEEESGGG CS
       AAA_5   5 vGppGtgKselaerlaaal.nreveyvqltrd...tteedlkgrreikngttslvdsplvraar.egeilvlDEver 76 
                 vG+pG+gK+ + e l +a+ n  v  ++ +++   ++   l+ +++++++ +++ + ++ + a+ +  il++DE+++
  AHX11255.1 213 VGEPGVGKTAILEGLVHAIvNGDVPHKLRNARvysLKIGSLLAGTRYRGDFEERIKMVINEIANcKNTILFIDEIHT 289
                 8******************9777777776665111445567788888788888888888877778889999999986 PP

  == domain 2  score: 34.9 bits;  conditional E-value: 2.4e-11
                 E--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------...G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-SS CS
       AAA_5   5 vGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar...egeilvlDEveraesevlnsLlslleerrllleegg 100
                  G++G+gK+ela+++a+ l+ +++ + +++++++  +   +   +g   + ++ +  +a       ++++DE+e+a+++++n+Ll++++   +  ++ g
  AHX11255.1 496 GGETGIGKTELAKQIAKNLCMQFVRIDMSEYMESHSVSRLLGAPPGYVGHDKGGFLVEALfkhGNTLILFDEIEKAHKDIQNILLQIMDYGCIT-DSTG 593
                 69***********************************999997777777766665555555755567788********************9998.6666 PP

                 SEEE---......-EEEEEESS- CS
       AAA_5 101 elvkaknddllerfrviatanpl 123
                 +  k++n        vi t+n  
  AHX11255.1 594 RKSKFQN------CIVICTTNVG 610
                 6666666......7888888865 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0    0.0019         1      20     105 ..     205     290 ..     188     296 .. 0.77
   2 !   31.9   0.1   1.7e-10   9.3e-08      25     143 ..     493     609 ..     486     620 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0019
                      TSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBS.SSSSTTTSS-BEHHHHHTTTSEEEEETGGGS CS
  Sigma54_activat  20 ktdlsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhe.kGaFtGAekekkGlfekadgGtlfLDeigel 105
                      +t+ + + +Ge G+GK+ + + + +a  + + p    n   + +  + s L G++ +G F    k     + ++++ +lf+Dei+++
       AHX11255.1 205 RTKNNPIYVGEPGVGKTAILEGLVHAIVNGDVPHKLRNARVY-SLKIGSLLAGTRyRGDFEERIKMVINEIANCKNTILFIDEIHTI 290
                      344556778*********999998888888888776665555.55578999998648***************************986 PP

  == domain 2  score: 31.9 bits;  conditional E-value: 1.7e-10
                      EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BEHHHHHT...TTSEE.EEETGGGS-HHHHHHHH CS
  Sigma54_activat  25 vlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekkGlfeka...dgGtl.fLDeigelplelQekLl 114
                       l  Ge+G GK+ la++i ++      +fv+++++++ e+   s+L G   G + G +  k G + +a   +g tl ++Dei++   ++Q+ Ll
       AHX11255.1 493 YLFGGETGIGKTELAKQIAKNLC---MQFVRIDMSEYMESHSVSRLLGAPPG-YVGHD--KGGFLVEAlfkHGNTLiLFDEIEKAHKDIQNILL 580
                      5788*************987655...78********************9998.78865..4566665544455555156*************** PP

                      HHHHHSEEESBTSSSEEE--EEEEEEESS CS
  Sigma54_activat 115 rvlqegevervGsskeikvdvriiaatne 143
                      ++++ g ++   ++k++  ++ +i++tn 
       AHX11255.1 581 QIMDYGCITDSTGRKSKFQNCIVICTTNV 609
                      *********99999999999*9***9985 PP

>> Clp_N  Clp amino terminal domain, pathogenicity island component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.5   0.8   3.6e-12     2e-09       1      52 [.      13      62 ..      13      63 .. 0.96
   2 ?    0.5   0.1       1.3   6.9e+02       1      40 [.      94     133 ..      94     138 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.5 bits;  conditional E-value: 3.6e-12
                HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSSHHHHHHHHHHHH CS
       Clp_N  1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvdldalrkaiekll 52
                A +lA s+ h+y++ EHLLlAL e++   + ++  + G++  +lr+ + ++l
  AHX11255.1 13 ALALAHSFSHSYVTLEHLLLALTEDE--EIVQIASNSGINFGKLRDLLLQFL 62
                7789********************99..********************9997 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 1.3
                 HHHHHHHTTCSSB-HHHHHHHHHHSCTSHHHHHHHHTTSS CS
       Clp_N   1 AqelAkslghqyistEHLLlALleeddGlaarlLkkaGvd 40 
                 Aq  A  +  ++i+  H+L+ ++ e d+ a   L + +++
  AHX11255.1  94 AQFHASIAELNQITGLHVLIEIFCEQDSHAFAFLTQSNIT 133
                 566777777899*********9999999999999888876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       5.3   2.9e+03      32     104 ..      67     134 ..      56     144 .. 0.66
   2 !   12.4   0.0   0.00023      0.12      12      92 ..     217     306 ..     209     359 .. 0.74
   3 !   16.0   0.0   1.7e-05    0.0093      12      90 ..     500     586 ..     492     600 .. 0.71

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 5.3
      AAA_14  32 silyinldderdkkladpe.kllelileklkeekktylflDEiqevpewekalkslvdegknldvivtGSnskl 104
                 s  y+++d  + +k++ p+  l ++i++      +    + E  +++++   +  +++++++   ++t Sn  +
  AHX11255.1  67 SLKYFSMDYSDISKIK-PTlGLKRVIQR-----AQFHASIAELNQITGLHVLIEIFCEQDSHAFAFLTQSNITM 134
                 5667777776666655.32122233332.....44557788888888888888899998888888888888776 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 0.00023
      AAA_14  12 rvGKTtllkqlikell.....vkkesilyinldderd....kkla.dpekllelileklkeekktylflDEiqevpewekalkslvdegkn 92 
                  vGKT +l+ l++         k ++   ++l+  ++    + ++ d+e+ ++++ +++ + k+t+lf+DEi+ + ++ ++ ++ +d g+ 
  AHX11255.1 217 GVGKTAILEGLVHAIVngdvpHKLRNARVYSLKIGSLlagtR-YRgDFEERIKMVINEIANCKNTILFIDEIHTIVGAGSTSNGSIDAGNL 306
                 689999999998666677766333444444444444433422.223666666677776666699***********9988888888887744 PP

  == domain 3  score: 16.0 bits;  conditional E-value: 1.7e-05
      AAA_14  12 rvGKTtllkqlikellvkkesilyinldderdkkladpe...........kllelileklkeekktylflDEiqev.pewekalkslvdeg 90 
                  +GKT l+kq++k+l     +++ i++ +  ++ +   +           +   ++ e l ++++t++++DEi ++ ++++++l +++d g
  AHX11255.1 500 GIGKTELAKQIAKNLC---MQFVRIDMSEYMESHSVS-RllgappgyvghDKGGFLVEALFKHGNTLILFDEIEKAhKDIQNILLQIMDYG 586
                 68************99...899999998877633221.12233344444333345555544469*********998467999999999866 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.6   0.0   0.00092       0.5       5     103 ..     207     290 ..     203     311 .. 0.70
   2 !   13.8   0.0   9.8e-05     0.053      12     117 ..     497     584 ..     491     608 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00092
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseellealeqalraravielliiDEaqh 102
                 ++  + +Ge+G+GKT  l+ l++               v  ++p++  + +    ++ + l   + +  ++ ee ++++ + + +++   +l iDE++ 
  AHX11255.1 207 KNNPIYVGEPGVGKTAILEGLVHAI-------------VNGDVPHKLrNARVYSLKIGSLLAGTRYR--GDFEERIKMVINEIANCKN-TILFIDEIHT 289
                 5555679**************9996.............44455555534444455555555544444..7777777888888888888.8888888776 PP

      AAA_22 103 l 103
                 +
  AHX11255.1 290 I 290
                 5 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 9.8e-05
      AAA_22  12 GesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhlrseeale 110
                 Ge+G+GKT l+++++++l         + ++v++++++ ++s ++     r lg +  +     +    ++e  +++  +  l++ DE+++  ++++ +
  AHX11255.1 497 GETGIGKTELAKQIAKNL---------CMQFVRIDMSEYMESHSV----SRLLGAPPGY--VGHDKGGFLVEALFKHGNT--LILFDEIEKA-HKDIQN 577
                 9*****************.........***********9966655....5555555555..2333333444444444444..7777777777.666666 PP

      AAA_22 111 eLrslln 117
                  L ++++
  AHX11255.1 578 ILLQIMD 584
                 6666666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00023      0.12       2      48 ..     188     231 ..     187     252 .. 0.75
   2 ?   -1.1   0.0       3.9   2.1e+03     119     145 ..     263     288 ..     237     303 .. 0.71
   3 !   12.6   0.0   0.00024      0.13       7      60 ..     468     523 ..     463     538 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00023
      AAA_16   2 lvGReeeleqL.lsalervrsgrpelvllsGesGvGKsslvrellral 48 
                 l+ Re+e+e+  + +l+r++ +     + +Ge+GvGK+++++ l +a+
  AHX11255.1 188 LINREKEIERTiEILLRRTK-NN---PIYVGEPGVGKTAILEGLVHAI 231
                 77899999766355665554.33...3458***********8777665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 3.9
      AAA_16 119 llellkrllallsrderplvlvlDdlq 145
                 + e +k  ++ +++  + ++l++D+++
  AHX11255.1 263 FEERIKMVINEIAN-CKNTILFIDEIH 288
                 44444455533333.3459******99 PP

  == domain 3  score: 12.6 bits;  conditional E-value: 0.00024
      AAA_16   7 eeleqLlsalervrsgrp.....elvllsGesGvGKsslvrellralekdggiflrgkc 60 
                 e +e+L + l++   g       +  l+ Ge G+GK+ l++++++ l+ +   f+r + 
  AHX11255.1 468 EIIERLVHSLRPGLLGLKgekpiGTYLFGGETGIGKTELAKQIAKNLCMQ---FVRIDM 523
                 56666666666433333333368999*******************99976...666555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   7.1e-07   0.00038      72     185 ..     231     347 ..     185     350 .. 0.85
   2 ?    2.4   0.0      0.16        88      32      58 ..     487     513 ..     464     524 .. 0.78
   3 ?   -3.3   0.0       9.2     5e+03      31      51 ..     594     614 ..     591     624 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 7.1e-07
        TniB  72 vlvvqappkpdekrlyaaiLealgaplkararvskleqqvlrllrelkvrvLiiDEihnll.agsark.qreflnalksLgnelkipivlvGt.eealr 167
                 ++  ++p+k  ++r y+  + +l a ++ r + ++  ++v++ + ++k  +L iDEih ++ ags ++    + n+lk +  +  +  +++ t +e  +
  AHX11255.1 231 IVNGDVPHKLRNARVYSLKIGSLLAGTRYRGDFEERIKMVINEIANCKNTILFIDEIHTIVgAGSTSNgSIDAGNLLKPFLTKGPLRCIGATTyKEYSA 329
                 55667899999999***99****************************************9833443331446789***999999888888887245566 PP

        TniB 168 alrtDpqlasRFepialp 185
                 ++++D+ l++RF+ i+++
  AHX11255.1 330 HFEKDAALNRRFQRIEIE 347
                 79***********99986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.16
        TniB  32 rkrmpnlllvGdsnnGKtmivekFarl 58 
                 +k +  +l+ G++ +GKt ++++ a++
  AHX11255.1 487 EKPIGTYLFGGETGIGKTELAKQIAKN 513
                 5555678999***********998875 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 9.2
        TniB  31 krkrmpnlllvGdsnnGKtmi 51 
                 ++++ +n++++  +n+G + i
  AHX11255.1 594 RKSKFQNCIVICTTNVGSSFI 614
                 678899***********8877 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0         2   1.1e+03       6      22 ..     214     230 ..     211     235 .. 0.82
   2 ?   -2.8   0.0       9.9   5.4e+03       7      34 ..     348     375 ..     346     380 .. 0.84
   3 !   22.9   0.0   1.1e-07     6e-05       4     111 ..     495     608 ..     492     613 .. 0.76

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2
       AAA_3   6 gvPGlaktllvkalaka 22 
                 g PG++kt + + l +a
  AHX11255.1 214 GEPGVGKTAILEGLVHA 230
                 78*******99988765 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 9.9
       AAA_3   7 vPGlaktllvkalakaldlefkriqftp 34 
                  P l  tl +   aka   +f+r+++t 
  AHX11255.1 348 EPSLQNTLSIIDGAKAYYEDFHRVRYTK 375
                 5888889999999999999*****9996 PP

  == domain 3  score: 22.9 bits;  conditional E-value: 1.1e-07
       AAA_3   4 legvPGlaktllvkalakaldlefkriqftpdllP...sdilGte..vfeekekefefkkGpvf...anllladeinrappktqsalleameerqvtve 94 
                 + g  G++kt l+k++ak l ++f ri +   +     s +lG+   ++ +++  f +   ++f   + l+l dei++a   +q  ll++m+   +t +
  AHX11255.1 495 FGGETGIGKTELAKQIAKNLCMQFVRIDMSEYMEShsvSRLLGAPpgYVGHDKGGFLV--EALFkhgNTLILFDEIEKAHKDIQNILLQIMDYGCITDS 591
                 56788***********************987775411256788852244444444443..44551124699**************************98 PP

       AAA_3  95 gethklpepflvlatqn 111
                   +++  ++ +v+ t n
  AHX11255.1 592 TGRKSKFQNCIVICTTN 608
                 88888888888898887 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.3     1e-07   5.6e-05       1      72 [.     655     726 ..     655     733 .. 0.94

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 1e-07
                    SCHHHHHHHHHHHHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTS CS
  ClpB_D2-small   1 LtkeelkkIvdlalkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsge 72 
                    L+k+ l+kI+++ + +++  l+ +g++l++ ++++++l     + +  AR++++ ++  i ++++ ++l+ +
     AHX11255.1 655 LDKNSLEKIINKSIIEMRLLLEGKGIKLKFAEDVVKHLTGSHASGKINARSVEKKVKDDIMQAISSKMLRSK 726
                    899*************************************************************99999876 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.0   0.00027      0.15       6      32 ..     213     239 ..     210     253 .. 0.88
   2 !    8.9   0.0    0.0024       1.3       4      24 ..     494     514 ..     492     526 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00027
                 EC-TTTCHHHHHHHHHHHHCTS-SCCC CS
       NACHT   6 qGeaGsGKTtLlqklalawaegklpqg 32 
                  Ge+G+GKT+ l++l++a+  g+ p++
  AHX11255.1 213 VGEPGVGKTAILEGLVHAIVNGDVPHK 239
                 7*********************99986 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0024
                 EEEC-TTTCHHHHHHHHHHHH CS
       NACHT   4 ilqGeaGsGKTtLlqklalaw 24 
                 +  Ge G+GKT L++++a  +
  AHX11255.1 494 LFGGETGIGKTELAKQIAKNL 514
                 567**************9875 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0029       1.6      30      57 ..     204     231 ..     192     289 .. 0.82
   2 !   12.1   0.0   0.00019      0.11      36      82 ..     493     536 ..     485     613 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0029
       AAA_7  30 lknkkpvllvGptGtGKtviikdllkkl 57 
                  + k++ ++vG+ G+GKt+i++ l++++
  AHX11255.1 204 RRTKNNPIYVGEPGVGKTAILEGLVHAI 231
                 345678899***********99977665 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 0.00019
       AAA_7  36 vllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdii 82 
                  l+ G+tG GKt ++k++ k+l    ++++ i +s +++++++ +++
  AHX11255.1 493 YLFGGETGIGKTELAKQIAKNLC---MQFVRIDMSEYMESHSVSRLL 536
                 5899******************9...999***********9999887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0     0.028        15       4      24 ..     213     233 ..     211     290 .. 0.82
   2 !   12.8   0.5   0.00022      0.12       3      36 ..     495     543 ..     493     609 .. 0.57

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.028
  RNA_helicase   4 yGpsgeGKStlakeLakallk 24 
                   +G++g+GK+ + + L++a+ +
    AHX11255.1 213 VGEPGVGKTAILEGLVHAIVN 233
                   7**************999984 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00022
  RNA_helicase   3 lyGpsgeGKStlakeLakallkkl...............klkkkdsvys 36 
                   + G++g+GK+ lak++ak+l+ ++                l  ++  y+
    AHX11255.1 495 FGGETGIGKTELAKQIAKNLCMQFvridmseymeshsvsRLLGAPPGYV 543
                   56888****************8886666666665555554444455555 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.2   5.8e-05     0.032       2      41 ..     189     228 ..     188     240 .. 0.86
   2 ?    2.5   0.0      0.21   1.1e+02     100     138 ..     261     298 ..     235     312 .. 0.77
   3 ?    0.3   0.2      0.98   5.4e+02      73     123 ..     415     465 ..     362     474 .. 0.69
   4 ?    5.3   0.0     0.029        16      27      44 ..     497     514 ..     482     534 .. 0.81
   5 ?    4.1   0.2     0.069        37     120     208 ..     561     642 ..     550     665 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 5.8e-05
    ATPase_2   2 fdRekelke.leeilerepneiyfiYGpegsGKtaLlkeii 41 
                 ++Reke+++ +e +l+r++n+++++ G  g+GKta+l  ++
  AHX11255.1 189 INREKEIERtIEILLRRTKNNPIYV-GEPGVGKTAILEGLV 228
                 7******863888899999999999.*********998776 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.21
    ATPase_2 100 klvfkaielllekikkkgkkiiiiiDelqklidlglnga 138
                  + ++ i+ ++++i +  k  i++iDe+  ++  g+ ++
  AHX11255.1 261 GDFEERIKMVINEIANC-KNTILFIDEIHTIVGAGSTSN 298
                 56778889999999887.679**********97776644 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.98
    ATPase_2  73 eekkklekalgiavpkaeleeilkeksklvfkaielllekikkkgkkiiii 123
                 +++k+ ++++  +  + +l + ++  +++++ a+e++l++++k+ k++i  
  AHX11255.1 415 KVNKRRDRKIDVKYVRETLAKRFNIPIAQLNCAVEDMLKSLEKNLKEVIYD 465
                 344444444444555555555566666777777777777777777777654 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.029
    ATPase_2  27 GpegsGKtaLlkeiienl 44 
                 G  g+GKt L k+i++nl
  AHX11255.1 497 GETGIGKTELAKQIAKNL 514
                 7789************98 PP

  == domain 5  score: 4.1 bits;  conditional E-value: 0.069
    ATPase_2 120 iiiiiDelqklidlglngaellvkeL.lnliesltkek...hlcvviclsSegl.fiervyneselegrhkyilvddldketalnflkegfkel 208
                   i++De+ k+   + + ++ l++ + + +i + t +k   + c+vic++  g  fie           h + + d ++ +   +f+k+  kel
  AHX11255.1 561 TLILFDEIEKAH--K-DIQNILLQIMdYGCITDSTGRKskfQNCIVICTTNVGSsFIE---------SNHLGFSKDCVKIDREDQFAKFFTKEL 642
                 5799*******9..3.66789999885678888887772235699*****97651555.........333334444444444455555554444 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0     0.034        19      23      64 ..     208     249 ..     188     266 .. 0.80
   2 ?   -0.9   0.0       1.7     9e+02     101     116 ..     273     288 ..     265     292 .. 0.86
   3 ?    5.8   0.0     0.014       7.7      26      65 ..     494     534 ..     490     543 .. 0.79
   4 ?    5.6   0.0     0.017       9.1     108     205 ..     561     658 ..     554     660 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.034
  Mg_chelatase  23 HnlllvGppGsGKtmlakrlpsllpplseeealevakiasva 64 
                    n + vG pG GKt + + l   + + +    l  a+++s++
    AHX11255.1 208 NNPIYVGEPGVGKTAILEGLVHAIVNGDVPHKLRNARVYSLK 249
                   566889**********99999988888888888888888875 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
  Mg_chelatase 101 eislahnGvLfLDElp 116
                   ei+  +n +Lf+DE+ 
    AHX11255.1 273 EIANCKNTILFIDEIH 288
                   89999*********86 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.014
  Mg_chelatase  26 llvGppGsGKtmlakrlpsllp.plseeealevakiasvag 65 
                   l+ G  G GKt lak++++ l+ +  + ++ e  + +sv++
    AHX11255.1 494 LFGGETGIGKTELAKQIAKNLCmQFVRIDMSEYMESHSVSR 534
                   7889***********99765542677778888888888876 PP

  == domain 4  score: 5.6 bits;  conditional E-value: 0.017
  Mg_chelatase 108 GvLfLDElpefkrkvlevLRePledgevtisrakakvefparfqlvaamNpcpc...gklkdkekectcsekeierYlsklsgplldRidlqvevkk 201
                    ++++DE+ + ++++ ++L + ++ g +t s   +k +f  ++ +++++N   +   +++   +k+c+ + ++ +++ +   + ll+R+dl +  ++
    AHX11255.1 561 TLILFDEIEKAHKDIQNILLQIMDYGCITDSTG-RKSKFQ-NCIVICTTNVGSSfieSNHLGFSKDCV-KIDREDQFAKFFTKELLNRLDLALVFNR 654
                   56789*********************9986654.456775.789999999987622223333456665.46667788999999********999888 PP

  Mg_chelatase 202 leae 205
                   l+++
    AHX11255.1 655 LDKN 658
                   7765 PP

>> Torsin  Torsin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.3e-06    0.0012      10      86 ..     446     523 ..     441     532 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.3e-06
                 XX.---HHHHHHHHHHH--S-HHHHHHHHHHHHHHHT-SS-SS-EEE.EEEE-TTSSHHHHHHHHHHHHSTTGGGSTT CS
      Torsin  10 krisanleeLekdlekklfGqhlvkklvvksvkaylenekpkkpLvl.sfhGwtGtGknfvaeiiaenlyrdGlrsdy 86 
                 + ++  l++Lek+l++ ++ q  + + +v+s++  l   k +kp+    f G tG Gk  +a++ia+nl  + +r d+
  AHX11255.1 446 CAVEDMLKSLEKNLKEVIYDQDEIIERLVHSLRPGLLGLKGEKPIGTyLFGGETGIGKTELAKQIAKNLCMQFVRIDM 523
                 55666799************************************965157789***************9877666555 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0       0.5   2.7e+02      37      50 ..     211     224 ..     189     255 .. 0.81
   2 ?    4.0   0.0      0.07        38      84      96 ..     278     290 ..     261     294 .. 0.79
   3 !    7.8   0.0    0.0046       2.5      31      61 ..     488     518 ..     457     531 .. 0.84
   4 ?   -0.2   0.0       1.3   7.3e+02      86     109 ..     561     584 ..     546     600 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.5
      RuvB_N  37 llyGpPGlGkttla 50 
                 + +G PG+Gkt++ 
  AHX11255.1 211 IYVGEPGVGKTAIL 224
                 678********975 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.07
      RuvB_N  84 ekdvlfideihrl 96 
                 ++ +lfideih +
  AHX11255.1 278 KNTILFIDEIHTI 290
                 578********86 PP

  == domain 3  score: 7.8 bits;  conditional E-value: 0.0046
      RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvkl 61 
                 +++   l+ G  G+Gkt lak iak+l +++
  AHX11255.1 488 KPIGTYLFGGETGIGKTELAKQIAKNLCMQF 518
                 566677999****************998765 PP

  == domain 4  score: -0.2 bits;  conditional E-value: 1.3
      RuvB_N  86 dvlfideihrlsraveevlysame 109
                  +++ dei + ++ ++++l + m+
  AHX11255.1 561 TLILFDEIEKAHKDIQNILLQIMD 584
                 45677**************99986 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.23   1.2e+02      21      40 ..     212     231 ..     194     237 .. 0.82
   2 !   13.4   0.0   6.3e-05     0.034      18      58 ..     492     530 ..     484     546 .. 0.87

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.23
  Zeta_toxin  21 lgGqpGAGKselaellkdel 40 
                  +G pG GK++++e l  ++
  AHX11255.1 212 YVGEPGVGKTAILEGLVHAI 231
                 579**********9887665 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 6.3e-05
  Zeta_toxin  18 lillgGqpGAGKselaellkdelerqgnvvrldpDdlRelh 58 
                  +l gG +G GK+ela+ ++++l    ++vr+d  ++ e h
  AHX11255.1 492 TYLFGGETGIGKTELAKQIAKNL--CMQFVRIDMSEYMESH 530
                 5899*******************..89******99998887 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       8.2   4.4e+03      58      82 ..     144     171 ..     141     181 .. 0.70
   2 ?    4.6   0.0     0.056        31       4      43 ..     192     231 ..     189     238 .. 0.77
   3 !   11.1   0.0   0.00055       0.3      22      46 ..     493     517 ..     455     527 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 8.2
                 EEEE..SS...EEEEE-TT-SSTHHHHH CS
        TsaE  58 eYelekeg...lyHfDlYRledeeelee 82 
                 +Y+++  +    +H+D+ R +d+++++e
  AHX11255.1 144 TYKNKLPEngaTCHADILRGTDASSFKE 171
                 5665544466799****99887776655 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.056
                 HHHHHHHHHHHHHCHTEEEEEEESTTSSHHHHHHHHHHHT CS
        TsaE   4 eeetealgkklakalgdvilLeGdLGaGKTtlvrglakal 43 
                 e+e+e+  + l + +++  +  G+ G+GKT++  gl++a+
  AHX11255.1 192 EKEIERTIEILLRRTKNNPIYVGEPGVGKTAILEGLVHAI 231
                 5666666666666666777889**************9987 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00055
                 EEEEESTTSSHHHHHHHHHHHTT-- CS
        TsaE  22 ilLeGdLGaGKTtlvrglakalgve 46 
                  l+ G+ G GKT l++++ak+l ++
  AHX11255.1 493 YLFGGETGIGKTELAKQIAKNLCMQ 517
                 7899****************99876 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.0    0.0051       2.8      45     103 ..     205     267 ..     186     291 .. 0.63
   2 !    7.9   0.0    0.0042       2.3      50      78 ..     493     521 ..     449     538 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0051
   IstB_IS21  45 ekkenivllGpsGvGKshlaialgveavrag..lsvlfvrvedL..veelkrarrdgklaral 103
                 ++k+n + +G +GvGK+ +   l ++ v+ +  ++ +  rv  L   + l+  r  g +++++
  AHX11255.1 205 RTKNNPIYVGEPGVGKTAILEGLVHAIVNGDvpHKLRNARVYSLkiGSLLAGTRYRGDFEERI 267
                 678999*************99999988874422444444444331134444444444444444 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.0042
   IstB_IS21  50 ivllGpsGvGKshlaialgveavraglsv 78 
                  ++ G +G+GK+ la  ++++ + + +++
  AHX11255.1 493 YLFGGETGIGKTELAKQIAKNLCMQFVRI 521
                 466799*************9999876655 PP

>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0    0.0001     0.056      20      46 ..     491     517 ..     483     532 .. 0.87
   2 ?    1.7   0.1      0.37     2e+02     106     127 ..     562     583 ..     552     584 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.0001
  DNA_pol3_delta2  20 hayLfeGdegigkkelalnlakallce 46 
                       +yLf G++gigk ela+++ak+l+ +
       AHX11255.1 491 GTYLFGGETGIGKTELAKQIAKNLCMQ 517
                      58**********************976 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.37
  DNA_pol3_delta2 106 iiiiedaekmtksAaNalLktl 127
                      +i+ +++ek +k  +N+lL+++
       AHX11255.1 562 LILFDEIEKAHKDIQNILLQIM 583
                      68899**************986 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.093        50       4      21 ..     212     229 ..     211     281 .. 0.86
   2 !   11.0   0.0   0.00067      0.36       3      33 ..     494     532 ..     493     604 .. 0.64

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.093
      AAA_33   4 lvGlpGsGKstlaerllk 21 
                  vG pG+GK+  +e+l+ 
  AHX11255.1 212 YVGEPGVGKTAILEGLVH 229
                 69************9984 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00067
      AAA_33   3 llvGlpGsGKstlaerllkklgavllssdt........l 33 
                 l+ G  G GK+ la++++k+l +++++ d         +
  AHX11255.1 494 LFGGETGIGKTELAKQIAKNLCMQFVRIDMseymeshsV 532
                 578999****************66666554334444440 PP

>> AAA_6  Hydrolytic ATP binding site of dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.9   0.0   3.7e-05      0.02      39      78 ..     497     536 ..     490     538 .. 0.93

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
       AAA_6  39 GpagtGKtEtvkdLakalakqvvvfncsdqldykslgkif 78 
                 G +g GKtE  k++ak+l +q+v ++ s+ ++ +s+++++
  AHX11255.1 497 GETGIGKTELAKQIAKNLCMQFVRIDMSEYMESHSVSRLL 536
                 899********************************99975 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.039        21       1      42 [.     191     229 ..     191     235 .. 0.78
   2 ?    6.0   0.2      0.01       5.7      26      44 ..     496     514 ..     484     603 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.039
                 -HHHHHHHHHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCC CS
      NB-ARC   1 reksvekviekLlekdelqslvvalvGmgGvGKttlakqiln 42 
                 rek++e+ ie Ll+  + +      vG +GvGKt +++  ++
  AHX11255.1 191 REKEIERTIEILLRRTKNN---PIYVGEPGVGKTAILEGLVH 229
                 5788999999999866555...3468*********9987665 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.01
                 EESTTSSHHHHHHHHCCSH CS
      NB-ARC  26 vGmgGvGKttlakqilnks 44 
                  G  G+GKt lakqi +++
  AHX11255.1 496 GGETGIGKTELAKQIAKNL 514
                 5899***********9983 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.7   9.2e+02      12      46 ..     195     229 ..     184     236 .. 0.69
   2 ?   -0.8   0.0       2.4   1.3e+03     131     146 ..     277     292 ..     254     308 .. 0.79
   3 ?    9.3   0.0     0.002       1.1       4      49 ..     462     515 ..     449     520 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
                 HHHHT......TTSEEEEEESTTSTHHHHHHHHHH CS
      ResIII  12 ienlleklkskrdkrglikmaTGtGKTlvaaklie 46 
                 ie+++e l  + +++ + + + G+GKT ++  l+ 
  AHX11255.1 195 IERTIEILLRRTKNNPIYVGEPGVGKTAILEGLVH 229
                 4444444443555666778899*****99866665 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.4
                 TT-SEEEEETGGGTTS CS
      ResIII 131 drfdviiiDEaHrlga 146
                  ++ +++iDE H + +
  AHX11255.1 277 CKNTILFIDEIHTIVG 292
                 4566999*****8876 PP

  == domain 3  score: 9.3 bits;  conditional E-value: 0.002
                 E-HHHHHHHHHHT...........TTS...EEEEEESTTSTHHHHHHHHHHHH- CS
      ResIII   4 lreyQeeaienlleklks.....krdk...rglikmaTGtGKTlvaaklierll 49 
                 + + Q e+ie+l+ +l       k++k    +l+  +TG GKT +a +++++l 
  AHX11255.1 462 VIYDQDEIIERLVHSLRPgllglKGEKpigTYLFGGETGIGKTELAKQIAKNLC 515
                 556788888888888877999996666677999*************99999885 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.0    0.0094       5.1       3      23 ..     211     231 ..     210     246 .. 0.86
   2 ?    3.2   0.0      0.18        97       6      22 ..     497     513 ..     493     528 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0094
                 EEESSTTSSHHHHHHCHCT-C CS
         Roc   3 vlvGdsgvGKtsllkrfvedk 23 
                 + vG+ gvGKt +l+ +v+  
  AHX11255.1 211 IYVGEPGVGKTAILEGLVHAI 231
                 579***********9998765 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.18
                 SSTTSSHHHHHHCHCT- CS
         Roc   6 GdsgvGKtsllkrfved 22 
                 G++g+GKt l+k++ ++
  AHX11255.1 497 GETGIGKTELAKQIAKN 513
                 9***********99876 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.0     0.057        31      97     121 ..     205     229 ..     162     245 .. 0.73
   2 ?    5.8   0.0     0.022        12     101     127 ..     492     518 ..     431     533 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.057
                  CTTSEEEEECSTTSSHHHHHHHHCT CS
  RsgA_GTPase  97 lkdktsvlvGqSGvGKStLinallp 121
                   +++  + vG+ GvGK+++++ l+ 
   AHX11255.1 205 RTKNNPIYVGEPGVGKTAILEGLVH 229
                  334567889**********998876 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.022
                  EEEEECSTTSSHHHHHHHHCTT----- CS
  RsgA_GTPase 101 tsvlvGqSGvGKStLinallpelelkt 127
                  t ++ G++G+GK+ L ++++ +l ++ 
   AHX11255.1 492 TYLFGGETGIGKTELAKQIAKNLCMQF 518
                  78899**************99876665 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.044        24       6      28 ..     214     236 ..     211     239 .. 0.84
   2 ?   -2.9   0.1        10   5.4e+03      81     104 ..     263     287 ..     257     288 .. 0.61
   3 ?    5.7   0.0     0.023        12       5      26 ..     496     517 ..     492     522 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.044
                 --TTSSHHHHHHHHHHHH...GG CS
    NTPase_1   6 GppGvGKtTlvkkvlellkssgv 28 
                 G+pGvGKt +++ +++++ + +v
  AHX11255.1 214 GEPGVGKTAILEGLVHAIVNGDV 236
                 9***********99998876655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 10
                 HHHHHHHHHHHHH.HHH-EEEE--- CS
    NTPase_1  81 feelalealrkal.seadviviDEi 104
                 fee +  ++++    ++ ++ iDEi
  AHX11255.1 263 FEERIKMVINEIAnCKNTILFIDEI 287
                 5555555555444245559999998 PP

  == domain 3  score: 5.7 bits;  conditional E-value: 0.023
                 E--TTSSHHHHHHHHHHHH... CS
    NTPase_1   5 TGppGvGKtTlvkkvlellkss 26 
                  G+ G+GKt l k+++++l  +
  AHX11255.1 496 GGETGIGKTELAKQIAKNLCMQ 517
                 699*************999655 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0      0.13        71       5      21 ..     214     230 ..     211     289 .. 0.69
   2 ?    5.7   0.0     0.037        20       4      25 ..     496     549 ..     494     588 .. 0.61

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.13
      AAA_18   5 GtpGvGKttlakeLskr 21 
                 G pGvGKt + + L   
  AHX11255.1 214 GEPGVGKTAILEGLVHA 230
                 88*********999655 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.037
      AAA_18   4 tGtpGvGKttlakeLskrlgf.................................g 25 
                  G  G GKt+lak ++k l +                                 g
  AHX11255.1 496 GGETGIGKTELAKQIAKNL-CmqfvridmseymeshsvsrllgappgyvghdkgG 549
                 677899**********998.33566655555555555555555555555444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0      0.01       5.6      37      61 ..     211     235 ..     179     252 .. 0.80
   2 ?   -0.8   0.0       1.8   9.7e+02     127     166 ..     264     302 ..     243     311 .. 0.79
   3 ?    0.1   0.0      0.92     5e+02      37      54 ..     494     511 ..     490     517 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.01
      AAA_25  37 llaGapgtGKttlaldlalavatGk 61 
                 + +G pg+GKt+++  l++a++ G+
  AHX11255.1 211 IYVGEPGVGKTAILEGLVHAIVNGD 235
                 679******************9987 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.8
      AAA_25 127 tadvdaleaaieevegvrlvviDplsralggdensnsdvg 166
                 ++ ++ ++++i   ++   + iD +  ++g++++sn  ++
  AHX11255.1 264 EERIKMVINEIAN-CKNTILFIDEIHTIVGAGSTSNGSID 302
                 5667788889999.569999***********999998863 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.92
      AAA_25  37 llaGapgtGKttlaldla 54 
                 l+ G +g GKt la ++a
  AHX11255.1 494 LFGGETGIGKTELAKQIA 511
                 789**********98887 PP

>> PP1_inhibitor  PKC-activated protein phosphatase-1 inhibitor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       7.9   4.3e+03      73      99 ..     184     208 ..     172     211 .. 0.68
   2 ?   10.3   0.3   0.00095      0.52      22      78 ..     412     470 ..     395     476 .. 0.77
   3 ?   -1.1   0.1       3.1   1.7e+03     103     129 ..     637     663 ..     630     672 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 7.9
                    HHHHHHCTSSTTHHHHHHHHHHTTCSS CS
  PP1_inhibitor  73 nidelldlesdeersrklqellksctn 99 
                    +id+l++ e + er+  ++ ll+  +n
     AHX11255.1 184 KIDKLINREKEIERT--IEILLRRTKN 208
                    688888877777665..5556666665 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00095
                    --SSSS-S-SSSSSSSS-SSSSCHHHHHH.HHHHHHHHHCSSSSSTTS-SSS.HHHHHH CS
  PP1_inhibitor  22 eaglsiqkrqarvtvkydrkelqkrldve.kWidesleelylGreeemPeev.nidell 78 
                    ++++  ++r+ ++ vky r  l kr+++    +++++e++ +  e+++ e + + de++
     AHX11255.1 412 DSSKVNKRRDRKIDVKYVRETLAKRFNIPiAQLNCAVEDMLKSLEKNLKEVIyDQDEII 470
                    4444445566779**************973579999**999999999988764556655 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 3.1
                    HHHHHHHHHCTTT--XX.....XXXXX CS
  PP1_inhibitor 103 afitellvklkGlqkqeelqkeGiehp 129
                     f++ell +l+     + l+k+ +e+ 
     AHX11255.1 637 FFTKELLNRLDLALVFNRLDKNSLEKI 663
                    578888888887777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (743 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       797  (0.0444531); expected 358.6 (0.02)
Passed bias filter:                      580  (0.0323498); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                        33  (0.00184059); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              33  [number of targets reported over threshold]
# CPU time: 0.71u 0.28s 00:00:00.99 Elapsed: 00:00:00.41
# Mc/sec: 5455.57
//
Query:       AHX11256.1  [L=103]
Description: hypothetical protein NHE_0297 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 859.52
//
Query:       AHX11257.1  [L=42]
Description: hypothetical protein NHE_0298 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       129  (0.00719505); expected 358.6 (0.02)
Passed bias filter:                      111  (0.00619109); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.22s 00:00:00.51 Elapsed: 00:00:00.34
# Mc/sec: 366.25
//
Query:       AHX11258.1  [L=225]
Description: ABC transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.7e-30  104.9   0.1      7e-30  104.3   0.1    1.2  1  ABC_tran     ABC transporter
    3.1e-08   33.8   0.2    0.00055   19.8   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.5e-06   28.2   0.0      0.022   14.5   0.0    2.1  2  AAA_15       AAA ATPase domain
    7.3e-05   22.3   0.2    0.00066   19.2   0.0    1.9  2  SMC_N        RecF/RecN/SMC N terminal domain
    0.00019   21.7   0.3     0.0029   17.9   0.3    2.2  1  AAA_22       AAA domain
     0.0004   20.8   0.2    0.00082   19.8   0.2    1.5  1  AAA_16       AAA ATPase domain
     0.0028   17.2   0.5       0.06   12.9   0.2    2.2  2  AAA_25       AAA domain
  ------ inclusion threshold ------
      0.016   15.0   0.1        3.6    7.3   0.0    2.2  2  IstB_IS21    IstB-like ATP binding protein
      0.019   14.7   0.2       0.21   11.3   0.0    2.1  2  AAA_30       AAA domain
      0.027   14.4   0.1      0.064   13.2   0.1    1.6  1  RsgA_GTPase  RsgA GTPase
      0.042   13.5   0.1      0.088   12.4   0.1    1.5  1  SRP54        SRP54-type protein, GTPase domain
       0.07   11.8   0.0       0.11   11.2   0.0    1.2  1  AAA_13       AAA domain
      0.098   12.8   0.5        0.3   11.2   0.5    1.9  1  AAA_33       AAA domain
       0.12   12.4   0.0       0.29   11.2   0.0    1.7  1  AAA_14       AAA domain
       0.14   11.8   0.0       0.18   11.5   0.0    1.2  1  AAA_24       AAA domain
       0.15   12.4   0.0        1.9    8.8   0.0    2.2  1  SbcCD_C      Putative exonuclease SbcCD, C subunit
       0.15   12.1   0.1       0.22   11.6   0.1    1.5  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.3   0.1   6.6e-33     7e-30       1     136 [.      26     172 ..      26     173 .. 0.96

  Alignments for each domain:
  == domain 1  score: 104.3 bits;  conditional E-value: 6.6e-33
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH.............HHHTC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx.............xxxxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke..qeleslrkeigvlpqepqlfpeltvren.............esdee 84 
                 lk  +l + ege+va+vG +G GK+t l+l   l ++++G i++d++++++    + + r++ig++ q ++l ++l+v +n              +++e
  AHX11258.1  26 LKGANLRIFEGEVVALVGASGVGKTTTLQLAGLLDQQDSGIIKIDDTEIEYfnSATAIRREKIGFIYQFHHLLEDLSVIRNimlplliagiqkkIAKAE 124
                 68899************************99999999**************9999999*******************99999*********99999999 PP

                 HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  85 iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +ek+l  l+l +++++ v     +LSgGq+qr+a+ara++kkpkl+++DEpt
  AHX11258.1 125 AEKVLGALNLGDVANKSV----VELSGGQRQRIAVARAIIKKPKLIIADEPT 172
                 ************999999....*****************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00013      0.14       2      40 ..      39      65 ..      38      94 .. 0.73
   2 !   19.8   0.0   5.2e-07   0.00055     233     302 ..     141     208 ..     115     209 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00013
      AAA_21  2 nvliGpNgsGKSnLLdaldllarldrdvegltdelsggg 40
                 +l+G+ g+GK++ L++  ll             ++++g
  AHX11258.1 39 VALVGASGVGKTTTLQLAGLLD------------QQDSG 65
                68****************9993............22222 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 5.2e-07
      AAA_21 233 parelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsrngaQviltTHSplll 302
                 ++ elS G+++ +a++ a++  +   +l++ DEp  +L+P+  + +++l+ + +++ +a v+l+TH+ ++l
  AHX11258.1 141 SVVELSGGQRQRIAVARAIIKKP---KLIIADEPTGNLDPENAENVFKLIlRFARQSKAAVLLATHNLSFL 208
                 46788999999988888888666...99*******************99965555599*********9887 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   2.1e-05     0.022      24      83 ..      37      92 ..      29     133 .. 0.78
   2 !   11.8   0.0   0.00013      0.14     318     367 ..     157     206 ..     142     208 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 2.1e-05
      AAA_15 24 eltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83
                e+  l+G+ ++GK++ l++  l+ +++    +  iki++ ++e+f++    ++ kI + +
  AHX11258.1 37 EVVALVGASGVGKTTTLQLAGLLDQQD----SGIIKIDDTEIEYFNSATAIRREKIGFIY 92
                3889**************999999988....899**********************9988 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 0.00013
      AAA_15 318 dekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                 + + +k+++++ +EP  +L p++ + ++kl+++ a+++k  v++ TH+  
  AHX11258.1 157 RAIIKKPKLIIADEPTGNLDPENAENVFKLILRFARQSKAAVLLATHNLS 206
                 4577899****************************************975 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.22   2.3e+02      22      39 ..      34      51 ..      25      56 .. 0.85
   2 !   19.2   0.0   6.3e-07   0.00066     135     213 ..     106     219 ..      58     223 .. 0.73

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.22
                TTSSEEEEEESTTSSHHH CS
                xxxxxxxxxxxxxxxxxx RF
       SMC_N 22 fsksftaivGpNGSGKsn 39
                f+ ++ a+vG+ G GK+ 
  AHX11258.1 34 FEGEVVALVGASGVGKTT 51
                778899**********96 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 6.3e-07
                 T.....................................CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHH..HHCTTSEEEE CS
                 x.....................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
       SMC_N 135 e.....................................lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellk..eksknaQfiv 194
                 +                                     +LSgG+++ +a+a   A   +k+  l + De   +LD +n ++v +l+   +++++a ++ 
  AHX11258.1 106 NimlplliagiqkkiakaeaekvlgalnlgdvanksvvELSGGQRQRIAVAR--A--IIKKPKLIIADEPTGNLDPENAENVFKLILrfARQSKAAVLL 200
                 255555555555556666666666666666667777779******9888764..3..355667999******************99845566679999* PP

                 E-SSHHHCCC-SCEEEEEE CS
                 xxxxxxxxxxxxxxxxxxx RF
       SMC_N 195 islreemlekadklvgvtk 213
                  +++  +le+ad++++++ 
  AHX11258.1 201 ATHNLSFLEEADRTLKISN 219
                 **************99976 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   2.8e-06    0.0029       6     126 ..      37     199 ..      32     209 .. 0.54

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.8e-06
      AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaee..............................erpevvfvtlpsstsskdllrellralglelka.... 70 
                  +++++G sG+GKTt+l+     +++++ + +                              e+ +v+                          +    
  AHX11258.1  37 EVVALVGASGVGKTTTLQLAGLLDQQDSGIIKiddteieyfnsatairrekigfiyqfhhllEDLSVI--------------------------Rniml 109
                 5789***************9999987655555555555555555555543333333333333233332..........................02222 PP

      AAA_22  71 ............................erlsseell.ealeqalrarav...ielliiDEaqh.lr..s.eealeeLrsllnlsrkgvqli 126
                                             +++s  el   + ++ + ara    ++l+i DE    l+  + e++++ + +++   +++ +++
  AHX11258.1 110 plliagiqkkiakaeaekvlgalnlgdvANKSVVELSgGQRQRIAVARAIikkPKLIIADEPTGnLDpeNaENVFKLILRFAR--QSKAAVL 199
                 22223333333334444444444444444777777776666666666666777777777776665754312444444444444..4444444 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8   0.2   7.8e-07   0.00082      23     131 ..      35     195 ..      25     218 .. 0.61

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 7.8e-07
      AAA_16  23 rpelvllsGesGvGKsslvrellralekdg.gif.lrgkcdql.esaipy........salaqalareellrqllde.....aesaeleawrekleeal 105
                 ++e+v l+G+sGvGK++ ++ +   l +++ gi  +  +  ++  sa++         +++  +l+  +++r +  +      +++ + a         
  AHX11258.1  35 EGEVVALVGASGVGKTTTLQLAG-LLDQQDsGIIkIDDTEIEYfNSATAIrrekigfiYQFHHLLEDLSVIRNIMLPlliagIQKKIAKAE-------- 124
                 4589***************7777.7888852333333333333433322222443334445555555555555555544433222222222........ PP

      AAA_16 106 a.............................................avpelagaeasrllellkrllalls 131
                 a                                             ++++l+++ a+ ++ l+ r++++++
  AHX11258.1 125 AekvlgalnlgdvanksvvelsggqrqriavaraiikkpkliiadePTGNLDPENAENVFKLILRFARQSK 195
                 23333444477777776666777777777778888888888888887778888777777777777775544 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   0.2   5.7e-05      0.06      30      50 ..      33      53 ..      25      58 .. 0.86
   2 ?    2.5   0.0     0.086        91     164     188 ..     179     203 ..     120     204 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.7e-05
      AAA_25 30 lpagelallaGapgtGKttla 50
                + +ge+++l+Ga+g+GKtt +
  AHX11258.1 33 IFEGEVVALVGASGVGKTTTL 53
                679***************965 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.086
      AAA_25 164 dvgalvealeriarrtgaavllvhH 188
                  ++ +++ + r+ar+ +aavll  H
  AHX11258.1 179 NAENVFKLILRFARQSKAAVLLATH 203
                 357788899999**********999 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.01        11      46      61 ..      35      50 ..      21      64 .. 0.86
   2 ?    7.3   0.0    0.0034       3.6      98     151 ..     152     207 ..     139     225 .] 0.70

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.01
   IstB_IS21 46 kkenivllGpsGvGKs 61
                + e ++l+G sGvGK+
  AHX11258.1 35 EGEVVALVGASGVGKT 50
                57899**********9 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0034
   IstB_IS21  98 klaralkrllkvdllilDdlgllpldqaeaellfevie..kryerrsiii.tsnlpf 151
                 ++a a + + k++l+i D+  + +ld ++ae++f++i   +r  ++++++ t nl+f
  AHX11258.1 152 RIAVARAIIKKPKLIIADEP-TGNLDPENAENVFKLILrfARQSKAAVLLaTHNLSF 207
                 45555556677788888875.689***********9962246666666663556665 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0002      0.21      19      43 ..      37      61 ..      29      82 .. 0.82
   2 ?    1.4   0.0      0.22   2.3e+02      81     112 ..     150     187 ..     111     204 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0002
      AAA_30 19 rvavltGpAGtGKttalkalreawe 43
                 v++l+G+ G GKtt+l+ +  + +
  AHX11258.1 37 EVVALVGASGVGKTTTLQLAGLLDQ 61
                5999*************98765555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.22
      AAA_30  81 k.....grarlepgtllivDE.agmvdtkqlaallkaa 112
                 +     +ra +++ +l+i DE +g +d +++++++k +
  AHX11258.1 150 RqriavARAIIKKPKLIIADEpTGNLDPENAENVFKLI 187
                 14455433445555888888856777777776665543 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1     6e-05     0.064      97     117 ..      34      54 ..      28      72 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6e-05
                  CTTSEEEEECSTTSSHHHHHH CS
  RsgA_GTPase  97 lkdktsvlvGqSGvGKStLin 117
                  +++++++lvG SGvGK+t + 
   AHX11258.1  34 FEGEVVALVGASGVGKTTTLQ 54 
                  67899************9775 PP

>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   8.3e-05     0.088       3      28 ..      38      62 ..      36      70 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                EEEEEESTTSSHHHHHHHHHHHHHHT CS
       SRP54  3 villvGlqGaGKTttlaKLaallkke 28
                v++lvG  G+GKTttl +La ll ++
  AHX11258.1 38 VVALVGASGVGKTTTL-QLAGLLDQQ 62
                899***********98.477666665 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0001      0.11     523     584 ..     159     218 ..     151     223 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0001
      AAA_13 523 eigkdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkkntkrk 584
                  i+k k ++ D P   LD +    vf li   +  +++ + +++ THnl+f+ e+++ +k +
  AHX11258.1 159 IIKKPKLIIADEPTGNLDPENAENVFKLILRFA--RQSKAAVLLATHNLSFLEEADRTLKIS 218
                 46899************************9998..45566799***********99988765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.5   0.00028       0.3       1      17 [.      38      54 ..      38     215 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
      AAA_33  1 lvllvGlpGsGKstlae 17
                +v lvG++G+GK+t ++
  AHX11258.1 38 VVALVGASGVGKTTTLQ 54
                799***********876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00028      0.29       3      43 ..      37      76 ..      35     105 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00028
      AAA_14  3 kilvitGaRrvGKTtllkqlikell.vkkesilyinldderd 43
                ++++++Ga  vGKTt l ql+  ll  +++ i+ i+  + ++
  AHX11258.1 37 EVVALVGASGVGKTTTL-QLA-GLLdQQDSGIIKIDDTEIEY 76
                799*************8.555.34423444444444333333 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00017      0.18       4      42 ..      38      73 ..      35     126 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00017
      AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtekGlksldadk 42
                 ++++G sg+GKTt++  +    l+ + + G  ++d+++
  AHX11258.1 38 VVALVGASGVGKTTTLQLA---GLLDQQDSGIIKIDDTE 73
                689************9988...33333333444444444 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.8   0.0    0.0018       1.9      62      88 ..     161     187 ..     131     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.0018
     SbcCD_C  62 palrlvfLDEAFsklDeesiatllell 88 
                 ++++l++ DE  ++lD+e+++++++l+
  AHX11258.1 161 KKPKLIIADEPTGNLDPENAENVFKLI 187
                 4689******************99985 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.1   0.00021      0.22       4      40 ..      41      75 ..      38     200 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.00021
                EESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSC CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  4 astkGGvGKTtlaanLaralarrglrVllvDaDpqan 40
                  + +GvGKTt+ + La +l ++   ++ +D D++ +
  AHX11258.1 41 LVGASGVGKTTT-LQLAGLLDQQDSGIIKID-DTEIE 75
                5689*****985.799999999999998888.54433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      417  (0.0232584); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.51u 0.29s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 1532.88
//
Query:       AHX11259.1  [L=266]
Description: hypothetical protein NHE_0300 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      583  (0.0325172); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.38
# Mc/sec: 2123.95
//
Query:       AHX11260.1  [L=41]
Description: hypothetical protein NHE_0301 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      228  (0.0127168); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 338.50
//
Query:       AHX11261.1  [L=542]
Description: comEC/Rec2-related domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.5e-51  174.1  10.2    4.4e-51  173.7  10.2    1.1  1  Competence  Competence protein
      0.004   16.8   0.0      0.004   16.8   0.0    3.1  2  DUF4131     Domain of unknown function (DUF4131)
  ------ inclusion threshold ------
      0.036   14.4   0.3       0.15   12.4   0.2    1.9  2  DUF4467     Domain of unknown function with cystatin-like fol


Domain annotation for each model (and alignments):
>> Competence  Competence protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.7  10.2   7.4e-55   4.4e-51       1     266 [.     110     415 ..     110     420 .. 0.89

  Alignments for each domain:
  == domain 1  score: 173.7 bits;  conditional E-value: 7.4e-55
  Competence   1 LllGdrselseevweafqktGlaHllAiSGlHvglvagllllllrrl.......llrlplrklaallallflllYallaGfspsvlRAllmlllvllal 92 
                 L++G++++++ +v + f+k+G+ HllAiSGlH+glv +++++l+rr         lr+ ++k+ a+++++  l+Y+ ++  ++s++RA++m++ + l +
  AHX11261.1 110 LTIGKKDGINNNVIATFRKSGTFHLLAISGLHMGLVGLFFFALFRRSctlseylTLRYDIKKISAFAGIASSLFYLQISCGQVSAQRACIMTCTFFLSI 208
                 899***************************************************9******************************************** PP

  Competence  93 llkrkaspldalalaallvllvdPlallsaGfqLSflavagilllaprlekalkrlskkvrelllla................................ 159
                 l++rk + +++  laa++++++ P+ ++++Gfq+ f av gi+ ++++  + l+r + k ++l  +                                 
  AHX11261.1 209 LIDRKPDIFRSTTLAAIILIVLYPENIFKPGFQMLFFAVSGICSCTSNNHDTLFRPTLKKKILGNFShlhnpsekkpghylirktlvtlsrllvytgki 307
                 **********************************************5555555555555554444445555555555556666666699********** PP

  Competence 160 ..vslaaqlallplllylfgqislvsllaNllavPlvsllvlplallallllllpslaalllqladlllelllellellaslplaslvlgkpsllllll 256
                   +s+ a+ a+ p+++y+f+++sl++++aN +a+P++++l++p ++++l+ +++   +  l  l ++ +e l++l+e++++l +    +  +s   lll
  AHX11261.1 308 akISIFATAATSPFVIYHFHYFSLTGIFANAVAIPVTTFLIIPTLIAILASMPI-CDSHTLYILLEIEIESLIRLMEAFNRLNFGYTDIHGFSGMTLLL 405
                 ***************************************************999.6666666678****************999998887777777777 PP

  Competence 257 lyllllllll 266
                 + ++ l+ll+
  AHX11261.1 406 ISFGTLILLI 415
                 7777666665 PP

>> DUF4131  Domain of unknown function (DUF4131)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   6.7e-07     0.004     107     163 ..      13      70 ..       7      74 .. 0.87
   2 ?   -3.3   4.1         1   6.1e+03      26      53 ..     155     196 ..     131     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 6.7e-07
     DUF4131 107 rvlvtvpkspae.glrpGdrlrltgrlkrprpatNpggFDyraYLarqgIfatlyvkg 163
                 + l+ +++ +   +l pGd +r+++ +++ r+a  p g  + ++    +I+at+++ g
  AHX11261.1  13 KSLLKLYSRQKLeELNPGDIVRFSAYIEPSRGAVTPSGHEFSKFHYFANIRATGRIVG 70 
                 55667777777778***************************************99865 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1
     DUF4131  26 r..............rprrrvllllllllllallgfalrapq 53 
                 r              ++   ++++++ l+ l  ++ +++a++
  AHX11261.1 155 RsctlseyltlrydiKKISAFAGIASSLFYLQISCGQVSAQR 196
                 234566677777776666666777777776666666666554 PP

>> DUF4467  Domain of unknown function with cystatin-like fold (DUF4467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.44   2.6e+03      23      45 ..       2      24 ..       1      28 [. 0.88
   2 ?   12.4   0.2   2.6e-05      0.15      21      65 ..     486     531 ..     478     539 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.44
     DUF4467 23 gndvevdikkedanvyVyedgKl 45
                gn + + i++e++  + y   Kl
  AHX11261.1  2 GNRISITIEHEKSLLKLYSRQKL 24
                6889999***********99986 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2.6e-05
     DUF4467  21 kkgndvevdikkedanvyVy.edgKlivlaykllknreevtyvaYe 65 
                  ++  ++++i+k d   y y ++gK+i+++y+  + +++ +yv  +
  AHX11261.1 486 TVSHSDNPEIEKTDQSSYLYrKNGKVILIDYNSQNPEQKQRYVFSN 531
                 566788999***********5579********99999999998655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      339  (0.0189079); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 4147.26
//
Query:       AHX11262.1  [L=37]
Description: hypothetical protein NHE_0303 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.12   12.3   0.0       0.15   12.0   0.0    1.3  1  DUF2847   Protein of unknown function (DUF2847)


Domain annotation for each model (and alignments):
>> DUF2847  Protein of unknown function (DUF2847)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.1e-06      0.15      12      35 ..       9      32 ..       2      37 .] 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-06
     DUF2847 12 ileeskekpvlifKhstrcsiSae 35
                il++s    +lifK+ t+c+ S+ 
  AHX11262.1  9 ILKNSAFLLALIFKANTTCPNSTP 32
                6677777789**********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       206  (0.0114898); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.19s 00:00:00.50 Elapsed: 00:00:00.34
# Mc/sec: 324.45
//
Query:       AHX11263.1  [L=258]
Description: glycine cleavage T-C-terminal barrel domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.1e-06   26.4   0.0      5e-06   26.1   0.0    1.2  1  GCV_T     Aminomethyltransferase folate-binding domain


Domain annotation for each model (and alignments):
>> GCV_T  Aminomethyltransferase folate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.1   0.0   2.8e-10     5e-06      52     135 ..      12      91 ..       7     168 .. 0.85

  Alignments for each domain:
  == domain 1  score: 26.1 bits;  conditional E-value: 2.8e-10
       GCV_T  52 evsGpdaaalLqrlltndisklkpgkatytlllnedGgvidDlivarldedefllvvnaankekdlawlekaaekkdldveved 135
                  ++G++++++Lq ++t++i  lk  ++ y+l+l+++G+ i Dl+v+  d+ ++ll + + nke +l+ l+ ++   ++++ev++
  AHX11263.1  12 LITGKNVKSFLQGIITRNIGYLK--DCIYALILTPKGRLICDLFVYSYDASSILLETHSCNKEAILSLLNLYNF--KKTIEVKE 91 
                 589*******************7..******************************************9988877..44444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1888.78
//
Query:       AHX11264.1  [L=82]
Description: preprotein translocase, YajC subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.6e-26   89.6   1.8    9.4e-26   89.5   1.8    1.0  1  YajC      Preprotein translocase subunit
  ------ inclusion threshold ------
       0.14   12.2   0.0       0.19   11.7   0.0    1.3  1  FixQ      Cbb3-type cytochrome oxidase component FixQ
       0.16   12.0   0.7        3.9    7.5   0.2    2.2  2  CusF_Ec   Copper binding periplasmic protein CusF


Domain annotation for each model (and alignments):
>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.5   1.8   1.6e-29   9.4e-26       1      78 [.       1      78 [.       1      80 [. 0.90

  Alignments for each domain:
  == domain 1  score: 89.5 bits;  conditional E-value: 1.6e-29
        YajC  1 ssllplvlifvifyfllirpqqkkqkehkemlasLkkGdeVvtigGivGkvvkvddde..vtveigesagvkikversai 78
                +sl+pl ++f++fy+++irpq kk keh++ml++Lk Gd +vt+gGi G ++k+d+++  + ++i+  + v++k+ +s++
  AHX11264.1  1 MSLVPLGIVFLVFYIFVIRPQSKKVKEHQAMLDALKIGDSIVTSGGISGVITKIDEKNnmIHLQIA--DAVVVKILKSFV 78
                57899**************************************************77634666664..56*******998 PP

>> FixQ  Cbb3-type cytochrome oxidase component FixQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   3.2e-05      0.19      15      40 ..       3      28 ..       1      32 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 3.2e-05
        FixQ 15 llflvllfygvviyafrpgnrkdfed 40
                l+ l ++f+  +i++ rp+++k  e+
  AHX11264.1  3 LVPLGIVFLVFYIFVIRPQSKKVKEH 28
                66799***************987665 PP

>> CusF_Ec  Copper binding periplasmic protein CusF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0     0.016        96      36      49 ..      28      41 ..      24      44 .. 0.85
   2 ?    7.5   0.2   0.00065       3.9       1      16 [.      49      64 ..      49      72 .. 0.92

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.016
                TTSEESS-STT-EE CS
     CusF_Ec 36 dpallaglkaGdkV 49
                ++a+l++lk Gd +
  AHX11264.1 28 HQAMLDALKIGDSI 41
                689*********98 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00065
                EEEEEEETTCTEEEEE CS
     CusF_Ec  1 GvVkavdaaagkvtls 16
                Gv++++d++++++ l+
  AHX11264.1 49 GVITKIDEKNNMIHLQ 64
                9************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       973  (0.0542696); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.28s 00:00:00.67 Elapsed: 00:00:00.44
# Mc/sec: 564.64
//
Query:       AHX11265.1  [L=244]
Description: pyridoxal phosphate biosynthesis PdxJ family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-66  223.1   0.1    2.8e-66  223.0   0.1    1.0  1  PdxJ      Pyridoxal phosphate biosynthesis protein PdxJ


Domain annotation for each model (and alignments):
>> PdxJ  Pyridoxal phosphate biosynthesis protein PdxJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.1   1.6e-70   2.8e-66       1     232 [.       3     240 ..       3     242 .. 0.96

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 1.6e-70
                 EEEEE-HHHHHHHHCCSSS-S-HHHHHHHHHCCT.SEEEEE--TT-SSS-HHHHHHHHHH-SS.....EEEEEEESSHHHHHHHHHH--SEEEEE--SC CS
        PdxJ   1 kLgVnidhvAtlRnarggnePdvveaaelaeeaGAdgitvhlreDrRhiqdeDveelkelvkt.....elnlEmalteemleialelkpeqvtLVPekr 94 
                 ++++n+++vA++Rnargg+ Pd+  +a+l    G++git+h+r D Rh + eDv+++ +l ++     e+nlE++l+ee+l++++++  +q t+VP ++
  AHX11265.1   3 RISINLNKVALIRNARGGDSPDIKYVANLGIMNGCTGITLHPRADARHSTVEDVQTILNLKEVssgevEFNLEGDLREELLDLVKSHGIHQFTIVPVRE 101
                 589****************************************************9998876666778******************************* PP

                 CCCSTTSSB-TGGCHCCHHHHHHHHHHT.T-EEEEEE-S-HHHHHHHHHCT-SEEEEETHHHHHHCCHHHHHHHHHHHHHHHHHHHHTT-EEEEETT-- CS
        PdxJ  95 eelttegGldvakeeeklkevikelkea.girvslFidpdkeqieaaaelgadvvELhtgaYaeaaeeeereeelerlkeaaklakelgLevnaGHgLn 192
                  e tte G+++++++++l ++ik+lk+a ++r+slFi+p++++++ aae+g+d+vELh++ Ya+a+ ++++++e++rl+ aa +a++lgL+vn GH+++
  AHX11265.1 102 GEKTTERGFSLNEKRDSLMSAIKDLKAArDVRISLFIEPEPASVAYAAEIGCDAVELHAKWYARAFCTHRESKEVRRLHFAALEARNLGLKVNLGHDIS 200
                 *************************98769************************************99999**************************** PP

                 TTTCHH.HHTSTTEEEEEE-HHHHHHHHHH-HHHHHHHHHH CS
        PdxJ 193 yenvka.iakipeieelnIGhaliaealfvGleeavremke 232
                 + n+++ i+ki+  +e+++Ghali e+ + G+ ++ r++ +
  AHX11265.1 201 LVNISTvINKIKP-DEVSVGHALIVESFLQGFPRTLRKYVS 240
                 ******6777766.***********************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      401  (0.022366); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1893.29
//
Query:       AHX11266.1  [L=50]
Description: hypothetical protein NHE_0307 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (50 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       545  (0.0303977); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 412.82
//
Query:       AHX11267.1  [L=296]
Description: lipoyl synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-10   41.6   0.1    4.6e-10   40.1   0.1    1.7  2  Radical_SAM   Radical SAM superfamily
  ------ inclusion threshold ------
      0.031   13.7   0.0      0.045   13.2   0.0    1.2  1  His_biosynth  Histidine biosynthesis protein


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.1   0.1   5.2e-14   4.6e-10       4     165 ..      58     216 ..      55     218 .. 0.88
   2 ?   -1.4   0.0       0.3   2.7e+03      76     100 ..     260     287 ..     235     292 .. 0.59

  Alignments for each domain:
  == domain 1  score: 40.1 bits;  conditional E-value: 5.2e-14
                  ESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC....CCTEEEEEEECSSCHGHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   4 trgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggepllypdfvellerlakla....vpgiritvetngtlpdeeklerl 97 
                  +  C+++C+fC++      +g++  l++ e ++++k +  + g k+v++++ + ++  d   + ++++ ++    + + +i v t+ +l      + l
   AHX11267.1  58 GSVCTRACRFCNVA-----TGKPDLLDPHEPEKLAKVI-SKLGLKHVVITSVDRDDLEDGGAAHFAECIRRiretSVDTTIEVLTPDFLGKASARDIL 149
                  678***********.....6******************.5999**************************9877777888888888888877999999* PP

                  HHTT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEEBTTTSHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  98 lelgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivglpGendeeleelle 165
                   e+++d++++++e++     + +++ +  +   l +le  +++  +   ++++++++ Ge + e+ ++++
   AHX11267.1 150 IEANPDVFNHNIETVPRL--HPKVRIKAKYFNSLSLLEEVKRK-NPAifTKSGLMVGLGEERGEILQVMD 216
                  ****************96..55555899999999999999999.566789**********9999988876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.3
                  CTEEEEEEECSSCHG...HHHHHHHHHT CS
                  xxxxxxxxxxxxxxx...xxxxxxxxxx RF
  Radical_SAM  76 pgiritvetngtlpd...eeklerllel 100
                  +g+ ++ +++ t+ +   +e  +rl+e+
   AHX11267.1 260 KGFLMVSSSPLTRSSyhaDEDFKRLREA 287
                  3444445555555446667777777766 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.1e-06     0.045     100     189 ..      30     123 ..      15     131 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.1e-06
                   EESHH..HHH-THHHHHHHHHHCGGGEEEEEEEEE.C.EEEEETTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS---HHHHHHHHHH CS
  His_biosynth 100 iigta..avknpelikelaekfgsqkivvaiDarr.g.ykvaikgwreetgldavelakkleelgageilltdidrdGtlsGpdleltkelaea 189
                   +++t+   + +p++ + +++k+    i  ++ +r+    +va+ + +     ++++lak +++lg++++++t++drd  ++G    + +++++ 
    AHX11267.1  30 SLNTVcqEAACPNVSECWSKKHVTVMILGSVCTRAcRfCNVATGKPDLLDPHEPEKLAKVISKLGLKHVVITSVDRDDLEDGGAAHFAECIRRI 123
                   566662233567788888888888777777777775245677777777788999****************************999988888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (296 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.20s 00:00:00.63 Elapsed: 00:00:00.35
# Mc/sec: 2525.17
//
Query:       AHX11268.1  [L=153]
Description: polyketide cyclase / dehydrase and lipid transport family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-18   67.6   0.0    1.3e-18   67.4   0.0    1.0  1  Polyketide_cyc   Polyketide cyclase / dehydrase and lipid tra
    0.00023   21.5   0.0     0.0003   21.1   0.0    1.2  1  Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid tra
     0.0074   16.0   0.0      0.011   15.5   0.0    1.2  1  COXG             Carbon monoxide dehydrogenase subunit G (Cox


Domain annotation for each model (and alignments):
>> Polyketide_cyc  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.4   0.0   2.2e-22   1.3e-18       2     130 .]      15     143 ..      14     143 .. 0.92

  Alignments for each domain:
  == domain 1  score: 67.4 bits;  conditional E-value: 2.2e-22
                     SS-HHHHHHHHTTTGGCCSCCCCEEEEEE.SSSEE...EEEECSTTSSCEEEEEEEEEEETTT.....EEECTTCCCCCEEEEEEEECTECCEEE CS
  Polyketide_cyc   2 papadqvyalvadvesypeflphcssvevleeaesglsadlevgfggltesftarvtldppee.....itfklvegdfkslegkWtieslppnsg 91 
                     p +a +v+++v d+e+y ef+p+c++ +v+++ae++++a+++ +f+g+ +++++ +   pp       i++k  eg fk+l + W++ + ++   
      AHX11268.1  15 PFSAMHVFEIVLDIECYHEFIPWCQKIRVISKAENEIKAEVVASFKGIVATYVSLIKFLPPGNeeagfIEVKSTEGAFKYLYNLWKFHPEGK--- 106
                     77999***************************************************9999999************************99976... PP

                     CEEEEEEEEEEEE-SSCHHHHHHHHHHHHHHHHHHHHHH CS
  Polyketide_cyc  92 gtrtkvalevdfkfaspllgalvgqvaervldellaale 130
                     g+  +v++ +++ f+s+++  +++++ + + ++++ a+e
      AHX11268.1 107 GS--RVTFYIEYSFRSKFMQLILNMMYNIAQRRIISAFE 143
                     66..56666666669*********999999999999986 PP

>> Polyketide_cyc2  Polyketide cyclase / dehydrase and lipid transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0     5e-08    0.0003       7     126 ..      11     134 ..       6     146 .. 0.70

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 5e-08
                      EEEESS-HHHHHHHHTTTTGGGGT-TTEEEEECSESTSSSTTTEEEEECCCSSEEEEEEEEE...ETTTTEEEEEEE...SSS-TSEEEE.EEE CS
  Polyketide_cyc2   7 svviaappekVwalvsdfenwprWhpevarveleggggpargvegtvrvggrgtvreelvev...dpegrllsyriv..kpvpvanyvat.wtv 94 
                      ++v + ++  V+++v d e +++ +p  ++ ++ ++ ++  +++ +v + ++  ++ + v +    p g   +  i+  ++ ++++y  + w++
       AHX11268.1  11 ERVLPFSAMHVFEIVLDIECYHEFIPWCQKIRVISKAEN--EIKAEVVASFK-GIVATYVSLikfLPPGNEEAGFIEvkSTEGAFKYLYNlWKF 101
                      6778889999******************99999986777..55444444442.24444444444454233333333235689*****8888*** PP

                      EECCETEEEEEEEEEEE.E--TT--HHHHHHHH CS
  Polyketide_cyc2  95 tpdgggtrvtwtgefda.gplggpfekpaaaka 126
                      +p+g g+rvt+++e+ + + +++++ + +   a
       AHX11268.1 102 HPEGKGSRVTFYIEYSFrSKFMQLILNMMYNIA 134
                      *************99976666666655555555 PP

>> COXG  Carbon monoxide dehydrogenase subunit G (CoxG)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.0   1.8e-06     0.011      11     134 ..      20     144 ..      13     146 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 1.8e-06
                 HHHHHHT-HHHHGGGSTTEEEEEEET.TEEEEEEEEESSSSEEEEEEEEEEEEEETTTEEE...EEEEEE-SSEEEEEEEEEEEEEETTEEEEEEEEEE CS
        COXG  11 avwefLndpeklarciPGvksvekeg.deykvkvklkvGplkgsfkarvelselekenstt.ieikGkGrgagvaidfalvvlveegggtrlswsakvn 107
                  v+e++ d+e   + iP ++++ +++  e ++k+++ v ++kg +++ v+l ++ ++++     i+ k +   ++   +l   + eg+g+r+ + +++ 
  AHX11268.1  20 HVFEIVLDIECYHEFIPWCQKIRVISkAENEIKAEV-VASFKGIVATYVSLIKFLPPGNEEaGFIEVKSTEGAFKYLYNLWKFHPEGKGSRVTFYIEYS 117
                 7999*****************988777555555555.3445666666777777776666554556777777788888888889999999********** PP

                 EEEHHHHS-HHHHHHHHHHHHHHHHHH CS
        COXG 108 vggllaslGsrlidsaarklinelfec 134
                  + +  +l   ++ ++a++ i  +fe+
  AHX11268.1 118 FRSKFMQLILNMMYNIAQRRIISAFEN 144
                 ***************999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (153 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1366.81
//
Query:       AHX11269.1  [L=269]
Description: kinase/pyrophosphorylase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.5e-80  269.5   0.0      4e-80  269.3   0.0    1.0  1  Kinase-PPPase  Kinase/pyrophosphorylase


Domain annotation for each model (and alignments):
>> Kinase-PPPase  Kinase/pyrophosphorylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.3   0.0   2.2e-84     4e-80       1     255 []       6     261 ..       6     261 .. 0.97

  Alignments for each domain:
  == domain 1  score: 269.3 bits;  conditional E-value: 2.2e-84
  Kinase-PPPase   1 ifvvSdstGetaeavaraalaqFeevevelevlpfvkteekleevleeakeeeaivvyTlvdeelrealeeaaeekgveavdllgpllealeeelg 96 
                    ++++Sd+  + + +v r +la+F+++ev ++v+p+ ++ ekl+++l++++  +a+++y + d+ +r++l+e++++++++++ +l++++++l+++l+
     AHX11269.1   6 VHLISDQGVDALLSVSRESLARFKNLEVIESVWPLTDSVEKLQRILTNING-KAFILYAIKDRLIRDTLKEFCQTMRIPCIPILSRIIRELSSYLN 100
                    89***********************************************75.799***************************************** PP

  Kinase-PPPase  97 vkpkeepgl.lhkldedYfkrieAieFalkhDDGkkprklkeADivLvGvSRtsKTPlSlyLaqkglkvaNvPLvpelelpkelfevdkkkvfgLt 191
                    + p+   +  +h+++edYf+ri+A+++ l+hDDG+++ +l+eAD+++vG SRtsK+P+S+yL+ +g+kvaN+P+v++++lp++l+++++  v+gLt
     AHX11269.1 101 QGPTDASKEeYHRFNEDYFARIDAMNYMLSHDDGQNTWDLDEADVIIVGPSRTSKSPTSVYLSYRGYKVANIPFVNNIPLPESLIKLKHVLVIGLT 196
                    ***98776669************************************************************************************* PP

  Kinase-PPPase 192 idperLveiRkeRlkslglkse.sYadlerveeeleeaeklfrklgipvidvtnksiEetAaeil 255
                    i+p+rL+eiRk+Rl+  + +++  Ya  e++ +el++a+++f ++++p+idvt++s+Ee+Aa+i+
     AHX11269.1 197 INPDRLIEIRKQRLSLSQNHDNpVYAGREQILDELTNAKRVFMQNNWPIIDVTHRSVEEIAATII 261
                    ***************66655558****************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (269 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       395  (0.0220313); expected 358.6 (0.02)
Passed bias filter:                      332  (0.0185175); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2041.93
//
Query:       AHX11270.1  [L=258]
Description: transporter associated domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.7e-14   51.9   0.0    1.4e-13   50.6   0.0    1.7  1  CorC_HlyC  Transporter associated domain
      3e-10   40.4   4.9    1.2e-07   32.0   0.5    2.9  2  CBS        CBS domain


Domain annotation for each model (and alignments):
>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.6e-17   1.4e-13       3      78 ..     177     252 ..     175     255 .. 0.91

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.6e-17
                 ECTTEEEEETT-BHHHHHHHHTSTTHH.CT-SBHHHHHHHHH-S---TT-EEEEEET.TEEEEEEEEETTCEEEEEEE CS
   CorC_HlyC   3 ldegsylvdGslpldeleeelglelpe.edyeTlgGlllellgriPkegesvevdle.glrftVlemdgrrIkkvrve 78 
                 l+e++++v+++++++e+ +  gle++  +++ TlgG++++  g++P +g+   v+ + g+ f +l++d++rI+ v v+
  AHX11270.1 177 LSEHKFEVSARIEMKEFLDKSGLEFEVgDNFRTLGGYIFSIAGKVPSVGD--IVTSPeGVMFSILDADNKRINVVLVD 252
                 789************************778********************..554444***************99986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   0.4   0.00014       1.3      29      53 ..      70      97 ..      17     101 .. 0.82
   2 !   32.0   0.5   1.4e-11   1.2e-07       6      56 ..     109     159 ..     103     160 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00014
                T..SSEEEEEETTT.BEEEEEEHHHHHH CS
         CBS 29 g..vsrlPVVdedg.klvGivtlrDllr 53
                +  +sr PV d++  k++G ++ +D+l+
  AHX11270.1 70 EisHSRTPVFDGNLdKIIGFIHIKDVLN 97
                33379*****544479**********97 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 1.4e-11
                 BSSCEEEETTSBHHHHHHHHHHHTSS.EEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   6 trdvvtvppdttleealelmrekgvs.rlPVVdedgklvGivtlrDllrall 56 
                  r++++vpp++ ++ +l +m+ ++v+ ++ VVde g  vGivt++D+++ +l
  AHX11270.1 109 LRKIICVPPSMKVSALLMKMKVAHVHmAI-VVDEFGATVGIVTMTDVVEQIL 159
                 4789****************767797455.99***************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1949.92
//
Query:       AHX11271.1  [L=692]
Description: hypothetical protein NHE_0313 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (692 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      215  (0.0119917); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.85u 0.32s 00:00:01.17 Elapsed: 00:00:00.47
# Mc/sec: 4417.55
//
Query:       AHX11272.1  [L=132]
Description: 4Fe-4S binding domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-09   34.8  26.1    7.8e-07   28.7   8.6    3.2  2  Fer4           4Fe-4S binding domain
    1.8e-07   30.9  16.5    0.00051   20.0   4.6    2.3  2  Fer4_2         4Fe-4S binding domain
    2.2e-07   31.7   8.1    0.00034   21.5   0.2    2.3  2  Fer4_16        4Fe-4S double cluster binding domain
    5.3e-07   29.7  25.0    0.00019   21.5   1.5    2.2  2  Fer4_10        4Fe-4S dicluster domain
    2.1e-06   27.7  13.7    0.00098   19.2   0.7    2.4  2  Fer4_21        4Fe-4S dicluster domain
      8e-06   25.7  21.3    0.00074   19.5   6.1    2.4  2  Fer4_6         4Fe-4S binding domain
    8.6e-06   26.3  16.2    5.6e-05   23.6  16.1    2.1  2  Fer4_7         4Fe-4S dicluster domain
      2e-05   24.7  13.3    4.4e-05   23.6  13.4    1.6  1  Fer4_9         4Fe-4S dicluster domain
    8.5e-05   22.8  13.2      0.001   19.4   0.6    2.6  2  Fer4_4         4Fe-4S binding domain
    9.8e-05   22.2   0.0    0.00016   21.6   0.0    1.3  1  DUF3470        Domain of unknown function (DUF3470)
    0.00011   22.7   6.9      0.003   18.0   0.1    2.3  2  Fer4_17        4Fe-4S dicluster domain
    0.00047   20.6   8.7     0.0048   17.3   0.0    2.3  2  Fer4_8         4Fe-4S dicluster domain
  ------ inclusion threshold ------
       0.33   11.1  11.1       0.92    9.7  10.6    1.9  2  Fer4_11        4Fe-4S dicluster domain
       0.34   11.5  15.5       0.42   11.2   4.3    2.7  2  Fer4_13        4Fe-4S single cluster domain of Ferredoxin I
       0.58    9.9   3.2        4.1    7.2   0.0    2.2  2  Thioredoxin_9  Thioredoxin
        1.4    9.7  11.8       0.11   13.2   2.8    2.5  2  Fer4_15        4Fe-4S single cluster domain
        1.9    9.6  21.0        5.3    8.2   8.2    2.3  2  Fer4_3         4Fe-4S binding domain
        2.6    7.9  14.2       0.76    9.6   5.0    2.3  2  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
        6.1    7.1  17.4        1.8    8.8   3.1    2.3  2  Fer4_18        4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   9.6    0.0012       1.1       2      23 ..       3      26 ..       2      27 .. 0.88
   2 !   28.7   8.6   8.3e-10   7.8e-07       2      23 ..      34      55 ..      33      56 .. 0.95

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.0012
                EEETTTSSS-TH..HHHHSTTTEE CS
        Fer4  2 videekCigCGa..CvevCPvgAI 23
                 + +ekC++C++  CvevCPv++ 
  AHX11272.1  3 HVVTEKCVKCKYtdCVEVCPVDCF 26
                5889*******888********85 PP

  == domain 2  score: 28.7 bits;  conditional E-value: 8.3e-10
                EEETTTSSS-THHHHHSTTTEE CS
        Fer4  2 videekCigCGaCvevCPvgAI 23
                vid+e Ci CG Cv  CP +AI
  AHX11272.1 34 VIDPEVCIDCGVCVPECPIEAI 55
                8********************9 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   4.1   6.9e-06    0.0065       3      21 ..       2      22 ..       1      23 [. 0.92
   2 !   20.0   4.6   5.4e-07   0.00051       2      21 ..      32      51 ..      31      51 .. 0.93

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.9e-06
      Fer4_2  3 vvvdtdrCigCg..aCvsaCP 21
                ++v+t++C+ C+   Cv +CP
  AHX11272.1  2 PHVVTEKCVKCKytDCVEVCP 22
                89*********889******* PP

  == domain 2  score: 20.0 bits;  conditional E-value: 5.4e-07
      Fer4_2  2 pvvvdtdrCigCgaCvsaCP 21
                + v+d++ Ci Cg Cv  CP
  AHX11272.1 32 YLVIDPEVCIDCGVCVPECP 51
                679****************9 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   2.9   0.00014      0.13       1      22 [.       8      31 ..       8      38 .. 0.83
   2 !   21.5   0.2   3.6e-07   0.00034       2      33 ..      40      70 ..      39      97 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00014
     Fer4_16  1 rCgtCgk..CaevCPtnaikekke 22
                +C++C+   C+evCP+++++e +e
  AHX11272.1  8 KCVKCKYtdCVEVCPVDCFHEGEE 31
                5****9888*********999854 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 3.6e-07
     Fer4_16  2 CgtCgkCaevCPtnaikekkekeiearecisy 33
                C++Cg C+  CP +ai ++ e+ i+ +  ++ 
  AHX11272.1 40 CIDCGVCVPECPIEAIVND-ETYIDGKSLEAI 70
                ******************9.556664443333 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.8  16.0   6.9e-07   0.00066       5      56 .]       5      51 ..       1      51 [. 0.94
   2 !   21.5   1.5     2e-07   0.00019       2      24 ..      33      61 ..      32      86 .. 0.71

  Alignments for each domain:
  == domain 1  score: 19.8 bits;  conditional E-value: 6.9e-07
     Fer4_10  5 dddtCirCg..kCvkaCPadltsvgakgeaseeeavrkkvekCtgcgaCveaCP 56
                 +++C++C+  +Cv++CP+         + ++ee   +++e C++cg Cv +CP
  AHX11272.1  5 VTEKCVKCKytDCVEVCPV-------DCFHEGEEYLVIDPEVCIDCGVCVPECP 51
                5789****9999*******.......99*************************9 PP

  == domain 2  score: 21.5 bits;  conditional E-value: 2e-07
     Fer4_10  2 vvidddtCirCgkCvkaCPadl......t 24
                +vid++ Ci Cg Cv  CP  +       
  AHX11272.1 33 LVIDPEVCIDCGVCVPECPIEAivndetY 61
                589*****************554444332 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   6.6   8.8e-05     0.083      35      57 ..       3      26 ..       1      28 [. 0.85
   2 !   19.2   0.7     1e-06   0.00098       2      29 ..      34      58 ..      30      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.8e-05
     Fer4_21 35 kvvedeCvGCnl..CssvCPvedci 57
                +vv+++Cv C+   C++vCPv dc 
  AHX11272.1  3 HVVTEKCVKCKYtdCVEVCPV-DCF 26
                689*******8656******9.985 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 1e-06
     Fer4_21  2 ridedkCigCgkCliaCedtshqaieid 29
                +id++ Ci+Cg C+  C+   ++ai  d
  AHX11272.1 34 VIDPEVCIDCGVCVPECP---IEAIVND 58
                589999999999999999...6777544 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   7.2   0.00023      0.21       2      22 ..       2      24 ..       1      26 [. 0.83
   2 !   19.5   6.1   7.8e-07   0.00074       3      24 .]      34      55 ..      33      55 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
      Fer4_6  2 veidpdkCigCgd..CvrvCPeg 22
                +++  +kC+ C    Cv vCP +
  AHX11272.1  2 PHVVTEKCVKCKYtdCVEVCPVD 24
                678899*****5558******76 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 7.8e-07
      Fer4_6  3 eidpdkCigCgdCvrvCPegai 24
                +idp+ Ci+Cg Cv  CP  ai
  AHX11272.1 34 VIDPEVCIDCGVCVPECPIEAI 55
                79****************8887 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.6   7.2    0.0015       1.4      33      51 ..       4      24 ..       2      25 .. 0.77
   2 !   23.6  16.1     6e-08   5.6e-05       1      52 []       8      54 ..       8      54 .. 0.89

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0015
      Fer4_7 33 idpekClgCga..CvavCPtg 51
                ++ ekC+ C+   Cv+vCP++
  AHX11272.1  4 VVTEKCVKCKYtdCVEVCPVD 24
                567899999755699999987 PP

  == domain 2  score: 23.6 bits;  conditional E-value: 6e-08
      Fer4_7  1 rCigCg..aCvaaCpvkaieldeeenekgtekveidpekClgCgaCvavCPtga 52
                +C++C+   Cv++Cpv+++   e       e+++idpe C++Cg+Cv +CP +a
  AHX11272.1  8 KCVKCKytDCVEVCPVDCFHEGE-------EYLVIDPEVCIDCGVCVPECPIEA 54
                7****8779*********98755.......589******************765 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6  13.4   4.6e-08   4.4e-05       1      51 []       8      55 ..       8      55 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 4.6e-08
      Fer4_9  1 kCtgCga..CveaCpagvvvedaaerkarlraaseeaCigCgaCveaCpkgai 51
                kC++C++  Cve+Cp + + e +    +  +      Ci+Cg Cv  Cp +ai
  AHX11272.1  8 KCVKCKYtdCVEVCPVDCFHEGEEYLVIDPE-----VCIDCGVCVPECPIEAI 55
                7****9888**********999999998875.....4************8876 PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.0   5.4    0.0048       4.5       2      16 ..       7      23 ..       6      24 .. 0.86
   2 !   19.4   0.6   1.1e-06     0.001       1      15 [.      37      51 ..      37      72 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0048
      Fer4_4  2 erCigCgs..CvaaCPq 16
                e+C+ C+   Cv +CP+
  AHX11272.1  7 EKCVKCKYtdCVEVCPV 23
                89*****666******7 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.1e-06
      Fer4_4  1 qerCigCgsCvaaCP 15
                +e Ci+Cg+Cv  CP
  AHX11272.1 37 PEVCIDCGVCVPECP 51
                588***********9 PP

>> DUF3470  Domain of unknown function (DUF3470)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   1.7e-07   0.00016       6      40 ..      92     126 ..      88     128 .. 0.92

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.7e-07
     DUF3470   6 lNaeLAkqWPnItekkdplpDAdewkgvpdKlekL 40 
                  N++ +++ P+I  kkdp+ +Ad w    +K + +
  AHX11272.1  92 FNRKRSAELPVIVAKKDPMVEADVWSAIDNKIQFI 126
                 69999999***********************9976 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   2.9     0.012        12       1      15 [.       8      24 ..       6      35 .. 0.76
   2 !   18.0   0.1   3.2e-06     0.003       2      21 ..      40      59 ..      39      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.012
     Fer4_17  1 rCiqCgy..ClpeCpsy 15
                +C +C+y  C+++Cp  
  AHX11272.1  8 KCVKCKYtdCVEVCPVD 24
                59999988899999864 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 3.2e-06
     Fer4_17  2 CiqCgyClpeCpsyeaydne 21
                Ci Cg C+peCp  ++ ++e
  AHX11272.1 40 CIDCGVCVPECPIEAIVNDE 59
                ************98886664 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   6.2     0.073        69      49      64 ..       7      24 ..       3      25 .. 0.75
   2 !   17.3   0.0   5.1e-06    0.0048       4      25 ..      39      61 ..      36     118 .. 0.67

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.073
      Fer4_8 49 wsCttcga..CtevCpvg 64
                ++C+ c+   C+evCpv+
  AHX11272.1  7 EKCVKCKYtdCVEVCPVD 24
                578888866688888875 PP

  == domain 2  score: 17.3 bits;  conditional E-value: 5.1e-06
      Fer4_8  4 kCieCgaCqsaCpvlrrtk.khl 25
                 Ci Cg C  +Cp+    + +  
  AHX11272.1 39 VCIDCGVCVPECPIEAIVNdETY 61
                6************5444432222 PP

>> Fer4_11  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7  10.6   0.00097      0.92       6      64 ..       5      60 ..       2      66 .. 0.88
   2 ?    7.7   0.9     0.004       3.7       4      32 ..      34      60 ..      31      94 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00097
     Fer4_11  6 lpeqCrhCleppCvasapseaivkdeetGaVlldektkkeevrevveacPykivrknee 64
                + e+C +C    Cv+++p++ +++ e     ++d++ +  ++  +v  cP +++ ++e+
  AHX11272.1  5 VTEKCVKCKYTDCVEVCPVDCFHEGE--EYLVIDPEVCI-DCGVCVPECPIEAIVNDET 60
                689****************9988877..68999*****7.***********99887764 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.004
     Fer4_11  4 lflpeqCrhCleppCvasapseaivkdee 32
                ++ pe C +C    Cv  +p eaiv+de+
  AHX11272.1 34 VIDPEVCIDCG--VCVPECPIEAIVNDET 60
                67899*****6..7***********9984 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   3.5     0.034        32       4      25 ..       7      31 ..       5      34 .. 0.79
   2 ?   11.2   4.3   0.00045      0.42       1      17 [.      35      51 ..      35      59 .. 0.96

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.034
     Fer4_13  4 dtCiac..gaCvelaP.dvFeedde 25
                ++C+ c  + Cve++P d+F+e +e
  AHX11272.1  7 EKCVKCkyTDCVEVCPvDCFHEGEE 31
                7999994458******889988877 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00045
     Fer4_13  1 VDrdtCiacgaCvelaP 17
                +D + Ci+cg+Cv  +P
  AHX11272.1 35 IDPEVCIDCGVCVPECP 51
                799*************9 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   1.4      0.12   1.2e+02      44      61 ..      31      48 ..      24      59 .. 0.89
   2 ?    7.2   0.0    0.0044       4.1      79     123 ..      81     125 ..      71     130 .. 0.89

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.12
                   EEEEE--TT-HHHHHHHH CS
  Thioredoxin_9 44 kilvltedwCgDaavnvP 61
                   + lv+  + C D+ v+vP
     AHX11272.1 31 EYLVIDPEVCIDCGVCVP 48
                   679999***********9 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0044
                    -HHHHHHHTTTTTT-SS--SSEEEEE-TT--EEEEEESS-HHHHH CS
  Thioredoxin_9  79 lrdenlelmdqyltngaraiPtliildeegeelgvwgerPaevqe 123
                     r++n ++m  + ++ +++ P+++  ++ + e  vw    +++q 
     AHX11272.1  81 ERQSNVKFMATFNRKRSAELPVIVAKKDPMVEADVWSAIDNKIQF 125
                    58999*********************99999999**999888875 PP

>> Fer4_15  4Fe-4S single cluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   1.8      0.45   4.3e+02      54      63 ..      16      25 ..       9      27 .. 0.81
   2 ?   13.2   2.8   0.00012      0.11       2      26 ..      34      59 ..      33     120 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.45
     Fer4_15 54 eAaraCPvdA 63
                + +++CPvd+
  AHX11272.1 16 DCVEVCPVDC 25
                56799****9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 0.00012
     Fer4_15  2 vvDrdaCigcglCvaeap.evfelde 26
                v+D + Ci cg+Cv e+p e +++de
  AHX11272.1 34 VIDPEVCIDCGVCVPECPiEAIVNDE 59
                79***************745666665 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   8.2    0.0056       5.3       1      14 [.       9      24 ..       9      25 .. 0.83
   2 ?    7.2   4.8     0.012        11       1      14 [.      40      53 ..      40      54 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0056
      Fer4_3  1 CtgCg..aCvevCPvg 14
                C+ C    CvevCPv+
  AHX11272.1  9 CVKCKytDCVEVCPVD 24
                999*5457******97 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.012
      Fer4_3  1 CtgCgaCvevCPvg 14
                C+ Cg Cv  CP  
  AHX11272.1 40 CIDCGVCVPECPIE 53
                9***********75 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   5.0   0.00081      0.76      22      39 ..       7      24 ..       3      29 .. 0.90
   2 ?    4.2   1.5     0.038        36      22      43 ..      38      57 ..      26      84 .. 0.81

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00081
                TT----TT-HHHHCSTT- CS
     Fer4_20 22 sRClqCkkapcvkgCPve 39
                ++C++Ck + cv+ CPv+
  AHX11272.1  7 EKCVKCKYTDCVEVCPVD 24
                79**************97 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.038
                TT----TT-HHHHCSTT---HH CS
     Fer4_20 22 sRClqCkkapcvkgCPveidip 43
                + C++C    cv +CP+e  ++
  AHX11272.1 38 EVCIDC--GVCVPECPIEAIVN 57
                669999..78******987654 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   5.8     0.032        30      59      74 ..       7      24 ..       3      35 .. 0.85
   2 ?    8.8   3.1    0.0019       1.8      60      79 ..      39      58 ..      26      89 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.032
     Fer4_18 59 gdcidces..cvkvcPtg 74
                 +c++c++  cv+vcP++
  AHX11272.1  7 EKCVKCKYtdCVEVCPVD 24
                68****9666******86 PP

  == domain 2  score: 8.8 bits;  conditional E-value: 0.0019
     Fer4_18 60 dcidcescvkvcPtgidirk 79
                 cidc++cv  cP++  + +
  AHX11272.1 39 VCIDCGVCVPECPIEAIVND 58
                5************9866555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (132 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       845  (0.0471303); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 964.08
//
Query:       AHX11273.1  [L=151]
Description: hypothetical protein NHE_0315 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1212.62
//
Query:       AHX11274.1  [L=452]
Description: cysteine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.1e-109  366.4   0.0   2.4e-109  365.3   0.0    1.5  2  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
      7e-14   51.4   0.0    1.2e-06   27.5   0.0    2.5  3  tRNA-synt_1g  tRNA synthetases class I (M)
    5.9e-10   39.5   0.1    1.2e-09   38.5   0.1    1.5  1  DALR_2        DALR domain
    1.2e-05   24.5   0.0      0.021   13.8   0.0    2.1  2  tRNA-synt_1f  tRNA synthetases class I (K)
    1.5e-05   23.5   0.0    8.6e-05   21.0   0.0    2.0  2  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)


Domain annotation for each model (and alignments):
>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  365.3   0.0  6.7e-113  2.4e-109       4     300 ..      18     313 ..      15     314 .. 0.97
   2 ?   -2.4   0.1      0.64   2.3e+03      21      74 ..     366     418 ..     364     443 .. 0.53

  Alignments for each domain:
  == domain 1  score: 365.3 bits;  conditional E-value: 6.7e-113
                   -SBTTEEEEEEEEEBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB--B CS
  tRNA-synt_1e   4 pleekkvtlYvCGptvydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptlepr 100
                   p++ ++v +YvCGptvyd  h+G+ R++v++Di+ r+l+++   v +v+n+tDidDkii+ +  ++ +++e+a ++++ f + l+ +n+l+p++epr
    AHX11274.1  18 PINGDEVRMYVCGPTVYDVPHIGNIRAAVVYDIVYRVLRKAFTRVVYVRNITDIDDKIINASLTQGVEYSEIALRYEKIFREHLKLMNCLPPSFEPR 114
                   567789******************************************************************************************* PP

                   GGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTTTTTT--HHHHHHT----S--S-SSTT-EEEEEE--TTS--B--TTSSEEE-SSHHHH CS
  tRNA-synt_1e 101 vsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYgklskqnleelelgaegevseekkdkkDfaLWkaskegepswdsPwgkGRPGWhieCs 197
                   ++e+++++i ++  l+e g aY +  g vyfdvs++++Yg lsk++++el  g ++++ e+k+++ Df+LWk+  ++e+ w+sPwg+GRPGWhieCs
    AHX11274.1 115 ATENIEQMISIIRSLVESGNAYRAG-GSVYFDVSSFKDYGALSKKKIDELVYGVRIDGDENKRHPGDFVLWKH--DDEVYWPSPWGNGRPGWHIECS 208
                   *************************.**********************************************7..6889****************** PP

                   HHHHHHH-SSEEEEEEEGGGTTTHHHHHHHHHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTT.S-HHHHHHHHHSS-TTS-EEE- CS
  tRNA-synt_1e 198 vmaskllgseidihsGGiDLafPhhenelaqseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkk.fdprqlRllllsahyrsqldfk 292
                   +m+ ++lg ++dih+GG+DL+fPhhene+aqs +a   +++++y++hng+l+++gekmsksL+n+i +  ++k+ ++p+++R++l+s+hy +++d+ 
    AHX11274.1 209 AMILTTLGADFDIHGGGADLKFPHHENEIAQSVCANPgSKFARYWIHNGFLTVNGEKMSKSLGNIINVDTLIKNgVTPNTIRFILISTHYSKPMDWC 305
                   ********************************999866**********************************97689******************99 PP

                   HHHHHHHH CS
  tRNA-synt_1e 293 eelleeak 300
                    + ++ea+
    AHX11274.1 306 PKIVQEAV 313
                   88888775 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.64
                   S--BHHHHHHHHHHHHHHHHHHH.TT-EEEEEEEBB--SHHHHHHHHHTTS-HHH CS
  tRNA-synt_1e  21 dashlGhaRslvafDilrrilqa.lgYdvqfvqnvtDidDkiikrareeeksvke 74 
                   d++hlG+  ++  + +l ++l   lg d+q  q v    +  i+   +e   +++
    AHX11274.1 366 DKIHLGDHSKAQQYAVLLNTLLLfLGIDLQASQSVI--SEDFITSQIQERVAFRQ 418
                   667777666666666655555444677766666653..33333333333333333 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   3.1e-08   0.00011      12     125 ..      35     147 ..      26     154 .. 0.88
   2 !   27.5   0.0   3.5e-10   1.2e-06     316     377 ..     254     315 ..     239     324 .. 0.82
   3 ?   -1.2   0.0      0.18   6.5e+02      63     132 ..     301     372 ..     297     375 .. 0.74

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 3.1e-08
                   S---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHHHHHHHHHHHHH CS
  tRNA-synt_1g  12 gklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrttseehkelvqeifkklk 108
                   +++H+G+++ ++  Di++R  r+  + v++v        +i  +   +gv+ +e++ +++++++e +k +n    +++   +e + e + +i++ l 
    AHX11274.1  35 DVPHIGNIRAAVVYDIVYRVLRKAFTRVVYVRNITDIDDKIINASLTQGVEYSEIALRYEKIFREHLKLMNCLPPSFEPRATE-NIEQMISIIRSLV 130
                   689****************************99999999**********************************9999866554.5555567899999 PP

                   HTT-EEEEEEEEEEETT CS
  tRNA-synt_1g 109 ekgliyekeieqlycpk 125
                   e g  y+   +++++++
    AHX11274.1 131 ESGNAYRAGGSVYFDVS 147
                   99999998888888765 PP

  == domain 2  score: 27.5 bits;  conditional E-value: 3.5e-10
                   EEE--EEE--------------HHHHHHH.H-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHH CS
  tRNA-synt_1g 316 vaheyltvegkKlSkSrgvvvkakealer.ldadllRYylaaeapekkDldfswedfvervNs 377
                   + +++ltv+g+K+SkS g+++ +++++++ ++++++R+ l++++  +k +d+  + ++e vNs
    AHX11274.1 254 IHNGFLTVNGEKMSKSLGNIINVDTLIKNgVTPNTIRFILISTH-YSKPMDWCPKIVQEAVNS 315
                   6789*************************9********999854.455666677777777775 PP

  == domain 3  score: -1.2 bits;  conditional E-value: 0.18
                   HHHHHHHHHHHHHHHHHHTT...---SEEEETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-G CS
  tRNA-synt_1g  63 peelvekvheeikelfkkln...isfdkygrttseehkelvqeifkklkekgliyekeieqlycpkderflpd 132
                   p + + k+ +e  + + k++   i +++ ++tt+++    ++++f  + + ++ +  +i+ ly  +d+  l d
    AHX11274.1 301 PMDWCPKIVQEAVNSLMKFKivlIDNNALSKTTEDDCDGYMEKFFISMSD-DFNTPAAIALLYELRDKIHLGD 372
                   55666666666666655555211578889999999999999999999876.7788888999999999888887 PP

>> DALR_2  DALR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.5   0.1   3.3e-13   1.2e-09       2      58 ..     344     397 ..     343     401 .. 0.91

  Alignments for each domain:
  == domain 1  score: 38.5 bits;  conditional E-value: 3.3e-13
                 HHHHHTBT--HHHHHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHGGGT-.S-S- CS
      DALR_2   2 FeeaMdDDFNTaeAiavlFelakeiNralkeedkaaasalkallrelaevLGl.lqee 58 
                 F  +M DDFNT++Aia l+el  +i       d+ +a++ + ll++l   LG+ lq +
  AHX11274.1 344 FFISMSDDFNTPAAIALLYELRDKIHL----GDHSKAQQYAVLLNTLLLFLGIdLQAS 397
                 6678**********************9....9999999999************88874 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0   0.00023      0.82      35      72 ..      35      72 ..      20      77 .. 0.80
   2 !   13.8   0.0   5.7e-06     0.021     274     340 ..     258     324 ..     199     339 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00023
  tRNA-synt_1f 35 GliHiGnlrevltadlvaralrkrgeevrlilisDdmD 72
                    +HiGn+r  +  d+v+r lrk   +v  +  + d+D
    AHX11274.1 35 DVPHIGNIRAAVVYDIVYRVLRKAFTRVVYVRNITDID 72
                  579********************999966665555555 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 5.7e-06
  tRNA-synt_1f 274 illkggekmssSkGnvltledwlev.aepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                   +l  +gekms+S Gn++ ++ +++  ++p+++rf++++++  k ++  ++  ++++v+   k++  ++
    AHX11274.1 258 FLTVNGEKMSKSLGNIINVDTLIKNgVTPNTIRFILISTHYSKPMDWCPK-IVQEAVNSLMKFKIVLI 324
                   6666788**************9986379******************9999.99999999888876666 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0     0.074   2.7e+02      30      58 ..      29      57 ..      22      68 .. 0.81
   2 !   21.0   0.0   2.4e-08   8.6e-05     523     601 ..     225     304 ..     216     305 .. 0.75

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.074
  tRNA-synt_1 30 gPPyvtGslHiGhalaktlkdivirykrm 58
                   P v   +HiG++ a ++ div r+ r 
   AHX11274.1 29 CGPTVYDVPHIGNIRAAVVYDIVYRVLRK 57
                 557888899***************98765 PP

  == domain 2  score: 21.0 bits;  conditional E-value: 2.4e-08
  tRNA-synt_1 523 GlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikk.ygadalRltlilsdvgrdinl 601
                  G D  +   ++ i +s+  +  + f +  +h   +  +G KmSKslgN+i+ +++ik+ +  + +R++li++++++ +++
   AHX11274.1 225 GADLKFPHHENEIAQSVCANPGSKFARYWIHNGFLTVNGEKMSKSLGNIINVDTLIKNgVTPNTIRFILISTHYSKPMDW 304
                  55555555556666666666666676666666667789**************999987255699*********9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       450  (0.025099); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.22s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3233.70
//
Query:       AHX11275.1  [L=60]
Description: hypothetical protein NHE_0317 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (60 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 480.68
//
Query:       AHX11276.1  [L=225]
Description: ribulose-phosphate 3-epimerase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-70  236.1   0.9    2.6e-70  235.9   0.9    1.1  1  Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
    4.5e-06   26.3   0.7      0.091   12.2   0.0    2.5  3  PcrB            PcrB family


Domain annotation for each model (and alignments):
>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  235.9   0.9   2.9e-74   2.6e-70       1     198 []       3     200 ..       3     200 .. 0.99

  Alignments for each domain:
  == domain 1  score: 235.9 bits;  conditional E-value: 2.9e-74
                     EEEEBGGGS-GGGHHHHHHHHHHTT-SEEEEEEEBSSSSS-B-B-HHHHHHHGGGE-S-EEEEEESSSHHHCHHHHHHCT-SEEEEE-ST-TTHH CS
  Ribul_P_3_epim   1 kiapSllsadfarlgeevkaveeagadllHvDvmDghfvpNltigplvvealrkltelpldvHLmveevdrivpefaeagasiisvHaEalehlk 95 
                     k++pSllsadf +lg ev+++e+ gad++H+DvmDg+fvpNlt+gpl++ +++ +t+lp+ vHLm++++++ ++++++aga++i+vH Ea+ h++
      AHX11276.1   3 KVSPSLLSADFLNLGAEVAQIENSGADSIHIDVMDGRFVPNLTFGPLIIRQVKGITNLPIMVHLMISNAEQTFQDYIDAGANTIFVHSEACVHVD 97 
                     699******************************************************************************************** PP

                     HHHHHHHHTTSEEEEEE-TT--GGGGTTTCCC-SEEEEESS-TT-SS----CCHHHHHHHHHHHHHHHT---EEEEESS--TTTCHHHHHHT--E CS
  Ribul_P_3_epim  96 rtiqeikeaGakaglvlnpatplealeyllekldlvllmsvePgfgGQkFipevlekikkvrklidekeldlkievDGGvkldnieqiaeagadv 190
                     r+++ ik++ +k+gl++np+t+ ++leyl +++d++l+m+v+Pgf  Q+F+ ++l ki+ ++++i++ + d++i vDGG++ + +  +++agadv
      AHX11276.1  98 RLLTMIKKQNVKVGLAINPSTHESVLEYLYSSIDTILVMTVNPGFAAQSFLMSQLRKIEVLKERITKLGNDIEIAVDGGIDYEIAGLVVSAGADV 192
                     *********************************************************************************************** PP

                     EEESHHHH CS
  Ribul_P_3_epim 191 lVagsavf 198
                     lV+gs++f
      AHX11276.1 193 LVTGSYLF 200
                     *****998 PP

>> PcrB  PcrB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.29   2.6e+03     146     165 ..       8      29 ..       4      37 .. 0.67
   2 !   12.1   0.1   1.1e-05       0.1      18      83 ..      70     138 ..      56     144 .. 0.87
   3 !   12.2   0.0     1e-05     0.091     169     215 ..     156     203 ..     148     215 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.29
                 HHHHHHTT-..SEEEEE-TTSS CS
        PcrB 146 llaakllgl..rliYlEasGal 165
                 ll+a++l+l   ++ +E sGa 
  AHX11276.1   8 LLSADFLNLgaEVAQIENSGAD 29 
                 6778887774357788888874 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.1e-05
                 -CHHHHHHHHCTT-SEEEEECSTCHHHHHHHHHHHHHCTSSS-EEEEESSGGG--TT....SSEEEEEEE CS
        PcrB  18 npdEiveiviesgtDavmigGsqsvtldntvrllkkvsriklPivlepsnvegvvry....aDalFvmsl 83 
                 n +   +  i+ g++++ +     v+ d+ ++++kk  ++k+ + + ps  e+v +y    +D + vm++
  AHX11276.1  70 NAEQTFQDYIDAGANTIFVHSEACVHVDRLLTMIKKQ-NVKVGLAINPSTHESVLEYlyssIDTILVMTV 138
                 556677778999********999*************9.9************9998763333688888887 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 1e-05
                 HHHHH.HHHHHSSSEEEEESS--SHHHHHHHHCC.SSEEEE-CHHHHHH CS
        PcrB 169 eevia.lkkklekarlivGGGirsaEkAkevvea.ADvivvGnvveekd 215
                 e +++ + k  +++++ v GGi+  E+A  vv a ADv+v+G  +  ++
  AHX11276.1 156 EVLKErITKLGNDIEIAVDGGID-YEIAGLVVSAgADVLVTGSYLFSEP 203
                 544441455567899*******6.79****************9988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1751.34
//
Query:       AHX11277.1  [L=262]
Description: methionine aminopeptidase, type I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.1e-53  181.1   0.0    2.4e-53  181.0   0.0    1.0  1  Peptidase_M24  Metallopeptidase family M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.0   0.0   1.3e-57   2.4e-53       1     209 []      13     244 ..      13     244 .. 0.89

  Alignments for each domain:
  == domain 1  score: 181.0 bits;  conditional E-value: 1.3e-57
                    HHHHHHHHHHHHHHHHHHHHHHTTCBHHHHHHHHHHHHHHHTT.....TCEESSSSEEEEGGGGGSTTTBCSSSB--TTEEEEEEEEEEETTEEEE CS
  Peptidase_M24   1 elirkaariasaaleavleaikpgvterelaaeieattlkrhg.....arglafppivasgenaavlhytpndrvlkegdlvlidagaeydgyasD 91 
                    e +r+a+r+a+++l+++ e +kp vt++el+++++++ + + g      ++ +fp+++++++n+ ++h++p++ +lk+gd+++id+++ +dg+++D
     AHX11277.1  13 EYMRRAGRLAAEVLDYITEFVKPDVTTNELDRLCHEF-IVKAGavpapLNYKGFPKSICTSKNNVICHGIPDEVPLKKGDILNIDVTVILDGWHGD 107
                    57*********************************99.5555669999************************************************ PP

                    EEEEEECSSGSHHHHHHHHHHHHHHHHHHHC-STTSBHHHHHHHHHHHHHHT.TBCCGBSSCSEEEESSSSSEEEEEESS...STTCSSB--TTBE CS
  Peptidase_M24  92 itrTvlvGkftpeqrelyeavleaqeaaikavkpGvtlseidaaarevlesa.glakffphglGHgvGlevhdegpsvsr...esndgrkleeGmv 183
                    ++r+++vG+++ + ++l+ea+  a+ a+i+ v+pG++l+ i+ a+++++ ++  + + + +++GHg+G+++h+  psv +   +s+++  le+Gm 
     AHX11277.1 108 TSRMYFVGTPSIKGARLCEATYGALMAGIEVVRPGIPLNRIGCAIEDYISQQySY-SIVDQYCGHGIGRSFHEP-PSVVHyatDSGNTIILEPGMF 201
                    ********77778999**********************************64378.8999************98.997555666669********* PP

                    EEEEEEEE..EET........TT.......E.EEEEBEEEEEES CS
  Peptidase_M24 184 ftiEpgiy..fap........ge.......g.gvriedtvlvte 209
                    ftiEp+i   + p        g+       + ++++e+t+ vte
     AHX11277.1 202 FTIEPMINegK-PhaivdkndGWtvrtkdlSlSAQFEHTIAVTE 244
                    *****999430.24444444455888889977***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (262 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       374  (0.0208601); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1999.97
//
Query:       AHX11278.1  [L=151]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1102.80
//
Query:       AHX11279.1  [L=175]
Description: ubiquinone biosynthesis COQ7 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-57  192.4   0.1    5.5e-57  192.3   0.1    1.0  1  COQ7          Ubiquinone biosynthesis protein COQ7
  ------ inclusion threshold ------
      0.015   15.7   0.0      0.034   14.5   0.0    1.6  1  Rubrerythrin  Rubrerythrin
      0.017   15.4   0.2          3    8.0   0.0    2.2  2  Ferritin_2    Ferritin-like domain


Domain annotation for each model (and alignments):
>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  192.3   0.1   9.2e-61   5.5e-57       2     172 .]       7     175 .]       6     175 .] 0.97

  Alignments for each domain:
  == domain 1  score: 192.3 bits;  conditional E-value: 9.2e-61
        COQ7   2 ldrllRvdhaGElgAvaiYkgqlavlakkdpelkpllkemleqEkeHlatfeellkerrvrpslllplwkvagfalGaltallGkeaamacteavEtvi 100
                 +dr+lRv+haGE++Av++Y+gql  l  +d e k+l++em++ E+ Hl++f++ + + ++rpslll  wk  +f+lG+l+a +G  +amact+a+E+vi
  AHX11279.1   7 IDRILRVNHAGECAAVQVYRGQLRGL-GDDLEKKKLVSEMMKSEQAHLQFFRSEIINLKTRPSLLLATWKSLAFGLGYLSARAGVPTAMACTVAIEEVI 104
                 89***********************9.6666669***************************************************************** PP

        COQ7 101 geHYneqlreleeleeeedkelleiikqfrddEleHldtAvendaekapaykllsaviklgcrvaiavaeri 172
                 +eHY++q+r le+++  +d++ll+ i qfr+dEl+H+++A+en+a+kap+y +++ + k++crv+i va+ri
  AHX11279.1 105 DEHYQKQIRLLEKIS-LSDTRLLKKIVQFRQDELDHRNIAMENEARKAPCYVAITGITKFCCRVGIFVAKRI 175
                 ************875.999****************************************************8 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   5.7e-06     0.034       2     106 ..      10     111 ..       9     146 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 5.7e-06
                   HHHHHHHHHHHHHHHHHHHHHCHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTHH.B.SSBBS-------TTGGHHHHHHHHHHHHHHHHHC CS
  Rubrerythrin   2 iLekAiagEssarrlYkelaekakegypqiaelFeelAeeEreHakilnklleklepelelevkekvreyaeakpkflttaknLeeaiegayaeeee 98 
                   iL  + agE+ a ++Y+   + + + ++  ++l  e+ + E+ H ++++  + +l+       +  +++ + +   +l+ +  + +a++   a ee 
    AHX11279.1  10 ILRVNHAGECAAVQVYRGQLRGLGDDLE-KKKLVSEMMKSEQAHLQFFRSEIINLKTRPS--LLLATWKSLAFGLGYLSARAGVPTAMACTVAIEEV 103
                   788999******************8887.69******************99999888888..78899999999999999999999777777777777 PP

                   HHHHHHHH CS
  Rubrerythrin  99 myrfyeel 106
                   + ++y++ 
    AHX11279.1 104 IDEHYQKQ 111
                   77777664 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0005         3      34      61 ..      33      60 ..       9      74 .. 0.76
   2 ?    5.3   0.1    0.0035        21      12      56 ..     100     142 ..      93     154 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0005
  Ferritin_2 34 lldaevrevaeeiakheeaHveflkaal 61
                + d e ++++ e++k e+aH++f+++ +
  AHX11279.1 33 GDDLEKKKLVSEMMKSEQAHLQFFRSEI 60
                556677999***************9977 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0035
  Ferritin_2  12 lEyleaafYtaalegaslddkalldaevrevaeeiakheeaHvef 56 
                  E +  + Y++ +     ++ +l+d++ ++ + +++++e +H+++
  AHX11279.1 100 IEEVIDEHYQKQIRLL--EKISLSDTRLLKKIVQFRQDELDHRNI 142
                 5666667777777744..3378889999**************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (175 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      375  (0.0209158); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.25s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1386.80
//
Query:       AHX11280.1  [L=167]
Description: disulfide bond formation DsbB family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-24   86.5   4.7    2.8e-24   86.2   4.7    1.0  1  DsbB      Disulfide bond formation protein DsbB
  ------ inclusion threshold ------
      0.091   12.5   0.1       0.14   11.8   0.1    1.3  1  TTC5_OB   Tetratricopeptide repeat protein 5 OB fold domain
       0.17   12.1   0.3       0.17   12.1   0.3    3.7  4  DUF3951   Protein of unknown function (DUF3951)


Domain annotation for each model (and alignments):
>> DsbB  Disulfide bond formation protein DsbB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.2   4.7   4.6e-28   2.8e-24       3     146 ..      17     160 ..      15     161 .. 0.90

  Alignments for each domain:
  == domain 1  score: 86.2 bits;  conditional E-value: 4.6e-28
                 HHHHHHHHHHHHHHHHHHHHHCTTTTSXXSHHHHHHHHHHHHHHHHHHTTSSSS.HHHHHHHHHHHHHHHHHHHHHHHHHHHSX-S.STSB-BSXXXTT CS
        DsbB   3 llllllalaslallalAlyfqhvlglePCelCvyqRlallliallallaaiapk.rllllllallaalvgaalaarhvgvellpwd.pasCgslptfpe 99 
                 l+++ l+l+sl++l++A+++++ +g++PC+lC+y+R+++++++l+++ +++  + + l+++la++a+ +ga++ ++h+g+e+++    +sC+   t+ +
  AHX11280.1  17 LVAFNLFLSSLFALVFAVILEYAFGYHPCTLCIYERWPYFIVLLISVRMLFLDEvTPLFFYLAIAALSAGALITLYHIGIEYHLFIkEESCS--ITYHN 113
                 678889*****************************************99977776669999***********************99778**5..44567 PP

                 SXHHHHSSTTTTTXX.SSSSSSSXECTTSEHHHHHHHHHHHHHHHHHH CS
        DsbB 100 alpldewlpevfkat.gdCgeadwkllglsmaqwnllifalllllllv 146
                 +  +d + +++++ +   C++++ +++g+ ++++nll+++l + ++l+
  AHX11280.1 114 IHEIDSLHKQLISNEiVRCNTPQ-TVFGIRLTHINLLYSMLSITVTLF 160
                 788999999999999888*9877.999*************99988876 PP

>> TTC5_OB  Tetratricopeptide repeat protein 5 OB fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.1   2.4e-05      0.14      25      99 ..      63     138 ..      55     140 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 2.4e-05
     TTC5_OB  25 vtslaseeevplal.llvDskgtvlvvtvYnilkgkgvvig.DtvaIpePfieqikielkskdiqfksiRVdtpevl 99 
                 v +l  +e  pl + l + + +  + +t+Y+i+ ++ + i+ ++ +I   +i++i+ +l ++ i+ +++R++tp+++
  AHX11280.1  63 VRMLFLDEVTPLFFyLAIAALSAGALITLYHIGIEYHLFIKeESCSITYHNIHEID-SLHKQLISNEIVRCNTPQTV 138
                 44566666777665155677777899******887776665167************.77779************986 PP

>> DUF3951  Protein of unknown function (DUF3951)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.2      0.32   1.9e+03      20      28 ..      16      24 ..       7      26 .. 0.73
   2 ?    2.7   1.0     0.024   1.4e+02      17      37 ..      56      77 ..      34      80 .. 0.73
   3 ?   12.1   0.3   2.9e-05      0.17       4      38 ..      78     112 ..      76     121 .. 0.84
   4 ?   -0.5   0.2      0.24   1.4e+03      13      30 ..     146     163 ..     137     165 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.32
     DUF3951 20 gfvayklFv 28
                 +va+ lF 
  AHX11280.1 16 KLVAFNLFL 24
                589999996 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.024
     DUF3951 17 viIgfva.yklFvkkesidiyY 37
                +i+ +++  +lF +  ++  +Y
  AHX11280.1 56 FIVLLISvRMLFLDEVTPLFFY 77
                45555541689****9999998 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 2.9e-05
     DUF3951   4 ltiGillltlvilviIgfvayklFvkkesidiyYT 38 
                 l+i +l  +++i +  + + y lF+k es  i Y 
  AHX11280.1  78 LAIAALSAGALITLYHIGIEYHLFIKEESCSITYH 112
                 5788899999998877777************9885 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.24
     DUF3951  13 lvilviIgfvayklFvkk 30 
                 + +l  +  ++  lF+ +
  AHX11280.1 146 INLLYSMLSITVTLFIHR 163
                 555555555677788876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       866  (0.0483016); expected 358.6 (0.02)
Passed bias filter:                      391  (0.0218082); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.21s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1402.55
//
Query:       AHX11281.1  [L=37]
Description: hypothetical protein NHE_0329 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       184  (0.0102627); expected 358.6 (0.02)
Passed bias filter:                      178  (0.00992805); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 298.27
//
Query:       AHX11282.1  [L=288]
Description: RNA polymerase sigma-32 factor [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-15   56.2   0.4    8.1e-14   50.9   0.3    2.9  3  Sigma70_r4    Sigma-70, region 4
    2.4e-15   56.0   0.0    5.6e-15   54.9   0.0    1.7  1  Sigma70_r2    Sigma-70 region 2
    0.00035   20.6   2.1      0.025   14.7   0.5    2.6  2  Sigma70_r3    Sigma-70 region 3
     0.0017   18.0   0.6      0.018   14.7   0.3    2.5  2  Sigma70_r4_2  Sigma-70, region 4
  ------ inclusion threshold ------
        0.1   12.5   0.4       0.29   11.0   0.1    1.9  2  HTH_5         Bacterial regulatory protein, arsR family
       0.11   12.6   0.1        0.4   10.8   0.0    2.1  2  HTH_16        Helix-turn-helix domain
       0.41   11.0   2.5        1.3    9.4   0.7    2.6  3  HTH_WhiA      WhiA C-terminal HTH domain


Domain annotation for each model (and alignments):
>> Sigma70_r4  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0         1   2.6e+03      13      32 ..      61      81 ..      61      85 .. 0.78
   2 ?    1.8   0.0     0.067   1.7e+02      23      41 ..     154     172 ..     143     174 .. 0.86
   3 !   50.9   0.3   3.2e-17   8.1e-14       1      50 []     225     276 ..     225     276 .. 0.96

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1
                HHHHH.TTT--HHHHHHHHTS CS
  Sigma70_r4 13 lelrf.geglTleEIgerlgi 32
                +++rf   gl+l +++ + +i
  AHX11282.1 61 VVMRFkNYGLPLMDLASEGNI 81
                589999999999988877666 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.067
                 HHHHHHHHTS-HHHHHHHH CS
  Sigma70_r4  23 leEIgerlgiSrerVrqie 41 
                  e I++ l+++++ V+  e
  AHX11282.1 154 VEKISKLLDVPESDVKEME 172
                 589***********99765 PP

  == domain 3  score: 50.9 bits;  conditional E-value: 3.2e-17
                 HHHHS-HHHHHHHHHHH..TTT--HHHHHHHHTS-HHHHHHHHHHHHHHHHH CS
  Sigma70_r4   1 aLasLpererevlelrf..geglTleEIgerlgiSrerVrqiekrAlrkLRk 50 
                 a +sL++r+r+++ lr     + Tl+E++e++ iS+erVrqi+ rA++k+++
  AHX11282.1 225 AVDSLDDRHRKIFILRSlsSTPSTLKELSEKFSISQERVRQIHVRAMEKVKE 276
                 5699***************9*****************************996 PP

>> Sigma70_r2  Sigma-70 region 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.9   0.0   2.2e-18   5.6e-15       1      68 [.      50     117 ..      50     120 .. 0.95

  Alignments for each domain:
  == domain 1  score: 54.9 bits;  conditional E-value: 2.2e-18
                 HHHHHHHHHHHHHHHCT-THHHHHHHHHHHHHHHHHHGGGTSTTTCHHHHHHHHHHHHHHHHHHHHTS CS
  Sigma70_r2   1 lverylplvkrlarrllgsgadaeDlvQeaflrlwraverfdpergvsfsawllriarnaaidrlRkr 68 
                 lve+yl+lv+++++r+ + g+   Dl++e++++l++a+++fd + g++  ++++++++ a+  ++ + 
  AHX11282.1  50 LVEAYLRLVVKVVMRFKNYGLPLMDLASEGNIGLMKAIKNFDNTLGYKIATYAVWWIKAAINEYIIRS 117
                 79*********************************************************998888665 PP

>> Sigma70_r3  Sigma-70 region 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.5   9.6e-06     0.025      23      75 ..     154     206 ..     153     208 .. 0.88
   2 ?    4.5   0.0     0.014        37      22      40 ..     248     266 ..     241     283 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 9.6e-06
                 HHHHHHHHTXXHHHHHHHHH.HHXXXEETTXBSSSSTTXBSTTTXBXSSSXXHH CS
  Sigma70_r3  23 peEiAeeLglseekVrevle.aarepvSldlpvgeeedtelgdlleddeaespe 75 
                 +e i + L+++e++V+e+   ++ + vSl+ ++ge++ te  d+l+   + ++e
  AHX11282.1 154 VEKISKLLDVPESDVKEMEAiLSSKDVSLNARIGEDDGTEVHDMLAGP-GPDQE 206
                 57899************966268899*******************998.77766 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.014
                 XHHHHHHHHTXXHHHHHHH CS
  Sigma70_r3  22 tpeEiAeeLglseekVrev 40 
                 t  E+ e+  +s+e+Vr++
  AHX11282.1 248 TLKELSEKFSISQERVRQI 266
                 668**************97 PP

>> Sigma70_r4_2  Sigma-70, region 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.21   5.3e+02      30      44 ..     155     169 ..     150     171 .. 0.88
   2 !   14.7   0.3   6.8e-06     0.018       3      53 ..     221     273 ..     219     274 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.21
                   HHHHHHHT--HHHHH CS
  Sigma70_r4_2  30 kEIAellgisegtVk 44 
                   + I++ll+++e+ Vk
    AHX11282.1 155 EKISKLLDVPESDVK 169
                   679*********998 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 6.8e-06
                   HHHHHHTTS-HHHHHHHHHHHTS-..--HHHHHHHHT--HHHHHHHHHHHHHH CS
  Sigma70_r4_2   3 alrealaeLperqreifllryleg..lsykEIAellgisegtVksrlsRArkk 53 
                    l ea+++L  r r+if+lr l    ++ kE +e++ is   V++   RA++k
    AHX11282.1 221 LLKEAVDSLDDRHRKIFILRSLSStpSTLKELSEKFSISQERVRQIHVRAMEK 273
                   6889*******************944578*********************998 PP

>> HTH_5  Bacterial regulatory protein, arsR family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.6     4e+03      18      32 ..     154     168 ..     149     170 .. 0.81
   2 ?   11.0   0.1   0.00011      0.29       7      34 ..     238     265 ..     233     274 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.6
                 HHHHHHHHTS-HHHH CS
       HTH_5  18 vcelaeelglsqstv 32 
                 v  +++ l++++s v
  AHX11282.1 154 VEKISKLLDVPESDV 168
                 678999999999876 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00011
                 HHHHHTTSSEEHHHHHHHHTS-HHHHHH CS
       HTH_5   7 ILklLaegelcvcelaeelglsqstvSh 34 
                 IL++L++ + +  el+e++ +sq  v++
  AHX11282.1 238 ILRSLSSTPSTLKELSEKFSISQERVRQ 265
                 9**********************88876 PP

>> HTH_16  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00016       0.4      11      65 .]      43      91 ..      39      91 .. 0.89
   2 ?   -3.8   0.0       5.3   1.4e+04      51      63 ..     264     276 ..     254     278 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00016
      HTH_16 11 DeeAieeiLkhYegyIrklSlrklydedgnvngyvdedlkqeleiklieaIlkFk 65
                D eA +++++ Y  +  k  +r+      + +g   +dl  e  i l++aI++F+
  AHX11282.1 43 DVEAAQKLVEAYLRLVVKVVMRF------KNYGLPLMDLASEGNIGLMKAIKNFD 91
                99*******************84......34777889*****************7 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.3
      HTH_16  51 qeleiklieaIlk 63 
                 +++ ++ +e+++ 
  AHX11282.1 264 RQIHVRAMEKVKE 276
                 5666666666665 PP

>> HTH_WhiA  WhiA C-terminal HTH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.7   4.3e+03      13      29 ..      41      57 ..      40      76 .. 0.73
   2 ?   -0.7   0.0      0.73   1.9e+03      24      58 ..     149     183 ..     133     185 .. 0.72
   3 ?    9.4   0.7    0.0005       1.3      21      73 ..     212     263 ..     208     275 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.7
                HHHHHHHHHHHHHHHHH CS
    HTH_WhiA 13 kKtvkaaakqieaieli 29
                 K v+aa+k +ea+ ++
  AHX11282.1 41 HKDVEAAQKLVEAYLRL 57
                57788888888876555 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.73
                 HHHHHHHHHT-GGGS-HHHHHHHHHHHH-TTS-HH CS
    HTH_WhiA  24 eaielieekkgleklpeklkevaelRlenpdaSLk 58 
                 e+ +++e+  +l ++pe+  + +e+ l+ +d+SL+
  AHX11282.1 149 EKGQMVEKISKLLDVPESDVKEMEAILSSKDVSLN 183
                 55566777777777777777777777888888876 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.0005
                 HHHHHHHHHHHHT-GGGS-HHHHHHHHHH.HH-TTS-HHHHHHTT..T--HHHH CS
    HTH_WhiA  21 kqieaielieekkgleklpeklkevaelR.lenpdaSLkeLgelleppisKSgv 73 
                 +q ++i+    k+++++l+++ ++++ lR l+   ++LkeL+e +   is   v
  AHX11282.1 212 EQQRRIKANLLKEAVDSLDDRHRKIFILRsLSSTPSTLKELSEKF--SISQERV 263
                 5666676666677899*************66788899******99..6665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (288 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2081.18
//
Query:       AHX11283.1  [L=329]
Description: cell division protein FtsZ [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-37  128.5   0.2    6.2e-37  127.7   0.2    1.4  1  Tubulin   Tubulin/FtsZ family, GTPase domain
    1.6e-33  114.8   1.7    1.6e-33  114.8   1.7    1.9  2  FtsZ_C    FtsZ family, C-terminal domain
  ------ inclusion threshold ------
       0.11   11.9   3.6      0.093   12.2   0.6    1.9  2  MafB      Neisseria toxin MafB


Domain annotation for each model (and alignments):
>> Tubulin  Tubulin/FtsZ family, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.7   0.2     1e-40   6.2e-37      52     197 .]       4     137 ..       1     137 [. 0.98

  Alignments for each domain:
  == domain 1  score: 127.7 bits;  conditional E-value: 1e-40
                 .EEESBHHHHHTS-GS......EEEE--CCCCTTC--TT-HHHHHHHHHHTHHHHHHHHTT-SE.SEEEEEEETTSSHHHHHHHHHHHHHHHTSTTSEE CS
     Tubulin  52 vaidtdpqvlneikagselfnpnklllgkegagnngaggypevgkeaaeeileeirkevekcdslqgffitaslgGGTGSGlgpvilevlkeeypkalv 150
                 +a++td+q+l+ + a+      +k++lg + ++++gag+ pe+g++aaee+ +ei + +e++d+   +fita++gGGTG+G++pvi+++++e   k+lv
  AHX11283.1   4 IAANTDAQALEYSLAD------TKVQLGVNLTKGLGAGSIPEIGRQAAEESINEIADVIEGVDM---LFITAGMGGGTGTGAAPVIAKLASEH--KVLV 91 
                 69**************......******************************************...**************************..**** PP

                 EEEEEE--GG.G-HHHHHHHHHHHHHHHHT-SEEEEEEHHHHHCCST CS
     Tubulin 151 vtvvvlPsefsevvvepynailalkelieesdavividNdaLlkiln 197
                 v+vv+ P+ f e+ ++ + a+ ++++l++++d++ivi+N++L+ki+n
  AHX11283.1  92 VAVVTKPFYF-EGGRRAKVAEAGVETLRKYVDTYIVINNQNLFKIAN 137
                 **********.*********************************986 PP

>> FtsZ_C  FtsZ family, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.92   5.5e+03      18      72 ..      43      56 ..      11      61 .. 0.54
   2 !  114.8   1.7   2.7e-37   1.6e-33       1      94 [.     185     279 ..     185     280 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.92
                HHHHHHHTSGGGT--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEE CS
      FtsZ_C 18 eaaeaaisspLLdvdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvi 72
                +aa                                         +e ++e a+vi
  AHX11283.1 43 QAA-----------------------------------------EESINEIADVI 56
                222.........................................23344444444 PP

  == domain 2  score: 114.8 bits;  conditional E-value: 2.7e-37
                 EEEEEEEEEEESTTHHHHHHHHHHTSGGGT.--GGG-SEEEEEEEE-TT--HHHHHHHHHHHHHHS-TTSEEEEEEEE-TT--SEEEEEEEEES- CS
      FtsZ_C   1 GvAmmgvGeasgedraeeaaeaaisspLLd.vdlsgAkgvlvnitggsdltlkEveevaetireevdeeanvivGavideeledeirvtvvatgl 94 
                 G+A+mg+Geasge+ra +aae++i++pLLd ++++ Akg+l+nitgg+d+tl+Ev+++a+ +re+++e++n+i+G++  e++++ +rv+vvatg+
  AHX11283.1 185 GKALMGTGEASGENRAIKAAENSIANPLLDnLSVQDAKGILMNITGGPDMTLFEVDAAANCVREKANENVNIIFGSTCTESMNNAVRVSVVATGI 279
                 89********************************************************************************************9 PP

>> MafB  Neisseria toxin MafB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1     0.054   3.2e+02     153     218 ..      13      74 ..       4      96 .. 0.58
   2 ?   12.2   0.6   1.6e-05     0.093     195     284 ..     176     266 ..     134     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.054
        MafB 153 isqrlldefanagsnlldradeankkifeydpeldrsgnameavnGvadgavnpflaagealGvGd 218
                 ++  l+d   ++g nl+++ + +    +  ++      ++++++  v++g+   f++ag + G G 
  AHX11283.1  13 LEYSLADTKVQLGVNLTKGLGAGSIPEIGRQAAE----ESINEIADVIEGVDMLFITAGMGGGTGT 74 
                 5555556666666666666655544333333333....4556666666677777777776655553 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 1.6e-05
        MafB 195 avnGvadgavnpflaagealGvGdivdgiseavdiaalhnlgllsaeaklaaitdladaaqlk.kdaaeavrdWadenPnaaetveavvnv 284
                 +v+ v++ +   ++ +gea G   +++++ +++    l nl+   a + l  it+  d++ ++ + aa++vr+ a+en n+  +  +  ++
  AHX11283.1 176 DVRSVMSKMGKALMGTGEASGENRAIKAAENSIANPLLDNLSVQDAKGILMNITGGPDMTLFEvDAAANCVREKANENVNIIFGSTCTESM 266
                 6778888888899999*******************************************98862667899**********96544333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       839  (0.0467957); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 2595.59
//
Query:       AHX11284.1  [L=528]
Description: penicillin binding transpeptidase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-48  166.0   0.0    1.5e-48  165.6   0.0    1.1  1  Transpeptidase  Penicillin binding protein transpeptidase dom
    3.4e-09   37.3   0.0    1.1e-08   35.7   0.0    1.8  2  PBP_dimer       Penicillin-binding Protein dimerisation domai


Domain annotation for each model (and alignments):
>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  165.6   0.0   1.7e-52   1.5e-48       3     305 ..     214     508 ..     212     509 .. 0.92

  Alignments for each domain:
  == domain 1  score: 165.6 bits;  conditional E-value: 1.7e-52
                     EEEEETTT-BEEEEEEESE-TTTHHCC.TCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTSS.ECTCCCC-SSSSEE. CS
  Transpeptidase   3 avvldaktgevlamaskpsydpnakvg.kneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqggqsikdweqdnkgsegi. 95 
                      +v+da+tgev+a++s p++dpn  +   +e+  nr+  ++ye GS++K++t+a a+e+gvi++++t+d  +  + +g +ikd  +++   + i 
      AHX11284.1 214 GIVMDANTGEVIALVSLPDFDPNHVQLsREEERFNRVSLGRYEFGSIMKIFTVACAMENGVISGEDTYDVVTPLKISGYTIKDLYKAR---KSIy 305
                     689*********************9988999999***********************************9886666666688888887...6677 PP

                     EHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS-SSSSSTT-B--.B--SSHHHHHHHHHTTTSBB-HHHHHHHHHHHHTT.TEEE--BSE CS
  Transpeptidase  96 tlrealekSsntyfvklaqklgadklrkylkkfglGnktgidlpgesaG.vptrkwlegatisfgiGltvtplqlaqayaaiang.GklvkPhlv 188
                     ++ e+l++Ssn++++++a k+g +  ++ ++++g+  + +++ p++s    p+++ l + t+s+g+G t t l++++a a ++n+ G l +  l+
      AHX11284.1 306 NVAEILKYSSNVGMAQIAMKMGSEVQYNCFQELGFFDDIKFEIPEKSIPsRPKESRLTSVTLSYGYGFTPTLLHVMKATAILINDtGCLPTITLL 400
                     *********************************************99884555566****************************87899999999 PP

                     EEEEECTTEEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCTTTTGCGTCTTS--EEEEEEEEECSSSTTSEEEEEEEEEEEEEESTTS-SEEEEE CS
  Transpeptidase 189 kaivdpdgvrkvkpkelnklpisketaekvkeglkgvvsrgsgtataavegykvagKTGTAevagkkgngkkegakiswfvgyapadnpkyavav 283
                     k+ +++++            +i++e  +++++ ++gvv +gsg+ +   +gy+v gKTG  e++   ++ + ++++ ++fv++ p +np+y++ +
      AHX11284.1 401 KGNKENNT---------CIPVIREEVRKEMRKFMRGVVLDGSGRRAD-AVGYQVGGKTGSSEKNI--NGIYLKDKNLASFVAVFPMENPRYVIGI 483
                     87777765.........899*********************887777.99**************8..677788888******************* PP

                     EECTCS...SSSSCCHHHHHHHHHH CS
  Transpeptidase 284 lieqpk...eaaggkaaapiakkil 305
                      +++pk     +gg ++apiakk++
      AHX11284.1 484 SVDEPKssrAVTGGVVSAPIAKKVI 508
                     *******99999**********986 PP

>> PBP_dimer  Penicillin-binding Protein dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.2e-12   1.1e-08       9     126 ..      54     160 ..      53     215 .. 0.75
   2 ?   -2.1   0.0      0.47   4.2e+03      35      74 ..     299     336 ..     287     351 .. 0.65

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.2e-12
                 EE-TTS-EEEEEEEEEEEEEEESSS-HHHHHHHHHHHHHHC.HHHTTS-HHHHHHHHCCCCTSSTTSCECCCCCEECHHHCCCHHHHHCSTT-EEEEEE CS
   PBP_dimer   9 IyDrngrlLAtnrpsytltitpsklkkkkalekikklakll.eseenldderleelalkknsykaykpvviaediseeevarikenakdlpGinievep 106
                 +yDrng+++A n p+++++   +kl  ++++    kla+ l +     + ++l     +k+ ++ + +v +++ ++ +e++ri   +  +pG+++++e 
  AHX11284.1  54 LYDRNGEIIAFNLPTVSVYTFVKKLRGDHSEI-STKLAEALlN----TSRQEL-----MKKFASTEGFVWLKRYLTPNELHRIL--LLGMPGLYFREEH 140
                 69***************999888888888765.8999999933....333333.....456777778888999**********8..56699******** PP

                 EEEETTTSTTHHHH-EEEEC CS
   PBP_dimer 107 kRyYpkgelaahvlGyvgki 126
                 kR+Y + +l+ahvlGyv + 
  AHX11284.1 141 KRVYISRNLFAHVLGYVDND 160
                 *****************987 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.47
                 HHHHHHHHHHHHHHCHHHTTS-HHHHHHHHCCCCTSSTTS CS
   PBP_dimer  35 kkkalekikklaklleseenldderleelalkknsykayk 74 
                 k++  ++i ++a++l+ ++n+  +++  ++ ++ +y+ ++
  AHX11284.1 299 KAR--KSIYNVAEILKYSSNVGMAQIAMKMGSEVQYNCFQ 336
                 333..33999999998888877777777555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (528 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      514  (0.0286686); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 4318.28
//
Query:       AHX11285.1  [L=189]
Description: ribosomal subunit interface protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.7e-14   53.3   0.0    6.5e-14   52.5   0.0    1.4  1  Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosoma
    2.6e-12   46.2   0.1    4.8e-12   45.4   0.1    1.3  1  Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein 
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.038   13.9   0.0    1.4  1  TnpB_IS66        IS66 Orf2 like protein


Domain annotation for each model (and alignments):
>> Ribosomal_S30AE  Sigma 54 modulation protein / S30EA ribosomal protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.5   0.0   1.1e-17   6.5e-14       2      86 .]       4      97 ..       3      97 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.5 bits;  conditional E-value: 1.1e-17
                     EEEECTS---HHHHHHHHHHH.CCGGGG....-EEEEEEEEE....EEEEEEEEEC..TTEEEEEEEEESSHHHHHHHHHHHHHHHHHHCHHTTX CS
  Ribosomal_S30AE  2 eitgrnievtdalkeyvekkl.eklekyf...ieadVtlskk....kkvevtirla..kgkviraeeesedlyaaidlavdklerqlrkykeklk 86
                     ++ g+++++  +l e+++++l + +ekyf   ++ +V ls k    + +++ ++    +++vi+a++es+d y a d+a+ ++  +lr+yk+klk
       AHX11285.1  4 IVAGHGFNLGSSLSEHITDHLsSSVEKYFshaVSGRVSLS-KvgrlFSADIVVNDGvpNKPVIKASAESSDPYLAADSAIARISAKLRRYKQKLK 97
                     689******************999****9999********.5577899*****88899999********************************86 PP

>> Ribosom_S30AE_C  Sigma 54 modulation/S30EA ribosomal protein C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.1     8e-16   4.8e-12       5      54 ..     124     173 ..     121     174 .. 0.95

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 8e-16
                      -EEEEE-S--S-B-HHHHHHHHHHHT-SEEEEEETTTTEEEEEEEETTSC CS
  Ribosom_S30AE_C   5 eivrtkrfelkpmsveeAilqmellghdFfvFrnaetgevnVvYrrkdgn 54 
                       +v+++++el+ +s+e+Ai++m+l+   +fvF+n e++++++++r + g+
       AHX11285.1 124 LVVKEEKIELRQLSLEDAIMHMDLISAAVFVFINIESNRLSIIHREDKGD 173
                      59*******************************************99885 PP

>> TnpB_IS66  IS66 Orf2 like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   6.4e-06     0.038      27      56 ..     143     172 ..     131     184 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 6.4e-06
   TnpB_IS66  27 lkldpfsgalFvFrnrrrdrlKiLlwdgnG 56 
                 +++d +s a+FvF+n +++rl i++ +++G
  AHX11285.1 143 MHMDLISAAVFVFINIESNRLSIIHREDKG 172
                 899***********************9999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       674  (0.0375927); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1481.96
//
Query:       AHX11286.1  [L=391]
Description: tyrosine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.8e-75  252.3   0.0    7.7e-75  251.9   0.0    1.2  1  tRNA-synt_1b  tRNA synthetases class I (W and Y)
    2.9e-07   30.1   0.0    7.1e-07   28.8   0.0    1.6  1  S4            S4 domain
  ------ inclusion threshold ------
      0.029   14.7   1.9       0.45   10.8   0.1    2.4  2  DUF4878       Domain of unknown function (DUF4878)


Domain annotation for each model (and alignments):
>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.9   0.0   1.3e-78   7.7e-75       4     293 .]      28     316 ..      25     316 .. 0.98

  Alignments for each domain:
  == domain 1  score: 251.9 bits;  conditional E-value: 1.3e-78
                   S--EEEEEEETSSS.-BGGGHHHHHHHHHHHHTTSEEEEEEEHHHHHTTTTT.-SSHHHHHHHHHHHHHH..HHHHHHHTCHTTTEEEEETHHHHTT CS
  tRNA-synt_1b   4 rplrvysGidPTgk.lHlGylvplkklvelqkaghevffliaDlhAiigdps.kaeerklrkreevlena..ikaqlakgldpekaevvlqsewleh 96 
                   ++l +y+G+d T++ +HlG+lvpl+ l+ + ++gh+v++l+++ +++igdps k ++r+++++ee ++n+  i +++++++    +++v++ ewle+
    AHX11286.1  28 GKLVFYLGFDCTSSsIHLGHLVPLMLLRLIKRYGHDVIILLGGGTTLIGDPSgKDKARQMLSKEEIQKNTesIGKIIKCLVGE--VRFVNNAEWLEN 122
                   67899*****************************************************************99*******9987..9*********** PP

                   HHHHHHHHHHHTTCBHHHHHHHHHCCHHCSSSC--BHHHHHHHHHHHHHHHHTCHS....EEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET CS
  tRNA-synt_1b  97 lelaellrdlgklgslnrmlqfksvkkrleegegislgeftYplLqaaDilllkad....lvpgGsDQkqnielgrdlarrfnkkevfkkpegltvp 189
                   l+++++lr++g+ +s+nrml f+svk+rle+++ +s+ ef+Y++Lqa+D++ l+      +++gGsDQ++ni+ g++l ++++ +    + +gltvp
    AHX11286.1 123 LSYIDFLREIGRYFSINRMLTFDSVKSRLERESHLSFLEFNYMILQAYDFVELNRLygcnVQIGGSDQWGNIVNGVELSKKLKGS----QLFGLTVP 215
                   *******************************889*******************9999999*************************....******** PP

                   -BBSTTSSSBTTCETTCGC-BTTCCHHHHHHHHHHCHCSTTCSHHHHHHHHHTHHHCHHHHHHHHCCSEEESSHHHHHHHHHCCCCHHHHHHHHHHH CS
  tRNA-synt_1b 190 lltgldGekKmSKSagnsaIfLddekesvkkkiqkavtdsdeevekllklktelsnelierleavsgkkpkreaeellaeevtklvhggdlkkalae 286
                   l+  ++G+ Km+K++ + a++Ld +  s+ +  q++ ++ d++v+k+l+l+tels++++e+l+++ g++  +ea+++la e+tk  hg d +k+++e
    AHX11286.1 216 LIMTASGK-KMGKTEAG-AVWLDADLYSPHDYWQYFRNTEDADVRKFLYLFTELSKKEVEELSKLEGSEL-NEAKKILATEATKICHGADTAKKVSE 309
                   ********.********.**********************************************999997.9************************* PP

                   HHHHHHH CS
  tRNA-synt_1b 287 alnelle 293
                   +l++++e
    AHX11286.1 310 SLIKAFE 316
                   ***9985 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   1.2e-10   7.1e-07      10      40 ..     341     371 ..     336     375 .. 0.87

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 1.2e-10
                 TTSSSSHHHHHHHHHTTTEEETTEEE--TT- CS
          S4  10 lglassrreArqlIehGrVlVNGkvvkdpsy 40 
                 +  assr++A+qlI+ G V+++++++    y
  AHX11286.1 341 IEAASSRSQAKQLIKSGAVRIDNQKISELEY 371
                 5679*********************988777 PP

>> DUF4878  Domain of unknown function (DUF4878)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.2     0.019   1.1e+02      16      56 ..     248     288 ..     243     297 .. 0.83
   2 ?   10.8   0.1   7.6e-05      0.45       3      60 ..     298     355 ..     296     381 .. 0.78

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.019
     DUF4878  16 FleavkeGdvedaikyltestreedalaeklkgkfkelkak 56 
                 ++ + ++ dv+++  + te +++e ++ +kl+g + +++ k
  AHX11286.1 248 YFRNTEDADVRKFLYLFTELSKKEVEELSKLEGSELNEAKK 288
                 7888999***********************99999874444 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 7.6e-05
     DUF4878   3 cgekqtpeeavknFleavkeGdvedaikyltestreedalaeklkgkfkelkakaekk 60 
                 c  ++t++++ +  ++a+++ d+ ++ +  te++ +++++  ++++ +   +ak   k
  AHX11286.1 298 CHGADTAKKVSESLIKAFEKHDFSQLPEVYTEKDPSIIEILIQIEAASSRSQAKQLIK 355
                 99999**************************************999888755552222 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       732  (0.0408277); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3026.23
//
Query:       AHX11287.1  [L=152]
Description: bacterioferritin [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-36  125.5   0.5    1.6e-36  125.4   0.5    1.0  1  Ferritin      Ferritin-like domain
    7.9e-06   26.3   0.9      0.076   13.4   0.1    2.1  2  Rubrerythrin  Rubrerythrin
  ------ inclusion threshold ------
      0.022   14.5   0.2       0.14   11.9   0.0    1.9  2  COQ7          Ubiquinone biosynthesis protein COQ7
      0.084   13.1   0.7       0.45   10.7   0.0    2.0  1  Ferritin_2    Ferritin-like domain


Domain annotation for each model (and alignments):
>> Ferritin  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.4   0.5   3.5e-40   1.6e-36       3     141 ..       8     141 ..       6     142 .. 0.98

  Alignments for each domain:
  == domain 1  score: 125.4 bits;  conditional E-value: 3.5e-40
                 HHHHHHHHHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS....SHHHHHHC-SSSSCS.SHHHHHHHHHHHHHHHHHHHH CS
    Ferritin   3 aLneqladeltaayqylamawyvkgpgleglaeffdeqaeeerehadklaerilalGgtpvltraeleeieapkefg.sveevleaalehekkvteslr 100
                 +Lne+la+el a++qy+ ++ ++k++g+ +l++ ++e+++ee++had l++ril + g p +++++ +++      + +ve +le++l++e ++++ ++
  AHX11287.1   8 KLNEALANELLAINQYFVHSKMFKDMGFLSLSKALREHSIEEMQHADSLIDRILYCKGLPKISYRDMGPL------SpTVEGMLEKDLKLECDAVNLYN 100
                 7********************************************************************9......77********************* PP

                 HHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Ferritin 101 elielaeeegDpatadfledfleeqeeheweleallekler 141
                 e+i++ e+++D+++a+++  +l+++e h+++le++l  ++ 
  AHX11287.1 101 EAIAYLEAHKDFGSASLIRTLLKDEEGHVEWLEHQLSLIKS 141
                 ************************************99875 PP

>> Rubrerythrin  Rubrerythrin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.1   1.7e-05     0.076       3      51 ..       9      58 ..       8      68 .. 0.95
   2 !   11.9   0.1   5.1e-05      0.23       3      52 ..      85     135 ..      83     145 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1.7e-05
                  HHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHH CS
  Rubrerythrin  3 LekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnk 51
                  L++A+a+E  a++ Y   ++ +k  g+ +++++++e + eE +Ha+ l++
    AHX11287.1  9 LNEALANELLAINQYFVHSKMFKdMGFLSLSKALREHSIEEMQHADSLID 58
                  899******************************************99876 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 5.1e-05
                   HHHHHHHHHHHHHHHHHHHHCHH.TT-HHHHHHHHHHHHHHHHHHHHHHHH CS
  Rubrerythrin   3 LekAiagEssarrlYkelaekak.egypqiaelFeelAeeEreHakilnkl 52 
                   Lek ++ E++a +lY+e    ++  +   +a l++ l ++E+ H ++l+  
    AHX11287.1  85 LEKDLKLECDAVNLYNEAIAYLEaHKDFGSASLIRTLLKDEEGHVEWLEHQ 135
                   888999***********999999988888*****************99865 PP

>> COQ7  Ubiquinone biosynthesis protein COQ7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.09   4.1e+02     121     139 ..      37      55 ..      13      61 .. 0.76
   2 ?   11.9   0.0   3.1e-05      0.14      10      56 ..      89     136 ..      80     141 .. 0.85

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.09
        COQ7 121 elleiikqfrddEleHldt 139
                 +l++++++   +E++H+d 
  AHX11287.1  37 SLSKALREHSIEEMQHADS 55 
                 5677888888888888875 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.1e-05
        COQ7  10 haGElgAvaiYkgqlavl.akkdpelkpllkemleqEkeHlatfeell 56 
                    E+ Av +Y+  +a l a+kd    +l++  l++E+ H++++e+ l
  AHX11287.1  89 LKLECDAVNLYNEAIAYLeAHKDFGSASLIRTLLKDEEGHVEWLEHQL 136
                 556899************777888899*****************9876 PP

>> Ferritin_2  Ferritin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   9.9e-05      0.45       6      61 ..      85     136 ..      61     146 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 9.9e-05
  Ferritin_2   6 LnfAlnlEyleaafYtaalegaslddkalldaevrevaeeiakheeaHveflkaal 61 
                 L+  l lE  + + Y++a++      +a  d     +++++ k+ee+Hve l+  l
  AHX11287.1  85 LEKDLKLECDAVNLYNEAIAYL----EAHKDFGSASLIRTLLKDEEGHVEWLEHQL 136
                 55568999999*******9966....78888888999***************9887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1237.99
//
Query:       AHX11288.1  [L=821]
Description: ATP-dependent protease La [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-83  278.9   0.9    3.6e-83  278.1   0.9    1.4  1  Lon_C            Lon protease (S16) C-terminal proteolytic do
    2.7e-33  115.6   1.0    2.7e-33  115.6   1.0    2.2  2  LON_substr_bdg   ATP-dependent protease La (LON) substrate-bi
    1.1e-21   77.6   0.0    2.9e-21   76.3   0.0    1.7  1  AAA              ATPase family associated with various cellul
    2.4e-10   40.5   0.0    6.1e-10   39.2   0.0    1.7  1  AAA_5            AAA domain (dynein-related subfamily)
    1.9e-06   28.4   1.7     0.0012   19.2   1.0    4.0  3  AAA_16           AAA ATPase domain
      2e-06   27.0   0.5    9.6e-06   24.7   0.0    2.1  2  AAA_PrkA         PrkA AAA domain
    2.4e-06   27.4   0.0    7.1e-06   25.9   0.0    1.9  1  ChlI             Subunit ChlI of Mg-chelatase
    3.6e-05   24.0   0.1     0.0037   17.5   0.1    2.8  1  AAA_22           AAA domain
    0.00013   21.8   0.4    0.00044   20.0   0.0    2.0  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
     0.0002   21.1   0.0    0.00043   20.0   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
    0.00023   21.4   0.3    0.00075   19.6   0.0    2.0  1  AAA_2            AAA domain (Cdc48 subfamily)
    0.00029   20.6   1.0    0.00062   19.5   0.0    2.1  2  IstB_IS21        IstB-like ATP binding protein
    0.00054   19.9   0.0      0.044   13.7   0.0    2.6  2  NACHT            NACHT domain
    0.00088   18.5   1.1      0.018   14.2   0.0    2.5  2  NB-ARC           NB-ARC domain
     0.0014   18.7   0.6     0.0014   18.7   0.6    2.3  2  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
     0.0016   19.0   0.0     0.0067   17.0   0.0    2.1  1  AAA_18           AAA domain
      0.003   17.5   0.0     0.0091   15.9   0.0    1.8  1  RsgA_GTPase      RsgA GTPase
     0.0052   16.8   0.2      0.019   15.0   0.0    2.1  1  AAA_14           AAA domain
     0.0061   16.9   0.0       0.13   12.7   0.0    2.8  2  RNA_helicase     RNA helicase
  ------ inclusion threshold ------
      0.013   15.9   1.0       0.15   12.5   0.0    2.9  2  AAA_17           AAA domain
      0.015   15.3   0.0      0.054   13.5   0.0    1.9  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.019   15.5   2.0      0.089   13.3   0.0    2.7  2  ABC_tran         ABC transporter
       0.02   15.1   0.1       0.07   13.4   0.0    2.0  2  AAA_28           AAA domain
       0.02   14.7   0.0      0.057   13.3   0.0    1.8  1  AAA_3            ATPase family associated with various cellul
      0.021   15.0   0.0      0.041   14.1   0.0    1.5  1  AAA_33           AAA domain
      0.039   13.7   0.8        4.5    7.0   0.0    2.8  2  PduV-EutP        Ethanolamine utilisation - propanediol utili
      0.041   13.0   0.0      0.081   12.0   0.0    1.4  1  Parvo_NS1        Parvovirus non-structural protein NS1
       0.05   13.2   0.1      0.099   12.2   0.1    1.4  1  AAA_25           AAA domain
      0.096   12.8   0.0       0.53   10.4   0.0    2.4  2  MMR_HSR1         50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> Lon_C  Lon protease (S16) C-terminal proteolytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  278.1   0.9   5.9e-86   3.6e-83       2     203 ..     598     799 ..     597     801 .. 0.98

  Alignments for each domain:
  == domain 1  score: 278.1 bits;  conditional E-value: 5.9e-86
                 E-TTTTHHHH-S-SS--SSSSS--BSSEEEEEEEETTEEEEEEEEEEEESS-S-EEEEES--HHHHHHHHHHHHHHTSS-GGGSS-SS-TTT-EEEEEE CS
       Lon_C   2 vtakeleellGkkrfrseeaekedqvGvvtGlawtevGGdlltieavllpgkgklkltGklgdvmkesaqaalsyvrsraeelgidkevfekkdihihv 100
                 +++k+l+++ G+++++ ++ae+++ vG++tGla+t++GGdl+tieavllpgkg+++ tGklg+vm+es+qaa+s+v s+++++g  +++f++kdih+hv
  AHX11288.1 598 ISTKNLKKYAGVSKYNFGTAETQNLVGMTTGLAYTQTGGDLITIEAVLLPGKGEIRSTGKLGEVMQESIQAAYSFVCSNCNKFGFTSKFFKSKDIHLHV 696
                 889************************************************************************************************ PP

                 -S-B-GGGGGGGHHHHHHHHHHHHTS--B-TTBEE--EE-TT-BEE--S-HHHHHHHHHHTT-SBEEEEGGGGGGTTTS-HHHHTS-B--EESBHHHHH CS
       Lon_C 101 PeGavPkdGPsaGvtlatalvslltgkkvrkdvamtGeitLrGrvlpiGGlkekllaakragikkvilPkenekdlediPeevreeleiilveevdevl 199
                 PeGa+ kdGPsaGv+++t++vs++tg++v + vamtGe++LrG+v+ iGGlkekllaa r+gi++v++Pk+nekdl diP++v+++++ii+v++v+e +
  AHX11288.1 697 PEGATSKDGPSAGVAICTSIVSVMTGIPVCSTVAMTGEVSLRGKVMEIGGLKEKLLAAVRGGIETVLIPKSNEKDLVDIPKSVKSAIKIIPVSTVSEAF 795
                 ***********************************************************************************************9988 PP

                 HHHB CS
       Lon_C 200 kaal 203
                    l
  AHX11288.1 796 TFTL 799
                 7666 PP

>> LON_substr_bdg  ATP-dependent protease La (LON) substrate-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.6   1.0   4.4e-36   2.7e-33       2     207 ..      32     227 ..      31     228 .. 0.93
   2 ?   -2.1   0.1       4.8     3e+03     128     139 ..     557     589 ..     509     620 .. 0.49

  Alignments for each domain:
  == domain 1  score: 115.6 bits;  conditional E-value: 4.4e-36
  LON_substr_bdg   2 lpllpldnkvlfPgitlpltvsrpksiaaierlldkdkp.yigvflvkesqkdaide.esiselysvGtvarIvqil.rlddgrikvvlegleRv 93 
                     +p+lpl+++++fPg +lp+ v+r++si+a+++++ +++     ++lv  +qkd+++e ++ ++ly++G++arI +    l+dg ik+++   +R+
      AHX11288.1  32 VPVLPLREVIFFPGDYLPIFVGRKASIKAMDKAIADSSDgAGKILLV--AQKDPKKEiPEGKDLYKIGVIARIAEPKiNLQDGGIKLMVIVESRA 124
                     7*********************************7777766779999..*************************9877999************** PP

  LON_substr_bdg  94 kikklekekeegylvaeveiieddsepedsdslqkelkalvqeiiekikkslarellkllleielllkyedlenpyrLadlvaailpfsneekqe 188
                     k+ ++  +k+ g l+a++  +    e+++ + l   ++a+ +eii+ ++k   + +l+   ++e+++ + ++++++r++dl++a ++++ +ekqe
      AHX11288.1 125 KVLSF--KKNGGILEAQIVAV----EEDKTTGL--DIEAYRREIIQDFEK---CVKLSETIPDEIIGLVSQIDSTSRVVDLITASISLKLSEKQE 208
                     *****..66*********888....55666666..9*************6...89999999********************************** PP

  LON_substr_bdg 189 lLeeldvedRlkkvlelLk 207
                     +Le++++++R+kkv  +L+
      AHX11288.1 209 ILETINLRERVKKVHVFLE 227
                     **************99997 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.8
  LON_substr_bdg 128 kelkalvqe.....................iie 139
                       ++++++e                     +ie
      AHX11288.1 557 ALIRQYTREsgvrslkrelanlmrkavkqlSIE 589
                     223333333333333333222222222222222 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.0   4.7e-24   2.9e-21       1     126 [.     379     514 ..     379     519 .. 0.93

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 4.7e-24
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSS.........STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellsk.........yvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLl 90 
                 ++l+GppG+GKT+la+a+a+ +g++f+++s+  ++++         y+g+++ ki + +k+ak ++   ++++DEid++  +       ++++ + +Ll
  AHX11288.1 379 LCLVGPPGVGKTSLAQAIAEATGRPFVRMSLGGIRDEseikghrrtYIGAMPGKIIQHMKKAKLSN--PVFLLDEIDKMSMD-------FRSDPAFALL 468
                 58*********************************778************************9888..***********544.......69******** PP

                 HHHHHTTTS............SSTEEEEEEESSGGGSTHHHHSTTSSE CS
         AAA  91 teldgvkkk............eskvivigatnrpdkldpallrgRfdr 126
                 ++ld +++              s+v++++++n+ ++++ all +R+++
  AHX11288.1 469 EVLDPEQNAhfvdhyleveydLSNVMFVATANSLNMIP-ALL-DRLEI 514
                 *********************888**********9986.566.67765 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.0   9.9e-13   6.1e-10       2     137 ..     379     511 ..     378     512 .. 0.77

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 9.9e-13
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------....G-SEEEEESGGG--....HHHHHHHHHHHHSS CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraar....egeilvlDEverae....sevlnsLlslleer 92 
                 ++LvGppG+gK++la+ +a+a++r+++ + l     e+++kg+r++        ++++ + ++    +  +++lDE+++++    s+ + +Ll +l+ +
  AHX11288.1 379 LCLVGPPGVGKTSLAQAIAEATGRPFVRMSLGGIRDESEIKGHRRT---YIGAMPGKIIQHMKkaklSNPVFLLDEIDKMSmdfrSDPAFALLEVLDPE 474
                 79*******************************************7...445556666666665557999*********97322255677899999865 PP

                 E.EE..-SSSEEE---......-EEEEEESS--.-TT-TTHHHHTT CS
       AAA_5  93 r.llleeggelvkaknddllerfrviatanpldrslnelspalrsR 137
                 +  ++ +   +v  +     ++++++atan+l+     + pal++R
  AHX11288.1 475 QnAHFVDHYLEVEYDL----SNVMFVATANSLN-----MIPALLDR 511
                 4145555555554444....4499999999999.....77777777 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.46   2.9e+02       2      29 ..      51      78 ..      50      79 .. 0.95
   2 ?    0.2   0.1       1.4   8.8e+02      50     106 ..     162     215 ..     147     272 .. 0.70
   3 !   19.2   1.0     2e-06    0.0012      18      51 ..     370     403 ..     357     590 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.46
      AAA_16  2 lvGReeeleqLlsalervrsgrpelvll 29
                +vGR++ ++++  a+ + ++g + ++l+
  AHX11288.1 51 FVGRKASIKAMDKAIADSSDGAGKILLV 78
                8*********************999998 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 1.4
      AAA_16  50 kdggiflrgkcdqlesaipy..salaqalareellrqlldeaesaeleawrekleeala 106
                 +d      +kc++l++ ip   + l+++++  + + +l +++ s +l++ +e le+   
  AHX11288.1 162 QD-----FEKCVKLSETIPDeiIGLVSQIDSTSRVVDLITASISLKLSEKQEILETINL 215
                 44.....5677777777766634599999999999999999999999998887776544 PP

  == domain 3  score: 19.2 bits;  conditional E-value: 2e-06
      AAA_16  18 rvrsgrpelvllsGesGvGKsslvrellralekd 51 
                 r++s  ++++ l+G++GvGK+sl++++++a  + 
  AHX11288.1 370 RTKSLKGSILCLVGPPGVGKTSLAQAIAEATGRP 403
                 444445599*******************755554 PP

>> AAA_PrkA  PrkA AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.2      0.88   5.4e+02      20      68 ..     187     234 ..     183     256 .. 0.77
   2 !   24.7   0.0   1.5e-08   9.6e-06      59     110 ..     347     398 ..     333     408 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.88
    AAA_PrkA  20 aaerlldlikdkglelvdtaederlsrifsnetikkypafeedffGlee 68 
                 + +r++dli+ + + l  ++++e l+ i   e +kk  +f e+  G+ +
  AHX11288.1 187 STSRVVDLITAS-ISLKLSEKQEILETINLRERVKKVHVFLEKELGVLQ 234
                 578999999998.777678888889999999999999888776666654 PP

  == domain 2  score: 24.7 bits;  conditional E-value: 1.5e-08
    AAA_PrkA  59 feedffGleetiekiveyfraaaqrleerkqilyllGPvggGksslverlkk 110
                 ++   +G+e++ e+i+ey+    +    +  il l+GP g Gk+sl++++ +
  AHX11288.1 347 LKASHYGMEKVKERIIEYLAVQNRTKSLKGSILCLVGPPGVGKTSLAQAIAE 398
                 56678******************************************99865 PP

>> ChlI  Subunit ChlI of Mg-chelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   1.1e-08   7.1e-06      40     121 .]     687     768 ..     642     768 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-08
        ChlI  40 fpakkitvnLaPadlkkeGsafDLpiAigilaaleqieaeeetlflGeLsldGslrpvkgvlpialaakkegikkvivpken 121
                 f++k i + +      k+G++   +i  +i++++  i++ +++ + Ge+sl G++ ++ g+ + +laa + gi++v++pk+n
  AHX11288.1 687 FKSKDIHLHVPEGATSKDGPSAGVAICTSIVSVMTGIPVCSTVAMTGEVSLRGKVMEIGGLKEKLLAAVRGGIETVLIPKSN 768
                 6677777788778899***************************************************************998 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   5.9e-06    0.0037       5     103 ..     376     455 ..     372     481 .. 0.68

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 5.9e-06
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalrarav.ielliiDEaqh 102
                  +il+++G++G+GKT l++ ++e           ++++v++ l +  + +++  +    +g           ++  ++ q++++++   +++++DE+++
  AHX11288.1 376 GSILCLVGPPGVGKTSLAQAIAEAT---------GRPFVRMSLGGIRDESEIKGHRRTYIG-----------AMPGKIIQHMKKAKLsNPVFLLDEIDK 454
                 689*******************998.........777777776666655555444333333...........345566666666666666677777777 PP

      AAA_22 103 l 103
                 +
  AHX11288.1 455 M 455
                 6 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.1       4.5   2.8e+03      44     106 ..     230     291 ..     209     297 .. 0.71
   2 !   20.0   0.0   7.2e-07   0.00044       9      61 ..     351     404 ..     346     421 .. 0.75

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.5
      RuvB_N  44 lGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsraveevlys 106
                 lG   + + i ++ ++++k +       + +l ++ ++l ek+    dei  l+++v+++  s
  AHX11288.1 230 LGVLQIKQQIKEKTESQIKKSHKVY-LLNEQLKTITKELYEKEGGEYDEITDLEKKVNNIKLS 291
                 5556666666677777777654443.3456788888889888888899999999999887655 PP

  == domain 2  score: 20.0 bits;  conditional E-value: 7.2e-07
      RuvB_N   9 yigqekvkeklkifieaakkreealdh..vllyGpPGlGkttlakiiakelgvkl 61 
                 + g ekvke++     a ++r+++l    + l+GpPG+Gkt+la+ ia+  g  +
  AHX11288.1 351 HYGMEKVKERIIE-YLAVQNRTKSLKGsiLCLVGPPGVGKTSLAQAIAEATGRPF 404
                 5688999998854.4577788888765114479***************9887665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.9e-07   0.00043      23     119 ..     377     473 ..     353     504 .. 0.77

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.9e-07
                      S-EEEECSTTSSHHHHHHHHHHHSTTTTS-EEEEETTTS-TTCHHHHHHEBSSSSSTTTSS-BE.HHHHHTT..TSEEEEETGGGS-HHHHH.. CS
  Sigma54_activat  23 lsvlitGesGtGKellaraiheaskrkekpfvavncaaipeelleseLFGhekGaFtGAekekk.Glfekad..gGtlfLDeigelplelQe.. 111
                      + + ++G  G+GK+ la+ai ea+    +pfv++  + i +   ese+ Gh++ ++ GA   k    ++ka+  + + +LDei ++++++ +  
       AHX11288.1 377 SILCLVGPPGVGKTSLAQAIAEATG---RPFVRMSLGGIRD---ESEIKGHRR-TYIGAMPGKIiQHMKKAKlsNPVFLLDEIDKMSMDFRSdp 463
                      445689**************88765...8**********99...6******88.7999999998788998863367899*********987622 PP

                      ..HHHHHHHH CS
  Sigma54_activat 112 ..kLlrvlqe 119
                         Ll+vl+ 
       AHX11288.1 464 afALLEVLDP 473
                      2357777765 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   1.2e-06   0.00075       7     132 ..     380     504 ..     374     539 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 1.2e-06
                 EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS......EEEEETGGG-------------HHHHHHH CS
       AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG......ivllDEidKihpkessgadvSregVqrdL 99 
                  l+gp gvGkt la+a+ae       ++++r+    +  e e++      iga pg + +  +       + llDEidK +       d  r +   +L
  AHX11288.1 380 CLVGPPGVGKTSLAQAIAEATG----RPFVRMSLGGIRDESEIKGHRRTYIGAMPGKIIQHMKKaklsnpVFLLDEIDKMSM------D-FRSDPAFAL 467
                 578******************8....7************99*************99875555445999*************9......3.355667789 PP

                 HHHHH...--EE-----.--EE-TT-EEEEEE--TTH CS
       AAA_2 100 Lqile...ggtltdkqg.rkvdtknilfImtgafgss 132
                 L +l+   +++  d++   + d +n++f++t +    
  AHX11288.1 468 LEVLDpeqNAHFVDHYLeVEYDLSNVMFVATANSLNM 504
                 9999943334444776558999999999999986555 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0     1e-06   0.00062      11      72 ..     338     401 ..     332     478 .. 0.79
   2 ?   -2.9   0.0       7.8   4.8e+03      11      90 ..     535     562 ..     528     583 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1e-06
   IstB_IS21  11 aklpaqktledidfraarsldkrkvkeLatlsfiek..kenivllGpsGvGKshlaialgveav 72 
                 a l a++t+ +  +   +++++r+++ La  + +++     ++l+Gp+GvGK+ la a++ ++ 
  AHX11288.1 338 ADLSASETILKASHYGMEKVKERIIEYLAVQNRTKSlkGSILCLVGPPGVGKTSLAQAIAEATG 401
                 667766666666666677899999999988888875114568999**************98765 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.8
   IstB_IS21  11 aklpaqktledidfraarsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveavraglsvlfvrvedLveel 90 
                 akl++++ l++ +++ +r++ k+ +++                                                     
  AHX11288.1 535 AKLRKEHGLKKGEWSISRDALKALIRQ----------------------------------------------------Y 562
                 566666666666666666555555544....................................................3 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.0   7.1e-05     0.044       2      23 ..     378     399 ..     377     405 .. 0.89
   2 ?    3.4   0.0      0.11        65      84     164 ..     442     534 ..     416     536 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.1e-05
                 CEEEEC-TTTCHHHHHHHHHHH CS
       NACHT   2 lvilqGeaGsGKTtLlqklala 23 
                 +++l G++G+GKT L+q +a+a
  AHX11288.1 378 ILCLVGPPGVGKTSLAQAIAEA 399
                 689****************987 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.11
                 E....EEEE-STT-SS-TCH..................HHHHHCTTT.TT--EEEEEEECCCHHHHCTTSSCE..EEEE--TCCHHHHHHHHCTT CS
       NACHT  84 L....lilDglDelvtdlgq.........kekqpvrtlLselirkkl.lpeasllltvrpralrdleeqleeaivlevegfsesrrkqlvrkyfs 164
                 L    ++lD +D+++ d++           ++++  +   + ++ ++ l+++++++t+ + +   ++ +l + +++ +e+ se++ +++++ y+ 
  AHX11288.1 442 LsnpvFLLDEIDKMSMDFRSdpafallevLDPEQNAHFVDHYLEVEYdLSNVMFVATANSLNM--IPALLDRLEIIRLEAYSEEEKVEIASNYLI 534
                 244449999999999999988899999995555555555555554443788888888888888..999999999999999999999999999876 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.6      0.15        93      43     101 ..     158     227 ..     147     247 .. 0.81
   2 !   14.2   0.0   2.9e-05     0.018       2      42 ..     355     398 ..     354     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                 SHCCCCCCBTEEEEE..........EEESXXHHHHHHHXXHHHHHCCCTTSSSS-STTS...HHHHHHHHCC CS
      NB-ARC  43 ksdevegrFdsvawv..........vvsktdkseeiletilkeLslseddleekeeves...lkrklvrlLl 101
                    e+++ F+ ++ +           vs+ d+ +++++ i + +sl+ ++ +e  e  +   + +k++ +L+
  AHX11288.1 158 R--EIIQDFEKCVKLsetipdeiigLVSQIDSTSRVVDLITASISLKLSEKQEILETINlreRVKKVHVFLE 227
                 4..78888888888888888888889******************9999999998888885556666666665 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 2.9e-05
                 HHHHHHHHHHHHC...TTTSCSEEEEEEESTTSSHHHHHHHHCC CS
      NB-ARC   2 eksvekviekLle...kdelqslvvalvGmgGvGKttlakqiln 42 
                 ek +e++ie L      ++l+  ++ lvG +GvGKt la+ i +
  AHX11288.1 355 EKVKERIIEYLAVqnrTKSLKGSILCLVGPPGVGKTSLAQAIAE 398
                 67789999999751124556667*****************9976 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.4       6.1   3.8e+03       5      38 ..     259     302 ..     255     306 .. 0.59
   2 !   18.7   0.6   2.2e-06    0.0014       3      79 ..     522     598 ..     521     600 .. 0.91

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 6.1
                    HHHHHHHH..........HHHHHHHHSCTTTEEEEEHHHHHHHH CS
  ClpB_D2-small   5 elkkIvdl..........alkklekrlkergvelevtdealdal 38 
                    +lk I ++          ++ +lek++++ +++ e ++++l+ l
     AHX11288.1 259 QLKTITKElyekeggeydEITDLEKKVNNIKLSAEAKEKVLKEL 302
                    55555555555555555566777777776666666666666655 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 2.2e-06
                    HHHHHHHHHH.HHHHHHHHSCTTTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSSSTTSEE CS
  ClpB_D2-small   3 keelkkIvdl.alkklekrlkergvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgelkegdtv 79 
                    +ee ++I+ +  ++kl+k    ++ e +++ +al+al+++ y +e G R+L+r + + + +++ ++ +++++k+g ++
     AHX11288.1 522 EEEKVEIASNyLIAKLRKEHGLKKGEWSISRDALKALIRQ-YTRESGVRSLKRELANLMRKAVKQLSIEKNVKSGINI 598
                    6778899999778899999999****************97.9*****************************9988665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   1.1e-05    0.0067       2      24 ..     380     402 ..     379     460 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 1.1e-05
      AAA_18   2 lltGtpGvGKttlakeLskrlgf 24 
                 +l G+pGvGKt+la+++++ +g 
  AHX11288.1 380 CLVGPPGVGKTSLAQAIAEATGR 402
                 799***************99843 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   1.5e-05    0.0091      71     122 ..     348     399 ..     319     424 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 1.5e-05
                  HHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT CS
  RsgA_GTPase  71 elealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpe 122
                  + +++g+e ++ +  +  ++++ ++ lk+++ +lvG+ GvGK++L  a+++ 
   AHX11288.1 348 KASHYGMEKVKERIIEYLAVQNRTKSLKGSILCLVGPPGVGKTSLAQAIAEA 399
                  44555566666666666677888899********************999876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0   3.1e-05     0.019       3      77 ..     377     474 ..     375     523 .. 0.68

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.1e-05
      AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpe......kllelileklke..ekktylflDEiqev................. 76 
                  il+++G+  vGKT l++ +++      + ++ ++l   rd+++ + +       ++  i +++k+    + +++lDEi ++                 
  AHX11288.1 377 SILCLVGPPGVGKTSLAQAIAEATG---RPFVRMSLGGIRDESEIKGHrrtyigAMPGKIIQHMKKakLSNPVFLLDEIDKMsmdfrsdpafallevld 472
                 6999************999998777...99*****99998854332212334564444444443334456789******99866666555555555555 PP

      AAA_14  77 .p 77 
                  +
  AHX11288.1 473 pE 474
                 53 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.0   0.00021      0.13       1      36 [.     379     426 ..     379     499 .. 0.74
   2 ?    0.6   0.0       1.2   7.5e+02      15      50 ..     530     565 ..     528     569 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00021
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl............klkkkdsvys 36 
                   ++l+Gp+g+GK++la+ +a+a  + +            + k + ++y+
    AHX11288.1 379 LCLVGPPGVGKTSLAQAIAEATGRPFvrmslggirdesEIKGHRRTYI 426
                   589**************9999887666666666666665555555555 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 1.2
  RNA_helicase  15 akeLakallkklklkkkdsvysrnpeddfwdgYtgq 50 
                   +++L+++l k+ +lkk ++ +sr + +    +Yt++
    AHX11288.1 530 SNYLIAKLRKEHGLKKGEWSISRDALKALIRQYTRE 565
                   789************************999999986 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.7       1.6     1e+03      89     124 ..     236     272 ..     192     309 .. 0.60
   2 ?   12.5   0.0   0.00024      0.15       1      27 [.     382     408 ..     382     473 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 1.6
                 EESSHHHHHHHH..SE.EEEEE--HHHHHHHHHHHTT CS
      AAA_17  89 ldglpkevleelkpda.iilleadpeeilerrlkdrt 124
                  ++++++++ ++k ++ + ll+ + ++i++++ ++++
  AHX11288.1 236 KQQIKEKTESQIKKSHkVYLLNEQLKTITKELYEKEG 272
                 3444555555665544144466777777777766532 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00024
                 EE-TTSSHHHHHHHHHHHHTEEEEEHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsaG 27 
                 +G+PG+GK+ +++ ++e  g +++ ++
  AHX11288.1 382 VGPPGVGKTSLAQAIAEATGRPFVRMS 408
                 7******************98888664 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   8.8e-05     0.054      18      44 ..     369     401 ..     350     407 .. 0.74

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 8.8e-05
                 H......TEEEEEEESTTSSHHHHHHHHHHHTT CS
        TsaE  18 l......gdvilLeGdLGaGKTtlvrglakalg 44 
                        g++++L G+ G+GKT l++++a+a g
  AHX11288.1 369 NrtkslkGSILCLVGPPGVGKTSLAQAIAEATG 401
                 1222335778*******************9986 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.5       1.4   8.9e+02      31      93 ..     263     286 ..     194     366 .. 0.54
   2 ?   13.3   0.0   0.00014     0.089      10      34 ..     375     399 ..     367     451 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 1.4
                 HTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH......HHHTCHHHHHHHST CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx RF
    ABC_tran  31 lagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren......esdeeiekalsklg 93 
                 +++                                             +       + +ei+++ +k++
  AHX11288.1 263 ITK---------------------------------------------ElyekegGEYDEITDLEKKVN 286
                 111.............................................022223312222222222222 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 0.00014
                 TTSEEEEEESTTSSHHHHHHHHTTS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  10 egekvaivGenGaGKStLlkllagl 34 
                 +g+++ +vG+ G GK++L++++a+ 
  AHX11288.1 375 KGSILCLVGPPGVGKTSLAQAIAEA 399
                 799*******************975 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       9.2   5.7e+03      23      68 ..     252     294 ..     245     299 .. 0.70
   2 ?   13.4   0.0   0.00011      0.07       3      28 ..     380     406 ..     378     450 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 9.2
      AAA_28  23 gypvvpEaareileeklakgedalpwvedllafaervleeqleeea 68 
                 ++  + E   +i++e+++k++++ +   ++ +++++v + +l++ea
  AHX11288.1 252 KVYLLNEQLKTITKELYEKEGGEYD---EITDLEKKVNNIKLSAEA 294
                 5556688899999999999998554...556677766666665554 PP

  == domain 2  score: 13.4 bits;  conditional E-value: 0.00011
      AAA_28   3 vitGgestGKTtlleaLaar.gypvvp 28 
                 +++G+++ GKT+l++a+a+  g p v+
  AHX11288.1 380 CLVGPPGVGKTSLAQAIAEAtGRPFVR 406
                 89****************765999875 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   9.3e-05     0.057       4     113 ..     381     502 ..     378     508 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.3e-05
       AAA_3   4 legvPGlaktllvkalakaldlefkriqftpdllPsdilGtevfeeke....kefefkkGpvfanllladeinrappktqs....alleameerq.vtv 93 
                 l g PG++kt l++a+a+a +  f r+ +      s+i G++     +       ++kk  + + ++l dei++ +   +s    alle+++ +q   +
  AHX11288.1 381 LVGPPGVGKTSLAQAIAEATGRPFVRMSLGGIRDESEIKGHRRTYIGAmpgkIIQHMKKAKLSNPVFLLDEIDKMSMDFRSdpafALLEVLDPEQnAHF 479
                 6789*************************999999****9864333322332334577888889999******99887766555689999985541444 PP

       AAA_3  94 egethklp...epflvlatqnPi 113
                  ++  +++   ++ + +at n +
  AHX11288.1 480 VDHYLEVEydlSNVMFVATANSL 502
                 44333333111234456777766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.6e-05     0.041       2      29 ..     379     408 ..     378     439 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.6e-05
      AAA_33   2 vllvGlpGsGKstlaerllkklg..avlls 29 
                 + lvG+pG+GK+ la+ +++++g  +v+ s
  AHX11288.1 379 LCLVGPPGVGKTSLAQAIAEATGrpFVRMS 408
                 568*****************9998877765 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.2     0.059        36      85     137 ..     171     222 ..     158     228 .. 0.81
   2 ?    7.0   0.0    0.0073       4.5       4      23 ..     379     398 ..     376     401 .. 0.87

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.059
   PduV-EutP  85 asvfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieel 137
                 ++++  e+iG++ +id ++   ++ ++   Lk    ++i e+ ++++  ++++
  AHX11288.1 171 SETIPDEIIGLVSQIDSTSRVVDLITASISLKLSEKQEILETINLRE-RVKKV 222
                 5677889***********99999999999999999999998877754.35555 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0073
   PduV-EutP   4 illiGkvgsGKttLtqalkg 23 
                 + l+G+ g+GKt+L+qa+ +
  AHX11288.1 379 LCLVGPPGVGKTSLAQAIAE 398
                 579**************976 PP

>> Parvo_NS1  Parvovirus non-structural protein NS1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00013     0.081     105     138 ..     366     400 ..     344     407 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00013
   Parvo_NS1 105 awlskqlgkrntv.wfyGpantGktnlaeaIakav 138
                 a+ +++++ ++ + +++Gp+  Gkt la+aIa+a+
  AHX11288.1 366 AVQNRTKSLKGSIlCLVGPPGVGKTSLAQAIAEAT 400
                 45566666777661567****************97 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00016     0.099      32      64 ..     375     405 ..     370     413 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00016
      AAA_25  32 agelallaGapgtGKttlaldlalavatGkpwl 64 
                 +g++  l+G+pg+GKt la   a+a atG+p+ 
  AHX11288.1 375 KGSILCLVGPPGVGKTSLAQ--AIAEATGRPFV 405
                 689999**********9985..66788999985 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.1       7.5   4.6e+03      90     100 ..     232     242 ..     179     284 .. 0.57
   2 ?   10.4   0.0   0.00085      0.53       3      23 ..     380     402 ..     378     497 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 7.5
                 SHHHHHHHHHH CS
    MMR_HSR1  90 lkpldeeleel 100
                 + +++++++e 
  AHX11288.1 232 VLQIKQQIKEK 242
                 22333333332 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00085
                 EEEESTTSSHHHHHHHHHTS..T CS
    MMR_HSR1   3 aivGrpNvGKStLinaltge..k 23 
                 ++vG p vGK++L +a+ ++  +
  AHX11288.1 380 CLVGPPGVGKTSLAQAIAEAtgR 402
                 79***************986444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (821 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1503  (0.0838307); expected 358.6 (0.02)
Passed bias filter:                      676  (0.0377043); expected 358.6 (0.02)
Passed Vit filter:                        87  (0.00485247); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.83u 0.30s 00:00:01.12 Elapsed: 00:00:00.48
# Mc/sec: 5146.19
//
Query:       AHX11289.1  [L=184]
Description: thiamine monophosphate synthase/TENI family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-13   48.3   0.0    7.9e-13   48.1   0.0    1.0  1  TMP-TENI  Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.1   0.0   4.4e-17   7.9e-13      29     175 ..      28     177 ..       7     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 48.1 bits;  conditional E-value: 4.4e-17
    TMP-TENI  29 lvqlRekeldarellelaeklaalcrkygvpliindrvdlalavgadgvHlgqddl.pvaearellgpdliiGlSvhsleeaeeaealgadYigvGpif 126
                 +v lR  e     +++ a  l + cr+ +  +++  ++ +a++ +a g+Hl   d  ++++ ++l++ ++++ +  hsl+   e+++++ d   ++p+f
  AHX11289.1  28 IVLLRSYE--HPHRKNIAFWLSRQCRRLNLFFVVAGDLPIAIESHASGIHLRDADFhKMKKWKNLTHGRWFVSAASHSLRRNFEIQSANLDAALYSPVF 124
                 56666666..34445566678899*****************************99857899999**********************************9 PP

    TMP-TENI 127 pTdtKkdaeplgleglkelaealeiPvvaiGGitlenvaevl....eagadgv 175
                  ++  k ++   l ++k++  + +i ++a+GG +++n+  +     +ag++g+
  AHX11289.1 125 TSKDSKTKTIGHLRFIKHCYLTRKINIFALGGTSKSNIRLLKrphkKAGIAGI 177
                 888777778888888888888888***************99865555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (184 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       299  (0.0166769); expected 358.6 (0.02)
Passed bias filter:                      263  (0.014669); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1434.36
//
Query:       AHX11290.1  [L=95]
Description: hypothetical protein NHE_0338 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-24   87.3   3.8    1.2e-24   87.2   3.8    1.0  1  UPF0093   Uncharacterised protein family (UPF0093)
  ------ inclusion threshold ------
      0.022   15.1   4.1      0.027   14.9   4.1    1.1  1  CopD      Copper resistance protein D
        8.7    6.1  11.3        1.6    8.5   7.8    1.5  2  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> UPF0093  Uncharacterised protein family (UPF0093)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.2   3.8     2e-28   1.2e-24      49     146 .]       1      95 []       1      95 [] 0.97

  Alignments for each domain:
  == domain 1  score: 87.2 bits;  conditional E-value: 2e-28
     UPF0093  49 merrLlkiimtpamiltlvlGllllalaeglvalssgWlhvKlllvllllayhlvlaklrkklaagentksekfyrilNEvptlllivivllvvvkpf 146
                 merrL+++imtpam+++l lG l+lala+g+  + s Wlh+K+++v +l+++h+++ +++ ++++g+n++ + f+++lNE +t+ +i+iv+l+v+kpf
  AHX11290.1   1 MERRLFYYIMTPAMVASLSLG-LILALATGH--IVSLWLHLKFIFVGILVLLHIFFWRCLVAFREGRNHHPSGFFKLLNESVTISFIIIVILAVIKPF 95 
                 9********************.999999988..5669***********************************************************98 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   4.1   4.5e-06     0.027       7     103 ..       6      91 ..       2      93 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.5e-06
        CopD   7 FsrlalaavavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprleaatgaggqalrhrlrrsaalelvlalvvlllaa 103
                 F  ++++a+++ l  G+++al     + +++     +l++K +++ +l++l+   ++ lv       ++++ ++   ++ + + +++ ++++++la+
  AHX11290.1   6 FYYIMTPAMVASLSLGLILALAT---GHIVS----LWLHLKFIFVGILVLLHIFFWRCLVAFR----EGRNHHPSGFFKLLNESVTISFIIIVILAV 91 
                 66788889999999999997776...67777....8****************99997666544....344444443344444444444444444433 PP

>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   7.8   0.00027       1.6       6      60 ..       5      59 ..       4      61 .. 0.91
   2 ?   -2.3   0.1      0.54   3.3e+03      13      26 ..      77      91 ..      70      94 .. 0.50

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.00027
        MNHE  6 lvWllltgs.lgelllGlllallvalllrrlllplrrvllrllayllvflweivka 60
                l++ ++t   +++l lGl+lal++  ++ +l+l+l+ +++++l++l +f+w+ ++a
  AHX11290.1  5 LFYYIMTPAmVASLSLGLILALATGHIV-SLWLHLKFIFVGILVLLHIFFWRCLVA 59
                5788889889******************.688999999999**********99887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.54
        MNHE 13 gs.lgelllGlllal 26
                +s + ++++ ++la+
  AHX11290.1 77 ESvTISFIIIVILAV 91
                444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 702.32
//
Query:       AHX11291.1  [L=470]
Description: glutamine synthetase, type I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
   1.2e-103  346.8   0.0   1.4e-103  346.5   0.0    1.0  1  Gln-synt_C  Glutamine synthetase, catalytic domain
    5.5e-24   83.7   0.1    1.2e-23   82.6   0.1    1.6  1  Gln-synt_N  Glutamine synthetase, beta-Grasp domain
  ------ inclusion threshold ------
       0.11   12.1   0.0       0.22   11.1   0.0    1.4  1  HofP        DNA utilization proteins HofP


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.5   0.0  2.4e-107  1.4e-103       2     345 .]     107     467 ..     106     467 .. 0.96

  Alignments for each domain:
  == domain 1  score: 346.5 bits;  conditional E-value: 2.4e-107
                 T-HHHHHHHHHHHHHHTTC..EEEEEEEEEEEEESEECCCE.SSEEEEEEE.T..............B...B.TSS-TTBHCCCCCTCCHHHHHHHHHH CS
  Gln-synt_C   2 rdPRsvlkralarlaeeGl..tvvvgpElEFflfdkeedke.asksllevdse..............ekgrpaekggyfsvapvdeaedlrreiveale 83 
                 ++PR ++++a++ l+++G+  + ++g+E+EFf++d+ +++   ++ ++e+ds               +++r+++k+ y   +p d+ +d+r+ei+e+l+
  AHX11291.1 107 HNPRATARKAMQFLRSTGIadKSYFGFEMEFFVLDDARFAVrDNGAFFELDSAegsynsgkryeynnHGHRNQRKSCYLASQPSDSLNDIRAEILETLK 205
                 57******************99*****************9999*********9**************99****************************** PP

                 HTT--EECCEEECCCTEEEEEE--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTTEESSB-TTSGGGB-HHHHHHH CS
  Gln-synt_C  84 algieveashhEvatgQvEinlkfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdgknlfadeddeyalselarhfi 182
                 +++++   +hhEva +Q+Ei++++ +a+k+ Dn++  K+v+++vA+++g++atFmpKp+++dnG+gmH+h Slw k ++nlfa ++ + ++sel+ ++i
  AHX11291.1 206 EVKVKPLLHHHEVASSQCEISFQYGEAVKTSDNAQKCKHVIHNVASSYGKSATFMPKPFKNDNGNGMHIHTSLW-KGDRNLFAPDNSRGDVSELCTYYI 303
                 **************************************************************************.999********9999********* PP

                 HHHHHHHHHHHHHHS-SCCHHHHCSSSTTSSSBEEEESS-TTCSEEEE-...TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S- CS
  Gln-synt_C 183 gGllkhakaltaltaptvnSYkRlvpgyeaPvalawgarNRsallRipa...skekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekd 278
                 gG++k+ kal+a+++p +nSYkRl+pgyeaP++l  +   Rsa++Rip+   ++++akrvE+R+pda +NPYL ++all+Ag+ Gi++k++p+ ++  +
  AHX11291.1 304 GGVIKYGKALNAILNPLTNSYKRLIPGYEAPCNLDCSPLSRSAAIRIPHspgGEPSAKRVEVRFPDAGTNPYLGTSALLMAGIAGINEKITPESATA-E 401
                 *************************************************9999**************************************987764.3 PP

                 SSSS-TTTHTSS-B--SSHHHHHHHHHCS.HHHCC..SS-HHHHHHHHHHHHHCHHHHHCT--HHHHHHH CS
  Gln-synt_C 279 lyelspeerkgieelPasleeAlealeed.ellke..vlgeevieaylalkraEleeleeevsdwelery 345
                 l + ++    g  +l++sleeAl +l+++ ++l e  v+++  i+ay+alk +++eel++++ ++e+ +y
  AHX11291.1 402 LKKSAD----GSISLCRSLEEALVSLDKNrDFLLEgnVFTNAQIDAYIALKTEDIEELMKHPVPIEFIKY 467
                 444443....4469***************99*99999*****************************9776 PP

>> Gln-synt_N  Glutamine synthetase, beta-Grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.1   2.1e-27   1.2e-23       2      83 .]      17      99 ..      16      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.1e-27
                --EEEEEEE-SSS-EEEEEEEHHHHHHHTTTT-EEEETTSSTTT------EEEEEEEGG..GEEE-SS-SS-.EEEEEEEEE-T CS
  Gln-synt_N  2 vkfvdlqFtDikgklkhvtipadelsedaleegvsFDGSsiegfaeieeSDmlLkPdls..tavidPfreekktarvicdvydp 83
                +k vd++Ft++ gk+ h+t ++d+++e++l++gvsFDGSs+ g+ ++ +SDmlL+Pdl+  t ++dPf +++ t++++cdv++p
  AHX11291.1 17 IKLVDFRFTSVSGKFLHITHHSDSVTEKTLTNGVSFDGSSVPGWSSVGKSDMLLIPDLEagTSFLDPFAAQP-TLCILCDVVEP 99
                899******************************************************76337**********.********987 PP

>> HofP  DNA utilization proteins HofP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   3.6e-05      0.22      14      63 ..     279     328 ..     272     340 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 3.6e-05
        HofP  14 ltgmrdPfkPPedrcriaelslwryqGvvkkGerltgilkdsqkkwrrve 63 
                   g r+ f+P + r  ++el  +  +Gv+k G+ l +il+   + ++r+ 
  AHX11291.1 279 WKGDRNLFAPDNSRGDVSELCTYYIGGVIKYGKALNAILNPLTNSYKRLI 328
                 46889**********************************99888888865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (470 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       448  (0.0249875); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.27s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3439.32
//
Query:       AHX11292.1  [L=150]
Description: transcriptional regulator NrdR [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-13   51.1   0.8      2e-13   50.7   0.8    1.2  1  ATP-cone         ATP cone domain
    5.8e-05   23.4   0.2     0.0001   22.6   0.2    1.4  1  Lar_restr_allev  Restriction alleviation protein Lar
     0.0079   15.7   1.1       0.11   12.0   0.1    2.3  2  TF_Zn_Ribbon     TFIIB zinc-binding
  ------ inclusion threshold ------
       0.01   15.7   1.1       0.63    9.9   0.1    2.3  2  TFIIS_C          Transcription factor S-II (TFIIS)
      0.012   15.0   0.3        4.7    6.8   0.1    2.3  2  zf-ribbon_3      zinc-ribbon domain
      0.041   13.9   1.1      0.077   13.0   1.1    1.5  1  Zn_Tnp_IS1595    Transposase zinc-ribbon domain
       0.14   11.9   0.4         10    5.9   0.1    2.4  2  A2L_zn_ribbon    A2L zinc ribbon domain
       0.16   12.3   0.3       0.36   11.1   0.2    1.6  1  DUF3268          zinc-finger-containing domain
        0.7   10.6   2.7        7.4    7.3   0.2    2.4  2  zf-ISL3          zinc-finger of transposase IS204/IS1001/IS10
          1   10.3   3.1         19    6.4   0.1    2.8  3  zf-C2H2_4        C2H2-type zinc finger


Domain annotation for each model (and alignments):
>> ATP-cone  ATP cone domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.7   0.8   1.1e-16     2e-13       1      86 []      49     137 ..      49     137 .. 0.97

  Alignments for each domain:
  == domain 1  score: 50.7 bits;  conditional E-value: 1.1e-16
                 -EEE-TTS-EEE--HHHHHHHHHHHHHH...-HHHHHHHHHHHHHHHHHHHIIT-BHHHHHHHHHHHHHHSS-HHHHHHHHHHHHHHHH CS
    ATP-cone   1 ikViKRdGtvepfdvekIkraiekAceg...seeeideiaeeveaevrkrlrdgisteeIqdlvektliehpdyavaaayilyrnlrke 86 
                 ikV K+dG+ e+fd+ek  r+ie A+++   ++e +d++ + v+ ++++  + +++ + I++l++++l   + +a+++++++y n+ +e
  AHX11292.1  49 IKVLKKDGSCESFDREKAMRSIEVALRKrpvTRESVDALMNSVVYKIERVHDTKVTAKMIGELIMEQLSILDRVAFIRFASVYMNFSDE 137
                 68*************************************************999*******************************9875 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.2   5.7e-08    0.0001       5      47 ..       2      44 ..       1      54 [. 0.83

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 5.7e-08
  Lar_restr_allev  5 pCPfCggravlersqrvvaeigq...cvyCadCgastpwfkiaede 47
                      CPfCg+ ++ +++ r v+ +++     +C++Cga   +f++ e  
       AHX11292.1  2 KCPFCGNTDTSVKDSRSVNRGAFikrRRSCDECGA---KFTTFEMI 44
                     5*****************98887999*********...56665554 PP

>> TF_Zn_Ribbon  TFIIB zinc-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   6.3e-05      0.11       1      15 [.       1      16 [.       1      25 [. 0.80
   2 ?    2.1   0.1     0.078   1.4e+02      22      27 ..      31      36 ..      28      42 .. 0.56

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 6.3e-05
                  EEETTTTCEE.CHEET CS
  TF_Zn_Ribbon  1 ykCPnCgstn.lveDp 15
                  +kCP Cg+t+  v D 
    AHX11292.1  1 MKCPFCGNTDtSVKDS 16
                  89*******9558885 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.078
                  ESSSSB CS
  TF_Zn_Ribbon 22 CtdCGl 27
                  C +CG+
    AHX11292.1 31 CDECGA 36
                  555554 PP

>> TFIIS_C  Transcription factor S-II (TFIIS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.1     0.017        30       2      12 ..       2      12 ..       1      16 [. 0.86
   2 ?    9.9   0.1   0.00035      0.63       2      19 ..      30      47 ..      29      49 .. 0.93

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.017
     TFIIS_C  2 kCpkCgsreay 12
                kCp Cg+++++
  AHX11292.1  2 KCPFCGNTDTS 12
                8******9886 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00035
     TFIIS_C  2 kCpkCgsreayffqlQtR 19
                 C +Cg + ++f ++Q+R
  AHX11292.1 30 SCDECGAKFTTFEMIQLR 47
                6****************9 PP

>> zf-ribbon_3  zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.1    0.0026       4.7       4      10 ..       2       8 ..       1      14 [. 0.68
   2 ?    6.3   0.0    0.0037       6.6       4      11 ..      30      38 ..      27      44 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0026
  zf-ribbon_3  4 rCPnCGa 10
                 +CP CG+
   AHX11292.1  2 KCPFCGN 8 
                 4666665 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0037
  zf-ribbon_3  4 rCPnCGa.p 11
                 +C +CGa  
   AHX11292.1 30 SCDECGAkF 38
                 788888855 PP

>> Zn_Tnp_IS1595  Transposase zinc-ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   1.1   4.3e-05     0.077      20      45 ..       2      36 ..       1      37 [. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 4.3e-05
  Zn_Tnp_IS1595 20 vCPhCgsr.kayrikt........rglfqCkeCrk 45
                    CP+Cg++ ++ + ++         ++  C eC++
     AHX11292.1  2 KCPFCGNTdTSVKDSRsvnrgafiKRRRSCDECGA 36
                   6*******955554445666*************86 PP

>> A2L_zn_ribbon  A2L zinc ribbon domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.1    0.0059        10      24      30 ..       3       9 ..       1      12 [. 0.82
   2 ?    4.0   0.0     0.024        42      22      32 ..      29      39 ..      27      40 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0059
  A2L_zn_ribbon 24 CieCgas 30
                   C++Cg++
     AHX11292.1  3 CPFCGNT 9 
                   *****98 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.024
  A2L_zn_ribbon 22 lvCieCgasfp 32
                   ++C eCga f+
     AHX11292.1 29 RSCDECGAKFT 39
                   58*****9876 PP

>> DUF3268  zinc-finger-containing domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.2    0.0002      0.36       3      40 ..       1      38 [.       1      54 [. 0.81

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0002
     DUF3268  3 trCpyCGekvilvsaseiYkerskgkllylCpkCdayv 40
                ++Cp+CG++ + v++s   +  ++ k    C +C+a  
  AHX11292.1  1 MKCPFCGNTDTSVKDSRSVNRGAFIKRRRSCDECGAKF 38
                58*****99888777766656778888889*****976 PP

>> zf-ISL3  zinc-finger of transposase IS204/IS1001/IS1096/IS1165
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   0.2    0.0041       7.4       4      19 ..       2      17 ..       1      21 [. 0.71
   2 ?    3.1   0.3     0.088   1.6e+02      39      47 .]      26      34 ..      24      40 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0041
     zf-ISL3  4 rCPnCgsktvvkhgkk 19
                +CP Cg++   +++++
  AHX11292.1  2 KCPFCGNTDTSVKDSR 17
                7*******55555544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.088
     zf-ISL3 39 krRyrCkeC 47
                krR  C+eC
  AHX11292.1 26 KRRRSCDEC 34
                677788777 PP

>> zf-C2H2_4  C2H2-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.1     0.077   1.4e+02       2       8 ..       2       8 ..       1      16 [. 0.85
   2 ?    6.4   0.1     0.011        19       2      14 ..      30      42 ..      29      47 .. 0.82
   3 ?   -3.2   0.0        10   1.8e+04       6      16 ..      58      67 ..      57      68 .. 0.65

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.077
   zf-C2H2_4 2 kCpiCgk 8
               kCp+Cg 
  AHX11292.1 2 KCPFCGN 8
               7****75 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.011
   zf-C2H2_4  2 kCpiCgksFsskk 14
                 C+ Cg+ F++ +
  AHX11292.1 30 SCDECGAKFTTFE 42
                5********8865 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 10
   zf-C2H2_4  6 CgksFsskkaL 16
                C +sF + ka+
  AHX11292.1 58 C-ESFDREKAM 67
                5.788776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       850  (0.0474092); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        86  (0.0047967); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.39u 0.27s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1104.45
//
Query:       AHX11293.1  [L=287]
Description: hypothetical protein NHE_0341 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        5.5    7.3   8.1          6    7.2   4.8    2.7  3  DUF948    Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.8   0.00034         6       2      28 ..       7      30 ..       5      89 .. 0.83
   2 ?   -0.7   0.0     0.097   1.7e+03      37      58 ..     166     187 ..     148     194 .. 0.83
   3 ?   -1.9   0.0      0.24   4.3e+03      71      84 ..     242     255 ..     223     273 .. 0.61

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00034
      DUF948  2 AglIaAiAFvvLviflivvllklkktl 28
                A ++aA+AFv+L+++l+++ ++   t+
  AHX11293.1  7 A-VLAAVAFVILAVVLFCLYKQC--TI 30
                4.56*************999987..44 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.097
      DUF948  37 elekqvdpilkevedllakvne 58 
                  l+  +dpi   +e+ ++k+n+
  AHX11293.1 166 ALNFTADPIKASTEGNIEKTNK 187
                 5666789999999999999998 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.24
      DUF948  71 dplteavadlgesv 84 
                 ++++ a +++++++
  AHX11293.1 242 EEIFGATQEASDNF 255
                 34455555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (287 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1042  (0.0581181); expected 358.6 (0.02)
Passed bias filter:                      718  (0.0400469); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.43
# Mc/sec: 1994.91
//
Query:       AHX11294.1  [L=617]
Description: uvrD/REP helicase N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-76  257.4   5.2    2.2e-76  257.4   5.2    2.5  2  UvrD-helicase    UvrD/REP helicase N-terminal domain
    3.6e-66  223.9   2.1    3.6e-66  223.9   2.1    2.1  2  UvrD_C           UvrD-like helicase C-terminal domain
    1.4e-31  109.8   0.1    3.7e-31  108.4   0.1    1.7  1  AAA_19           AAA domain
    1.2e-09   38.1   0.1    0.00089   19.0   0.1    2.4  2  AAA_30           AAA domain
    7.9e-09   35.2   0.0    4.1e-08   32.9   0.0    2.2  1  UvrD_C_2         UvrD-like helicase C-terminal domain
    7.7e-06   25.8   0.1       0.45   10.2   0.0    3.5  3  Viral_helicase1  Viral (Superfamily 1) RNA helicase
    1.6e-05   24.9   0.0    5.8e-05   23.0   0.0    2.0  1  AAA_11           AAA domain
  ------ inclusion threshold ------
      0.031   14.1   0.1      0.079   12.8   0.1    1.7  1  Helicase_RecD    Helicase


Domain annotation for each model (and alignments):
>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  257.4   5.2     1e-79   2.2e-76       1     315 []       3     267 ..       3     267 .. 0.95
   2 ?   -1.6   0.1      0.68   1.5e+03     187     228 ..     454     508 ..     286     533 .. 0.63

  Alignments for each domain:
  == domain 1  score: 257.4 bits;  conditional E-value: 1e-79
                    SSHHHHHHHHS-SSEEEEEE-TTSSHHHHHHHHHHHHHHTSSSTGGGEEEEESSHHHHHHHHHHHHHHHHHCCHHCTT-HHHHHHHHHCTTSEEEE CS
  UvrD-helicase   1 lnpeqreaiaslggpilveAsAGsGKTfvlaerilrlikeeeiepdrilvvTFTnkAaeElkeRieealkkaeqessdderlrlalqnlseanisT 96 
                    ln+eqr ai++ +gp+l++A+AG+GKT++l++ri++like+   p++i++vTF nkAa+E+ +Ri+e++++a+                   +i+T
     AHX11294.1   3 LNNEQRLAIETINGPLLILAGAGTGKTKTLVHRIANLIKEGYAYPNQIMAVTFANKAAKEMMHRITEIVGEAQ-----------------FNWIGT 81 
                    799*******************************************************************985.................57**** PP

                    HHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHHHHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHT CS
  UvrD-helicase  97 lHsfcqkilkkeanrigldpnfrildeedeedlkqqellkelleksaddslnldkkkleklikelsksrnikkeelslskskaeelrelvskakek 192
                    +H+++ kil+ ea++ig++p+f+ild +d     q ++l+++ +   +  ++++++k                          +++  ++s++k+k
     AHX11294.1  82 FHAIAAKILRIEAEKIGFRPDFTILDTDD-----QMRMLQKIAK---E--VQIETDKSLI-----------------------KKYLTIISNWKDK 144
                    *****************************.....9999999997...3..5566555552.......................37899******** PP

                    TCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCEEHHHHHHHHHHHHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTTEEE CS
  UvrD-helicase 193 qlspkelkkafekasdlqkkiaeflkeyqeqkkeenalDfsdllhallelleeneelaealrerykeiliDEyQDTnkiQyrilkllasgheelfm 288
                     ++p + k ++ +++ ++k++  +++ yqe++ke+n +Df dll+  ++l++++ e++e++re++k+i++DEyQDTn +Qy +l+lla++h+++++
     AHX11294.1 145 AFTPGRVKYNNAANTWFEKQALCIYELYQERLKENNSMDFGDLLMHNVSLFKKDAEVLERYREKFKYIMVDEYQDTNLCQYLWLRLLAQKHSNICC 240
                    ******9999999*********************************************************************************** PP

                    EE-GGG--GGGGTB-THHHHHHHHHST CS
  UvrD-helicase 289 vGDpkQsIYgFRgAdielflkkkkdfk 315
                    vGD++QsIYg+RgA+++++l++++df+
     AHX11294.1 241 VGDDDQSIYGWRGAEVGNILRFSQDFD 267
                    ************************996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.68
                    HHHHHTTCCTTHHCHSS.............TSCSHHHHHHHHHHHHHHHHHHHHT CS
  UvrD-helicase 187 skakekqlspkelkkaf.............ekasdlqkkiaeflkeyqeqkkeen 228
                    +k+k+ ql++ ++  +                 ++ ++ ++++++ +    ++ n
     AHX11294.1 454 EKVKKWQLESVNYSLHDflkkitiesgyisALREQDESRLENIDEIFRVVQEFDN 508
                    3333333322222221122222222222222222233334444444444444444 PP

>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.2      0.86   1.9e+03     203     217 ..     127     141 ..      53     217 .. 0.55
   2 !  223.9   2.1   1.6e-69   3.6e-66       1     347 [.     272     593 ..     272     595 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.86
                 xxxxxxxxxxxxxxx RF
      UvrD_C 203 rqalvskyadlfkel 217
                  ++l++ky    +++
  AHX11294.1 127 DKSLIKKYLTIISNW 141
                 233333333333333 PP

  == domain 2  score: 223.9 bits;  conditional E-value: 1.6e-69
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      UvrD_C   1 ivLekNyRStksLlkaankflenilnrralekek..ktvekgekivvleaeteeeEaekiaatikallekneklediavLvRsnkdadkiskaLkkegi 97 
                 i+Le+NyRSt+++l aa ++++n+  r   +++k  +++  ge+i++l+  ++e+Ea+ i++ ik+ +    +++d+a+LvR   +++ +++a  ++++
  AHX11294.1 272 IKLEQNYRSTNKILSAAHNVIRNNQAR---LTKKlwTAEPGGEEIQILTYIDSEQEARAIVRMIKERA-SVCDYSDTAILVRAGFQTRAFEEAAISQQL 366
                 79*******************998888...444567999999**************************.9***************************** PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx RF
      UvrD_C  98 pfnvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlgigkatveriseelkklglsltDfikedtleygeeFieliraleeknl..elllk 194
                 p++v+++ +f++r+e+kdi+ayl+ + n++d++a++ri++++++g+g+a++++i            +f  e+       F   ir  e+++l  + +l 
  AHX11294.1 367 PYKVIGGLRFYDRKEVKDIIAYLRFVTNPSDNLAFERIINSPKRGLGTASLNKI-----------YNFSLENGCS---MFEASIRLSEDGTLkgK-ILP 450
                 ******************************************************...........4555555544...45555566666666432.566 PP

                 x.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      UvrD_C 195 k.iektaeerqalvskyadlfkelaeklaelkekseskrkkee.klenlreLysllkelekkeeeeeveeklneileiatLseseleeskkkekipiiT 291
                   iek ++ + + v+   ++f    +k++      +  r+++e +len++e++++++e+++            ++l++ +L  +++ ++ + + i+i+T
  AHX11294.1 451 DfIEKVKKWQLESVNYSLHDF---LKKITIESGYISALREQDEsRLENIDEIFRVVQEFDN----------AIDFLQHVSLLTDNDSQLYNSNAINIMT 536
                 668888877766665544444...33344334444444444445*****************..........679************999999******* PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      UvrD_C 292 iHqAKGlEFdvVflagleegtfPsyrskk.ekrleEEkRlfYVaiTRAkkrLfisys 347
                 +H++KGlEF+ Vfl g e+gtfP+ rs    +++eEE+Rl YV+iTRAkk L+i+ +
  AHX11294.1 537 LHASKGLEFEQVFLPGWEDGTFPHARSLYsADQIEEERRLAYVGITRAKKFLTITNA 593
                 **************************998889**********************975 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.4   0.1   1.7e-34   3.7e-31       1     144 [.       7     250 ..       7     252 .. 0.94

  Alignments for each domain:
  == domain 1  score: 108.4 bits;  conditional E-value: 1.7e-34
      AAA_19   1 qreavealkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgae.....atTiHrlal................. 77 
                 qr a+ ++ +++ll++aG+GtGKT++l+h++a l+++g   p++i++v+f+++Aake+  r++++ +e     + T+H++a                  
  AHX11294.1   7 QRLAI-ETINGPLLILAGAGTGKTKTLVHRIANLIKEGYAYPNQIMAVTFANKAAKEMMHRITEIVGEaqfnwIGTFHAIAAkilrieaekigfrpdft 104
                 77888.88899***************************************************9999998999999*****99***************** PP

      AAA_19  78 .............................................................................ldfddlltealelle.eaeeek 98 
                                                                                              +df dll++ ++l++ +ae  +
  AHX11294.1 105 ildtddqmrmlqkiakevqietdkslikkyltiisnwkdkaftpgrvkynnaantwfekqalciyelyqerlkennsMDFGDLLMHNVSLFKkDAEVLE 203
                 *****************************************************************************9999999999999885444455 PP

      AAA_19  99 klqeee.llivDEfqdvdelqyrLlkallgekkklllvGDpdQliyv 144
                   +e++ +++vDE+qd++  qy  l+ l++++ +++ vGD+dQ+iy 
  AHX11294.1 204 RYREKFkYIMVDEYQDTNLCQYLWLRLLAQKHSNICCVGDDDQSIYG 250
                 6667778**********************88888***********96 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.0   0.1     4e-07   0.00089       2      65 ..       3      66 ..       2     125 .. 0.77
   2 !   16.7   0.0     2e-06    0.0045      84     175 ..     203     298 ..     172     307 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.0 bits;  conditional E-value: 4e-07
      AAA_30  2 lnaeQaaavealltsgdrvavltGpAGtGKttalkalreaweaag....grviglAptgkaAkvLaee 65
                ln+eQ+ a+e++ +++    ++ ++AGtGKt +l +  + + ++g     ++++++  +kaAk++ + 
  AHX11294.1  3 LNNEQRLAIETI-NGP---LLILAGAGTGKTKTLVHRIANLIKEGyaypNQIMAVTFANKAAKEMMHR 66
                8999*9999866.444...689999******88877655555565578899*************7654 PP

  == domain 2  score: 16.7 bits;  conditional E-value: 2e-06
      AAA_30  84 arlepg.tllivDEagmvdtkqlaallkaaekagakvilvGDerQl....asVeaGgvlrdlveaagigtaeLtevvRqkeseeraaalalregdae 175
                 +r++++ + ++vDE   ++  q   l   a+k +  + +vGD++Q        e G++lr  ++ +g+++++L++++R +++   aa + +r+++a+
  AHX11294.1 203 ERYREKfKYIMVDEYQDTNLCQYLWLRLLAQK-HSNICCVGDDDQSiygwRGAEVGNILRFSQDFDGAKVIKLEQNYRSTNKILSAAHNVIRNNQAR 298
                 4566777999****987777777766666665.9***********644446788899999999889*************998888888888888766 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.9   0.0   1.8e-11   4.1e-08       4      51 ..     534     590 ..     531     591 .. 0.83

  Alignments for each domain:
  == domain 1  score: 32.9 bits;  conditional E-value: 1.8e-11
    UvrD_C_2   4 altihkaQGsefpaVivfdpdlaaarmgel.........rrrlLYtavTRAreklil 51 
                 ++t h ++G+ef+ V++   +  ++++ +           rrl+Y+++TRA++ l++
  AHX11294.1 534 IMTLHASKGLEFEQVFLPGWEDGTFPHARSlysadqieeERRLAYVGITRAKKFLTI 590
                 79***************6555444444444799999*****************9987 PP

>> Viral_helicase1  Viral (Superfamily 1) RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.5   0.0      0.09     2e+02       2      21 ..      19      38 ..      18      71 .. 0.73
   2 !    9.7   0.0   0.00029      0.64      61     106 ..     207     253 ..     169     331 .. 0.73
   3 !   10.2   0.0    0.0002      0.45     169     232 ..     519     590 ..     464     592 .. 0.72

  Alignments for each domain:
  == domain 1  score: 1.5 bits;  conditional E-value: 0.09
  Viral_helicase1  2 vvhGvpGcGKStlirkllrt 21
                     ++ + +G GK++ +++ + +
       AHX11294.1 19 LILAGAGTGKTKTLVHRIAN 38
                     67889******999988866 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00029
  Viral_helicase1  61 tkgkililDEylllhaG.yill.laalskaklvilfGDplQipfhsrn 106
                       k+k++ +DEy+  + + y++l l+a+ + ++++++GD  Q+ +  r 
       AHX11294.1 207 EKFKYIMVDEYQDTNLCqYLWLrLLAQKH-SNICCVGDDDQSIYGWRG 253
                      569*********99998456667777777.59*********9876555 PP

  == domain 3  score: 10.2 bits;  conditional E-value: 0.0002
  Viral_helicase1 169 yltftqalkealgvrevttvhevqGltfdkVtlvllketdlelis.........esrenllvAlTRhrkslvi 232
                      +     +l+++   + ++t h   Gl+f+ V l   ++ +   ++         e+r   +v++TR++k l+i
       AHX11294.1 519 LTDNDSQLYNSNAIN-IMTLHASKGLEFEQVFLPGWEDGTFPHARslysadqieEERRLAYVGITRAKKFLTI 590
                      333334444445555.9**************9986654432222245557777788*************9988 PP

>> AAA_11  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   2.6e-08   5.8e-05       2     130 ..       3     129 ..       2     217 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 2.6e-08
      AAA_11   2 lndsqreaiksalseseitliqGPPGtgKTktivellsqllsrrkseeeksakpriLvCapSNaAvDellerllr.....gll.dsegekykpkivRvg 94 
                 ln++qr ai+++       ++ G  GtgKTkt+v+ +++l+     +e  +++++i + +  N+A  e++ r+ +     +++  ++   +  ki+R+ 
  AHX11294.1   3 LNNEQRLAIETINGPL--LILAGA-GTGKTKTLVHRIANLI-----KEGYAYPNQIMAVTFANKAAKEMMHRITEivgeaQFNwIGTFHAIAAKILRIE 93 
                 7888888887665433..345555.***************4.....56889***********************97754322112456677779****9 PP

      AAA_11  95 neeeriseavksvsleekvekrlekeekaqlakeis 130
                 +e+  ++++   + ++ +++  ++  +++q+  ++s
  AHX11294.1  94 AEKIGFRPDFTILDTDDQMRMLQKIAKEVQIETDKS 129
                 999777777777777777777776666555533333 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.5e-05     0.079       2      80 ..      20     101 ..      19     122 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.5e-05
  Helicase_RecD   2 ltAdRGRGKSaalGlalaaliaegk...snilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyia 80 
                    + A+ G+GK+ +l   +a+li+eg+   ++i+ +   ++++k++++++++ + + +++   +++    + lr++ ++i + +
     AHX11294.1  20 ILAGAGTGKTKTLVHRIANLIKEGYaypNQIMAVTFANKAAKEMMHRITEIVGEAQFNWIGTFHAIAAKILRIEAEKIGFRP 101
                    889***********************999999999999*********99999888887766666666666777766666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (617 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      526  (0.0293379); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.69u 0.25s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 4004.52
//
Query:       AHX11295.1  [L=43]
Description: hypothetical protein NHE_0343 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       147  (0.00819901); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 333.48
//
Query:       AHX11296.1  [L=257]
Description: hydrolase, TatD family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.3e-69  234.5   0.1    1.4e-69  234.3   0.1    1.0  1  TatD_DNase  TatD related DNase
  ------ inclusion threshold ------
       0.17   12.2   0.0       0.34   11.2   0.0    1.5  1  DUF365      Domain of unknown function (DUF365)


Domain annotation for each model (and alignments):
>> TatD_DNase  TatD related DNase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  234.3   0.1   1.6e-73   1.4e-69       1     254 [.       3     251 ..       3     253 .. 0.96

  Alignments for each domain:
  == domain 1  score: 234.3 bits;  conditional E-value: 1.6e-73
                 EEEEE-TTSCCCTTTHHHHHHHHHHTTEEEEEEE-SSGGGHHHHHHHHTT.TTTEEEEE---GGGGGCC.CCHHHHHHHHHHCCCTSEEEEEEEEEET- CS
  TatD_DNase   1 iDaHcHldskefeedreeileraeeagvaavvvvgtsskdskavlelakkypnkvyavlGiHPnevdeasedlleelkelanvkhskvvaiGeiGLDyy 99 
                 +D+HcHl + + e++ e+i++ a+ +gv+ + ++ t++ + +++++  +++++ vy+++G+HPn vd    +  +++ +l  ++h+kv+ +Ge+GLDy 
  AHX11296.1   3 FDSHCHLIFYQ-EDELEGIVADAQSNGVKILHTIATRLSEYEELIATCERFSD-VYCSIGVHPNHVDA-GRQAYQDIINL--AAHPKVISVGETGLDY- 95 
                 7********33.45577777********************************9.*************5.688889*****..****************. PP

                 CCCCCGHHHHHHHHHHHHHHHHHTTEEEEEEEES-HHHHHHHHHHCG.GCCSEEEETT--S-HHHHHHHHHTTEEEEE-GGGGTTTTHHHHHHHHHS-G CS
  TatD_DNase 100 sreestkeaqeevFeeqlrlAkelklplviHlrkaeedlleilkeaa.eakakvvlHsfsgsaeeakkflklgyyislsglltfknakelrelvkavpl 197
                 + ++  ke q+  F e++++A +l+lp+++H+r+ae+d+++il+ +  ++++ v+lHsf +s e  ++++   +y+s+sg+ltfkna e+++++++ pl
  AHX11296.1  96 YYNHTAKEDQRISFIEHIKAATDLNLPIIVHSRNAEADTIKILETESkDSGIPVILHSFASSRELFEAAVRNSWYLSFSGILTFKNALEIQQIARETPL 194
                 6778******************************************977888*********************************************** PP

                 GGEEE---TTSSEECCCTTSE--GGGHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHH CS
  TatD_DNase 198 drlLiETDaPyltpkpyrgkrnepanvayvveklaelkaltleelaeitaeNakrlf 254
                 +r+LiETDaPyl+p+p rg+rn+p  v +v+++l+ l++++le+l++i+ eN+  +f
  AHX11296.1 195 NRILIETDAPYLAPVPVRGQRNYPVHVLHVLRYLSSLRDMNLEKLSHILLENFFNAF 251
                 *****************************************************9999 PP

>> DUF365  Domain of unknown function (DUF365)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   3.8e-05      0.34       2      40 ..       8      46 ..       7      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 3.8e-05
                EEEE---STT-B--EEEEEEEEEEES-THHHHHHTSTTB CS
      DUF365  2 klvfyasredtGfvGeaeikrvvlsedpleifekygdrv 40
                +l+fy+  e +G+v +a+ + v++ + + + +++y++ +
  AHX11296.1  8 HLIFYQEDELEGIVADAQSNGVKILHTIATRLSEYEELI 46
                58**************************99999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2030.59
//
Query:       AHX11297.1  [L=42]
Description: hypothetical protein NHE_0345 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       349  (0.0194657); expected 358.6 (0.02)
Passed bias filter:                      232  (0.0129399); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 355.49
//
Query:       AHX11298.1  [L=171]
Description: protein-export chaperone SecB [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-43  147.3   0.0    3.2e-43  147.0   0.0    1.0  1  SecB      Preprotein translocase subunit SecB


Domain annotation for each model (and alignments):
>> SecB  Preprotein translocase subunit SecB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.0   0.0   1.8e-47   3.2e-43       5     140 ..      26     170 ..      22     171 .] 0.94

  Alignments for each domain:
  == domain 1  score: 147.0 bits;  conditional E-value: 1.8e-47
        SecB   5 qpqlriqkqYvkDlSfenpnapeifleaeeqPevkvnlnveakkleee..vyevvlkitvtaka.......eektlFlvevkyaGiftienipeeqlep 94 
                  p  r + q++k +S+++pn+pe+f+ +++ Pev+v++n++++ ++e+  +yev l+i+++a++       +++++F++ +ky+G+fti+n++++ql++
  AHX11298.1  26 LPMARPEGQFMKSISLDTPNSPEVFSIMKNPPEVDVQCNIDSRIIDEQngIYEVLLDIKTEARIsdenspdGKHIAFVCKLKYCGVFTIRNLTQDQLKQ 124
                 56778899*****************877******************8778************998999987789************************* PP

        SecB  95 llliecPrilFPyaReivsdlvreggfppllLepinFealyqqqla 140
                 +ll+e+P++lFP+aR+i++++++++gfppl+L+pinF++ y+++++
  AHX11298.1 125 ALLVEAPTLLFPFARRIIATATTDAGFPPLMLAPINFAQKYTESQK 170
                 *****************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       311  (0.0173462); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1421.44
//
Query:       AHX11299.1  [L=207]
Description: tim44-like domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-30  106.5   0.0      2e-30  105.8   0.0    1.2  1  Tim44     Tim44-like domain
  ------ inclusion threshold ------
      0.098   13.1   0.0       0.18   12.3   0.0    1.6  1  DUF4440   Domain of unknown function (DUF4440)


Domain annotation for each model (and alignments):
>> Tim44  Tim44-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.8   0.0   2.2e-34     2e-30       5     144 ..      66     205 ..      63     207 .] 0.97

  Alignments for each domain:
  == domain 1  score: 105.8 bits;  conditional E-value: 2.2e-34
                 HHHHHHH-TT--HHHHHHHHHHTHHHHHHHHHHT-HHHHHHHB-HHHHHHHHHHHHHHHHTT-EE--EEEEEEEEEEEEEEEETTEEEEEEEEEEEEE- CS
       Tim44   5 laaikqrdpsFdkeeFleeakeayepileayakgDletLrkllteevyeefkaeikerakqgltldaellgirevdlkeakiegdtavltvrfrtqqis 103
                  ++i++  +sF++++F+e+a++a+e    a+a  Dl+ L +ll++++++ ++++i+er+++g+tl+ +l+++++  l +  + +++ ++tv+f+++qis
  AHX11299.1  66 KKEIESSGKSFSTDQFMEGAERAFELFISAFASCDLKILARLLSKDAFAIVSRKINERKSRGNTLERTLVALQSKSLLKLNVAKGMIYATVKFVSEQIS 164
                 57899999******************************************************************************************* PP

                 EE-TTS.-EEEE-TT--EEEEEEEEEEE--S-GGG-EEEEE CS
       Tim44 104 vtddatGevveGdedkvvevrevwtfeRdlgsedpnWrLve 144
                 +++d+ G +v+Gd+d+++ ++++w+feR l+s +  W +++
  AHX11299.1 165 LMRDEAGSIVSGDKDTIEVIEDLWVFERCLSSASNSWTVSQ 205
                 *9999********************************9986 PP

>> DUF4440  Domain of unknown function (DUF4440)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     2e-05      0.18       4      47 ..      88     133 ..      69     185 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
                 HHHHHHHHHHCT-HHHHHHCEEEEEEEE-TT..S-EEEHHHHHHHH CS
     DUF4440   4 leealeeafvagdaealaallapdavlvgps..gtvldkeelleal 47 
                 ++e + +af+++d++ la+ll++da  + ++   ++ ++ + le+ 
  AHX11299.1  88 AFELFISAFASCDLKILARLLSKDAFAIVSRkiNERKSRGNTLERT 133
                 5667889******************988665454444555555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      548  (0.030565); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 1679.54
//
Query:       AHX11300.1  [L=265]
Description: dimethyladenosine transferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.9e-44  150.1   0.0    7.5e-44  149.8   0.0    1.0  1  RrnaAD           Ribosomal RNA adenine dimethylase
  ------ inclusion threshold ------
      0.023   14.3   0.0      0.056   13.1   0.0    1.6  1  Methyltransf_28  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.8   0.0   8.4e-48   7.5e-44       5     261 ..       7     260 ..       4     263 .. 0.93

  Alignments for each domain:
  == domain 1  score: 149.8 bits;  conditional E-value: 8.4e-48
                 XXGCG--EE--HHHHHHHHHHH-GGTTSEEEEES-TTTCCHHHHHCC-.SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHHCTTTCCCC CS
      RrnaAD   5 rksygqnflknkkvineIldklnleekltvleigpGkGilTeeLakra.kqvvvlElderLakllqkklskdeklkvvhqDflkfetpeevtekdsihq 102
                 +ks+gq+f+ ++ v+ +I+ ++  ++ + ++eigpG G lT+e++      ++++E+d+r+ k+     +++e+ + +  D+l   +   +     +++
  AHX11300.1   7 NKSLGQHFIYDRVVLGKIIGAATQTKGKHIVEIGPGIGTLTKEILATDpSLLTSIEKDQRFEKEHLSLERQYENYQFIIGDALSIPLERVY-----KGE 100
                 89*****************************************97777699**********999888566**************9999954.....8** PP

                 EEEEEEE--TTTHHHHHHHHHHGGGGCEEEEEEEEEHHHHHHHH--TTSTT-SHHHHHHHHHEEEEEEEEC-GGCECS--SSSEEEEEEEE-SS-S--S CS
      RrnaAD 103 eflvvanlPyeistqlvkqlleesrfglvkmllwlqkefarrllarpgskkrsrlsvlreaftdvklvakveksifsPppkvdsalvelerkdedlpqk 201
                 + +++anlPy+i t l   +lees   +++m+l++qke+a r++a+p +k++++lsvl ++ + +++  ++ +++f+Pppk+ s+++++++ + +  q 
  AHX11300.1 101 KVIIIANLPYNIATRLLLNWLEESNL-IQEMILMFQKEVADRICAEPRNKNYGALSVLIQIRCKLEPQFILQPEVFTPPPKILSSVLKITPLEIPKWQY 198
                 **********************9999.9***************************************************************99965566 PP

                 -HHHHHHHHHHHHCTTTSBCCCHCCCTSTCHHHHHCTT...T--TTTCCCCSGHHHHHHHHH CS
      RrnaAD 202 dlkkyesvvrkllnrkrktlstslksllpggelqalsst..gindnalvkklsaeqtldifk 261
                 +  +++ ++r+ ++ +rkt++t l+ ++ g++   +  +  g n  +++++l+++q++ ++ 
  AHX11300.1 199 KKIRLDTILRHGFAHRRKTMNTTLQGIFGGQKQLHVALEsiGANPSMRIEELTPGQICALSL 260
                 66789***********************998866655555899*************998875 PP

>> Methyltransf_28  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   6.2e-06     0.056      17      39 ..      31      53 ..      21      66 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 6.2e-06
  Methyltransf_28 17 skklrliElGpGkGtLmadvLrt 39
                      k+ +++E+GpG GtL +++L t
       AHX11300.1 31 TKGKHIVEIGPGIGTLTKEILAT 53
                     35579****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       512  (0.0285571); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2148.84
//
Query:       AHX11301.1  [L=379]
Description: hypothetical protein NHE_0349 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.019   14.4   0.2      0.035   13.6   0.2    1.4  1  NMD3      NMD3 family


Domain annotation for each model (and alignments):
>> NMD3  NMD3 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.2   1.9e-06     0.035     148     230 ..      50     133 ..      40     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.9e-06
        NMD3 148 ivQvRqk.relteeehkrtfelleqlilkhdahafiskikevkeGlDfyfgsksaArklveflksevggkvkeseklvsedkks 230
                  vQ+    ++ te   k++ el  +++ ++  +++isk +e+++Gl +y  +++   k+++ +++ v  +v+   +l ++  +s
  AHX11301.1  50 SVQIEFVtEQATEWLYKKIAELYDKVLDNEFIEREISKFNEENDGLSVYWIKQESDLKILDSVNDDVLSRVSIGRSLLQKSFES 133
                 5788888788999999***********9989*************************************9999888888776664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (379 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1081  (0.0602934); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.22s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3044.87
//
Query:       AHX11302.1  [L=706]
Description: response regulator [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.9e-21   76.1   1.0    9.6e-21   74.4   0.3    2.1  2  HATPase_c     Histidine kinase-, DNA gyrase B-, and HSP90-lik
    7.5e-20   71.2   0.6    2.3e-19   69.6   0.6    1.9  1  Response_reg  Response regulator receiver domain
    5.4e-10   39.2   0.0    1.5e-09   37.8   0.0    1.8  1  HisKA         His Kinase A (phospho-acceptor) domain
     0.0026   17.5   0.1     0.0048   16.6   0.1    1.4  1  HAUS4         HAUS augmin-like complex subunit 4
  ------ inclusion threshold ------
      0.014   15.3   0.0      0.032   14.1   0.0    1.6  1  HATPase_c_3   Histidine kinase-, DNA gyrase B-, and HSP90-lik
      0.026   14.7   1.0        1.2    9.4   0.1    2.6  2  TFIID_NTD2    WD40 associated region in TFIID subunit, NTD2 d
       0.13   12.6   0.0       0.69   10.2   0.0    2.4  1  PAS_9         PAS domain
       0.13   12.3   0.0       0.37   10.9   0.0    1.7  1  PAS_8         PAS domain


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.4   0.3   4.3e-24   9.6e-21       2     110 ..     433     558 ..     432     560 .. 0.86
   2 ?   -0.7   0.0      0.88     2e+03       8      56 ..     592     659 ..     591     678 .. 0.59

  Alignments for each domain:
  == domain 1  score: 74.4 bits;  conditional E-value: 4.3e-24
                 HHHHHHHHHHHHHHHHHHHHSTTTEEEEEEEE............EE........TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHH CS
   HATPase_c   2 dekrLrqiisnlvdNavkfatkageieveika............se........ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsi 80 
                 d+++L+q + nlv Na ++  ++g i ve++             s+        ++++++veDnG Gi+++ l+k+f +f +   tk+  +gtGlGls 
  AHX11302.1 433 DKTQLEQSLMNLVVNARDALESGGAIVVEVRNvlvdkkrtvlvgSQneevvlkgEYVSVTVEDNGSGISMDVLPKIFNPFFS---TKSVDKGTGLGLST 528
                 7899**************9779999999888788776665555511456777779**************************9...777779******** PP

                 HHHHHHHTTTEEEEEEETTTEEEEEEEEES CS
   HATPase_c  81 vkklvelmgGeiwvesepgrGttftftlpl 110
                 v  ++++m+G i+ves +++G+tft+ +p 
  AHX11302.1 529 VYGIIKQMRGYINVESIEKQGSTFTLLIPV 558
                 ***9999******************99885 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.88
                 HHHHHHHHHHHHHHS....TTTEEEEEEEE....EETEEEEEEEE......SSSSSTTHHHT......G CS
   HATPase_c   8 qiisnlvdNavkfat....kageieveika....seddlvisveD......nGiGipkedlk......k 56 
                 ++++n++  a++ ++    ++++ +v +k+    + +++++ ++D      +G+ +  ++++       
  AHX11302.1 592 KMVRNFLVKALRKQSfnvvECESSQVALKTflemK-QRIELVITDivmpgiDGPEMVTAMREdkpnlkV 659
                 57888888888873344456666666666554422.588888998644444444444433335555554 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.6   0.6     1e-22   2.3e-19       1     111 [.     585     695 ..     585     696 .. 0.92

  Alignments for each domain:
  == domain 1  score: 69.6 bits;  conditional E-value: 1e-22
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHH..HHHHESEEEEESSCSSSEHHHHHHHHHHCTTTSEEEEEESSTSHHHHHHHHHCTES CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealell..keekvdlillDinmpgmdGlellkeireedpelpviiltahseeedavealkagad 95 
                   +l+v+D+++vr+ l ++l+++ + +v e+e+++ al+ +   ++++ l+++Di mpg+dG e+++ +re++p+l+v+++++++ ++   +  +   +
    AHX11302.1 585 ILLVEDEKMVRNFLVKALRKQSF-NVVECESSQVALKTFleMKQRIELVITDIVMPGIDGPEMVTAMREDKPNLKVLFMSGYTRDKLHLDDHN-HNE 679
                   89*********************.9*************9656666*************************************99777766655.569 PP

                   EEEESSG-HHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkal 111
                   df++Kpf+ +eL++++
    AHX11302.1 680 DFIAKPFEVNELISKI 695
                   ************9987 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   6.6e-13   1.5e-09       1      65 [.     325     389 ..     325     391 .. 0.95

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 6.6e-13
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHHHHHHHCCHH CS
       HisKA   1 slgrflagvaHELrtPLsailgnaeaLkregklteelkeyletiesearrldhlvedlLdlsrie 65 
                 slg++  g+aH++++ L+ailg+ae+L ++++l  +    +++i+ +a+  ++lve +L +sr +
  AHX11302.1 325 SLGELSGGIAHDFNNILTAILGFAEMLLDDVPLKSKHYYDIAQIKYSAKKGQALVEKILAFSRNQ 389
                 799************************999899999999***********************987 PP

>> HAUS4  HAUS augmin-like complex subunit 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   0.1   2.2e-06    0.0048     107     157 ..     335     385 ..     310     420 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 2.2e-06
       HAUS4 107 aeYlqvLlqclqlLqklvkdhrLktqsdlDrlkkeyleakCeamllKlrvl 157
                 + ++++L+ +l+  + l+ d+ Lk+++ +D ++++y ++k +a++ K+ ++
  AHX11302.1 335 HDFNNILTAILGFAEMLLDDVPLKSKHYYDIAQIKYSAKKGQALVEKILAF 385
                 6799*******************************************9654 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.4e-05     0.032       3      65 ..     437     520 ..     435     578 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.4e-05
  HATPase_c_3   3 lekAlaelvdNsldAdaen.................vkievnknrgkt......geivieDdGkGmseeelknalrlatsskeakr 65 
                  le++l+ lv N+ dA                     v +  ++++  +       ++++eD+G+G+s + l + +++  s+k+ ++
   AHX11302.1 437 LEQSLMNLVVNARDALESGgaivvevrnvlvdkkrtVLVGSQNEE--VvlkgeyVSVTVEDNGSGISMDVLPKIFNPFFSTKSVDK 520
                  578999999999999777767666655555555544333333333..134444489********************9999998643 PP

>> TFIID_NTD2  WD40 associated region in TFIID subunit, NTD2 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.1     0.044        99      28      79 ..      16      67 ..       8     119 .. 0.70
   2 ?    9.4   0.1   0.00054       1.2      80     126 ..     589     637 ..     560     640 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.044
                HHGGGHHHHHHHHHHHHHHTT-HHHHHHHHHHHGGGGGGGHH.HHHHHTT-- CS
  TFIID_NTD2 28 eLsrllyPvFvhlyLelvakgaeeeakkFfekfkedhealhkedlkkLasis 79
                +++ + y v v ++++lv++ ++ +      +f++ + ++ ++ l+++ +i 
  AHX11302.1 16 QVRVVCYCVAVLTFFSLVYNLKKLHLVLVAAEFQNMFYSNAAKALTAFYMII 67
                567889**************99999666666666666666666666555543 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00054
                 SHHHHHHSHHHHHHHHS-EEEEEEHHHHHHHHHHHHHTT-H..HHHHHH CS
  TFIID_NTD2  80 spehleenelakafrenkyriklskaafelLlrfLeekeka..vllkil 126
                 + e++ +n l+ka+r++ +++  +++++  L++fLe k+++  v+++i+
  AHX11302.1 589 EDEKMVRNFLVKALRKQSFNVVECESSQVALKTFLEMKQRIelVITDIV 637
                 4577889999***************************999988888876 PP

>> PAS_9  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00031      0.69       4      40 ..     233     271 ..     230     309 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00031
       PAS_9   4 ilidnpdgrilyaNeaalrllGys..peevlgksitdlf 40 
                 +++ ++d ++l++N+a+++++G +   e++   +i dl 
  AHX11302.1 233 VAFMTKDLKVLDVNDAFREVFGGKcnLEQFFRSKINDLS 271
                 555459****************66558888888888887 PP

>> PAS_8  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.37      11      35 ..     230     254 ..     222     278 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
       PAS_8  11 pdgiavvdlgdrivdvNqaalellG 35 
                 + g+a    + +++dvN+a+ e +G
  AHX11302.1 230 AIGVAFMTKDLKVLDVNDAFREVFG 254
                 567775444458************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (706 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       698  (0.0389313); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4990.05
//
Query:       AHX11303.1  [L=433]
Description: proline--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-37  127.1   0.0      1e-36  126.6   0.0    1.2  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    1.5e-09   37.9   0.0      4e-09   36.5   0.0    1.7  1  HGTP_anticodon  Anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.6   0.0   1.1e-40     1e-36       2     178 ..      99     333 ..      98     334 .. 0.90

  Alignments for each domain:
  == domain 1  score: 126.6 bits;  conditional E-value: 1.1e-40
                   EEEETTSEEEEE-SSSHHHHHHHHHHHEEEB.GGSSEEEEEEEEEEBTTTSTBC.TTTB-SEEEEEEEEEEES.GGGHHHHHHHHHHHHHHHHHHTT CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   2 kledrndreyiLkPtneetfvelirdevlrs.krLPlklyqiqtkyRdEksdsr.GLlRvreFhqkdgyvfha.easlddslrdlikaisriferlg 95 
                   k+ dr d+e+  +Ptnee +++++rd  + s k+LP  ly+iq k+RdE +  r GL+R reF +kd+y+f   e+s++ s+ ++ +a+ rif+rlg
    AHX11303.1  99 KFRDRHDNEMLFGPTNEEVITSIVRDS-ITSyKQLPKILYHIQWKFRDEIR-PRfGLMRAREFLMKDAYSFDVdEQSARLSYDKVYQAYLRIFNRLG 193
                   6889***********************.888688*****************.888******************89999******************* PP

                   .SCEEEEEEGTTSC.........................................................BTTSEEEEEEEEETTTSEEEEEEEEE CS
                   xxxxxxxxxxxxxx.........................................................xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  96 lefraiielmsaks.........................................................adykdkkefeavsesltkgieigtiq 135
                   l+    + + + +                                                           + kd+k+  + + s ++gie+g+i+
    AHX11303.1 194 LNPIPCRADAGVIGgnlnhefhiatdaggecsifypseveslvqefcntdpgdaaavkamtarlqaldcftDECKDSKDRVMEMISTKQGIEVGHIF 290
                   *9977777766554566677889999999999999999999999999999999999999999999999998556666665555555699******** PP

                   EEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHHHHHH CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 136 klgtrlserlgatvldennreksvimicaaigveRllsaileq 178
                     g+++s  ++a++ld+++++ + +m+ ++ig++Rll+ai+e+
    AHX11303.1 291 LFGDKYSLPMKAQFLDKDGNRSNFYMGSYGIGISRLLAAIIEV 333
                   *****************************************97 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.5   0.0   4.5e-13     4e-09      14      82 ..     356     425 ..     345     432 .. 0.83

  Alignments for each domain:
  == domain 1  score: 36.5 bits;  conditional E-value: 4.5e-13
                     HHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEET.TTCEEEEE CS
  HGTP_anticodon  14 leeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdr.dtreqerv 82 
                     l+++   lae L a+  +v +dd  +s g k++++dl+g pf ++vG+++le+g+v+++ r d+ e+  +
      AHX11303.1 356 LHQESAALAENLFANLNNVIYDDTLDSQGVKFARMDLIGAPFQIIVGKRSLETGIVNLKYRlDSSEESCI 425
                     55667778888888877899999**************************************777776554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3120.67
//
Query:       AHX11304.1  [L=239]
Description: hypothetical protein NHE_0352 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.028   14.0   1.2       0.16   11.6   0.1    2.3  2  SPW       SPW repeat
       0.43   10.2   6.0      0.089   12.4   1.5    1.9  2  Saf_2TM   SAVED-fused 2TM effector domain
       0.84    9.9   7.1       0.82   10.0   1.2    2.5  2  DUF3082   Protein of unknown function (DUF3082)
        5.8    6.7   7.8        3.7    7.4   1.1    2.1  2  VIT1      VIT family


Domain annotation for each model (and alignments):
>> SPW  SPW repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.1       0.1   4.7e+02      18      45 ..     110     137 ..     108     140 .. 0.73
   2 ?   11.6   0.1   3.5e-05      0.16      26      46 ..     161     181 ..     155     182 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.1
         SPW  18 lGfsattgaawnnvivGavvavLalafa 45 
                   fs+t+++++n     ++++v ++ + 
  AHX11304.1 110 ARFSDTQNLVVNLCYYSIALLVAGFLCF 137
                 5689999999998777777777777665 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.5e-05
         SPW  26 aawnnvivGavvavLalafaa 46 
                 +++ +++vG+++a+L++ f++
  AHX11304.1 161 TIVVSIVVGICTAFLGVLFSS 181
                 6899*************9986 PP

>> Saf_2TM  SAVED-fused 2TM effector domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.2      0.18   8.2e+02      65      82 ..      55      72 ..      10      88 .. 0.58
   2 ?   12.4   1.5     2e-05     0.089      12      84 ..     106     178 ..     102     184 .. 0.87

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.18
     Saf_2TM 65 eivlaiilvigvllivvG 82
                  + + +++++++l ++ 
  AHX11304.1 55 VRITMYVMALCIVLPILA 72
                234444555555554333 PP

  == domain 2  score: 12.4 bits;  conditional E-value: 2e-05
     Saf_2TM  12 idwlfRkrsaell...lftigvalllailgtdwalkialklaggslevsfssseipeivlaiilvigvllivvGav 84 
                  +w+ R +  ++l   l  +++all+a++    ++++++  +  +l  s+++s  +e + ++++v+g+++  +G++
  AHX11304.1 106 QRWWARFSDTQNLvvnLCYYSIALLVAGFL--CFVQYIAVKGIAELFKSLEKSR-IETTIVVSIVVGICTAFLGVL 178
                 5899999999998566677889*****998..9999999999999******999.9999**********9999965 PP

>> DUF3082  Protein of unknown function (DUF3082)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.5     0.028   1.2e+02      13      64 ..      25      75 ..      20      80 .. 0.76
   2 ?   10.0   1.2   0.00018      0.82      11      58 ..     130     178 ..     120     188 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.028
     DUF3082 13 agvlavvlyklttsiaatfarkplssdnqlvqriavavRtlvvGlcyLatfv 64
                ++v a v++++   i    +r+ +s+ +++++ri++ v  l++ l  La ++
  AHX11304.1 25 SAVAAAVSFFVKVGIP-VISRQWFSEGKEFAVRITMYVMALCIVLPILACVI 75
                5555555555555554.46788899999**********99999999998877 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00018
     DUF3082  11 liagvlavvlyklttsiaatfarkplss.dnqlvqriavavRtlvvGlc 58 
                 l+ag+l++v y +++ ia+ f++ + s  + ++v++i v + t  +G+ 
  AHX11304.1 130 LVAGFLCFVQYIAVKGIAELFKSLEKSRiETTIVVSIVVGICTAFLGVL 178
                 78*******************9987766577888888888888888875 PP

>> VIT1  VIT family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.1   0.00082       3.7     137     178 ..      25      67 ..       6     131 .. 0.62
   2 ?    2.9   1.7     0.019        85     143     184 ..     127     179 ..     110     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.00082
        VIT1 137 aAlssalsfliGgliPllpylfve.svglalvvsiavtllall 178
                 +A++ a+sf++   iP+++   ++     a+++ + v++l+++
  AHX11304.1  25 SAVAAAVSFFVKVGIPVISRQWFSeGKEFAVRITMYVMALCIV 67 
                 89******************66662333333333333333322 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.019
        VIT1 143 lsfliGgliPllpylfve...........svglalvvsiavtllalllfGavk 184
                 ++ l+ g++  + y+ v+           s+++ ++v+ +v++++ +++G++ 
  AHX11304.1 127 IALLVAGFLCFVQYIAVKgiaelfkslekSRIETTIVVSIVVGICTAFLGVLF 179
                 55666666667777666666655554544577888888899999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (239 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       989  (0.055162); expected 358.6 (0.02)
Passed bias filter:                      532  (0.0296726); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 1665.40
//
Query:       AHX11305.1  [L=93]
Description: hypothetical protein NHE_0353 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.6   0.1     0.0093   16.2   0.1    1.1  1  DUF525    ApaG domain
  ------ inclusion threshold ------
      0.074   12.6   0.2       0.32   10.6   0.1    2.0  3  F-box_5   F-box


Domain annotation for each model (and alignments):
>> DUF525  ApaG domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1     1e-06    0.0093      19      85 ..       1      66 [.       1      67 [. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-06
                EEE-SSS-EEEEEEEEEEEETTS-EEEEEE.ESBTTB--EE-TTEEEEEEEEEEESSSEEEEEEEEEE CS
      DUF525 19 ieneseesvqLlsRhweitdadgkveeveg.eGvvGeqPlLepgesFeYtSgvsletpsGsmeGsytm 85
                ++n s+e v+++++  e+ d++g+v++v++ +Gv  +  +++++e+ eY  gv l++ sG+++  y++
  AHX11305.1  1 MTNCSSEDVKIIECWAEVIDSRGMVTKVRSvDGVWNK--IIKKNEALEYVTGVYLKSVSGVLRSWYEV 66
                68999***********************652666655..8********************99987775 PP

>> F-box_5  F-box
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.27   2.4e+03       5      13 ..      31      39 ..      28      41 .. 0.79
   2 ?   -3.6   0.0      0.98   8.8e+03       7      12 ..      43      48 ..      41      50 .. 0.64
   3 ?   10.6   0.1   3.6e-05      0.32      24      36 ..      55      67 ..      54      69 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.27
                GGGTHHHHH CS
     F-box_5  5 pDeVlecVl 13
                +D V+ +++
  AHX11305.1 31 VDGVWNKII 39
                799999998 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 0.98
                GTHHHH CS
     F-box_5  7 eVlecV 12
                e+le V
  AHX11305.1 43 EALEYV 48
                667766 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 3.6e-05
                HHTTS-HHHHHHH CS
     F-box_5 24 AvSlVCkrWYeie 36
                +vS V ++WYe+e
  AHX11305.1 55 SVSGVLRSWYEVE 67
                8**********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 736.55
//
Query:       AHX11306.1  [L=867]
Description: pyruvate, phosphate dikinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-84  284.1   0.0    2.1e-84  283.1   0.0    1.5  1  PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
    1.7e-52  178.8   0.0    3.1e-40  138.4   0.0    3.2  2  PPDK_N           Pyruvate phosphate dikinase, PEP/pyruvate bi
    2.4e-25   88.0   3.6    3.1e-25   87.7   1.9    2.0  2  PEP-utilizers    PEP-utilising enzyme, mobile domain


Domain annotation for each model (and alignments):
>> PEP-utilizers_C  PEP-utilising enzyme, TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.1   0.0   3.5e-88   2.1e-84       5     293 ..     517     857 ..     514     858 .. 0.94

  Alignments for each domain:
  == domain 1  score: 283.1 bits;  conditional E-value: 3.5e-88
                      TSCCCCCCCHCCCXBCEEEEEESSCHHHHHHHHCTXSSEEEEEHHHHCTTSCCHHHHHH....................HHHHHHHHHHHTTTS CS
  PEP-utilizers_C   5 gklktllavtkdgkkikvlaNidtpedaekalengaeGiGLlRtEflfmareelpteee....................qaeaykkvleamngr 78 
                      ++++ +++++++ kki v +N++t ed+e al++ a+GiGL+RtE++f++ +++ +++e                    q e++ ++++ m+++
       AHX11306.1 517 EEFEIFMSWVDEFKKIGVRVNAETEEDIEVALKFAADGIGLCRTEHMFFSEDRINIVREmiiaeesqqrsealkkllpiQQEDFVAIFRGMQSK 610
                      5677899*************************************************************************************** PP

                      EEEEEXXXSSCCGGSGGC.....................HHHH.XSXGGGSSXTHHHHCCSHHHHHHHHHHHHHHCCCC...EEEEEESSXXSH CS
  PEP-utilizers_C  79 pvvvRtlDiggdkelpel.....................keepeevNPmlGfRgirlglsepelfetqlrAllrasaag...kleimlPmvasv 148
                       v++R+lD++ +++lp                       ++ ++e+NPmlG+Rg+rlg+s+pe++e+ql A++ a++++     eim+P+v ++
       AHX11306.1 611 CVTIRLLDPPLHEFLPSDeaslesfkkhsvlaesfiqrrIKSLKEENPMLGHRGCRLGISHPEIYEMQLHAIFGAAQEVkniAPEIMIPFVMNA 704
                      ****************9889*******************99**********************************996655689********** PP

                      HHHHHHHHHHHHHHHHHHHCTCTXXTTXEEEEEEXSHHHHHTHHHHCTTSSEEEEXHHHHHHHHHTXXCCCHC....HHHH.......SXTTTC CS
  PEP-utilizers_C 149 eeleeakkiieevkeelekegvkkkkkvkvGiMiEvpsaalladklakevdFfSiGtNDLtQytlavdRdnee....vakl.......ydplep 231
                      eel   k+++e+v         +++ ++++G MiE psaa+la+++a++ dFfS+GtNDLtQ tl+++Rd+      +           dp+  
       AHX11306.1 705 EELLLIKRLVESV-------AANYSVEYSFGNMIELPSAAILANRIAEHSDFFSFGTNDLTQTTLGISRDDCGmflnI--YkekgllkDDPFVT 789
                      ************9.......3468899********************************************9965442..15578898899999 PP

                      HHCCCHHHHHHHHHHCC......XEEEEESCCCCSCCCHHHHHHCTXSEEEEXGGGHHHHHHHHHCTT CS
  PEP-utilizers_C 232 avlrlikevikaaeekg......lkvgiCGelagdpsavellvglGldelSmsaasvpaaraalaqve 293
                         + ++ +i+ a +kg      +k+giCGe++gdp +ve+++ lG+d++S+s+++vp+a+ a+aq e
       AHX11306.1 790 IQTENVGVLIRDAINKGratkknIKIGICGEHGGDPDSVEFFASLGVDYVSCSPYRVPIAKVAAAQYE 857
                      99999999999999998888888*****************************************9975 PP

>> PPDK_N  Pyruvate phosphate dikinase, PEP/pyruvate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.4   0.0   5.3e-44   3.1e-40       2     230 ..      22     300 ..      21     306 .. 0.94
   2 !   34.6   0.1   2.1e-12   1.2e-08     270     325 ..     301     354 ..     288     357 .. 0.89

  Alignments for each domain:
  == domain 1  score: 138.4 bits;  conditional E-value: 5.3e-44
      PPDK_N   2 elvGGKganLaellneagipvPpgfaitadafrefleengleekideelkeldvddvdelrkaskeirelilsaelPeeleeaikeayeelgkkfgde. 99 
                 +++GGKganLa++  + g+pvPpgf+i++ a++ ++++    e+ +++l+                            e+++a +++++++gk fg+  
  AHX11306.1  22 DILGGKGANLAQM-CNMGLPVPPGFTISSRACDLYYKDR---EHFRSLLDV---------------------------EVQKAFHSLESATGKVFGSPt 89 
                 589**********.66********************999...889998887...........................99****************999 PP

      PPDK_N 100 .elpvaVRSSataEDlpkasfaGqqdtyLnvggeeevle............................................................ 137
                  +l+v+VRS+      ++ s++G+ dt+Lnvg ++e++                                                             
  AHX11306.1  90 nPLLVSVRSG------SRFSMPGMLDTVLNVGLNNEIVAaldskfildsyrrliqmygnvvlkvdsyhfeealydykharlllndsdlskehlrqiiel 182
                 89********......9********************************************************************************** PP

      PPDK_N 138 .......................aikavfaSlfnerAilYrkekgldheevalavvvqkmvnsdlg...asGVafsldpetG...fkdevlinasyGlG 207
                                         i+avf+S+ nerA +Yr  ++++ ee+++av+vq+mv+++ +   asGV f+++p++G     +e++ na   +G
  AHX11306.1 183 fqdiiekhshegmpqdvyaqvmnCIEAVFQSWSNERAKTYRMIHNIP-EEIGTAVNVQSMVFGNFNehsASGVLFTRNPSNGrkeIFGEYIKNA---QG 277
                 ***********************************************.****************999***************554456788888...** PP

      PPDK_N 208 eaVVaGrvtpdefvvekstrkil 230
                 e+VV+G +tp  +   +s+++ l
  AHX11306.1 278 EDVVSGVRTPMPIEEMQSDNPSL 300
                 **********8887777766655 PP

  == domain 2  score: 34.6 bits;  conditional E-value: 2.1e-12
      PPDK_N 270 veeLaeiakkiekhygtpmdiEfaideeegklyllQaRpetrtsekkekkaaetle 325
                  ++L ++   +ekhy++ +diEf+i+  ++ ly+lQ+R  +r  e++ k+a ++  
  AHX11306.1 301 YKQLSDVCDVLEKHYKDVQDIEFTIE--DDVLYVLQTRSAKRSAEAAIKIAVDMVG 354
                 5899**********************..******************9999998875 PP

>> PEP-utilizers  PEP-utilising enzyme, mobile domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   1.9   5.1e-29   3.1e-25       4      73 .]     419     501 ..     416     501 .. 0.97
   2 ?   -1.8   0.0      0.45   2.7e+03      41      57 ..     692     708 ..     685     717 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 5.1e-29
                    S-EEEEES---HHHHTTS-GEEEEEES--TTHHHHHHHHHHTT--EEE--SSHH..............HH--TEEEEEETTTT CS
  PEP-utilizers   4 egvILvaeetspsdiagldkaaGivterGGmtSHaAivArelgiPaVvgvgeati.............elkegdlitvDgstG 73 
                    e+vILv +etsp+diag+++a +ivt rGGmtSHaA+vAr++g+P+++ +++ ++             +l++gd++tvDg++G
     AHX11306.1 419 EKVILVKSETSPEDIAGMHAAVAIVTTRGGMTSHAAVVARGMGKPCICALSGGSVdqysgilkispdiVLNKGDRVTVDGASG 501
                    56****************************************************9*************9************99 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.45
                    HHHHTT--EEE--SSHH CS
  PEP-utilizers  41 vArelgiPaVvgvgeat 57 
                    +A e  iP V++++e++
     AHX11306.1 692 IAPEIMIPFVMNAEELL 708
                    678899*******9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (867 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       566  (0.031569); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.72u 0.29s 00:00:01.01 Elapsed: 00:00:00.44
# Mc/sec: 5935.27
//
Query:       AHX11307.1  [L=186]
Description: pyridoxamine 5'-phosphate oxidase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-18   66.9   0.0      2e-18   66.3   0.0    1.3  1  Putative_PNPOx   Pyridoxamine 5'-phosphate oxidase
    3.5e-12   46.2   0.2    5.9e-12   45.5   0.2    1.4  1  PNP_phzG_C       Pyridoxine 5'-phosphate oxidase C-terminal d
    0.00025   21.6   0.0    0.00048   20.7   0.0    1.5  1  Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
     0.0035   16.9   0.0     0.0049   16.4   0.0    1.2  1  Pyrid_ox_like    Pyridoxamine 5'-phosphate oxidase like
  ------ inclusion threshold ------
       0.06   13.4   0.0       0.11   12.6   0.0    1.4  1  SH3_14           Dda helicase SH3 domain


Domain annotation for each model (and alignments):
>> Putative_PNPOx  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.3   0.0   5.6e-22     2e-18      12      83 ..      21      89 ..      12      94 .. 0.92

  Alignments for each domain:
  == domain 1  score: 66.3 bits;  conditional E-value: 5.6e-22
                    SSEEEEEEEETTSEEEEEEEEEEEETTTTEEEEEEETTSHHHHHHHHH-EEEEEEEETTGSEEEEEEEEEEE CS
  Putative_PNPOx 12 skavvlATvdedGrPnvspvllkagdgrdgivfatnadsrklrnleenprvallflddelgrgvrieGtael 83
                      a+ l+T+++ G P++++vl k  +++ g++f+tn  s+k++nl+enp++a++f++d+  ++v+++G + l
      AHX11307.1 21 KTAAILSTCTKAGIPSARTVLIKDVNDD-GFTFYTNVNSNKGKNLRENPKAAMVFYWDS--KQVTVRGDVYL 89
                    57899******************99999.******************************..9******9866 PP

>> PNP_phzG_C  Pyridoxine 5'-phosphate oxidase C-terminal dimerisation region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.5   0.2   1.6e-15   5.9e-12       1      43 []     145     186 .]     145     186 .] 0.96

  Alignments for each domain:
  == domain 1  score: 45.5 bits;  conditional E-value: 1.6e-15
  PNP_phzG_C   1 WgGyrvvPeeiEFWqgrpsRlHdRfrYereeedgkWkierLsP 43 
                 W G+r++P+++EF+   + Rl +Rf Y+ ++ d++Wki rL+P
  AHX11307.1 145 WEGFRLKPDSMEFFIADKYRLNKRFLYTLQP-DETWKISRLYP 186
                 ****************************877.67********9 PP

>> Pyridox_oxase_2  Pyridoxamine 5'-phosphate oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   1.3e-07   0.00048      16      97 ..      17      88 ..       6      91 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 1.3e-07
                     T-GGGGEEEEEEE-T.TS-EEEEEEE---B-TT...SS-.EEEEEETTSHHHHHHH.H--EEEEEEEETTTTEEEEEEEEEE CS
  Pyridox_oxase_2 16 kkkkstefqlaTvdeeegkPrvRtvvfRgfleekkeesdvltfttDvrseKvkqlessnaaveavfylketreQfRisGkaf 97
                     + +++t   l+T + ++g P++Rtv +++  ++       +tf t v s+K k+l+ +n+++ +vfy  +  +Q  ++G++ 
       AHX11307.1 17 NVPDKTAAILSTCT-KAGIPSARTVLIKDVNDD------GFTFYTNVNSNKGKNLR-ENPKAAMVFYWDS--KQVTVRGDVY 88
                     56788889999999.6899*******9998664......59***************.8*********976..5777777765 PP

>> Pyrid_ox_like  Pyridoxamine 5'-phosphate oxidase like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.4e-06    0.0049      12      96 ..      20     100 ..      15     117 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.4e-06
  Pyrid_ox_like  12 diktamLttteadgklksrPMatqkveedgdlwfltkkdsdkvkeirkdsqvnlafsdeskkkyvsvsGtaevvedrakieelWs 96 
                    d  +a+L t ++ g   +r   +++v++dg + f+t+ +s+k k++r+++++ ++f    ++k v+v+G + + e ++k++ +++
     AHX11307.1  20 DKTAAILSTCTKAGIPSARTVLIKDVNDDG-FTFYTNVNSNKGKNLRENPKAAMVFYW--DSKQVTVRGDVYLAE-KEKADAYFN 100
                    667889999999999999999999888887.6799***************88887766..45679*****99865.566666665 PP

>> SH3_14  Dda helicase SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0     3e-05      0.11      82     124 ..      39      81 ..      23      86 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3e-05
                 EE--SHHHHHHHHHHHHHHHHHHHS--SSSS--THHHHHHHTT CS
      SH3_14  82 kvlsddeekekfalflakaaetykslrkgtkaywsdfwdlkeq 124
                 +vl +d + + f+ +  + ++  k+lr++ ka    +wd k+ 
  AHX11307.1  39 TVLIKDVNDDGFTFYTNVNSNKGKNLRENPKAAMVFYWDSKQV 81 
                 8999***********************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       712  (0.0397122); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1436.75
//
Query:       AHX11308.1  [L=280]
Description: bacterial transferase hexapeptide family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.4e-17   62.9   0.4    3.8e-17   62.3   0.4    1.3  1  THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-ter
    3.5e-16   58.2  13.5    5.2e-07   29.1   0.7    3.8  4  Hexapep    Bacterial transferase hexapeptide (six repeats)
    9.6e-14   50.8  12.5    7.4e-13   48.0   2.6    3.1  3  Hexapep_2  Hexapeptide repeat of succinyl-transferase


Domain annotation for each model (and alignments):
>> THDPS_N_2  Tetrahydrodipicolinate N-succinyltransferase N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.3   0.4   6.3e-21   3.8e-17       3      67 .]       7      66 ..       5      66 .. 0.89

  Alignments for each domain:
  == domain 1  score: 62.3 bits;  conditional E-value: 6.3e-21
                HHHHHHHHHTGGG--SSS--HHHHHHHHHHHHHHHTTSS-SEEEETTEEEE-HHHHHHHHHHHHH CS
   THDPS_N_2  3 esdIeaawerrdelepetagaearaaveevleaLdaGelRvAekkdgeWevneWvKkAiLLsFrl 67
                +s Ie+awe  +  +    +++  + +e+v+++++ G+lRvAek++ +We+n+WvK+AiL+++r+
  AHX11308.1  7 KSVIEDAWESSN-YS----DKSLLKSIEAVIQLIEMGKLRVAEKQGSSWETNQWVKQAILIYMRI 66
                789******644.33....4679*********************8889**************997 PP

>> Hexapep  Bacterial transferase hexapeptide (six repeats)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.0    0.0015         9       8      28 ..     100     122 ..      98     125 .. 0.64
   2 !   28.0   3.0     2e-10   1.2e-06       2      36 .]     131     165 ..     130     165 .. 0.96
   3 !   29.1   0.7   8.7e-11   5.2e-07       2      35 ..     175     208 ..     174     209 .. 0.96
   4 ?   -1.7   0.0      0.48   2.9e+03      10      20 ..     226     236 ..     225     237 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0015
                 EEE-T..TEEEETTEEE-TTEEE CS
     Hexapep   8 vlIgp..faviggnVkIGdnvkI 28 
                 ++I++  ++ ++  + IG +v+I
  AHX11308.1 100 AKIRAvpGSFVRKSAYIGTDVVI 122
                 56666666677777777777777 PP

  == domain 2  score: 28.0 bits;  conditional E-value: 2e-10
                 EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEES CS
     Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvigg 36 
                 + +G +++I+ +a ig+ ++IG+n++I+ gv+igg
  AHX11308.1 131 AYVGAKTMIDTWASIGSCAQIGKNCHIAGGVGIGG 165
                 789******************************97 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 8.7e-11
                 EEEETTEEE-TTEEEETTEEE-TTEEEETTEEEE CS
     Hexapep   2 tvIGsnvlIgpfaviggnVkIGdnvkIgagvvig 35 
                 ++I++n++Ig+ + i ++V IG++++++ g++ig
  AHX11308.1 175 VIIEDNCFIGARSEIVDGVLIGEGSVLAMGCYIG 208
                 79*******************************8 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.48
                 E-TTEEEETTE CS
     Hexapep  10 IgpfaviggnV 20 
                 I p++v+ ++ 
  AHX11308.1 226 IPPYSVVVPGS 236
                 77999999886 PP

>> Hexapep_2  Hexapeptide repeat of succinyl-transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.48   2.9e+03      14      20 ..     114     120 ..     112     122 .. 0.62
   2 !    8.3   0.8   0.00033         2      16      31 ..     145     162 ..     130     164 .. 0.77
   3 !   48.0   2.6   1.2e-16   7.4e-13       1      33 [.     174     208 ..     174     209 .. 0.96

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.48
                 -EESEEE CS
   Hexapep_2  14 agiGvsl 20 
                 a+iG+++
  AHX11308.1 114 AYIGTDV 120
                 6777654 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00033
                 ES..EEE-TT-EE-TT-E CS
   Hexapep_2  16 iG..vslGdncvvgaGvv 31 
                 iG   ++G+nc+++ Gv 
  AHX11308.1 145 IGscAQIGKNCHIAGGVG 162
                 555568999999999995 PP

  == domain 3  score: 48.0 bits;  conditional E-value: 1.2e-16
                 .EEE-TT-EE-TT-EE..SEEE-TT-EE-TT-EE- CS
   Hexapep_2   1 pviIGdnCliGanagi..GvslGdncvvgaGvvit 33 
                 pviI+dnC+iGa+++i  Gv +G+++v+++G++i 
  AHX11308.1 174 PVIIEDNCFIGARSEIvdGVLIGEGSVLAMGCYIG 208
                 8**************88****************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       412  (0.0229795); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2098.41
//
Query:       AHX11309.1  [L=286]
Description: hypothetical protein NHE_0357 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (286 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       543  (0.0302861); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2093.27
//
Query:       AHX11310.1  [L=317]
Description: TIM-barrel, nifR3 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.2e-107  358.8   0.4   2.5e-107  358.5   0.4    1.0  1  Dus           Dihydrouridine synthase (Dus)
    5.2e-06   26.1   0.1    9.9e-06   25.2   0.1    1.4  1  His_biosynth  Histidine biosynthesis protein
    0.00011   21.5   0.6        0.2   10.9   0.1    2.2  2  DHO_dh        Dihydroorotate dehydrogenase
    0.00024   20.6   0.1    0.00054   19.5   0.0    1.6  2  NMO           Nitronate monooxygenase
    0.00063   19.3   0.1      0.006   16.1   0.1    2.5  2  PEP_mutase    Phosphoenolpyruvate phosphomutase
     0.0018   17.3   0.1     0.0034   16.4   0.1    1.4  1  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0031   17.2   0.8        4.1    7.0   0.0    2.8  3  DeoC          DeoC/LacD family aldolase
     0.0075   16.1   0.9       0.77    9.5   0.0    2.5  2  SOR_SNZ       SOR/SNZ family
     0.0082   16.3   0.0      0.016   15.4   0.0    1.5  1  PIN_10        PIN like domain
  ------ inclusion threshold ------
       0.01   15.3   0.0      0.022   14.2   0.0    1.5  1  G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
      0.034   13.8   0.9        3.6    7.2   0.0    2.7  3  Pterin_bind   Pterin binding enzyme
      0.042   13.2   0.1       0.19   11.1   0.1    2.1  2  TMP-TENI      Thiamine monophosphate synthase


Domain annotation for each model (and alignments):
>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  358.5   0.4  1.7e-110  2.5e-107       1     301 [.       2     302 ..       2     310 .. 0.97

  Alignments for each domain:
  == domain 1  score: 358.5 bits;  conditional E-value: 1.7e-110
                 EE---TTTS-HHHHHHHHHTT-SSEEEEEEEE-SSS---HHHHHHH-GGGGGTSCEEEEEE-S-HHHHHHHHHHHHHTT-SCEEEEESSTTEEETTEEE CS
         Dus   1 llaPmagvtdlpfRelvrefgataLvvtemvtakaivreekvrirmlseeeeetplavQlggsdpallaeaAklvadlgadeIdlNvGCPskkvtrgga 99 
                 +laPm+gvtd+p+R lv+ fga+ Lvv+emv+++a++ +++ +i+++  +e+e  +a+Ql+g +p+++aeaAk+++++ga +Id+N+GCP+kkv +g a
  AHX11310.1   2 ILAPMSGVTDMPYRSLVKTFGAG-LVVSEMVASRAMILQTRDTIKKIAISENEDITAIQLAGFEPDVMAEAAKMNEEMGARIIDINFGCPVKKVVNGYA 99 
                 59*********************.*************************************************************************** PP

                 GGGGGGSHHHHHHHHHHHHCCSSS-EEEEEESESSTTTC.HHHHHHHHHHCT-SEEEEESSECCCTT-CG--CHHHHHHHHH-SS-EEEESS--SHHHH CS
         Dus 100 GaaLlrkpdlvaqivkavvkaveiPvtvkirigiddeeenalelakiveaaGaqaltvHgRtraqnyegtadweaIkevkqavsipviaNGdIkdaeda 198
                 G+ L++++ ++a+i++a+v+av+iPvt+k+r+g+d++++na +laki+e+ G++++t+HgRtraq+y+g+ dw+ I evk+av+ipviaNGdIk+ +d+
  AHX11310.1 100 GSYLMKDELHAAKILEATVNAVKIPVTLKMRTGWDENHKNATRLAKIAENLGIKMITIHGRTRAQMYKGKSDWNFIGEVKNAVKIPVIANGDIKTYDDV 198
                 *************************************************************************************************** PP

                 HHHHHHH--SEEEESCHHCCSTTHHHH.HHHHHHSC------HHHHHHHHHHHHHHCHHTTCCCCCCHHHHHHHHHHHHHHTTTTCHHHHHHHHHHHHC CS
         Dus 199 qaileetGadgvmigrgalgnPwlfae.stavktgeaepapplaeeaeiveehlkkleeelgedkglrkirkhlawylkglkkaaelrreleevsdkee 296
                 +++ +e+Gadg+migrga+g+Pw++++  + +ktge   +p+++e+++i+ +h++++++++ge++g+r +rkh+ wy+ + k++ae+r e+   s+ e+
  AHX11310.1 199 EKAFSESGADGIMIGRGAYGKPWIIRNiLHFLKTGERLAEPNIQEKVKIITRHIRAMVNHYGEETGVRIARKHVLWYSATYKNSAEFRCEICGESSSER 297
                 ****************************************************************************************98877666666 PP

                 CHHCH CS
         Dus 297 alenl 301
                  l ++
  AHX11310.1 298 MLSKI 302
                 66655 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.1   6.6e-09   9.9e-06     139     224 ..     131     217 ..     100     220 .. 0.88

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.6e-09
                   TTTTEEEEEEHHHHHHHHHHTT-SEEEEEETTTTTTSS-.--HHHHHHHHHHHSSEEEEESS--SHHHHHHHH.HTTCSEEEESHHHH CS
  His_biosynth 139 kgwreetgldavelakkleelgageilltdidrdGtlsG.pdleltkelaeavkipviasGGvgsledlkelk.segvdavivgsaly 224
                    gw+e+ + +a+ lak +e+lg++ i ++   r  + +G  d +++ e+++avkipvia G +++ +d+++++ ++g+d++++g+  y
    AHX11310.1 131 TGWDEN-HKNATRLAKIAENLGIKMITIHGRTRAQMYKGkSDWNFIGEVKNAVKIPVIANGDIKTYDDVEKAFsESGADGIMIGRGAY 217
                   578888.999********************9999999995589******************************77888******8655 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.2   0.1   0.00042      0.63     111     202 ..      64     164 ..      20     172 .. 0.67
   2 !   10.9   0.1   0.00013       0.2     232     291 ..     173     230 ..     169     233 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00042
                 HHHHHHHHHHHG..GGESEEEEES-SCTCC.....TSCCCGCHHHHHHHHHHHHHHHHSSEEEEEE-S..SSSHHHHHHHHHHHHHHTECEEEE...BS CS
      DHO_dh 111 vddyvevvrkig..pfadilelNvSsPntp.....glrdlqekeelkaillkvvkevskvpvlvKlaP..dltdeekkdiadvllelkldgiivtNttv 200
                 + d ++ ++k++    a i+ +N  +P  +      +  l ++e  +a++l++  ++ k+pv  K+    d ++++ +  a+ + +l++++i +   t 
  AHX11310.1  64 EPDVMAEAAKMNeeMGARIIDINFGCPVKKvvngyAGSYLMKDELHAAKILEATVNAVKIPVTLKMRTgwDENHKNATRLAKIAENLGIKMITIHGRTR 162
                 456666777777545689*********76522221233444455556788888888889******9872255555666677777799999999876665 PP

                 EE CS
      DHO_dh 201 qr 202
                  +
  AHX11310.1 163 AQ 164
                 55 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00013
                 HHHHHHHHHTTT.S-EEEESS--SHHHHHHHH.HHTECEEEESHHHHHHGTCHHHHHHHHH CS
      DHO_dh 232 kvirelykrlkkeipiIgvGGiesgeDaleki.eaGAslvqvytalvfegpkiakkikkel 291
                 ++i e+++ +k  ip+I+ G i++ +D+   + e GA  + ++ +  +  p+i+++i + l
  AHX11310.1 173 NFIGEVKNAVK--IPVIANGDIKTYDDVEKAFsESGADGIMIGRGA-YGKPWIIRNILHFL 230
                 67889999999..**************97654389**********9.*******9998765 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       4.1   6.1e+03     180     196 ..     109     125 ..      97     127 .. 0.67
   2 !   19.5   0.0   3.6e-07   0.00054     176     222 ..     166     213 ..     139     215 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 4.1
         NMO 180 glfaLvpqvldavdiPv 196
                    ++++  ++av+iPv
  AHX11310.1 109 HAAKILEATVNAVKIPV 125
                 45567777788888887 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 3.6e-07
         NMO 176 vgdkglfaLvpqvldavdiPviAaGGiidrrgvaaaLa.lGAsgvqig 222
                 +++k+  + + +v++av+iPviA G i +  +v+ a++  GA g+ ig
  AHX11310.1 166 YKGKSDWNFIGEVKNAVKIPVIANGDIKTYDDVEKAFSeSGADGIMIG 213
                 33488899999**********************9999747*****998 PP

>> PEP_mutase  Phosphoenolpyruvate phosphomutase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1     4e-06     0.006      58     175 ..     111     212 ..      97     233 .. 0.80
   2 ?    2.2   0.1     0.068     1e+02     163     176 ..     200     213 ..     173     286 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4e-06
  PEP_mutase  58 laavraiaevvslPlivDledGygespeevaetvrrliaaGvvgvniEDkkkndaerqlldieefaekiaaaraaaeeagfvinARtdalllsagagle 156
                  ++++a +++v++P+++ +++G+ e+ ++  +  + ++++G+ +++i  +    ++ q+++ ++  + i ++++a    ++ ++A  d  +   ++++e
  AHX11310.1 111 AKILEATVNAVKIPVTLKMRTGWDENHKNATRLAKIAENLGIKMITIHGR----TRAQMYKGKSDWNFIGEVKNAV---KIPVIANGDIKT---YDDVE 199
                 56788999***************************************999....5678888888888888886665...357777777733...45555 PP

  PEP_mutase 157 eaieRaraYaeAGAdgvfv 175
                 +      a+ e GAdg+++
  AHX11310.1 200 K------AFSESGADGIMI 212
                 4......577777777776 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.068
  PEP_mutase 163 raYaeAGAdgvfvp 176
                 +a+ e GAdg+++ 
  AHX11310.1 200 KAFSESGADGIMIG 213
                 57888888888874 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   2.3e-06    0.0034     201     237 ..     177     214 ..     160     218 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 2.3e-06
                 HHHCTCT-EEEEES---SHHHHHHHHH.TT-SEEEESC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx RF
       IMPDH 201 eaakkagvpviaDGGikysgdivkAla.aGadavmlGs 237
                 e+ +  ++pvia G ik+  d+ kA++  Gad +m+G+
  AHX11310.1 177 EVKNAVKIPVIANGDIKTYDDVEKAFSeSGADGIMIGR 214
                 4567789*******************856********7 PP

>> DeoC  DeoC/LacD family aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.9   0.2    0.0057       8.6     148     205 ..      63     133 ..      44     148 .. 0.80
   2 !    6.2   0.0    0.0047       7.1      81     147 ..     105     170 ..      95     186 .. 0.79
   3 !    7.0   0.0    0.0027       4.1     178     233 ..     166     217 ..     161     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.0057
                 CHHHHHHHHHHHHTCCT-SEEEE--S............SCC.B.HHHHHHHHHHHHHCHSSTE.EEEETTS CS
        DeoC 148 vdpdlvaeAarvsaelGaDiiKvevp............kevvnateedaevfkdvikaapvpg.vvlsGGv 205
                  +pd+ aeAa++  e+Ga ii  +++             + ++ +  +a++ +  ++a+++p+ ++++ G 
  AHX11310.1  63 FEPDVMAEAAKMNEEMGARIIDINFGcpvkkvvngyagSYLMKDELHAAKILEATVNAVKIPVtLKMRTGW 133
                 6899**********************999888888888777788888888888888888888668888887 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0047
                 ETTCHHHHHHHTT-SEEEEEEEEHTTTTCHHHHHHHHHHHHHHHHHHHTEEEEEE.EEE-CTTBSSTT CS
        DeoC  81 devasveeakalGAdavkvvvyyradgseeeqqklaeikrvkeacheeglplile.lylrdeaikdek 147
                  +++ +++++++  +avk+ v +  ++   + +++++  r ++ ++++g+++i   + +r +  k+++
  AHX11310.1 105 KDELHAAKILEATVNAVKIPVTL--KMRTGWDENHKNATRLAKIAENLGIKMITIhGRTRAQMYKGKS 170
                 45667777777777888888888..88899*********************99777888887777666 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0027
                 B.HHHHHHHHHHHHHCHSSTEEEEETTSSHHHHHHHHHHHHHHHTHCEEEESHHHH CS
        DeoC 178 nateedaevfkdvikaapvpgvvlsGGvseedfletvedAvkeagasGvlsGRaif 233
                 ++++ d +++ +v +a+++p v+  G +   +  + ve+A +e+ga G+++GR ++
  AHX11310.1 166 YKGKSDWNFIGEVKNAVKIP-VIANGDI---KTYDDVEKAFSESGADGIMIGRGAY 217
                 66778888899999999999.5444444...67799*****************887 PP

>> SOR_SNZ  SOR/SNZ family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.1   0.5    0.0058       8.7      59      96 ..     111     155 ..      48     156 .. 0.63
   2 !    9.5   0.0   0.00051      0.77      26      79 ..     144     192 ..     137     199 .. 0.80

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0058
                 HHHHHHHHHH-SS-EEEEEETT....-...HHHHHHHHHTT-SEE CS
     SOR_SNZ  59 pklikeikeavsipvmakvriG....h...fveaqilealgvdyi 96 
                  k+++  ++av+ipv  k+r G    h   +  a+i e+lg+ +i
  AHX11310.1 111 AKILEATVNAVKIPVTLKMRTGwdenHknaTRLAKIAENLGIKMI 155
                 567788899************943333211233677777777776 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.00051
                 HHHHHHHT-SEEEE-SS-HHHHHHH-S------HHHHHHHHHH-SS-EEEEEET CS
     SOR_SNZ  26 akiaeeaGavavmalervpadirkeggvarmsdpklikeikeavsipvmakvri 79 
                 akiae+ G   +    r  a++ k       sd ++i e+k+av+ipv+a   i
  AHX11310.1 144 AKIAENLGIKMITIHGRTRAQMYK-----GKSDWNFIGEVKNAVKIPVIANGDI 192
                 888888888888777777777665.....369*****************98655 PP

>> PIN_10  PIN like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.016       3      82 ..     131     212 ..     129     214 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
      PIN_10   3 fflDenlppalakaLrelleeeghevvhlrdkf....aagtkDeeWiaalaeggwvvltkDrrirkrpaEraalreaglrvfil 82 
                    Den+    a  L +++e+ g+++++++ ++     +g +D + i  +++   + + +  +i++ ++  +a+ e+g+ ++++
  AHX11310.1 131 TGWDENHKN--ATRLAKIAENLGIKMITIHGRTraqmYKGKSDWNFIGEVKNAVKIPVIANGDIKTYDDVEKAFSESGADGIMI 212
                 556999999..99********************999999************99999999999****************999877 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.5e-05     0.022     129     167 ..     173     212 ..     167     216 .. 0.88

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.5e-05
                   HHHCTSTTS...EEEEESS--SHHHHHHHC.TT.SSEEEE CS
  G3P_antiterm 129 kvikeikkelkipiiaGGLietkedveeal.kaGaiavst 167
                   ++i e+k+++kip+ia G i+t +dve+a+ ++Ga++++ 
    AHX11310.1 173 NFIGEVKNAVKIPVIANGDIKTYDDVEKAFsESGADGIMI 212
                   57999**********************9983579999876 PP

>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0024       3.6     110     165 ..      15      66 ..       6      69 .. 0.84
   2 ?    5.6   0.1    0.0072        11      21      42 ..      66      87 ..      63      96 .. 0.81
   3 ?   -2.7   0.0       2.5   3.8e+03     107     131 ..     141     165 ..     134     183 .. 0.62

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0024
                  HHHHHHHT-EEEEESECSSTTTHCCCC.CCCSSHHHHHHHHHHHHHHHHHHTT--GG CS
  Pterin_bind 110 lelvaeagaavvvmhmrgtpktmqeee.gqyedvveeveaflearveaaeeaGvape 165
                   +lv+ +ga +vv  m       ++   +q++d+++++++  ++ + a++ aG++p+
   AHX11310.1  15 RSLVKTFGAGLVVSEMV-----ASRAMiLQTRDTIKKIAISENEDITAIQLAGFEPD 66 
                  579**************.....33444479************************984 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0072
                 HHHHHHHHHHHHTT-SEEEEES CS
  Pterin_bind 21 dkalaqarkmveeGAdilDigg 42
                 d + ++a+   e GA+i+Di+ 
   AHX11310.1 66 DVMAEAAKMNEEMGARIIDINF 87
                 5566777888899*******96 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 2.5
                  TTHHHHHHHHT-EEEEESECSSTTT CS
  Pterin_bind 107 pkmlelvaeagaavvvmhmrgtpkt 131
                   ++++++ + g +++  h r++++ 
   AHX11310.1 141 TRLAKIAENLGIKMITIHGRTRAQM 165
                  5667777777888888887744443 PP

>> TMP-TENI  Thiamine monophosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.62   9.2e+02     136     161 ..     137     162 ..     104     169 .. 0.59
   2 ?   11.1   0.1   0.00013      0.19     137     177 ..     170     212 ..     144     216 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.62
    TMP-TENI 136 plgleglkelaealeiPvvaiGGitl 161
                   + ++l+++ae+l i ++ i G t 
  AHX11310.1 137 HKNATRLAKIAENLGIKMITIHGRTR 162
                 34445555555555555555555555 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00013
    TMP-TENI 137 lgleglkelaealeiPvvaiGGitl.envaevl.eagadgvav 177
                  +++++ e+++a++iPv+a G+i++ ++v++++ e+gadg+ +
  AHX11310.1 170 SDWNFIGEVKNAVKIPVIANGDIKTyDDVEKAFsESGADGIMI 212
                 57999******************873567666569****9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      642  (0.0358079); expected 358.6 (0.02)
Passed Vit filter:                        71  (0.00396006); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.25s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 2317.05
//
Query:       AHX11311.1  [L=232]
Description: survival SurE family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-35  121.8   0.1    7.8e-35  120.4   0.0    1.6  2  SurE      Survival protein SurE
  ------ inclusion threshold ------
      0.041   12.3   0.0      0.052   12.0   0.0    1.1  1  FMO-like  Flavin-binding monooxygenase-like


Domain annotation for each model (and alignments):
>> SurE  Survival protein SurE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.4   0.0   8.7e-39   7.8e-35      27     190 ..       5     159 ..       2     166 .. 0.84
   2 ?   -1.7   0.0      0.23     2e+03     122     134 ..     169     181 ..     164     200 .. 0.62

  Alignments for each domain:
  == domain 1  score: 120.4 bits;  conditional E-value: 8.7e-39
                 EEEEEEESSS-TTCTTS--SSSEEEEEEEECSTTTCEEEESS-HHHHHHHHHHTTTTTS......SSEEEEEEEES---GGGGGG-HHHHHHHHHHHTT CS
        SurE  27 evvvvaPdserSgigkaltleeplrveseeeeeeeeeyavsGtPadcvklaleellkek.....kpdlVvSGiNhGaNlgtdvlySGTvgAaleaaleg 120
                 ++vvvaP++++ ++g+al++++ l++e+     e++ +av+GtP+dcv +a+      +     +p++V SG+N GaNlg d++ySGTv+Aa+++++ g
  AHX11311.1   5 DIVVVAPKTDKTASGHALSIHKRLKIEEI----ENNTFAVDGTPVDCVITAFYD---PRctgngTPEVVFSGVNIGANLGIDTMYSGTVAAAMQGMFFG 96 
                 89**********************98744....4799***************54...334456799********************************* PP

                 SEEEEEEEESSSSS-SSS---HHHHHHHHHHHHTTETTS-...SS-EEEEEEESS.GCG-SEEEE-B--C CS
        SurE 121 ipaiAvSlaskkeeekkeedtfeaaakvaaklveklieklllekvellnvNvPeleeeeikgvkvtrlgr 190
                 +p+ A+S+ +++         ++  ++++++ +  ++e+  + k+++ln+N+P+   ++i g+k  ++ +
  AHX11311.1  97 VPSFALSQFYESGV----GIRWNVHSSHLKDYILGVLENRQTFKNCVLNINLPS---KRIIGIKHVKQYN 159
                 ********986422....3457777788888888888888899**********5...6666666666655 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 0.23
                 EEEEEEEESSSSS CS
        SurE 122 paiAvSlaskkee 134
                  aiA+S++s ++e
  AHX11311.1 169 SAIAISTHSIDNE 181
                 6788887765322 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   5.9e-06     0.052     267     343 ..     123     204 ..     102     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 5.9e-06
    FMO-like 267 nyglk.pkkralakepvlndelparilaGavkvks...svkeltetsaifedgtv.eedidvvifatGytfafpfleeslvk 343
                 +y l   ++r++ k+ vln +lp++ ++G+ +vk+   + k+ t++sai   +   +++  + i +tG   +  fl    v 
  AHX11311.1 123 DYILGvLENRQTFKNCVLNINLPSKRIIGIKHVKQyntEEKKATDASAIAISTHSiDNEEYITIETTGSPQSCQFLSSGYVT 204
                 5655415789999*****************9999621145668899999776655055555678899999999998876665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1686.55
//
Query:       AHX11312.1  [L=52]
Description: hypothetical protein NHE_0360 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       225  (0.0125495); expected 358.6 (0.02)
Passed bias filter:                      164  (0.00914719); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 398.42
//
Query:       AHX11313.1  [L=597]
Description: succinate dehydrogenase, flavoprotein subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     3e-123  412.0   2.4   3.9e-123  411.6   2.4    1.1  1  FAD_binding_2   FAD binding domain
    2.1e-44  150.6   0.1    3.2e-44  150.0   0.1    1.3  1  Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
    1.3e-05   24.5   1.0    0.00047   19.5   0.2    2.6  2  Thi4            Thi4 family
    8.6e-05   21.9   1.1    0.00034   20.0   0.4    2.3  2  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
     0.0034   16.5   2.7       0.08   12.0   1.6    2.4  2  GIDA            Glucose inhibited division protein A
  ------ inclusion threshold ------
      0.019   14.2   0.8      0.042   13.1   0.8    1.6  1  FAD_binding_3   FAD binding domain
      0.044   13.1   6.2       0.71    9.2   1.3    2.5  3  FAD_oxidored    FAD dependent oxidoreductase
      0.054   12.2   1.0       0.18   10.4   0.6    2.0  2  HI0933_like     HI0933-like protein
      0.055   13.0   0.4       0.25   10.9   0.2    2.0  2  DAO             FAD dependent oxidoreductase
       0.18   11.1   0.6        5.4    6.2   0.1    2.4  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
       0.34   11.4   2.8        9.7    6.7   0.0    3.1  2  NAD_binding_7   Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  411.6   2.4  2.4e-126  3.9e-123       1     417 []      14     408 ..      14     408 .. 0.98

  Alignments for each domain:
  == domain 1  score: 411.6 bits;  conditional E-value: 2.4e-126
                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S-EE-TT..SSGGSTC.CHHHHHHHHHHHHTTT-S-HHHHHHHHHTHHHHHHHH CS
  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqGgidavlspeqkkagikdspelhrtdtlkaldeladqplveafveaapeavdeL 96 
                    Dv+V+G+G++GL+A+l +a +Glkva+++k+++++++t+++qGgi a+l + +     +d++++h++dt+k++d+l+dq+++e+++++a+ea+ eL
     AHX11313.1  14 DVVVVGAGGSGLRATLGIASQGLKVACISKVFPTRSHTVAAQGGISAALGNVS-----EDDWRWHAYDTVKGSDWLGDQDAIEYMCKNAAEAIIEL 104
                    9************************************************4444.....699*********************************** PP

                    HHTT----BCCTSSB-EEE-TT-SST......EEEE-.STT-......HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTC CS
  FAD_binding_2  97 eelgvpfsrtedgpvdvrelGglsat......artlhdaadarretlvtghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgr 186
                    e++gvpfsrt++g++++r++Gg++ +       rt++ a d+      tgha+l++l+++  k++++f+ ++ +++L+++++ + G++++++++g+
     AHX11313.1 105 ENFGVPFSRTAEGKIYQRPFGGMTTHygngsaIRTCA-AEDK------TGHAILHTLYQQSIKHKTTFFVEYIVLDLLMDGQVCKGVIAWDLKDGS 193
                    **************************99999999999.9999......************************************************ PP

                    EEEEEESEEEE-----GG..........GSSSBSSGTT-S-HHHHHHHCTTSSEES..TT-EEEEEEEET....TTTBB--THHHHTT-EEE-TTS CS
  FAD_binding_2 187 evrirakavvlatgGfgrallkellgaaaeaettnapavtGdglalalragaalnddrmeevqfhPtslvpirdgsgiLitealrgeGgilvdkdG 282
                     +r+ra+ vv+atgG+gr          +++++t+a+++tGdg+a +lrag++l+d  me+vqfhPt+++    g+g+Li+ea+rgeGg+lv+++G
     AHX11313.1 194 LHRFRAHIVVIATGGYGR----------VYFSATGAHTCTGDGNAFVLRAGLPLQD--MEFVQFHPTGIY----GAGCLISEAVRGEGGYLVNSEG 273
                    ******************..........****************************..************....********************** PP

                    SBTH.......GGGS-HHHHHHHHH.HHHHTTTS....CCBEEEE-TT.SSHHHHHHHSHHHHHHHHHCCT......S-TTTSEEE.......EEE CS
  FAD_binding_2 283 rrFm.......nelasrdvvsrailekeiaeggs....eanvyldashgldaegleatleaineeaangldkdfgrgidpadrpipgpfyavkvvp 367
                    +rFm       ++lasrdvvsr+i+  ei+ g++    +++++l +sh ld++ +e++l++i e+a+ ++       +d +++pip       v p
     AHX11313.1 274 ERFMpryaptaKDLASRDVVSRSIT-MEIRAGRGvgpkKDHIFLQVSH-LDRDIIEKRLPGISETARIFAN------VDVTKEPIP-------VQP 354
                    *************************.999999999*************.**********************......*********.......*** PP

                    EEEEES-EEEBETTSBE....STTEEESSBTEEE-STCEESSSSTTS--TTHHH CS
  FAD_binding_2 368 aqhytmgGvetdengrv....ldadgqpipGLYAaGevaaggvhganrlgGnsl 417
                    ++hy+mgG++t+ +++v     d++++++pGL A+Ge+a+ +vhganrlg+nsl
     AHX11313.1 355 TVHYNMGGIPTNRHAEVltvdGDDKEKVVPGLMAIGEAACISVHGANRLGSNSL 408
                    *****************9988788899*************************98 PP

>> Succ_DH_flav_C  Fumarate reductase flavoprotein C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.0   0.1     2e-47   3.2e-44       1     128 []     463     597 .]     463     597 .] 0.99

  Alignments for each domain:
  == domain 1  score: 150.0 bits;  conditional E-value: 2e-47
                     .HHHHHHHHHHSSSSB-HHHHHHHHHHHHHHHHHHTTB--S---SSS-HHHHHHHHHHHHHHHHHHHHHHHHH--S-BTTBEBTTS-SEETTT-S CS
  Succ_DH_flav_C   1 rkeLgkimqkkvgvfRteegLkealkelkelrerlknvkvtdkskvaNqelvealelanllelAeaiaksAlaRkESrGaHaredfperdDenwl 95 
                     rk++++imq++++vfR ++ L+e++++++e+ ++lk+vkvtd+s ++N++lve+lel+n++  A a+++sA +RkESrG+Hared+per+D++wl
      AHX11313.1 463 RKKMQSIMQEHASVFRVQSVLDEGCRKMREVLKELKEVKVTDRSLIWNTDLVETLELDNMVGQAIATIESASNRKESRGSHAREDYPERNDNDWL 557
                     79********************************************************************************************* PP

                     EEEEE...TT-SS-EEEEEE--GGG-.......-S---SS CS
  Succ_DH_flav_C  96 khtlasldaakeeveleyepveletl.......kpkeRsY 128
                     khtl++l++ +++++++y+pv+l+++       +pk+R+Y
      AHX11313.1 558 KHTLFWLNPGSGKTKFDYRPVHLQPMtneiesfPPKKRVY 597
                     **************************************99 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.2   2.9e-07   0.00047      17      49 ..      12      43 ..       6      59 .. 0.90
   2 ?    2.6   0.0      0.04        65     200     233 ..     369     405 ..     355     406 .. 0.76

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 2.9e-07
                EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
        Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailer 49
                e Dvv+vGaG sGL a+  +a + +lkva + +
  AHX11313.1 12 EYDVVVVGAGGSGLRATLGIASQ-GLKVACISK 43
                78*********************.*****9865 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.04
                 HHHHHH..HHECEEETTEEE-THHH.HHHHT-EB--S CS
        Thi4 200 aedaiv..kktrevvpnlyvaGmev.aevdganRmGp 233
                 ae   v   + ++vvp+l++ G ++   v+ganR+G+
  AHX11313.1 369 AEVLTVdgDDKEKVVPGLMAIGEAAcISVHGANRLGS 405
                 5555554445679*****99997651689******96 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.4   2.1e-07   0.00034       1      58 [.      13     149 ..      13     255 .. 0.65
   2 ?   -3.3   0.0       2.5   4.1e+03     249     278 ..     362     393 ..     353     403 .. 0.60

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 2.1e-07
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH..................................... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx..................................... RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias..................................... 57 
                  +dvvv+G+G  Gl+a l +a +g+kv++++     + +++  +  +s al +v+ed    +                                     
   AHX11313.1  13 YDVVVVGAGGSGLRATLGIASQGLKVACISkvfpTRSHTVAAQGGISAALGNVSEDDWRWHaydtvkgsdwlgdqdaieymcknaaeaiielenfgvp 110
                  69***************************888888888888888888888888877654446666666666666666666666666666666666666 PP

                  ......................................H CS
                  ......................................x RF
  Pyr_redox_2  58 ......................................e 58 
                                                         
   AHX11313.1 111 fsrtaegkiyqrpfggmtthygngsairtcaaedktghA 149
                  666666666666666555555555555555555555550 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.5
                  T-EEEETTEE.E--TTSBES.STTEEE-GGGC CS
                  xxxxxxxxxx.xxxxxxxxx.xxxxxxxxxxx RF
  Pyr_redox_2 249 glelderggi.vvdeflrtn.vpgiyaiGDva 278
                  g++++++  +  vd   + + vpg+ aiG  a
   AHX11313.1 362 GIPTNRHAEVlTVDGDDKEKvVPGLMAIGEAA 393
                  55555555443455444444477777777766 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.6   4.9e-05      0.08       1      29 [.      14      42 ..      14      68 .. 0.82
   2 ?    3.0   0.0     0.027        43     113     155 ..     166     213 ..     129     229 .. 0.67

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.9e-05
                CEEEE-SSHHHHHHHHHHHHTT--EEEEE CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLit 29
                dv+V+G+G +G+ A l +a  G+kv+ i 
  AHX11313.1 14 DVVVVGAGGSGLRATLGIASQGLKVACIS 42
                79***********************9883 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.027
                 EEES-EEEEEECTTEEEEEE...ETTS-..EEEECEEEE--TT-BT-E CS
        GIDA 113 iieeeveeliveekkvkgvv...tedge..tikakavviatGtflkgk 155
                  +e  v +l+++ + +kgv+   ++dg+   ++a++vviatG + +  
  AHX11313.1 166 FVEYIVLDLLMDGQVCKGVIawdLKDGSlhRFRAHIVVIATGGYGRVY 213
                 55666777777778888877333355542268888********87765 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.8   2.6e-05     0.042       1      36 [.      12      47 ..      12      59 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.6e-05
                   EEEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSS CS
  FAD_binding_3  1 etdVlIVGaGpaGlmlallLseaGvrvvlvekrstt 36
                   e+dV++VGaG +Gl ++l  +++G +v ++ k   t
     AHX11313.1 12 EYDVVVVGAGGSGLRATLGIASQGLKVACISKVFPT 47
                   589***************************997555 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.3   0.00043      0.71       1      29 [.      14      42 ..      14      47 .. 0.94
   2 ?    6.2   0.0    0.0034       5.5      83     151 ..     141     215 ..      92     250 .. 0.76
   3 ?   -3.9   0.2       3.9   6.4e+03     396     409 ..     382     395 ..     381     400 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00043
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLve 29
                  DvvVvG+g +G+ A +  a +G kv+ ++
    AHX11313.1 14 DVVVVGAGGSGLRATLGIASQGLKVACIS 42
                  9************************8775 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0034
  FAD_oxidored  83 tfepevakavleeml...aeagvtvllntrlvevekegkriesvtveske.g.rktirAkvfiDATg.dGdlaal 151
                   + e ++  a+l+ +     +++ t + +  + +  ++g+ +++v++++ + g  +++rA++++ ATg  G +   
    AHX11313.1 141 AAEDKTGHAILHTLYqqsIKHKTTFFVEYIVLDLLMDGQVCKGVIAWDLKdGsLHRFRAHIVVIATGgYGRVYFS 215
                   445555555555555433335999999**********988**********999**********999724666554 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 3.9
  FAD_oxidored 396 vepvcmalGqAaGv 409
                   v p  ma+G+Aa +
    AHX11313.1 382 VVPGLMAIGEAACI 395
                   67899******976 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.6   0.00011      0.18       1      31 [.      13      43 ..      13      57 .. 0.92
   2 ?   -1.2   0.0       0.4   6.5e+02     150     166 ..     194     210 ..     144     225 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00011
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                 +dv+v+G+G +Gl a++ +a++g +V+ + k
   AHX11313.1 13 YDVVVVGAGGSGLRATLGIASQGLKVACISK 43
                 59************************98866 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.4
                  TEEEEESEEEE----SS CS
  HI0933_like 150 eeeleadklvlAtGGlS 166
                   ++++a+ +v+AtGG  
   AHX11313.1 194 LHRFRAHIVVIATGGYG 210
                  46789999******975 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   0.00015      0.25       1      52 [.      14      66 ..      14     123 .. 0.78
   2 ?   -0.4   0.0      0.42   6.8e+02     181     205 ..     183     211 ..     146     248 .. 0.66

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00015
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSEEEEESSSSTHH CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrnsgllhsglrylp 52
                dvv++G+G  Gl + +  a +g  V+ + k  ++ +  + +++g ++++l +  
  AHX11313.1 14 DVVVVGAGGSGLRATLGIASQGlkVACISKV-FPTRSHTVAAQGGISAALGNVS 66
                9******************99*********9.8887888888888888773333 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.42
                 EEE..EECTEEEEEEEE..EEE--GGGHH CS
         DAO 181 gve..rttpgendaada..vVnaaGawsd 205
                 gv   + ++g+ ++++a  vV+a+G + +
  AHX11313.1 183 GVIawDLKDGSLHRFRAhiVVIATGGYGR 211
                 4444433446554345556999*999965 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1    0.0033       5.4     165     198 ..      13      46 ..       6      64 .. 0.84
   2 ?    2.6   0.0     0.042        68     122     139 ..     196     213 ..     191     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0033
  Pyr_redox_3 165 qkvvViGgknSavDaAlelvrkgaeVtvvtrgse 198
                   +vvV+G++ S+  a l ++++g +V  + +  +
   AHX11313.1  13 YDVVVVGAGGSGLRATLGIASQGLKVACISKVFP 46 
                  589**********************999887655 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.042
  Pyr_redox_3 122 tyeAkkviiAtGefdkPn 139
                   ++A+ v+iAtG +++ +
   AHX11313.1 196 RFRAHIVVIATGGYGRVY 213
                  689***********9765 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0     0.006       9.7       9      40 ..      14      45 ..      11     105 .. 0.73
   2 ?    3.0   0.7     0.086   1.4e+02      15      46 ..     414     448 ..     409     545 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.006
  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapev 40
                    v+vvG+G  ++r    ++++g kv  +++ +
     AHX11313.1 14 DVVVVGAGGSGLRATLGIASQGLKVACISKVF 45
                   69***************************985 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.086
  NAD_binding_7  15 gGevAarkvrklleagakvtvvapevkeele...e 46 
                     G+ Aa +++ ++++g k   +++e+++ +    +
     AHX11313.1 414 FGRAAAMRAKEVIKQGEKHSTISEEITDRILarfD 448
                    68999999999999999999999996322223332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (597 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      474  (0.0264376); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4181.30
//
Query:       AHX11314.1  [L=247]
Description: DNA polymerase III, delta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-23   81.2   5.3    1.3e-19   70.6   4.1    2.3  2  DNA_pol3_delta2  DNA polymerase III, delta subunit
  ------ inclusion threshold ------
      0.024   15.0   0.4      0.041   14.3   0.4    1.4  1  AAA              ATPase family associated with various cellul


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0     7e-05      0.62      17      47 ..      14      44 ..       3      50 .. 0.86
   2 !   70.6   4.1   1.4e-23   1.3e-19      79     160 ..      56     135 ..      43     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 7e-05
  DNA_pol3_delta2 17 rlahayLfeGdegigkkelalnlakallcee 47
                     + +ha+Lf+G +  + +e+a+n+ak +l +e
       AHX11314.1 14 KKSHAWLFTGIHVDNIFEIANNYAKWILKSE 44
                     568**********************998765 PP

  == domain 2  score: 70.6 bits;  conditional E-value: 1.4e-23
  DNA_pol3_delta2  79 kersikldqirelieelsrkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfs 160
                      k   +k+++ r+++e+l  ++   ++k+iii++ e mt sAaNa+Lk+lEE ++ a++i+it++ ++++ tirSRc +l+f 
       AHX11314.1  56 K--ILKIEHARKITEFLRLTTSSCTQKVIIISHFESMTLSAANAMLKILEETNQLATIIIITKHAHQVISTIRSRCFNLHFP 135
                      3..689**************************************************************************97 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   4.6e-06     0.041      41     124 ..      61     129 ..      33     135 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 4.6e-06
                 HHHHHHHHHHHHHHHTS.TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTS CS
         AAA  41 esekkirelfkeakeka.kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRf 124
                 e ++ki e+++   + + ++++++i  +++++ s            +n++l+ l++ ++     ++i++t++ +++ + ++ +R+
  AHX11314.1  61 EHARKITEFLRLTTS-ScTQKVIIISHFESMTLSA-----------ANAMLKILEETNQL---ATIIIITKHAHQVISTIR-SRC 129
                 678899999977554.4477************999...........***********995...689***************.887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       789  (0.0440069); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.21s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1944.48
//
Query:       AHX11315.1  [L=336]
Description: zinc-binding dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-10   40.4   0.0    4.5e-10   39.6   0.0    1.4  1  ADH_zinc_N    Zinc-binding dehydrogenase
    1.8e-09   38.8   0.0    3.4e-09   37.8   0.0    1.4  1  ADH_zinc_N_2  Zinc-binding dehydrogenase
    7.6e-06   25.8   0.0    1.5e-05   24.8   0.0    1.5  1  ADH_N         Alcohol dehydrogenase GroES-like domain


Domain annotation for each model (and alignments):
>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.6   0.0   7.5e-14   4.5e-10       2     116 ..     160     283 ..     160     295 .. 0.82

  Alignments for each domain:
  == domain 1  score: 39.6 bits;  conditional E-value: 7.5e-14
                 HHHHHHHHHH..HTT-EEEEEESSHHHHHHHHHTTESEEEETTTC.H.HHHHHHHHTTTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSCTSSEEE CS
  ADH_zinc_N   2 vGlaavqlAk..alGaeviavdsseeklelakklGadevinykea.d.lverikeltggegvdvvfecvGsgatleaalkllkpgGrlvvvGggkgeee 96 
                 vG +++q+ k  a  +++++++ss++k+e  k + +d ++ny+++ + l e+++++t+g gv +v++c+G ++t+  +l++l   G  v++   +ge +
  AHX11315.1 160 VGDMLCQWIKarAPECKIVGTVSSRRKIESIKNIRCDMLLNYSDDlEvLREKVQKFTRGYGVSAVYDCIG-KDTYLFSLNSLCTFGIYVLYEQRSGEIP 257
                 6788888865337788**************************6644359*********************.*************999999987444444 PP

                 ......EEHHHHHHTT-EEEEE-SSC CS
  ADH_zinc_N  97 ......fdlrnlllkeksilGsllgs 116
                       f++r l++++ s+    + +
  AHX11315.1 258 pmswkaFRARSLFFTHPSLFHYSRNH 283
                 56777777777888777776666655 PP

>> ADH_zinc_N_2  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   5.8e-13   3.4e-09       6     133 .]     207     334 ..     201     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 5.8e-13
                   EEETTSTTHHHHH-TT-EEEEEES-HHHHH.HHHHHHEEEEEEEEE----..S-EEE-CHHHCTTT-EEEE--GGG...-.-HHHH..HHHHHHHHH CS
  ADH_zinc_N_2   6 vidyrtedfeaatggegvDvvldtvggealleaslkvlpggGrlvsiggpp.lsaallkpakkrkgrsvkyeflfsmkasaqadil..eelaaliee 99 
                   v+  + + f   t+g gv++v+d++g++++   sl+ l   G +v + +++     ++++a+++++  ++   lf  ++++ + +l  +e++++++ 
    AHX11315.1 207 VLREKVQKF---TRGYGVSAVYDCIGKDTY-LFSLNSLCTFGIYVLYEQRSgEIPPMSWKAFRARSLFFTHPSLFHYSRNHMESVLavAEVFHYMKT 299
                   666777778...6789************99.5666666466***999965543333344444455555555556655555555555669******** PP

                   HH----EEEEEE.GGGHHHHHHHHHSS--SSEEEE CS
  ADH_zinc_N_2 100 Gklrpvvdrvfp.leeaaeAhrylesgrarGKiVl 133
                   Gk+ p +  +++ le++  Ah+ +e+g + G  V+
    AHX11315.1 300 GKIVPNIANRYKgLEQIHVAHKEIEAGNVSGATVV 334
                   ********99644****************998876 PP

>> ADH_N  Alcohol dehydrogenase GroES-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   2.5e-09   1.5e-05       2      62 ..      29      95 ..      28     106 .. 0.91

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 2.5e-09
                TEEEEEEEEEEE-HHHHHHHTTS.....TTTTSSSSEE---EEEEEEEEESTT-CS.--TT-EEEE- CS
       ADH_N  2 gevlikvkaagiCgsDlhilkgg.....kelevklplilGHEivGeveevgpevkk.lkvGdrVvve 62
                +e+l+k ++ g++  D++  +g      + ++ +lp i+G  +vG+v+++g++ +  +k GdrV+  
  AHX11315.1 29 NEALVKHTVIGVNYIDIEQRSGFynlreNASRLRLPAIVGCQAVGVVKALGEGASAdVKPGDRVCYT 95
                799**************9999878888899999*******************99877*******974 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (336 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2833.62
//
Query:       AHX11316.1  [L=92]
Description: hypothetical protein NHE_0364 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-25   88.6   0.1    2.6e-25   88.5   0.1    1.0  1  ETC_C1_NDUFA4  ETC complex I subunit conserved region


Domain annotation for each model (and alignments):
>> ETC_C1_NDUFA4  ETC complex I subunit conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.5   0.1   1.4e-29   2.6e-25       2      91 ..       4      92 .]       3      92 .] 0.97

  Alignments for each domain:
  == domain 1  score: 88.5 bits;  conditional E-value: 1.4e-29
                   EEEE--SS--STTTT-SS--EEEEEEEESSS---TTT-SSSS--SEEECEEEESSHHHHHHHHHHCT-EEEEE-SST-XXXXXXXXXXXX CS
  ETC_C1_NDUFA4  2 vrIykpaknamqsGkaktkkWklefeeqekrwenplmGWtssaDtlsqvslkFdskedAiayaekqgweyeveepkkrkvkpksYadnfs 91
                   ++Iy p+ + +qsG+ k +kW+l+f +++ ++++ lmGW +s +t sqvsl+F++ e+A +ya+++g+ y+v  p++++++ ksYadnf+
     AHX11316.1  4 AVIYMPSASVVQSGRGK-RKWVLKFVSRRGKYQEALMGWVGSFETNSQVSLEFSTLESAESYAKRNGIPYNVIYPQESHMRFKSYADNFK 92
                   89************986.78*********************************************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       359  (0.0200234); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.25s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 717.78
//
Query:       AHX11317.1  [L=376]
Description: ubiquinone biosynthesis hydroxylase, UbiH/UbiF/VisC/COQ6 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-26   92.9   0.0    2.7e-26   92.6   0.0    1.1  1  FAD_binding_3  FAD binding domain
    0.00084   19.5   0.1      0.002   18.3   0.1    1.6  1  NAD_binding_8  NAD(P)-binding Rossmann-like domain
  ------ inclusion threshold ------
      0.027   13.5   0.0      0.041   12.9   0.0    1.3  1  SE             Squalene epoxidase
      0.038   12.7   0.0        5.8    5.5   0.0    2.1  2  HI0933_like    HI0933-like protein
      0.047   12.9   0.0       0.48    9.6   0.0    1.9  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
       0.07   12.4   0.0        5.7    6.1   0.0    2.1  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase


Domain annotation for each model (and alignments):
>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.6   0.0   9.1e-30   2.7e-26       2     348 ..       3     331 ..       2     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 92.6 bits;  conditional E-value: 9.1e-30
                    EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSSSSCCSSS--EEEHHHHHHHHHTT-HHHHHHHSEECCCCEEEEEEECCCCCEEEEEHH...CHH CS
  FAD_binding_3   2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrsttvvlpradglnqrtmellrqlGledrilaegapnelmgealynelsdtpkaradle...les 94 
                    +d +I GaG++G+++a+lL++ G +  + +k +   v+ r + ++ ++ + +++lGl+d i+  ++p   + ++ +++      + ++ e   ++ 
     AHX11317.1   3 CDFIISGAGLSGVLAAQLLKKLGFSYYIFDKSNGSRVDYRTSAISYESARFFETLGLWDAIAPSAVPILDIYTFQEKS-----ASFLHFEsgdADI 93 
                    677899***********************************************************9999888888888.....4444444333556 PP

                    CST-CEE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT-HHHHHHTGGEEEEEEEEEEEEEEE CS
  FAD_binding_3  95 spervtvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgrStvrktlgiefegeetvyeagvldv 190
                      ++ +v+p   l+ +L+   e  ++q ++k ++       + v+ +++d    +   v+ +Y+  a+G +S ++  lg+++++ +  y+   +  
     AHX11317.1  94 DSPMSYVVPNLVLQDVLYRGIEINYAQAYEKIDYS-----HDRVRVNFQDD---T--IVEGRYMLVAEGRNSNTAGLLGFKMISAG--YRQACVVC 177
                    67777788888888888888777777777777776.....77777777766...3..599*********************99999..55666666 PP

                    EEEC-SCCCTTC..CEEEEECCTTEEEEEECCETEEEEEEEEECCE-GGGSCCCHHHHHHHHHHHHHHTTSSCEEEEEEEEEEEEEEEEESSSEET CS
  FAD_binding_3 191 lfdadlsdivep..lvlilsaesrgvmviPlentlerfyvqvearaekeersekfteeevkarlreivgektldveieevsawtvaqrvaekyrkg 284
                    + ++  +   e+  + + l  e + ++++Pl++ +++f ++++++ + +e+ ++++e++   ++++i+g+++ +v   ++s +++    + + rkg
     AHX11317.1 178 NLRSTGR---EHynIAVELFLEGGPFALLPLSK-KTDFSLIWTVKFPFAETLKNMDEQQFLGEVQKISGIEFKKVLTPRIS-YPLLLSFCISPRKG 268
                    6666444...4444344444555557*******.88999999999999**********************99888766666.66666666777*** PP

                    TEEE-GGGTEEE-STTSHHHHHHHHHHHHHHHHHHHHHTTSS-GGGGHHHHHHHHHHHHHHHHH CS
  FAD_binding_3 285 rvflaGDAaHihpPtgGqGlNtaiqDavnLawkLaavlkGeAkeelLdtYeeerravaqavvdf 348
                     v l+GD+ H+  P++GqG N+a+ D  +L+  L +    +A + l+dtY ++rr+ +  +v f
     AHX11317.1 269 PVILIGDSFHAIHPVAGQGFNLAVYDLRDLYNVLNKYGL-DAFDGLIDTYISKRRKSVLSMVAF 331
                    **********************************99877.9**************998888876 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   6.7e-07     0.002       3      30 ..       9      36 ..       7      45 .. 0.94

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 6.7e-07
                   --SHHHHHHHHHHHCCTEEEEEE-SSSS CS
  NAD_binding_8  3 GaGlsGlvaAylLakagfdvlllekrdr 30
                   GaGlsG +aA+lL+k gf+  +++k+++
     AHX11317.1  9 GAGLSGVLAAQLLKKLGFSYYIFDKSNG 36
                   9************************975 PP

>> SE  Squalene epoxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.4e-05     0.041     131     167 ..     269     305 ..     257     357 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.4e-05
          SE 131 GlillGDalnmRHPltggGmtvalnDivllskllkpl 167
                  +il+GD++   HP+ g G   a+ D   l ++l++ 
  AHX11317.1 269 PVILIGDSFHAIHPVAGQGFNLAVYDLRDLYNVLNKY 305
                 489***********************99888888776 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.5   0.0    0.0019       5.8       2      33 ..       4      35 ..       3      39 .. 0.92
   2 ?    5.0   0.0    0.0027       8.1     114     166 ..     104     155 ..      94     162 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.5 bits;  conditional E-value: 0.0019
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekak 33
                 d i+ G+G +G++aA  ++k g +  +++k +
   AHX11317.1  4 DFIISGAGLSGVLAAQLLKKLGFSYYIFDKSN 35
                 78999************************976 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0027
                  HHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
  HI0933_like 114 allkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                  + l+ +  +g+++++ ++ +++++++d+ +rv+ ++++ +e +++++A G +S
   AHX11317.1 104 LVLQDVLYRGIEINYAQAYEKIDYSHDR-VRVNFQDDTIVEGRYMLVAEGRNS 155
                  556777789*************999998.*******************99887 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0     0.071   2.1e+02       5      30 ..       7      32 ..       4      58 .. 0.64
   2 ?    9.6   0.0   0.00016      0.48     195     257 ..     111     170 ..      96     175 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.071
                 EE--SHHHHHHHHHHHHHTS-EEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  5 viGgGpAGlaaaltlaqagakvtlve 30
                 + G+G  G+ aa+ l++ g+  ++++
   AHX11317.1  7 ISGAGLSGVLAAQLLKKLGFSYYIFD 32
                 44555555555555555555555553 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00016
                  HTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 195 keGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelleeklgleldergg 257
                   +G+e+   +  ++id  +++++v  +d + ++ ++++va G+  +t++l   lg ++ ++g+
   AHX11317.1 111 YRGIEINYAQAYEKIDYSHDRVRVNFQDDTIVEGRYMLVAEGRNSNTAGL---LGFKMISAGY 170
                  57******************9**************************998...8888877766 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0019       5.7       1      31 [.       6      35 ..       6      56 .. 0.90
   2 ?    4.2   0.0    0.0071        21     221     271 ..     109     157 ..      84     175 .. 0.75

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0019
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgn 31
                 iI GaG  G+ aa  lkk+g+ +y i +k n
   AHX11317.1  6 IISGAGLSGVLAAQLLKKLGF-SYYIFDKSN 35
                 788******************.799***987 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.0071
  Pyr_redox_3 221 lvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdl 271
                  ++ ++ i++ + + +++i+ ++ +++v+++d  ++ +   +++a G ++++
   AHX11317.1 109 VLYRG-IEINYAQAYEKIDYSHDRVRVNFQDD-TIVEGRYMLVAEGRNSNT 157
                  33334.999**********************5.444556666777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (376 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.38
# Mc/sec: 2966.64
//
Query:       AHX11318.1  [L=290]
Description: porphobilinogen deaminase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-61  206.2   0.0    4.8e-61  205.8   0.0    1.1  1  Porphobil_deam   Porphobilinogen deaminase, dipyromethane cof
    3.7e-08   33.6   0.5    7.6e-08   32.6   0.1    1.8  2  Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain


Domain annotation for each model (and alignments):
>> Porphobil_deam  Porphobilinogen deaminase, dipyromethane cofactor binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  205.8   0.0   5.3e-65   4.8e-61       1     202 [.       4     202 ..       4     204 .. 0.94

  Alignments for each domain:
  == domain 1  score: 205.8 bits;  conditional E-value: 5.3e-65
  Porphobil_deam   1 irigtRkSkLAlaqaelvaeaLke.eeeveivtiktkGDkildkpLakiggkglFtkeleeaLlegeidlaVhSlKDlptelpeglelaavlkre 94 
                     +rigtR+S+LAlaq+e+v++aL+   +++e++++kt+GD +   pL++iggk+lF kele  Ll++eid+aVhS+KD+p+  +++l+++ vlkr+
      AHX11318.1   4 LRIGTRSSPLALAQTEIVRKALSPyCKKIEVIQVKTSGDATD-IPLTEIGGKALFLKELEGSLLKDEIDIAVHSMKDVPAFYHPDLQVVPVLKRA 97 
                     79********************5544569**********887.9*************************************************** PP

  Porphobil_deam  95 dprDvlvv..kssleelpegavvgTsSlRRkaqlkklrpdlevkdlRGnvdtRlrkldegeydaiiLAaAGLkRlgleerisevlspeellpavg 187
                     +++Dv++    s+++++p+ga++g++S+RR +ql ++   ++ ++lRG + tR++k +  ++d+iiLA +G++Rlg+++ +sevl+++ ++pavg
      AHX11318.1  98 SHNDVFISfyYSNMASMPDGARIGSCSPRRVIQLDRR---FQSTPLRGSIGTRIEKAK--NLDGIILALCGIERLGITDFVSEVLHEDLMIPAVG 187
                     *******655338**********************96...67789***********97..9********************999*********** PP

  Porphobil_deam 188 QGalavevrkedeel 202
                     QG+lave +++++++
      AHX11318.1 188 QGTLAVELKRNNHWV 202
                     *********999876 PP

>> Porphobil_deamC  Porphobilinogen deaminase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       1.6   1.4e+04      10      16 ..      57      63 ..      57      64 .. 0.88
   2 !   32.6   0.1   8.5e-12   7.6e-08       2      74 ..     216     283 ..     215     284 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 1.6
                     HHHHTT- CS
  Porphobil_deamC 10 llkeLeG 16
                     +lkeLeG
       AHX11318.1 57 FLKELEG 63
                     89****9 PP

  == domain 2  score: 32.6 bits;  conditional E-value: 8.5e-12
                      HHHHHHHHHHHHTT--TTSSEEEEEEEETTE.EEEEEEEE-TTS..S-EEEEEEEE-GGGHHHHHHHHHHHHH CS
  Porphobil_deamC   2 levlaERallkeLeGGCsvPiGvyaeveaneelkLkglvlsldglksaveeaeakgeleeaeelGkklaeell 74 
                      ++++aERa+l+e +G C++ +G+ a++ ++  l +kg++++ +      + +e+ g+  +a+ +G  +a ell
       AHX11318.1 216 TCAIAERAFLEEINGDCKTALGGLATMRGDI-LHFKGMLGKGNQ----PFFVEKSGPARDAARIGRCAASELL 283
                      79************************99878.********9888....577788887799*****99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      280  (0.0156172); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2331.10
//
Query:       AHX11319.1  [L=311]
Description: saccharopine dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.9e-16   58.2   0.0    4.3e-11   42.4   0.0    2.3  2  RmlD_sub_bind    RmlD substrate binding domain
    4.9e-15   55.3   0.1    1.8e-10   40.3   0.1    2.2  2  3Beta_HSD        3-beta hydroxysteroid dehydrogenase/isomeras
    6.3e-15   55.3   0.0    1.7e-13   50.6   0.0    2.1  1  Epimerase        NAD dependent epimerase/dehydratase family
    1.4e-11   44.6   0.0    2.5e-11   43.8   0.0    1.3  1  NAD_binding_10   NAD(P)H-binding
    2.9e-11   43.4   0.0    6.7e-11   42.2   0.0    1.5  1  NmrA             NmrA-like family
      7e-06   26.3   0.0    1.1e-05   25.7   0.0    1.3  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
      8e-06   25.2   0.0       0.05   12.8   0.0    2.8  2  NAD_binding_4    Male sterility protein
    0.00052   19.5   0.1     0.0011   18.4   0.0    1.6  2  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0055   15.9   0.0     0.0083   15.3   0.0    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
  ------ inclusion threshold ------
      0.021   14.8   0.0      0.064   13.2   0.0    1.7  2  KR               KR domain
      0.029   13.8   0.0      0.051   13.0   0.0    1.4  1  adh_short        short chain dehydrogenase
      0.031   13.9   0.0      0.047   13.3   0.0    1.3  1  ApbA             Ketopantoate reductase PanE/ApbA
       0.22   11.8   0.0       0.46   10.8   0.0    1.5  1  Nif11            Nif11 domain


Domain annotation for each model (and alignments):
>> RmlD_sub_bind  RmlD substrate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.5   0.0     2e-05     0.028       2     100 ..       3     115 ..       1     118 [. 0.90
   2 !   42.4   0.0   3.1e-14   4.3e-11     123     234 ..     124     233 ..     120     242 .. 0.87

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 2e-05
                    EEEEESTTSHHHHHHHHHCTTTSEEEEEE-TT...................T--TTSHHHHHHHHHHH--SEEEE------HHHHHHSHHHHHHHH CS
  RmlD_sub_bind   2 kilvtGanGqlGseLakqlaeeglevlaltre...................eldltdaeavaellkeakpdvvvnaAAytavDkaEseeeaayavn 78 
                    ki ++G++G +G  ++++la+++++++ ++r+                   + d+++++ +++ +     ++v+n+ A          + +  ++n
     AHX11319.1   3 KITIFGGSGFIGPYVVRELAKANYQITVVSRSmikekelklsgnlgqisvrRGDIRNPDDIRTSIMG--SEIVINLVAILGGN----SSSSMDEIN 92 
                    699****************************9*******************************9988..789****9986544....4556678** PP

                    THHHHHHHHHHHHCT-E.EEEEE CS
  RmlD_sub_bind  79 aeavealAeaaaavgal.LihvS 100
                      a +alA+  a++g++ +ih S
     AHX11319.1  93 NLACGALAKISAECGVKrFIHFS 115
                    ***************95489988 PP

  == domain 2  score: 42.4 bits;  conditional E-value: 3.1e-14
                    SHHHHHHHHHHHHHHHH-SSEEEEEE-SEESSSSS-HHHHHHHHHHH-S..EEEEESS-EE--EEHHHHHHHHHHHHHHCHH.GGG-EEEE---BS CS
  RmlD_sub_bind 123 nvYGrtKlaGEqavlaagkkalivRtswvygekgknfvktmlrlakere..elkvvaDqlgsPTsardlAevllqllekaaeekelagvyHlaneg 216
                    + YG++K++GE+av+aa ++ +i+R s+v+ge + nf++ +++l k+    +l +    + +P +++dl++++  +++        ++vy +++ +
     AHX11319.1 124 TRYGKSKIEGENAVRAAFPDSIIIRPSVVFGE-EDNFINSFIKLGKRLRiiPLPLGGKAVFQPVYVADLSRFVCRVVQDDNL---RNKVYTVTGPK 215
                    67*****************************9.89*********98765226778899999****************99886...57899999999 PP

                    -EEHHHHHHHHHHHHCHT CS
  RmlD_sub_bind 217 etswlefArailkeagad 234
                    e +  ++   i ++++++
     AHX11319.1 216 EYTLGQICSIIRENLKMK 233
                    999888888888887765 PP

>> 3Beta_HSD  3-beta hydroxysteroid dehydrogenase/isomerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.3   0.1   1.3e-13   1.8e-10       2     134 ..       6     135 ..       5     144 .. 0.80
   2 !   13.5   0.0     2e-05     0.027     174     223 ..     145     193 ..     123     214 .. 0.80

  Alignments for each domain:
  == domain 1  score: 40.3 bits;  conditional E-value: 1.3e-13
   3Beta_HSD   2 vtGgaGFlGralvkeLvrleelkevrvlDlrespelleelskvnvkkviegDvtdkdkleealegvdvvihlaslvdvagkltedeimkvnvkGTrnvl 100
                 + Gg+GF+G ++v+eL +++   +v +  + +++el + + +++ ++v  gD+++ d+++  + g+++vi l ++       ++ +++++n      + 
  AHX11319.1   6 IFGGSGFIGPYVVRELAKANYQITVVSRSMIKEKEL-KLSGNLGQISVRRGDIRNPDDIRTSIMGSEIVINLVAILGG---NSSSSMDEINNLACGALA 100
                 78******************7666655555555555.7888999999************************9555444...555667777777777888 PP

   3Beta_HSD 101 eacvkagvrvlvYtSs.aevvgpnslgeeilngdE 134
                 +   ++gv+++++ S+ ++ +g   +g+  ++g+ 
  AHX11319.1 101 KISAECGVKRFIHFSAlVGCAGTTRYGKSKIEGEN 135
                 8899********99983577888888887777765 PP

  == domain 2  score: 13.5 bits;  conditional E-value: 2e-05
   3Beta_HSD 174 caLRpagiyGegdkllvpllkqlaklglalfkigdeevlsdrvYvgNvaw 223
                 + +Rp++++Ge d+++  ++k  ++l+ + + +g +  ++++vYv  ++ 
  AHX11319.1 145 IIIRPSVVFGEEDNFINSFIKLGKRLRIIPLPLGGKA-VFQPVYVADLSR 193
                 579**********************997777777665.599***998875 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.6   0.0   1.2e-16   1.7e-13       1     231 [.       4     203 ..       4     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 50.6 bits;  conditional E-value: 1.2e-16
                 EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC....EEEE--TT-HHHHHHHHHHHT-SEEEE--S.---HHHHHHSHHHHHHHHTHH CS
   Epimerase   1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl....elveldltdrsalerlfkeeqpdavihlAa.vggvaassedpadfieknlqg 94 
                 i + G++GfiG ++v++l++++y++++++r   ++++ +l       ++ ++d++++++++  +   + ++vi+l a  gg + ss d     e+n   
  AHX11319.1   4 ITIFGGSGFIGPYVVRELAKANYQITVVSRSMIKEKELKLSGNlgqiSVRRGDIRNPDDIRTSIM--GSEIVINLVAiLGGNSSSSMD-----EINNLA 95 
                 7899***************************7777776666669999******************..9*******8866666665555.....566677 PP

                 HHHHHHHHHHHTCTEEEEEEEGGGGTSCSSSSBSTCSTTS----SSHHHHHHHHHHHHHHHHHHHHT-EEEEEEESEEESTTS-TTSTTSHHHHHHHHH CS
   Epimerase  95 tlnlleaarkagvkrllflsSsevYGkdaeqpkeettltgplkpnspYaaaKlageklveayaaqyglnaiilrlfnlyGprngegevsrvipalirki 193
                    l++ + ++gvkr++++s   + G                + ++ Y+ +K+ ge+ v+a+  +     ii+r++ ++G+       +++i  +i+  
  AHX11319.1  96 CGALAKISAECGVKRFIHFSA--LVGC---------------AGTTRYGKSKIEGENAVRAAFPDS----IIIRPSVVFGEE------DNFINSFIKLG 167
                 7789****************9..7772...............33479*************987766....***********9......77888887765 PP

                 HTTSSSEEEETTST-EEEEEEHHHHHHHHHHHHHHHTT CS
   Epimerase 194 legkqevtllgdgtalRdflyveDvaeaillvlehvda 231
                 ++ +  + l   g+a+ + +yv D+ + +++v++  d+
  AHX11319.1 168 KRLR-IIPLPLGGKAVFQPVYVADLSRFVCRVVQD-DN 203
                 5555.67777799********************98.43 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.0   1.8e-14   2.5e-11       1      99 [.       8     117 ..       8     161 .. 0.72

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.8e-14
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHH..CT.TTCEEEE--TT-CCHHHHHHTT-SEEEES-...--TCC....HHHH....HHHH CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaele..ae.eglevvegdvtdvedlaealkgadaVvsal...ggggk....deeg....akni 81 
                     G++G +G ++v+el+++ ++++t++ R+  k +el+   +  +++v  gd+ +++d++  + g ++V+  +   gg+++    +  +    + ++
      AHX11319.1   8 GGSGFIGPYVVRELAKA-NYQITVVSRSMIKEKELKlsGNlGQISVRRGDIRNPDDIRTSIMGSEIVINLVailGGNSSssmdE--InnlaCGAL 99 
                     9****************.6*********6555555433445899***********************87775563333345430..255669999 PP

                     HHHHHHCT--EEEEEEET CS
  NAD_binding_10  82 vdaakeagvkRfvlvsai 99 
                     ++   e gvkRf+  sa+
      AHX11319.1 100 AKISAECGVKRFIHFSAL 117
                     9999**********9996 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.2   0.0   4.9e-14   6.7e-11       1     224 [.       4     229 ..       4     241 .. 0.79

  Alignments for each domain:
  == domain 1  score: 42.2 bits;  conditional E-value: 4.9e-14
                 EEESSTTSHHHHHHHHHHHHHT-EEEEEES-S-SHHHHHHH.HSTTEEE.ES-TT-HHHHHHHHTT-SEEEE---GG.......S-HHHH..HHHHHHH CS
        NmrA   1 IlviGaTGrqGksvvrallkaghkvralvRdtkselakslk.eaGvelv.kgdlddkeslvealkgvdvvfsvtgfy.......skeied..gkklvdA 88 
                 I+++G++G +G +vvr l+ka++++ ++ R   +e+  +l+ + G   v  gd+ + + +++ + g++ v+  +++         +ei+     +l++ 
  AHX11319.1   4 ITIFGGSGFIGPYVVRELAKANYQITVVSRSMIKEKELKLSgNLGQISVrRGDIRNPDDIRTSIMGSEIVINLVAILggnssssMDEINNlaCGALAKI 102
                 89******************************666666666267999999**********************999889999887555554114589999 PP

                 HHHHS-SEEE.EEE---GG.GT.SSS---TTTHHHHHHHHHHHHCTS-EEEEE..E-EE..GGG-BSSS-SS-BEEE-TTS.-EEEEESS-TTS-EE.- CS
        NmrA  89 akeaGvkhfi.ySslgddndrsnaeepavphfdsKaeieeyvralgipytfvy..agff..menflsllaqlkvgdtappedkvtllgpgnpkavll.d 181
                  +e Gvk+fi +S l+ +   +          +sK+e e++vra+ +p ++++  +++f    nf+ ++ +      +  +   +++ p   kav+  +
  AHX11319.1 103 SAECGVKRFIhFSALVGCAGTT-------RYGKSKIEGENAVRAA-FPDSIIIrpSVVFgeEDNFINSFIK----LGKRLR---IIPLPLGGKAVFQpV 186
                 99********779999998555.......4457999999****97.5555543113345113466665555....555555...889999999999999 PP

                 HHHHHHHHHHHHHHHHHHHTTEEEEE-SEEE-HHHHHHHHHHH CS
        NmrA 182 aeeDiGafvikilkdprklkgkriklagntlsgneivelfekk 224
                  ++D  +fv+ +++d +  + ++     +++++ +i++++ ++
  AHX11319.1 187 YVADLSRFVCRVVQDDNLRNKVYTVTGPKEYTLGQICSIIREN 229
                 ***************8888666666666678999***998776 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   8.1e-09   1.1e-05       2      77 ..       5      77 ..       4      87 .. 0.90

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 8.1e-09
                     EEE--.SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTSSEEEE-S CS
  Sacchrp_dh_NADP  2 liiGa.GsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkegdlvvnls 77
                      i+G+ G++G  v+++la+ + +  +itv++rs  k ++l+ + +  +++ +  d+ n+++ +   + + ++v+nl+
       AHX11319.1  5 TIFGGsGFIGPYVVRELAKAN-Y--QITVVSRSMIKEKELKLSGNLGQISVRRGDIRNPDD-IRTSIMGSEIVINLV 77
                     688888*************85.7..9**********999998889999999999*******.999999*******97 PP

>> NAD_binding_4  Male sterility protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00048      0.67       3      33 ..       8      36 ..       6     125 .. 0.90
   2 !   12.8   0.0   3.6e-05      0.05     174     211 ..     124     157 ..     120     178 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00048
                   -TTSHHHHHHHHHHHHHS-.TEEEEEE-SSS CS
  NAD_binding_4  3 GaTGFLGkvLlekLLrttpevkiyllvRaks 33
                   G++GF+G +++++L + +   +i+++ R+  
     AHX11319.1  8 GGSGFIGPYVVRELAKANY--QITVVSRSMI 36
                   9**************9998..7888877654 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 3.6e-05
                    CHHHHHHHHHHHHHHHHHHHH---EEEEEE-EEE--SS CS
  NAD_binding_4 174 ntYeqsKalaEklvrearrrsglpvvivRpsiitgesk 211
                    + Y +sK ++E+ vr+a+       +i+Rps++ ge  
     AHX11319.1 124 TRYGKSKIEGENAVRAAFPD----SIIIRPSVVFGEED 157
                    57****************33....58*******99654 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.0     8e-07    0.0011       2      84 ..       6      78 ..       5     117 .. 0.77
   2 ?   -3.1   0.0       2.8   3.9e+03     225     264 ..     187     228 ..     186     235 .. 0.67

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 8e-07
                   EETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT-SEEEE--S CS
  GDP_Man_Dehyd  2 iTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevqpdevynLAA 84
                   i G++GfiG y+++ L + +y+++++ r     + +++ +l       + +++++ +gD+++ + ++  +     + v+nL A
     AHX11319.1  6 IFGGSGFIGPYVVRELAKANYQITVVSRSM--IKEKEL-KLSG-----NLGQISVRRGDIRNPDDIRTSIMGS--EIVINLVA 78
                   88********************98875433..333333.3333.....23689999******99999988777..45777766 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 2.8
                    EHHHHHHHHHHHHHCSS---..EEE-TT-EEECHHCHHCCHH CS
  GDP_Man_Dehyd 225 hvkDyveamwlmlqqdkped..yviatgethsvrefvelafl 264
                    +v D  + + +++q d+ ++  y +   +++++++++ +  +
     AHX11319.1 187 YVADLSRFVCRVVQDDNLRNkvYTVTGPKEYTLGQICSIIRE 228
                    788889999999998875441155666677887777766555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0     6e-06    0.0083       1     151 [.       4     139 ..       4     153 .. 0.81

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6e-06
                      EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHTT..T-SEEEE------HHHHH CS
  Polysacc_synt_2   1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekaleelkvdvvfhaAAlKhVPlve 94 
                      + + G++G iG  +vr+++k +  +i +++r+  k  e++ +   +l   +++v+     gd+r+ + +++ +   + ++v++  A+       
       AHX11319.1   4 ITIFGGSGFIGPYVVRELAKANY-QITVVSRSMIKEKELKLSG--NLG--QISVR----RGDIRNPDDIRTSIM--GSEIVINLVAIL--GGNS 84 
                      6789*************998875.7999999999988887764..233..45555....8***********999..9*****998863..2333 PP

                      HSHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEGGGSS--SHHHHHHHHHHHHHHH CS
  Polysacc_synt_2  95 enpleaiktNvlgtenvieaaieagvkkvvliStDKAvnPtnvmGatKrlaekllqa 151
                      +  ++    N l+   +++++ e+gvk+++  S+   +  t  +G +K   e  + a
       AHX11319.1  85 SSSMDE--INNLACGALAKISAECGVKRFIHFSALVGCAGTTRYGKSKIEGENAVRA 139
                      334444..4666667789999***************************998887766 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   4.7e-05     0.064       5      72 ..       6      67 ..       3      77 .. 0.83
   2 ?   -1.8   0.0       1.8   2.5e+03     118     144 ..      98     124 ..      95     134 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 4.7e-05
                EETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHH CS
          KR  5 itGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdaveall 72
                i GG G +G  ++r la+ ++ ++ ++sRs       k++  +l+ +  +++v++ D+ ++d++++ +
  AHX11319.1  6 IFGGSGFIGPYVVRELAK-ANYQITVVSRSMI-----KEKELKLSGNLGQISVRRGDIRNPDDIRTSI 67
                89**************96.6789*******33.....3333468888889*************99876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.8
                 HHHHHTTTS--SEEEEEEEHHHHH--T CS
          KR 118 nLhelledesldffvlfSSiagllgsa 144
                  L ++++++ ++ f+ fS + g+ g++
  AHX11319.1  98 ALAKISAECGVKRFIHFSALVGCAGTT 124
                 577888888899999999998888865 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   3.7e-05     0.051       1      66 [.       2      65 ..       2      94 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.7e-05
                SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHH CS
   adh_short  1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevea 66
                k + + G+s+ IG  +++elak++++++vv+rs  k +e++ +   +  ++ + ++D+++ +++++
  AHX11319.1  2 KKITIFGGSGFIGPYVVRELAKANYQITVVSRSMIKEKELKLS--GNLGQISVRRGDIRNPDDIRT 65
                67899***************************97666544333..334689999999999998876 PP

>> ApbA  Ketopantoate reductase PanE/ApbA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   3.4e-05     0.047       5      54 ..       9      54 ..       4      88 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.4e-05
                S-SHHHHHHHHHHHHHTHCEEEE-SCHHHHHHHHHCEEEEETTCEEEEEE CS
        ApbA  5 GaGaiGsllaakLakagadvtlilrsrrlealkknGlrltseggeeilrp 54
                G+G iG ++  +Laka++++t++ rs     +k++ l+l+++ g+  +r 
  AHX11319.1  9 GSGFIGPYVVRELAKANYQITVVSRSM----IKEKELKLSGNLGQISVRR 54
                89*************************....6777777777666665554 PP

>> Nif11  Nif11 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00033      0.46       4      30 ..     189     215 ..     188     228 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00033
       Nif11   4 eqlkaFlekvkqDpalreqlkacsdhe 30 
                  +l++F+ +v qD++lr+++ +++ + 
  AHX11319.1 189 ADLSRFVCRVVQDDNLRNKVYTVTGPK 215
                 699****************99887555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       439  (0.0244855); expected 358.6 (0.02)
Passed bias filter:                      408  (0.0227564); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.50u 0.29s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2187.51
//
Query:       AHX11320.1  [L=120]
Description: DNA processing chain A domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-05   23.9   0.1    0.00012   22.1   0.1    1.8  2  DprA_WH   DprA winged helix domain


Domain annotation for each model (and alignments):
>> DprA_WH  DprA winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.11     2e+03      16      31 ..      24      39 ..      16      40 .. 0.82
   2 !   22.1   0.1   6.8e-09   0.00012      11      58 ..      62     109 ..      53     110 .. 0.92

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.11
     DprA_WH 16 rvLaaLgpePvhvDqL 31
                 vL+ L +++++ D L
  AHX11320.1 24 DVLNTLRNTSRTTDYL 39
                5999999999999976 PP

  == domain 2  score: 22.1 bits;  conditional E-value: 6.8e-09
     DprA_WH  11 ddlerrvLaaLgpePvhvDqLvrrtglpaaevsaaLleLELaGlverl 58 
                   +++++L++L+ +Pv++ +L+ r+ l  ++++ a +eLE++ ++ rl
  AHX11320.1  62 KNTKAQILEQLELTPVSMYELMHRLYLNESTLLKAIIELEIERKISRL 109
                 56789****************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (120 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       730  (0.0407162); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 857.45
//
Query:       AHX11321.1  [L=73]
Description: hypothetical protein NHE_0369 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (73 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       199  (0.0110993); expected 358.6 (0.02)
Passed bias filter:                      180  (0.0100396); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 561.58
//
Query:       AHX11322.1  [L=108]
Description: putative DNA processing DprA domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
     0.0012   18.2   0.0     0.0016   17.7   0.0    1.2  1  DNA_processg_A  DNA recombination-mediator protein A


Domain annotation for each model (and alignments):
>> DNA_processg_A  DNA recombination-mediator protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.0   9.1e-08    0.0016       6      43 ..      59      96 ..      54      99 .. 0.88

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 9.1e-08
  DNA_processg_A  6 giklltledkeYPeklkeikdpPlvLfvkGnlellekr 43
                    + ++++  +++Y +kl++i+d+P+++ +kGn+ell+++
      AHX11322.1 59 DGTIIVSCEEKYSSKLRRIRDAPPIIATKGNVELLKTQ 96
                    55789999**************************9964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       607  (0.0338558); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 867.94
//
Query:       AHX11323.1  [L=148]
Description: sensory box protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-08   34.7   0.0    1.6e-08   34.4   0.0    1.0  1  PAS_5     PAS domain
  ------ inclusion threshold ------
      0.013   15.7   0.0      0.019   15.2   0.0    1.3  1  PAS_4     PAS fold


Domain annotation for each model (and alignments):
>> PAS_5  PAS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.0   1.8e-12   1.6e-08       8     132 ..      13     139 ..       6     143 .. 0.87

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 1.8e-12
       PAS_5   8 elfayWdelrggralPrRsdidPaklrelLgdvFile...rdaegelrfRlAGtrlcallGrelrgksfsalfteasreeleevvevvlkeelpvlval 103
                 +l +yW++ +gg++ P++sd+d +++ +++++  +++   +d++  +++   G+++ + + + + ++ f + f   + e+ +e +++vl+++ p+  + 
  AHX11323.1  13 QLCEYWKQIQGGNKFPKKSDLDVDEIGHIMPYCVVVDvhqDDGKIDYHVGYVGSKVRQFADKGIFHETFIQ-FVSPDTETFQEYLDEVLETQEPMTDSG 110
                 799****************************999986211444555677779***************9986.666778899****************** PP

       PAS_5 104 eaeaesgrslelellllPlatesgeqsrl 132
                 ea + ++++++++  +lPl+ + ++ +++
  AHX11323.1 111 EALNGNQEEVRFRQCILPLSDDGEKVTSM 139
                 *******************9997777665 PP

>> PAS_4  PAS fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   2.1e-06     0.019      42      94 ..      83     134 ..      44     143 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 2.1e-06
       PAS_4  42 ellpeedaarleralrrvlegeepiefleelll.pgeerhyelrllPlrdesGe 94 
                 +++++ d + ++++l++vle++ep ++  e l  ++ee+ +   +lPl d +Ge
  AHX11323.1  83 QFVSP-DTETFQEYLDEVLETQEPMTDSGEALNgNQEEVRFRQCILPLSD-DGE 134
                 44444.9******************99999999899999999999***76.887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (148 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1120.42
//
Query:       AHX11324.1  [L=176]
Description: peptide deformylase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-44  151.2   0.0      2e-44  151.0   0.0    1.1  1  Pep_deformylase  Polypeptide deformylase


Domain annotation for each model (and alignments):
>> Pep_deformylase  Polypeptide deformylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  151.0   0.0   1.1e-48     2e-44      16     157 ..       3     152 ..       1     154 [. 0.94

  Alignments for each domain:
  == domain 1  score: 151.0 bits;  conditional E-value: 1.1e-48
                      -B---BSSHHHHHHHHHHHHHHHHHCT-SEEEGGGGT--BSEEEEECCSS-ETT....S.........EEEEEEEEEEECSCEEECCEE--TTS CS
  Pep_deformylase  16 akpvekfeskelekllekmletmkeakgvgLAApQigvnkrlfvielpseeeeeeenke.........ltvliNPkitskseetitdeEgClSv 100
                      ++pv+++  +e++k++++mletm+e+ g+gLAA+Q+gv kr++v+++++++e + ++ +         ++ + NP+i++ se+ +   EgClSv
       AHX11324.1   3 SEPVDSVC-NETKKFMDDMLETMYESGGIGLAAVQVGVLKRIIVVDISEGKEWRYSPLDhpdytscggPYYMANPEIIEFSENHVLAYEGCLSV 95 
                      67788665.559*************************************9997766555999******************************** PP

                      TT--CEEEEESCEEEEEE-TTS-EEEEEEEHHHHHHHHHHHHHCTT--GGGGC-TTX CS
  Pep_deformylase 101 pgieakVeRskrikvkyldltgkeveleaegllArvlqHEiDhlnGklfidridkse 157
                      p+++ +V R++ i+vkyl ++gke  l+a+g+l r++qHEiDh++Gklfi ++++++
       AHX11324.1  96 PEQKYEVSRPDAITVKYLGYDGKETVLKANGWLGRCIQHEIDHIDGKLFISHLSRLK 152
                      ****************************************************99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1334.21
//
Query:       AHX11325.1  [L=322]
Description: delta-aminolevulinic acid dehydratase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     1e-110  369.8   0.0   1.2e-110  369.6   0.0    1.0  1  ALAD      Delta-aminolevulinic acid dehydratase
  ------ inclusion threshold ------
       0.18   11.4   0.0       0.36   10.4   0.0    1.4  1  DUF2674   Protein of unknown function (DUF2674)


Domain annotation for each model (and alignments):
>> ALAD  Delta-aminolevulinic acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  369.6   0.0  1.3e-114  1.2e-110       3     316 ..       8     318 ..       6     319 .. 0.96

  Alignments for each domain:
  == domain 1  score: 369.6 bits;  conditional E-value: 1.3e-114
                 -GGGGGSSHHHHHHC-S----GGGEEEEEEEESS-SS-EE-TTSTT-EEEEGGGHHHHHHHHHHTT--EEEEEEE-.SS.-BSS-GGGGSTTSHHHHHH CS
        ALAD   3 rlrrlrksealrelvretrlsasdlilplfvkegeeekeeiksmpgvyrlsvdelvkeveelvklgikavllFgvp.ee.kdeegsealnedglvqrai 99 
                 rlrr+r+++ +r+lv++t +s+s++i+p+fv+ege+ + ++++m gv  +s+d l k ++++++ g+++++lF    e+ k+++++ea+n+d+l++ra+
  AHX11325.1   8 RLRRIRENPIMRDLVADTFISPSQFIFPVFVVEGENLELSVEEMLGVNVYSIDMLGKVIDRALSCGVRSFMLFPRVdESkKSDNAEEAYNPDNLICRAV 106
                 99***********************************************************************54443369****************** PP

                 HHHHHH-.TTSEEEEEE-STTTBSS-SSSEEESS.EEHHHHHHHHHHHHHHHHHCT-SEEEE-S--TTHHHHHHHHHHHTT-TT-EEB---EEB--CGG CS
        ALAD 100 raikeev.pelvvitDvclceytshGhcgileekevdndetlellakvavsqaeaGadivapSdmmDgrvaaireaLdeagfeevailsYsaKyaSafY 197
                 r ++e++ +e+v+itDv+ ++yt +Gh+g+l++++++ndetlellak+a++q+ aG d++apSdmmDgr+ air+aLd  ++++v+ilsYs+KyaS++Y
  AHX11325.1 107 RGLRERFsSEIVIITDVAADPYTISGHDGLLQNGKILNDETLELLAKQALVQVAAGSDMIAPSDMMDGRILAIRNALDLGNLSSVPILSYSVKYASKLY 205
                 ******9778***************************************************************************************** PP

                 HHHHHHHT---S.S--TTTSB-TT-HHHHHHHHHHHHHTT-SBEEEES-TTGHHHHHHHHTT-SS-EEEEE-HHHHHHHHHHHHTTSS-HHHHHHHHHH CS
        ALAD 198 gPFrdaaesapsfgdrktYqmdpansrealreveldleeGADivmvKPalaylDiirevkeefdlpvaayqvSGEYamikaaaengwldekkvvlEsll 296
                 +PFr a++ ++   d+++Yq+d++ns ea+re+e d++eGADivm+KPa  +lD+i ++ ++f++p++ayqvSGEY+m +++   g +   ++++Esl+
  AHX11325.1 206 KPFRSAIGVNKGPIDKRSYQVDCRNSGEAMREIEVDIAEGADIVMIKPANLFLDVIGKAVDQFSVPIFAYQVSGEYQMFRQY---GGI---EMLIESLI 298
                 **********9999****************************************************************9865...555...589***** PP

                 HHHHTT-SEEEETTHHHHHH CS
        ALAD 297 sikRAGadliltYfakevak 316
                 +ikRAG + i tY a eva+
  AHX11325.1 299 GIKRAGVSSICTYAAIEVAE 318
                 *****************997 PP

>> DUF2674  Protein of unknown function (DUF2674)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0     4e-05      0.36      17      50 ..     234     266 ..     226     270 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 4e-05
     DUF2674  17 DikkIekeleeGWvIvnlvPyedaFlcvLEKsie 50 
                  +++Ie +++eG  Iv ++P  + Fl v+ K ++
  AHX11325.1 234 AMREIEVDIAEGADIVMIKPA-NLFLDVIGKAVD 266
                 599*****************7.589999988876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (322 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       325  (0.0181271); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2536.13
//
Query:       AHX11326.1  [L=270]
Description: yihY family inner membrane domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-52  178.9  20.5    1.6e-52  178.7  20.5    1.0  1  Virul_fac_BrkB  Virulence factor BrkB
  ------ inclusion threshold ------
      0.033   14.2   0.2      0.033   14.2   0.2    2.8  3  DUF1304         Protein of unknown function (DUF1304)
        1.6    7.9  10.6        1.4    8.2   9.6    1.3  1  CcmF_C          Cytochrome c-type biogenesis protein CcmF C-t


Domain annotation for each model (and alignments):
>> Virul_fac_BrkB  Virulence factor BrkB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  178.7  20.5   2.7e-56   1.6e-52       2     253 ..       3     258 ..       2     262 .. 0.91

  Alignments for each domain:
  == domain 1  score: 178.7 bits;  conditional E-value: 2.7e-56
  Virul_fac_BrkB   2 eddlsllAaalayytllSlfPlllvllavlgl.lg....lddelqeqlldllaevlpegaaevvedilqrllnqaslgllglavll..wsasggv 89 
                     ++++s++A+ l++ +llS+fP+l++++av+g  ++    ++ e++++ll+l+++ +pe+++e ++++++++l++++++ll++++l   w+as++v
      AHX11326.1   3 YHGGSEYAGYLSFLLLLSIFPFLFFFTAVAGHiGSivdeSSYEITRKLLSLFIDGVPENIIEGIMPYIKEILEGPTQSLLTFTILGaiWTASSIV 97 
                     6899**************************9954488998889999999999999*****************************9999******* PP

  Virul_fac_BrkB  90 salrralnkiygv...eesrsflrkrllsllllllllvllllslvlsvflqslllasapllglglelsellllqllrwlvallllvlafallYrv 181
                     ++l++a+n++y+        +++ +r +s++ +l++ + +ll+l+++++ + l+++++ +l l         +   ++ ++++++++++a+lY +
      AHX11326.1  98 EGLKAAVNRAYNFstdALVYEYIFRRCISIVQFLMISMTILLFLLFPTIYPLLTKNLK-FLSLVVKP--D--WIPYNI-LTTFCMFFFVAALYIF 186
                     ************964322447*******************************999987.65655433..2..333444.56679*********** PP

  Virul_fac_BrkB 182 lpnvkvrlraalpGallaallwllvkilfslylsnfasynaiYGslgaliilllWlylsalilLlGaelnae 253
                     +p++++++ +++pG++++++lw+++++ fs+yl++f +++ iYGs++++i+++ ++yl++l++++Gaelna 
      AHX11326.1 187 FPKERQKFIDVIPGSVAVVALWIITSVSFSFYLRSFTQMSLIYGSIAGIIVIMTYFYLINLCFIYGAELNAL 258
                     **********************************************************************96 PP

>> DUF1304  Protein of unknown function (DUF1304)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.24   1.4e+03      72      92 ..      22      42 ..      12      59 .. 0.73
   2 ?   14.2   0.2   5.5e-06     0.033      58     109 ..     157     207 ..     145     211 .. 0.76
   3 ?    0.8   0.8     0.078   4.7e+02      53      89 ..     203     240 ..     200     250 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.24
     DUF1304 72 vlfflgcvvvaglygaltask 92
                  f+ ++ +vag +g++ +++
  AHX11326.1 22 FPFLFFFTAVAGHIGSIVDES 42
                557788889999999988755 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 5.5e-06
     DUF1304  58 wglllgseavglalvlfflgcvvvaglygaltaskkillvQglpallAlvll 109
                 ++l+++ + + ++++++f+++ +va+ly+++ ++++  ++  +p+ +A+v+l
  AHX11326.1 157 LSLVVKPDWIPYNILTTFCMFFFVAALYIFFPKERQ-KFIDVIPGSVAVVAL 207
                 6777777788999******************98663.345555555555554 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.078
     DUF1304  53 Aagliwgl.llgseavglalvlfflgcvvvaglygalt 89 
                 A++++w +  ++ + + ++++ + l++  +ag+++++t
  AHX11326.1 203 AVVALWIItSVSFSFYLRSFTQMSLIYGSIAGIIVIMT 240
                 44444444222333445556666677777888877777 PP

>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2   9.6   0.00023       1.4      44     153 ..     134     243 ..     103     262 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00023
      CcmF_C  44 LvvaaavVllGTLyPlvldalglgkiSVGaPyFnavfvplmvplllllgvGpllrWkraklaellkrllvalvlalvlalllalllgelkvlaalglal 142
                  +++++  l+ T+yPl+++ l+  ++ V + +    ++  +++++++ ++  ++   r+k+ +++   +++++l +++++ + ++l++++ + ++   +
  AHX11326.1 134 SMTILLFLLFPTIYPLLTKNLKFLSLVVKPDWIPYNILTTFCMFFFVAALYIFFPKERQKFIDVIPGSVAVVALWIITSVSFSFYLRSFTQMSLIYGSI 232
                 3567788899**********************8888888888888899999999999999999999888887888888888888665666666655555 PP

      CcmF_C 143 avwvvlaalae 153
                 a ++v+++   
  AHX11326.1 233 AGIIVIMTYFY 243
                 55555555544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (270 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       832  (0.0464053); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.46
# Mc/sec: 1769.41
//
Query:       AHX11327.1  [L=243]
Description: ATP synthase F0, A subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.1e-53  182.4  33.3    1.3e-53  182.1  33.3    1.0  1  ATP-synt_A      ATP synthase A chain


Domain annotation for each model (and alignments):
>> ATP-synt_A  ATP synthase A chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.1  33.3   7.2e-58   1.3e-53       3     210 ..      31     236 ..      29     237 .. 0.86

  Alignments for each domain:
  == domain 1  score: 182.1 bits;  conditional E-value: 7.2e-58
                 HHHHHHHHHHCCC.CCSS.T.TTTSHHHHHHHHHHHHHHHHHHHHCTSSSTXHHHHHHHHHHHHHHHHHCCHCCS..STTTTTTCHHHHHHHHHHHHHH CS
  ATP-synt_A   3 ttlivllilllllllatrkkkkklpgklqnlvealvefvdnlvksvigkkkkkkffpliltlflfilvsNllgli..PglraatadinvtlalAlivfl 99 
                 ++++++++  l+l+     +++ +pg +q+++e++++fv ++vks+ gk  +  ++pli+t+fl+il++Nl g++  P+++++t++i vtlalA++vf+
  AHX11327.1  31 YMVLAVVLASLFLFSGI-VRTRIVPGSMQSFIEIVYNFVADIVKSNCGK-AGLDYLPLIFTVFLYILFANLAGMLplPMSFTVTSHIVVTLALAIVVFV 127
                 45555554444443333.233445***********************95.889********************974577******************** PP

                 HHHHHHHHHHGG..GGCHHHSS...SCCCCHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCTGCCCTTCHHHHHHHHHHHHHHHHHH CS
  ATP-synt_A 100 lvlilgikkkglkgyfkklfvp...plllvplllpielisefarpvsLalRLfgNifAGelllallagllllllllavllsvlilllavlllllelfvg 195
                 +v+++g++k+g  ++f ++f p   pl+++pl++++e+ ++f rp+sLa+RL++N++AG+++l+++ag++     +++l+s+l++++ v+l+++e+f++
  AHX11327.1 128 YVTVIGFRKQGK-AFF-SIFLPngtPLWIAPLMILLEVCTYFFRPISLAIRLTANMIAGHTILKVIAGFVQ---PISLLVSPLSFAFVVVLIVFEVFIA 221
                 **********95.677.67745588******************************************9962...2345678888888999********* PP

                 HHHHHHHHHHHHHHH CS
  ATP-synt_A 196 fiQAfvFtlLtlvYi 210
                 ++QA++F++L +vY+
  AHX11327.1 222 MLQAYIFVVLVCVYL 236
                 **************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1837.31
//
Query:       AHX11328.1  [L=75]
Description: ATP synthase subunit C family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.4e-11   43.8   3.6    2.9e-11   43.6   3.6    1.0  1  ATP-synt_C  ATP synthase subunit C


Domain annotation for each model (and alignments):
>> ATP-synt_C  ATP synthase subunit C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.6   3.6   1.6e-15   2.9e-11       1      60 []       9      71 ..       9      71 .. 0.98

  Alignments for each domain:
  == domain 1  score: 43.6 bits;  conditional E-value: 1.6e-15
                HHHHHHH.GGGHHHHHHHHHHHHHHHHHHHHSG....HHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  ATP-synt_C  1 lgaglavGlsalgsGigiGkagsagiravarnp....klftksliilafaeaialygLivalil 60
                lg+g++v +++lg+++g+ +++s +++++arnp    kl   +  ++a+ ea++l+ ++ al+l
  AHX11328.1  9 LGIGFSV-IGMLGAALGVSNIFSMMLNGIARNPeseeKLKKYVYAGAALTEAMGLFSFVLALLL 71
                79*****.******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (75 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       742  (0.0413855); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 658.41
//
Query:       AHX11329.1  [L=177]
Description: ATP synthase B/B' CF family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.7e-15   55.6   3.7    1.3e-12   48.3   1.7    2.5  3  YMF19       Plant ATP synthase F0
    1.9e-07   31.2   0.0    2.3e-07   30.9   0.0    1.1  1  ATP-synt_B  ATP synthase B/B' CF(0)
  ------ inclusion threshold ------
      0.054   12.5   0.2       0.18   10.8   0.2    1.7  1  DUF4015     Putative glycosyl hydrolase domain
      0.065   13.3   0.7      0.095   12.8   0.7    1.2  1  DivIVA      DivIVA protein
       0.25   11.8   2.4        0.5   10.9   2.4    1.5  1  ATP-synt_8  ATP synthase protein 8
        2.7    7.5   6.5        7.4    6.1   0.1    2.1  2  SieB        Super-infection exclusion protein B


Domain annotation for each model (and alignments):
>> YMF19  Plant ATP synthase F0
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   1.7   4.4e-16   1.3e-12       1      78 [.       2      79 ..       2      96 .. 0.91
   2 ?   -0.8   0.0       0.9   2.7e+03      45      75 ..      89     119 ..      77     131 .. 0.48
   3 !    6.9   0.0    0.0036        11      22      60 ..     137     175 ..     128     177 .] 0.89

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 4.4e-16
       YMF19  1 PQLDkftyftQffWlclfFitlYivllknilpkiarilklrkkllsslssevsklkkeqknlivskdsalanvslste 78
                PQ D  tyf Q+fW+++ F++lY+++   +lpk++ +l  r ++l +++  +++++++     ++ d al+++++  e
  AHX11329.1  2 PQFDISTYFGQIFWFFISFFLLYFFVRFVFLPKLSVSLGTRAAFLGENKRLLEDINSDLVRFKEKRDAALSDARFAAE 79
                9********************************************************999999999999999988554 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.9
       YMF19  45 lsslssevsklkkeqknlivskdsalanvsl 75 
                 +s+l+++ ++  +    +  +++ al n++l
  AHX11329.1  89 ISQLEKSANEKLSAIVADLREENVALINNFL 119
                 3444444444444444444444444444444 PP

  == domain 3  score: 6.9 bits;  conditional E-value: 0.0036
       YMF19  22 lYivllknilpkiarilklrkkllsslssevsklkkeqk 60 
                  Y+v++ +++p+ a + +lr + +s + s ++k++k q+
  AHX11329.1 137 CYVVVYGRFMPQSADTDSLRHRVSSDFTSIFEKFRKCQS 175
                 6***************************99999998775 PP

>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.0   7.8e-11   2.3e-07       2     124 ..      13     135 ..      12     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 7.8e-11
  ATP-synt_B   2 lvvnliallilvgllikfawkplkkvLdkReekIadeiaeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesA 100
                 +++  i++ +l++++ ++  ++l+  L +R +   ++ +  e   +++  +++++ ++l +Ar  A++i k+A  ++++l + ++++ +a ++ l+e+ 
  AHX11329.1  13 IFWFFISFFLLYFFVRFVFLPKLSVSLGTRAAFLGENKRLLEDINSDLVRFKEKRDAALSDARFAAENILKDASIAISQLEKSANEKLSAIVADLREEN 111
                 7999**********************************************************************************************9 PP

  ATP-synt_B 101 aaeIeqekdralaeLreqvvalav 124
                  a I+   +   + L++  ++l++
  AHX11329.1 112 VALINNFLADNADVLEQLFFELSL 135
                 999998777777777777777766 PP

>> DUF4015  Putative glycosyl hydrolase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2     6e-05      0.18     138     197 ..      53     140 ..      35     154 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 6e-05
                 -SEEEEE--S---..------EE---TT--............................HHHHHHHHHHHHHHHST..T--EE-BGGGT CS
     DUF4015 138 fdeiqfDYvRfpe..dskkkeleyseeeteee..........................rveaisdflayareelesygvfvsvdvfGy 197
                 +++i+ D vRf e  d   +++++ +e+  ++                          +v+ i++fla   + le+    +s d + +
  AHX11329.1  53 LEDINSDLVRFKEkrDAALSDARFAAENILKDasiaisqleksaneklsaivadlreeNVALINNFLADNADVLEQLFFELSLDCYVV 140
                 5799********9777788889999999888877777777777777777777777777777777777777777777777777776655 PP

>> DivIVA  DivIVA protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.7   3.2e-05     0.095      55     117 ..      46     108 ..      34     114 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      DivIVA  55 lkeykeleetLkktlvvaqetaeevkanakkeaeliikeAekkaekiveeaeeeakkiaeeie 117
                 l e k l e+++  lv  +e  + + + a+  ae+i+k+A  + +++ + a+e++  i +++ 
  AHX11329.1  46 LGENKRLLEDINSDLVRFKEKRDAALSDARFAAENILKDASIAISQLEKSANEKLSAIVADLR 108
                 778899999***********************************************9998876 PP

>> ATP-synt_8  ATP synthase protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   2.4   0.00017       0.5       1      24 [.       1      24 [.       1      37 [. 0.93

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00017
  ATP-synt_8  1 MPQLdtstWltiillmwltLfili 24
                MPQ d st +  i+ +++++f+l 
  AHX11329.1  1 MPQFDISTYFGQIFWFFISFFLLY 24
                *********************995 PP

>> SieB  Super-infection exclusion protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   2.8     0.014        42      33      57 ..       8      32 ..       3      83 .. 0.69
   2 ?    6.1   0.1    0.0025       7.4      50      97 ..      80     126 ..      71     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.014
        SieB 33 lwiglvflisiayllaqvvskllae 57
                 ++g++f ++i+++l +++++++ +
  AHX11329.1  8 TYFGQIFWFFISFFLLYFFVRFVFL 32
                689****************999844 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0025
        SieB  50 vvskllaeikekikkkreqkkvekklknLteeekavLreflnqgksvl 97 
                 ++ k   +++++++ k  ++k  + + +L ee  a++  fl+++  vl
  AHX11329.1  80 NILKDASIAISQLE-KSANEKLSAIVADLREENVALINNFLADNADVL 126
                 55555566667776.999************************999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       900  (0.050198); expected 358.6 (0.02)
Passed bias filter:                      570  (0.0317921); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1359.01
//
Query:       AHX11330.1  [L=164]
Description: ATP synthase B/B' CF family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-08   33.7   5.1    4.3e-08   33.3   5.1    1.1  1  ATP-synt_B      ATP synthase B/B' CF(0)
     0.0022   18.0   1.1     0.0024   17.9   0.3    1.5  2  Laminin_II      Laminin Domain II
     0.0038   17.4   1.2     0.0079   16.4   0.2    1.8  2  Fib_alpha       Fibrinogen alpha/beta chain family
     0.0081   16.4   0.5      0.022   15.0   0.3    1.8  1  SpoU_sub_bind   RNA 2'-O ribose methyltransferase substrate b
     0.0082   15.3   0.8      0.011   14.8   0.8    1.1  1  CKAP2_C         Cytoskeleton-associated protein 2 C-terminus
     0.0098   16.0   1.8      0.011   15.9   0.6    1.5  2  DUF4449         Protein of unknown function (DUF4449)
  ------ inclusion threshold ------
      0.011   15.6   2.8      0.011   15.6   2.8    1.7  2  Apolipoprotein  Apolipoprotein A1/A4/E domain
      0.011   15.9   0.6      0.036   14.3   0.4    1.9  2  DUF948          Bacterial protein of unknown function (DUF948


Domain annotation for each model (and alignments):
>> ATP-synt_B  ATP synthase B/B' CF(0)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.3   5.1   1.9e-11   4.3e-08       6     115 ..       9     118 ..       5     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 33.3 bits;  conditional E-value: 1.9e-11
  ATP-synt_B   6 liallilvgllikfawkplkkvLdkReekIadeiaeAeerrkeaaallaeaeqqlkeAraeAaeiiknAkkeaeklkeeieaeaeaeaerlkesAaaeI 104
                  +a++  v ll++ + k ++++Ldk ++ Ia++ ++ eer   a++ l +a q  ++  +e +ei + Ak +a+k+ e+ +++ e+e ++  e A+  I
  AHX11330.1   9 NVAFVAAVSLLFRPVTKAIRNILDKYSKGIATGVDSLEERLHVAKESLRSAIQSSAQLDDEVEEILARAKTRAAKITEAGKKRIEKEFASALERARVAI 107
                 579************************************************************************************************ PP

  ATP-synt_B 105 eqekdralaeL 115
                   e    l  L
  AHX11330.1 108 TEENRIFLVRL 118
                 99987766665 PP

>> Laminin_II  Laminin Domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.3   1.1e-06    0.0024      13      76 ..      14      78 ..       9     104 .. 0.89
   2 ?   -3.4   0.0       4.1   9.1e+03      21      90 ..     153     156 ..     137     163 .. 0.48

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 1.1e-06
                XXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHH CS
  Laminin_II 13 kevleqlaplsqnlentkeklse.inrsveetnekvkdankairdArrsvkkLeklapqLldklk 76
                ++v     p+ + + n+ +k+s+ i++ v+  +e ++ a++ +r+A +s+ +L+ +++++l++ k
  AHX11330.1 14 AAVSLLFRPVTKAIRNILDKYSKgIATGVDSLEERLHVAKESLRSAIQSSAQLDDEVEEILARAK 78
                677778899************8549************************************9965 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.1
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX--TTTTTGGGHHHHHHHHHH...HHH CS
  Laminin_II  21 plsqnlentkeklseinrsveetnekvkdankairdArrsvkkLeklapqLldklkelkqleeassslsd 90 
                 +                                                                  ls 
  AHX11330.1 153 Q------------------------------------------------------------------LSM 156
                 1..................................................................222 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.2   3.5e-06    0.0079      21      91 ..      26      97 ..      21     120 .. 0.84
   2 ?   -0.0   0.1      0.41   9.1e+02      70      95 ..     139     163 ..     110     164 .] 0.70

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 3.5e-06
                HHHHCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHCCC CS
   Fib_alpha 21 glqdlllkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn.dnvikksskeleeeil 91
                 ++++l+ky k + + +++le++l+ +++s ++a + + +++d ++e  + +k    ++++  +k++e+e +
  AHX11330.1 26 AIRNILDKYSKGIATGVDSLEERLHVAKESLRSAIQSSAQLDDEVEEILARAKTRaAKITEAGKKRIEKEFA 97
                6999*****************************************999998887656667777777877654 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.41
                 HHHHHHHHHHHHHHHHHHHCCCHHHH CS
   Fib_alpha  70 kskkdndnvikksskeleeeilrlke 95 
                 ++++ ++ +i++++++l  + +rlke
  AHX11330.1 139 QNSE-HEVMISRMTEQLSMNFTRLKE 163
                 3333.578888888888888888776 PP

>> SpoU_sub_bind  RNA 2'-O ribose methyltransferase substrate binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.3   9.7e-06     0.022       3      56 ..      40      94 ..      38     100 .. 0.92

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 9.7e-06
  SpoU_sub_bind  3 yGlhaVleaLksgrr.iekllvtegradkrleellklakkrgikvelvdkekLdk 56
                    G+ + +e L+  ++ +++ + ++ + d+++ee+l++ak r  k+ ++ k++++k
     AHX11330.1 40 TGVDSLEERLHVAKEsLRSAIQSSAQLDDEVEEILARAKTRAAKITEAGKKRIEK 94
                   6889999*****9998999999999**************************9986 PP

>> CKAP2_C  Cytoskeleton-associated protein 2 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.8   4.9e-06     0.011     146     219 ..      21      94 ..      16     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.9e-06
     CKAP2_C 146 EpitspieniiaiyEkailagAqpieelrhvladiltmKsqekvelgenveeakatkeeikevktedveaelek 219
                  p+t  i ni+  y k i++g   +ee  hv ++ l+   q++++l+++vee+ a  ++  +  te  +  +ek
  AHX11330.1  21 RPVTKAIRNILDKYSKGIATGVDSLEERLHVAKESLRSAIQSSAQLDDEVEEILARAKTRAAKITEAGKKRIEK 94 
                 589999**********************************************9887766555555533444443 PP

>> DUF4449  Protein of unknown function (DUF4449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.6   4.8e-06     0.011      21     120 ..      19     114 ..      13     121 .. 0.81
   2 ?   -1.9   0.0       1.4   3.2e+03      10      20 ..     138     148 ..     130     163 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.8e-06
     DUF4449  21 lfKPlllkvirpaiqkalekqirdaleklDaelyevkqeaerakeeaksdpenapniysryldalkkkftkkkekaeekekakkadkkvniavtkedsi 119
                 lf+P+ +k+ir+ + k  +k+i +++  l++ l   k+   +a +++++ ++++++i  r  +++ k  +++k++ e++   ++a +++++a+t+e+ i
  AHX11330.1  19 LFRPV-TKAIRNILDKY-SKGIATGVDSLEERLHVAKESLRSAIQSSAQLDDEVEEILARAKTRAAKITEAGKKRIEKE--FASALERARVAITEENRI 113
                 45553.67777777774.789**************************99777777787777777777778888888773..5577999*********99 PP

     DUF4449 120 f 120
                 f
  AHX11330.1 114 F 114
                 8 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
     DUF4449  10 lkkSkHklLfk 20 
                 +++S+H+++++
  AHX11330.1 138 IQNSEHEVMIS 148
                 77788877765 PP

>> Apolipoprotein  Apolipoprotein A1/A4/E domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   2.8   4.9e-06     0.011      75     182 ..      27      97 ..      21     112 .. 0.47
   2 ?   -2.4   0.0       1.6   3.6e+03     167     183 ..     147     163 ..     139     164 .] 0.63

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
                     CCHHHHHHHHHHHHCHHCCHHCHCCHCHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-----..-----SSSHHHHHHHTS-TTSHH CS
  Apolipoprotein  75 lapyteelrerlaadaeelqeqlavyaeelrerlerhvealkarlapyveelrqklaerleelkeslaphaeeveerlssrveelrekleeqaee 169
                     + ++++++ + +a  ++ l+e+l v +e lr+ ++++                                      ++l+++vee+ +++++ a++
      AHX11330.1  27 IRNILDKYSKGIATGVDSLEERLHVAKESLRSAIQSS--------------------------------------AQLDDEVEEILARAKTRAAK 83 
                     3344444444444455555555555444433333333......................................34444444444444444444 PP

                     HHHS--XXXX.XXX CS
  Apolipoprotein 170 lrerleanle.elk 182
                     ++e   + +e e+ 
      AHX11330.1  84 ITEAGKKRIEkEFA 97 
                     44444444433333 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.6
                     SHHHHHS--XXXXXXXX CS
  Apolipoprotein 167 aeelrerleanleelka 183
                     ++ ++e+l  n  +lk+
      AHX11330.1 147 ISRMTEQLSMNFTRLKE 163
                     45666666666666665 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   1.6e-05     0.036       4      79 ..       6      86 ..       5      93 .. 0.61
   2 ?   -0.6   0.0      0.72   1.6e+03      38      81 ..      92     134 ..      79     142 .. 0.62

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.6e-05
      DUF948  4 lIaAiAFvvLviflivvllkl............kktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavad 79
                +++ +AFv+ v +l++++ k+            +  +d++++++++ ++ +++ ++ +++l ++v+e+l       ++ ++  +++ +
  AHX11330.1  6 IVINVAFVAAVSLLFRPVTKAirnildkyskgiATGVDSLEERLHVAKESLRSAIQSSAQLDDEVEEIL-------ARAKTRAAKITE 86
                57889**********999999888885555555555555555555555555555555555555555555.......544444444444 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.72
      DUF948  38 lekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                 +ek+  + l+ ++ ++++ n+    v+ kl  +d++ + v+d g
  AHX11330.1  92 IEKEFASALERARVAITEENR-IFLVRLKLSLMDEVCAFVKDFG 134
                 555555555555555555555.4446666666677666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (164 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1623  (0.0905237); expected 358.6 (0.02)
Passed bias filter:                      768  (0.0428356); expected 358.6 (0.02)
Passed Vit filter:                        82  (0.0045736); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1210.14
//
Query:       AHX11331.1  [L=97]
Description: frataxin-like domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-06   28.5   0.0    1.3e-06   28.4   0.0    1.0  1  Frataxin_Cyay  Frataxin-like domain


Domain annotation for each model (and alignments):
>> Frataxin_Cyay  Frataxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   7.3e-11   1.3e-06       6     101 ..       5      94 ..       1      97 [] 0.78

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 7.3e-11
                    HHHHHHHHHHHHHHHH.HHHHH--CTS.SEEEETTEEEEEETTS-EEEEEEEGGGTEEEEEES.SEEEEEEEET.TEEEETTTT-BHHHHHHHHHH CS
  Frataxin_Cyay   6 yhkladelldsleekleelaeeaeedeldveyssgvLtiefekkgtyvinkqppnkqIWlsspisgpkrfdydekgeWiskrdgseLkelLeeels 101
                    +++l+  +++++     +l e  ++  +d+e+ +  ++i + kkg + ink     ++W+s  + g+ rf++d+++  + ++dg+e+++ +++ ls
     AHX11331.1   5 FDELSAGVFEEVV----TLVEGCNS-CIDYECLASSVEILT-KKGVLLINKKLDLMELWISNTVIGSMRFSMDQDRGCFINKDGEEIFAWVNNFLS 94 
                    4444555555444....45577534.459999999999977.78******************************666777799***9999988776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       434  (0.0242066); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 720.24
//
Query:       AHX11332.1  [L=149]
Description: 6,7-dimethyl-8-ribityllumazine synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-36  125.2   0.0    1.8e-36  125.1   0.0    1.0  1  DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase


Domain annotation for each model (and alignments):
>> DMRL_synthase  6,7-dimethyl-8-ribityllumazine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.0     1e-40   1.8e-36       3     140 ..       4     132 ..       2     133 .. 0.96

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 1e-40
                    EEEEEEESTTHHHHHHHHHHHHHHHHHCTTSSCCEEEEEESSCCCHHHHHHHHCTSTT-.SEEEEEEEEE--SSCHHHHHHHHHHHHHHHHHHHCT CS
  DMRL_synthase   3 riaiVvarfneeitdkllegaldelkeagvaeenidvvtVPGafElplaakklaesskyldavialGvvirGetphfeyvaeavskglmrvsldtg 98 
                    +i+++ ++ n ei++kl+e a++elk++g    +++ v+VPGafElp a++ l ++  ++ +++ lG++ir +tphf+yv++++++g+m+vsl+++
     AHX11332.1   4 KILVICSKVNPEICKKLYETAIEELKQRGL---RYKAVYVPGAFELPSALNLLQAD--CFLGYVLLGCIIRSGTPHFDYVSSEACRGIMQVSLEKN 94 
                    899**************************7...6****************998773..68************************************ PP

                    S-EEEEEEEESSHHCCHHCCTSTCCCHHHHHHHHHHHHHHHH CS
  DMRL_synthase  99 vPvifgvltvdteeqaleraggkagnkGeeaaeaalemanll 140
                    ++ +fgv+t++++eqaler+      +++ a++a+++m+nl+
     AHX11332.1  95 LALGFGVITANNMEQALERI----VPYAKAAVAACVSMINLK 132
                    ********************....79**************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       570  (0.0317921); expected 358.6 (0.02)
Passed bias filter:                      522  (0.0291148); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1127.28
//
Query:       AHX11333.1  [L=567]
Description: membrane protein insertase, YidC/Oxa1 family [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-51  173.1   9.0      8e-51  172.2   9.0    1.5  1  60KD_IMP       60Kd inner membrane protein
    4.5e-49  167.9   0.1    5.6e-49  167.5   0.1    1.1  1  YidC_periplas  YidC periplasmic domain


Domain annotation for each model (and alignments):
>> 60KD_IMP  60Kd inner membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.2   9.0   8.9e-55     8e-51       1     164 [.     351     547 ..     351     549 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.2 bits;  conditional E-value: 8.9e-55
    60KD_IMP   1 yglaIilltiivrlillpltlkqlkssakmqelqPelkeiqekykkdkqklqqemmklYkkegvnplaGclplLiqlpifialyrvlrsla.....sf. 93 
                 +g+aIillt+++rl++lpl++k+  s+ k++elqPe+ +i++ yk+dk +l+++  +l+kk++v p++Gclp+++q+p+f+aly+v+  +       f 
  AHX11333.1 351 FGVAIILLTLFIRLLMLPLSVKSGVSMVKIKELQPEILKIKKLYKDDKIALNKASVALFKKYNVTPMSGCLPTILQVPVFFALYKVIFITIemrqaPFf 449
                 69*************************************************************************************996656655227 PP

    60KD_IMP  94 .wikdLsapd.......................lpillavttflqqklsksk..km.qkmmlyvmplmilffslsfpaglvlYwlvsnllsiaqqlii 164
                  wikdLs pd                       lpill++t+++qq+l++s+     q +m+  mp ++++++++fp+glvlYw+++n+ls++qq+ i
  AHX11333.1 450 lWIKDLSLPDptnlftlfglldwncptflsigiLPILLGLTMIVQQNLTPSQyeDGtQAFMIKSMPYVFMLLFANFPSGLVLYWVFNNILSVLQQFAI 547
                 89***********************************************7764422478999*********************************988 PP

>> YidC_periplas  YidC periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.5   0.1   6.2e-53   5.6e-49       4     281 ..      60     338 ..      57     340 .. 0.84

  Alignments for each domain:
  == domain 1  score: 167.5 bits;  conditional E-value: 6.2e-53
                    EE-SS-EEEEETBTTEEEEEEEEEEESSTT-SS.EEEECEEETTEE.EEEEEEEESTT-.TTSGG.S--B-B-S-SEEE--TT-SEEEEEEEEE-T CS
  YidC_periplas   4 vdtdvlegsislkGgriddleLkkYketldkdskpveLlspegaet.yvaqsglvgagggkaldp.rktvftaeegeyelaeltdelpvtLtwdng 97 
                    +++ +l+gsi lkG  +d l+Lk+Y ++ d+ +  ++Ll+p ++   y +  g+   ++ + + p ++t++++++++     lt+e pvt+ wdng
     AHX11333.1  60 LSNGKLQGSILLKGLVLDNLSLKEY-KS-DDGTDRYQLLRPVRTASaYSVNPGWSTGNDVELKTPdSNTQWKSDGTS-----LTPENPVTFFWDNG 148
                    67899********************.44.444449*********99*********877755455569********98.....99************ PP

                    TS-EEEEEEEEETT-SEEEEEEEEE--SSS-EEEEEEEEEEEE--.------------EEEEEEETTTCCEEEEHHHHHT......T---EEEEES CS
  YidC_periplas  98 nGltftktytldrdsYlitvtdeveNtsgapvtlapygqlkrdpeeaseeesmfaityegaagvtdeeklqkvkfkdlekd....kkakkekktgg 189
                    +Gl f+  +++d d+Y++t++++veN+s++ +++ap  ++++++++  +++s + i +eg++gv++ +kl ++k+ +l k+      +++ +    
     AHX11333.1 149 SGLLFKVLISID-DKYMFTFKQTVENKSSNDLSVAPHFTITKQSQD--TQKS-MLIMHEGPIGVIK-DKLIELKYNKLVKKnkslLIEEDPR---- 235
                    ************.*****************************9544..2445.568*********7.***********98865542222222.... PP

                    -...EEEEEETTEEEEEEEE.SSSEEEEEEEEEE.....TEEEEEEEE.--EEE-TT-EEEEEEEEEEEE--HHHHHH......HTTGGGHHHHHH CS
  YidC_periplas 190 g...WvamtqkYFlsAlipdqdaetnefyarkkk....kdlyqagylsapavtvapgasasvtarlfaGPkevktlka......ipgLdlavDyGw 272
                        W ++ +kY+l   i  +  ++ ++y + +     +d +q+ +  +p   +  g+s +++++lfaGPke + l++      i  +d+avD+G+
     AHX11333.1 236 NyskWFGFSEKYWLVSQILRN-PTEGKVYISHSLdnnnNDIFQVTTF-HPHRIIRSGSSITQETELFAGPKELALLEEysrsmkILFFDRAVDFGI 329
                    1344***************85.5577777777765543339999999.6***************************7655554567********** PP

                    HHHHTSHHH CS
  YidC_periplas 273 ltfitkplf 281
                    l+++tkp+ 
     AHX11333.1 330 LYVMTKPIS 338
                    *******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (567 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       544  (0.0303419); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 4061.60
//
Query:       AHX11334.1  [L=421]
Description: transporter associated domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.7e-38  131.4   5.9      4e-38  130.9   5.9    1.2  1  DUF21      Cyclin M transmembrane N-terminal domain
    6.7e-19   67.7   0.0    1.5e-17   63.4   0.0    2.3  2  CorC_HlyC  Transporter associated domain
    9.1e-05   22.8   0.6     0.0079   16.6   0.0    3.2  3  CBS        CBS domain


Domain annotation for each model (and alignments):
>> DUF21  Cyclin M transmembrane N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.9   5.9   6.7e-42     4e-38       1     147 [.      11     161 ..      10     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 130.9 bits;  conditional E-value: 6.7e-42
       DUF21   1 liivlllllsaffsgaEtAlvslsrlrleelaekgkkkakrllkllknperlLstlligntlvnillsalatalfvellaegalavviatvivtllilv 99 
                 +++++ llls +fsg+EtA++++++++l +l+ kg+ ka+ ll+l ++ er++st+l++n+++n+++s++ ++l+++++  g+l+++i+t++v+ +++v
  AHX11334.1  11 ILLFASLLLSCVFSGSETAITAVNPAKLTQLKNKGSTKAALLLELYDDKERVISTVLLCNNVANMFASSVSAFLVIDVF--GSLGIIISTFVVSAVVVV 107
                 4567777************************************************************************..69**************** PP

       DUF21 100 fgEilPkslalkyaekialalapplrvlmvllyPlvwllskllnlil......e 147
                 fgEilPk++a+ ++e + ++la++++++ +++ Plv  l+ ++++ l      +
  AHX11334.1 108 FGEILPKAYAISHPEDLGMFLAYFISFVVKIFGPLVQYLNIVIKISLkwfnplK 161
                 ************************************999999988775544432 PP

>> CorC_HlyC  Transporter associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8   0.0      0.04   2.4e+02      31      67 ..     169     205 ..     160     215 .. 0.66
   2 !   63.4   0.0   2.5e-21   1.5e-17       2      80 ..     340     416 ..     339     417 .. 0.95

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.04
                 T-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEE CS
   CorC_HlyC  31 dyeTlgGlllellgriPkegesvevdleglrftVlem 67 
                  y+T+ Gll+ + ++  +++ + ++++ g  + ++e+
  AHX11334.1 169 PYDTIRGLLVLHKKSHSQQNVQKNLEVIGNILDITEI 205
                 7********9999988887663333322444444444 PP

  == domain 2  score: 63.4 bits;  conditional E-value: 2.5e-21
                 EECTTEEEEETT-BHHHHHHHHTSTTHHCT-SBHHHHHHHHH-S---TT-EEEEEETTEEEEEEEEETTCEEEEEEEE- CS
   CorC_HlyC   2 eldegsylvdGslpldeleeelglelpeedyeTlgGlllellgriPkegesvevdleglrftVlemdgrrIkkvrvekl 80 
                 e ++g y+++G++p+++l++ +g+++p e+ +T +G+++++++riP ege   ++  g+ +++l+ + ++I++v+++++
  AHX11334.1 340 ESGDGAYIINGRIPIRDLNKKMGFNFPTENNHTFAGMIIDEIERIPSEGE--IFEMCGCVLEILKKKSNKIVSVKLKRV 416
                 5689**********************************************..88877*******************986 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.78   4.7e+03      22      46 ..      73      95 ..      71      97 .. 0.73
   2 ?    2.8   0.0     0.027   1.6e+02      19      49 ..     227     258 ..     207     265 .. 0.75
   3 !   16.6   0.0   1.3e-06    0.0079      25      55 ..     295     325 ..     273     327 .. 0.74

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.78
                HHHHHHHTSSEEEEEETTTBEEEEE CS
         CBS 22 lelmrekgvsrlPVVdedgklvGiv 46
                ++++  + vs+++V+d  g  +Gi+
  AHX11334.1 73 ANMF-ASSVSAFLVIDVFG-SLGII 95
                5667.44599999998777.77776 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.027
                 HHHHHHHHHHTSSEEEEE.ETTTBEEEEEEHH CS
         CBS  19 eealelmrekgvsrlPVV.dedgklvGivtlr 49 
                 e+++++  +++++ +P   d+d+++v ++  +
  AHX11334.1 227 EDIMRTVLSSRYRWIPLWkDKDDNFVKVLDAS 258
                 89999966999******998888888776655 PP

  == domain 3  score: 16.6 bits;  conditional E-value: 1.3e-06
                 HH.HHT.SSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS  25 mr.ekg.vsrlPVVdedgklvGivtlrDllral 55 
                 ++ +k+ + ++ V+de+g+ +G++t +D+++ +
  AHX11334.1 295 FKvNKNdF-SI-VIDEYGNAIGVITFSDIMEEI 325
                 54455557.89.******************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1019  (0.0568353); expected 358.6 (0.02)
Passed bias filter:                      585  (0.0326287); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 3201.57
//
Query:       AHX11335.1  [L=366]
Description: peptide chain release factor 1 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-67  225.9   0.1    3.8e-67  225.9   0.1    1.5  2  PCRF      PCRF domain
    3.9e-40  136.4   2.7      9e-40  135.2   2.7    1.6  1  RF-1      RF-1 domain
  ------ inclusion threshold ------
      0.032   14.1   0.2      0.057   13.3   0.2    1.5  1  MIR       MIR domain


Domain annotation for each model (and alignments):
>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.9   0.1   6.3e-71   3.8e-67       3     193 .]      13     205 ..      11     205 .. 0.96
   2 ?   -3.3   0.2       1.1   6.7e+03      38      38 ..     279     279 ..     256     305 .. 0.43

  Alignments for each domain:
  == domain 1  score: 225.9 bits;  conditional E-value: 6.3e-71
                 HHHTTTTTST.-GGGTTTGGGSSSTTHHHHHTHHHHHHHHHHHHHTTTHHH...HT.......-S-..-GGGTHHHHHHHHHH..HHHHHT-..SSSTT CS
        PCRF   3 eeleelekklsdpevwedqekakklskelaeleeivealeeleealedleeakelle...edeelaelaeeeleelekeleeleeelkklLlpkdende 98 
                 +++  le+kl  pe ++ ++++ klske+++l++ ve +++ +++++++e +++ll+   ed+e++e+a+ +l+el+  l +le ++kk+L+pkd++d+
  AHX11335.1  13 KRCLYLEEKLRFPEKID-SQEFAKLSKEYSDLRPKVELIDKRKKLQDEIEYLSALLKnssEDPEIREIAKTDLQELQVLLPKLELDIKKMLIPKDKDDS 110
                 56667899999999885.689999********************************5578*************************************** PP

                 SEEEEEEEE-SSTHHHHHHHHHHHHHHHHHHHTTT-EEEEEEEEESSS.SEEEEEEEEESTTHHHHHGGG-EEEEEEEE-TTSSS--EEEEEEEE CS
        PCRF  99 knaileiraGaGGdeaalfaedLlrmYtryaerkgwkvevldaseeeagGikevtleiegegaYgkLkfEsGvHRvqRvpetesqgrihTStatV 193
                  n+ile+raG+GGdeaalfa++L++mY++yaer++wk+e++++s++e+gG+ke+t++i+g+++++kLkfEsGvHRvqRvpetes+grihTStatV
  AHX11335.1 111 LNVILEVRAGTGGDEAALFAASLFNMYHKYAERMKWKFEIISISHNEIGGYKEATASISGSDVFSKLKFESGVHRVQRVPETESSGRIHTSTATV 205
                 **********************************************************************************************9 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.1
                 H CS
        PCRF  38 v 38 
                 +
  AHX11335.1 279 L 279
                 1 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.2   2.7   1.5e-43     9e-40       2     116 .]     213     322 ..     212     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 135.2 bits;  conditional E-value: 1.5e-43
                 CCCCE--GGGEEEEEE---SSSSSSGCSSSCEEEEEETTTTEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCHTTTTT-.S.-S---S.-- CS
        RF-1   2 eieieidekdleidtfrssGaGGQnVNktesaVrlthlptgvivvecqeeRsqekNrekAlerLkaklkekeleeekeeekkrrvkkekkkigtgs.se 99 
                 +++++i++kdl+id++rssG+GGQ+VN+t+saVr+th+ptg ivv  q+e+sq+kNr+kA+++Lk +l+e e+++ ++e +++r k   ++ig+g+ se
  AHX11335.1 213 DVDVKINDKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPTG-IVVMQQDEKSQHKNRAKAMKILKVRLYEIERSKVEKEISSMR-K---SQIGSGErSE 306
                 6899*************************************.8*************************8876777666666666.4...48******** PP

                 ECEEEECGCTTEEEETT CS
        RF-1 100 kiRtynkkpqsrvkdhr 116
                 k Rtyn+ pq+r++dhr
  AHX11335.1 307 KTRTYNF-PQGRITDHR 322
                 *******.********9 PP

>> MIR  MIR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   9.5e-06     0.057     114     167 ..     213     271 ..     182     312 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 9.5e-06
         MIR 114 d.....nDkveifekksttgmksaklvprdsyvrlqHvvtgcwLhstsvklkkekfekv 167
                 d     nDk +  +   ++g + +++ + ds vr+ H+ tg +++ +  k + ++  k 
  AHX11335.1 213 DvdvkiNDKDLRIDVYRSSGPGGQSVNTTDSAVRITHIPTGIVVMQQDEKSQHKNRAKA 271
                 24455677744455567889999*********************999999766644433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2663.35
//
Query:       AHX11336.1  [L=258]
Description: acyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-18   66.2   0.0    2.9e-18   65.8   0.0    1.2  1  Acyltransferase  Acyltransferase


Domain annotation for each model (and alignments):
>> Acyltransferase  Acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.0   1.6e-22   2.9e-18       2     134 ..      67     194 ..      66     195 .. 0.94

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 1.6e-22
  Acyltransferase   2 vrvtglenlpekgpailvaNHqsylDvlllwlllyksngprnvviiakkellsipllgflmrllgfifidRksnaraagslenise...lleeg 92 
                      ++v+g en+++ +++i+++ H s lDvlll+ l+       ++ +i+k++l +ip++g  m ++++i i+ ++++++  +l ++++   +l ++
       AHX11336.1  67 FEVRGRENIEVYEKFIVASKHHSPLDVLLLADLF------VKPAFILKRSLVYIPIFGLYMIATKMITITYSKKSNGVDVLRKMLRqakVLAKN 154
                      689*****************************99......79*****************************88888888888888888889999 PP

  Acyltransferase  93 klvviFPEGtrsregellpfkkGlvrlaakakkgvpivPvai 134
                      + ++++PEG+r++ g+ ++ k+G+v l  ++  ++p++Pva+
       AHX11336.1 155 RTIILYPEGGRTKVGQQVEYKRGIVALYKHL--KLPVIPVAL 194
                      99*****************************..*******85 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       790  (0.0440627); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 2022.46
//
Query:       AHX11337.1  [L=38]
Description: hypothetical protein NHE_0388 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       112  (0.00624686); expected 358.6 (0.02)
Passed bias filter:                      102  (0.00568911); expected 358.6 (0.02)
Passed Vit filter:                         3  (0.000167327); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 293.31
//
Query:       AHX11338.1  [L=520]
Description: S1 RNA binding domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.5e-55  183.9  22.6    1.3e-13   51.1   2.4    6.5  6  S1             S1 RNA binding domain
    1.2e-07   31.5   0.2       0.12   12.4   0.0    4.2  3  RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
    7.8e-06   26.6   0.2     0.0066   17.2   0.0    4.5  5  PCB_OB         Penicillin-binding protein OB-like domain
    4.3e-05   23.5   2.9         14    5.8   0.0    5.9  7  S1_2           S1 domain
  ------ inclusion threshold ------
      0.015   15.6   0.0        1.4    9.3   0.0    3.1  3  Phage_TAC_4    Phage tail assembly chaperone
      0.035   14.4   1.0         28    4.9   0.0    4.0  4  RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
        0.1   12.6   0.1         15    5.6   0.0    3.7  3  CusF_Ec        Copper binding periplasmic protein CusF
       0.15   11.6   2.0         15    5.1   0.0    3.5  4  DUF2110        Uncharacterized protein conserved in archaea (


Domain annotation for each model (and alignments):
>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.8   0.3   3.8e-13   8.5e-10       3      74 ..       3      67 ..       2      68 .. 0.96
   2 !   19.2   0.1   5.3e-07    0.0012       8      75 .]      91     154 ..      86     154 .. 0.91
   3 !   51.1   2.4   5.8e-17   1.3e-13       3      75 .]     173     249 ..     171     249 .. 0.92
   4 !   50.7   0.0   7.5e-17   1.7e-13       3      75 .]     264     332 ..     262     332 .. 0.95
   5 !   22.5   0.1   4.7e-08    0.0001      20      75 .]     367     423 ..     349     423 .. 0.82
   6 !   12.5   0.3   6.2e-05      0.14       3      39 ..     438     474 ..     436     498 .. 0.78

  Alignments for each domain:
  == domain 1  score: 38.8 bits;  conditional E-value: 3.8e-13
                TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEE CS
          S1  3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsi 74
                ++g+vveG+++sv+++ + V+lg + eg +p+ + ++        ++l++G  + v+v+k++   ++++ls+
  AHX11338.1  3 KEGDVVEGIIKSVSPHFVLVNLGLKSEGKIPIQQFPNV-------DELQIGSSIMVYVEKTETGGGSLVLSY 67
                79**********************************87.......************************996 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 5.3e-07
                 EEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1   8 veGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                 +eG++    k G +Ve++ g  +f+p s+l+ +   +++d    vG ++k+++lk++ ++++i +s+k
  AHX11338.1  91 IEGVILYTIKSGCIVEVE-GLNAFLPNSHLDVR---PVSDPATLVGVKLKFRILKMEPKTGKIFVSRK 154
                 7999999999********.************77...888888899*******************9986 PP

  == domain 3  score: 51.1 bits;  conditional E-value: 5.8e-17
                 TTTCEEEEEEEEEETTEEEEEET.....TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1   3 ekgevveGeVtsvtkgGafVelg.....ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                 ++ge+++G V+s+  +G+f+++      + v+g++ ++++s+  rv +p+  ++vG+ev+vkv++vd +++ri+l +k
  AHX11338.1 173 KEGEIIDGRVKSIASYGVFIQIHesdkvGVVDGLLYINDISWA-RVTHPSSIYSVGQEVRVKVIGVDTEKGRISLGVK 249
                 79********************865454569***********9.*******************************986 PP

  == domain 4  score: 50.7 bits;  conditional E-value: 7.5e-17
                 TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                   g+++ G+Vts++++G+fV+l++gveg+v+  e+s+      ++  + ++++v v +l vd++  +i+lsi+
  AHX11338.1 264 TPGNIYPGVVTSIEDYGVFVRLEEGVEGLVHSGEISWT----REKPLFLPNQKVNVMLLSVDEESHKIALSIR 332
                 679**********************************9....677789***********************97 PP

  == domain 5  score: 22.5 bits;  conditional E-value: 4.7e-08
                 EEEEET.TTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEETTTTEEEEEEC CS
          S1  20 afVelg.ngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdkdrrriilsik 75 
                 + V+ +   v+g+v ++++s+    ++  +++kvGdev +k+  v+ dr+r+ +s+k
  AHX11338.1 367 MLVDQDySYVRGYVRVANISWSQNPRKDLKRFKVGDEVQAKLVHVNADRGRVMFSLK 423
                 4566667789************88889999***********************9986 PP

  == domain 6  score: 12.5 bits;  conditional E-value: 6.2e-05
                 TTTCEEEEEEEEEETTEEEEEETTTEEEEEEGGGSSS CS
          S1   3 ekgevveGeVtsvtkgGafVelgngvegfvpaselsr 39 
                 ++ge +e+++ +v+++G+++e+ +g e f   +++sr
  AHX11338.1 438 NEGELIEAKIMRVEDDGIYIEVREGLEFFTAQADVSR 474
                 79********************999998877777774 PP

>> RNase_II_C_S1  RNase II-type exonuclease C-terminal S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   9.1e-05       0.2      34      56 ..     224     246 ..     214     249 .. 0.81
   2 ?    2.3   0.0     0.073   1.6e+02      36      56 ..     309     329 ..     269     331 .. 0.75
   3 !   12.4   0.0   5.3e-05      0.12      34      57 ..     398     421 ..     393     423 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 9.1e-05
  RNase_II_C_S1  34 lplGervrVrLveADvatrrvrF 56 
                      +G++vrV++  +D +++r+ +
     AHX11338.1 224 YSVGQEVRVKVIGVDTEKGRISL 246
                    579*****************986 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.073
  RNase_II_C_S1  36 lGervrVrLveADvatrrvrF 56 
                    + ++v V L ++D ++ ++ +
     AHX11338.1 309 PNQKVNVMLLSVDEESHKIAL 329
                    678899999999988888865 PP

  == domain 3  score: 12.4 bits;  conditional E-value: 5.3e-05
  RNase_II_C_S1  34 lplGervrVrLveADvatrrvrFe 57 
                     ++G++v+ +Lv+++ +++rv F+
     AHX11338.1 398 FKVGDEVQAKLVHVNADRGRVMFS 421
                    679********************8 PP

>> PCB_OB  Penicillin-binding protein OB-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       1.1   2.4e+03      32      63 ..       5      36 ..       2      60 .. 0.78
   2 ?    1.5   0.0      0.22     5e+02      31      98 ..     174     235 ..     151     251 .. 0.70
   3 !   17.2   0.0   2.9e-06    0.0066      25      69 ..     259     303 ..     244     334 .. 0.88
   4 ?   -0.5   0.0      0.92   2.1e+03      41      92 ..     358     403 ..     318     416 .. 0.65
   5 ?    0.4   0.0      0.47   1.1e+03      30      55 ..     438     463 ..     428     480 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 1.1
                TTEEEEEEEEEETTEEEEEETTS-EEEEEGGG CS
      PCB_OB 32 gelrpAvVlsvseksarvglrdgetgtipleg 63
                g+++++++ svs+  + v l  +++g ip+++
  AHX11338.1  5 GDVVEGIIKSVSPHFVLVNLGLKSEGKIPIQQ 36
                67778888888888888888777888887765 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.22
                 CTTEEEEEEEEEETTEEEEEETTS.....-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEEEEEEE- CS
      PCB_OB  31 sgelrpAvVlsvseksarvglrdg.....etgtipleglkwarkvlsdkkqgkapksasdvlkpGdvvlvrke 98 
                 +ge+  + V s+   ++ +++++        g + +++++war            + +s + ++G+ v+v+  
  AHX11338.1 174 EGEIIDGRVKSIASYGVFIQIHESdkvgvVDGLLYINDISWARV-----------THPSSIYSVGQEVRVKVI 235
                 56666677777777777777765555555778899999999998...........567777777777777765 PP

  == domain 3  score: 17.2 bits;  conditional E-value: 2.9e-06
                 CCTSSTCTTEEEEEEEEEETTEEEEEETTS-EEEEEGGGGTTTGC CS
      PCB_OB  25 lkklpdsgelrpAvVlsvseksarvglrdgetgtipleglkwark 69 
                 ++k  + g+++p+vV+s+++ ++ v l++g +g +   +++w r+
  AHX11338.1 259 ISKKYTPGNIYPGVVTSIEDYGVFVRLEEGVEGLVHSGEISWTRE 303
                 45666889**********************************997 PP

  == domain 4  score: -0.5 bits;  conditional E-value: 0.92
                 EEETTEEEEEETTS....-EEEEEGGGGTTTGCCTTTS-B---CCCHCCC--TTEE CS
      PCB_OB  41 svseksarvglrdg....etgtipleglkwarkvlsdkkqgkapksasdvlkpGdv 92 
                 +++++++ ++l d+     +g + +++++w ++          p++  +++k+Gd 
  AHX11338.1 358 EITDSGMVLMLVDQdysyVRGYVRVANISWSQN----------PRKDLKRFKVGDE 403
                 555555555554433333455556666666665..........5555555555554 PP

  == domain 5  score: 0.4 bits;  conditional E-value: 0.47
                 TCTTEEEEEEEEEETTEEEEEETTS- CS
      PCB_OB  30 dsgelrpAvVlsvseksarvglrdge 55 
                 ++gel +A +++v+++++ +++r+g 
  AHX11338.1 438 NEGELIEAKIMRVEDDGIYIEVREGL 463
                 678999***************99884 PP

>> S1_2  S1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.022        50       2      48 ..       5      53 ..       5      53 .. 0.83
   2 ?   -3.1   0.0       3.9   8.7e+03      15      34 ..     101     119 ..      94     121 .. 0.74
   3 ?    4.1   0.0     0.022        49       2      27 ..     175     200 ..     175     202 .. 0.93
   4 ?    3.3   0.0     0.038        86       2      34 ..     266     298 ..     265     305 .. 0.85
   5 ?   -0.5   0.0      0.59   1.3e+03       1      20 [.     348     367 ..     348     374 .. 0.78
   6 ?   -4.1   0.0       7.7   1.7e+04      38      45 ..     398     405 ..     396     405 .. 0.79
   7 !    5.8   0.0    0.0064        14       2      30 ..     440     468 ..     440     482 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.022
        S1_2  2 GkintlkvlretdfgyfLqkdesgevlLpkkevp..eeleiGdeveVFv 48
                G +++  ++  ++  + ++ + + e   p ++ p  +el+iG+++ V v
  AHX11338.1  5 GDVVEGIIKSVSPHFVLVNLGLKSEGKIPIQQFPnvDELQIGSSIMVYV 53
                556677788888888888877779999999999999**********986 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 3.9
        S1_2  15 fgyfLqkdesgevlLpkkev 34 
                  g  ++ ++  + +Lp++++
  AHX11338.1 101 SGCIVEVEG-LNAFLPNSHL 119
                 566677777.7889999875 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.022
        S1_2   2 GkintlkvlretdfgyfLqkdesgev 27 
                 G+i   +v+ + + g+f+q +es++v
  AHX11338.1 175 GEIIDGRVKSIASYGVFIQIHESDKV 200
                 8999***************9998876 PP

  == domain 4  score: 3.3 bits;  conditional E-value: 0.038
        S1_2   2 GkintlkvlretdfgyfLqkdesgevlLpkkev 34 
                 G i    v+ ++d g+f+  +e++e l++  e+
  AHX11338.1 266 GNIYPGVVTSIEDYGVFVRLEEGVEGLVHSGEI 298
                 556667899*************9**99999887 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.59
        S1_2   1 iGkintlkvlretdfgyfLq 20 
                 +G   + +v ++td g++L 
  AHX11338.1 348 LGVLLKCRVAEITDSGMVLM 367
                 57778899*********995 PP

  == domain 6  score: -4.1 bits;  conditional E-value: 7.7
        S1_2  38 leiGdeve 45 
                 +++Gdev+
  AHX11338.1 398 FKVGDEVQ 405
                 799**995 PP

  == domain 7  score: 5.8 bits;  conditional E-value: 0.0064
        S1_2   2 GkintlkvlretdfgyfLqkdesgevlLp 30 
                 G+  ++k+ r +d g++++  e+ e++  
  AHX11338.1 440 GELIEAKIMRVEDDGIYIEVREGLEFFTA 468
                 88999**************9998887755 PP

>> Phage_TAC_4  Phage tail assembly chaperone
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.24   5.4e+02      16      48 ..     230     262 ..     228     268 .. 0.89
   2 ?    9.3   0.0   0.00061       1.4      12      49 ..     309     346 ..     302     375 .. 0.90
   3 ?    0.8   0.0      0.26   5.9e+02      19      54 ..     407     442 ..     402     484 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.24
  Phage_TAC_4  16 lpvklprldgekakveftfkamdrkelaeleee 48 
                  + vk+  +d ek  + + +k+++ + +++++++
   AHX11338.1 230 VRVKVIGVDTEKGRISLGVKQLTDNPWKDISKK 262
                  57889999********************99876 PP

  == domain 2  score: 9.3 bits;  conditional E-value: 0.00061
  Phage_TAC_4  12 PtFklpvklprldgekakveftfkamdrkelaeleeer 49 
                  P+ k++v+l  +d+e+ k+ + +++ +++ ++++ e+ 
   AHX11338.1 309 PNQKVNVMLLSVDEESHKIALSIRQCNTNPWKKFLEAY 346
                  77799****************************99875 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.26
  Phage_TAC_4  19 klprldgekakveftfkamdrkelaeleeereqsea 54 
                  kl  ++ +   v f +k+++ + ++e+ e+ ++ e 
   AHX11338.1 407 KLVHVNADRGRVMFSLKYVEYDPFEEFIEAVNEGEL 442
                  7888999999***************99999887653 PP

>> RNA_pol_Rbc25  RNA polymerase III subunit Rpc25
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.0     0.013        28       4      39 ..       5      40 ..       3      79 .. 0.86
   2 ?    3.7   0.1      0.03        67       4      35 ..     175     206 ..     173     240 .. 0.86
   3 ?   -3.1   0.0       3.9   8.7e+03       3      24 ..     265     286 ..     264     286 .. 0.88
   4 ?    1.0   0.0      0.21   4.8e+02       4      23 ..     440     459 ..     438     472 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.013
                   TSEEEEEEEEEETTCEEEEBTTBSEEEEECCCCSTT CS
  RNA_pol_Rbc25  4 gevltgkiksstregikvslgffddifvpkelLfep 39
                   g+v++g iks + + + v+lg+ ++  +p +++++ 
     AHX11338.1  5 GDVVEGIIKSVSPHFVLVNLGLKSEGKIPIQQFPNV 40
                   89********************99999998888765 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.03
                    TSEEEEEEEEEETTCEEEEBTTBSEEEEECCC CS
  RNA_pol_Rbc25   4 gevltgkiksstregikvslgffddifvpkel 35 
                    ge++ g++ks    g+++++   d++ v   l
     AHX11338.1 175 GEIIDGRVKSIASYGVFIQIHESDKVGVVDGL 206
                    9*****************99877777666555 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 3.9
                    TTSEEEEEEEEEETTCEEEEBT CS
  RNA_pol_Rbc25   3 vgevltgkiksstregikvslg 24 
                    +g++  g ++s +  g++v+l+
     AHX11338.1 265 PGNIYPGVVTSIEDYGVFVRLE 286
                    6889999***********9985 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.21
                    TSEEEEEEEEEETTCEEEEB CS
  RNA_pol_Rbc25   4 gevltgkiksstregikvsl 23 
                    ge +++ki + + +gi +++
     AHX11338.1 440 GELIEAKIMRVEDDGIYIEV 459
                    99**************9986 PP

>> CusF_Ec  Copper binding periplasmic protein CusF
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.6   3.6e+03      40      59 ..      40      59 ..      38      65 .. 0.82
   2 ?    5.6   0.0    0.0068        15      37      58 ..     392     413 ..     387     419 .. 0.83
   3 ?    1.9   0.0       0.1   2.3e+02      36      53 ..     468     485 ..     464     494 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.6
                ESS-STT-EEEEEEEEETTC CS
     CusF_Ec 40 laglkaGdkVrFefekrdgg 59
                +++l+ G  +++ +ek++ g
  AHX11338.1 40 VDELQIGSSIMVYVEKTETG 59
                689999****9999999855 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0068
                 TSEESS-STT-EEEEEEEEETT CS
     CusF_Ec  37 pallaglkaGdkVrFefekrdg 58 
                  ++l+++k+Gd+V+ ++++ + 
  AHX11338.1 392 RKDLKRFKVGDEVQAKLVHVNA 413
                 679***********99988765 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.1
                 TTSEESS-STT-EEEEEE CS
     CusF_Ec  36 dpallaglkaGdkVrFef 53 
                  +a++++l++G++ +F +
  AHX11338.1 468 AQADVSRLAVGQRLKFVV 485
                 4689***********976 PP

>> DUF2110  Uncharacterized protein conserved in archaea (DUF2110)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       1.1   2.5e+03      69      93 ..       3      27 ..       2      43 .. 0.83
   2 ?    0.7   0.1      0.14   3.2e+02      66      95 ..     170     199 ..     155     250 .. 0.74
   3 ?    5.1   0.0    0.0066        15      56      89 ..     251     284 ..     224     305 .. 0.78
   4 ?    2.7   0.0     0.035        79      59      93 ..     428     462 ..     397     484 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 1.1
     DUF2110 69 eegevyvGtlesldedgfvldigve 93
                +eg+v+ G ++s++ +  +++ g +
  AHX11338.1  3 KEGDVVEGIIKSVSPHFVLVNLGLK 27
                6899999****99999889999987 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.14
     DUF2110  66 keveegevyvGtlesldedgfvldigvevr 95 
                 ++++ege++ G+++s+ + g  ++i  + +
  AHX11338.1 170 STIKEGEIIDGRVKSIASYGVFIQIHESDK 199
                 45899*************999999877644 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.0066
     DUF2110  56 llreefgeitkeveegevyvGtlesldedgfvld 89 
                 l  + + +i k+ ++g++y G+++s+++ g  + 
  AHX11338.1 251 LTDNPWKDISKKYTPGNIYPGVVTSIEDYGVFVR 284
                 4556799*********************998654 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.035
     DUF2110  59 eefgeitkeveegevyvGtlesldedgfvldigve 93 
                 + f+e  ++v+ege +   +  +++dg+++++   
  AHX11338.1 428 DPFEEFIEAVNEGELIEAKIMRVEDDGIYIEVREG 462
                 568899999********************998554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (520 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       583  (0.0325172); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.56u 0.25s 00:00:00.81 Elapsed: 00:00:00.39
# Mc/sec: 3988.46
//
Query:       AHX11339.1  [L=308]
Description: signal peptide peptidase SppA, 36K type [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      1e-37  129.5   0.3    1.4e-37  129.0   0.3    1.2  1  Peptidase_S49  Peptidase family S49
      6e-08   32.0   1.0    8.5e-08   31.5   1.0    1.1  1  SDH_sah        Serine dehydrogenase proteinase
    3.6e-07   30.2   2.2    9.7e-07   28.8   1.1    2.0  2  CLP_protease   Clp protease
     0.0042   16.9   0.1     0.0079   16.0   0.1    1.4  1  Succ_CoA_lig   Succinyl-CoA ligase like flavodoxin domain


Domain annotation for each model (and alignments):
>> Peptidase_S49  Peptidase family S49
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.0   0.3   3.2e-41   1.4e-37       4     149 ..     110     256 ..     107     260 .. 0.96

  Alignments for each domain:
  == domain 1  score: 129.0 bits;  conditional E-value: 3.2e-41
                    HTT--EEEEEEEEEETHHHHHHTTSSEEEE-TT-EEE---EEEEEEE-HHHHHHTT-EEEEEESSTTCCCCCTTSS--HHHHHHHHHHHHHHHHHH CS
  Peptidase_S49   4 kakkPvvasaenvaaSggYylasaadkivanpstivgsiGvitqllnlenlldklgvevqvvkaGeyksavslrrelteeereilqrlldetyqqF 99 
                    ++ kP+v++  +v+aSg+Y++a+aad+i+a  s+ivgs+Gv+ q +nl++l+ ++gv+++vv++G +k   s+++++++e r +lqr++++  ++F
     AHX11339.1 110 AQVKPLVVVSHGVMASGAYMAAMAADHIIAHNSSIVGSVGVMVQVTNLHDLASRIGVKMEVVRSGRLKALPSTFEKVPNETRFALQRSVNAAGEYF 205
                    689********************************************************************************************* PP

                    HHHHHHHHTS-HHH.HHCHHCCHEEEHHHHHHTTSSSEETSHHHHHHHHHH CS
  Peptidase_S49 100 vqtVaknRnlsveq.vdkiAegrvltgqqAlklgLvdelgtvddavaelee 149
                    ++ V k R +s  + +++i +g+v++g++A++  L+de+g  ++av++l++
     AHX11339.1 206 LSLVTKRRRISDPAvIEEISTGKVFLGTEAIAISLIDEIGDENNAVEWLKQ 256
                    *********987662699******************************998 PP

>> SDH_sah  Serine dehydrogenase proteinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   1.0   1.9e-11   8.5e-08      77     157 ..      68     150 ..      55     166 .. 0.82

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.9e-11
     SDH_sah  77 dseevlrairltpkdkpidliihtpGGlvlaatqiakalkeh.kaktrvivphyamsGGt.lialaadeiildenavlGpvdp 157
                 d ++ + +    pk k + l i +pGG v a++ + +alk+  + k  v+v h  m+ G+ + a+aad+ii  + +++G v  
  AHX11339.1  68 DRDRRIASFAYNPKIKAVILHINSPGGAVAASEALYNALKSVaQVKPLVVVSHGVMASGAyMAAMAADHIIAHNSSIVGSVGV 150
                 556666677789999************************985267889*******9777625689**************9864 PP

>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   1.1   2.2e-10   9.7e-07      44      98 ..      80     136 ..      71     172 .. 0.83
   2 ?    0.0   0.0      0.15   6.7e+02     145     181 ..     211     247 ..     195     248 .. 0.74

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 2.2e-10
                   -SSS-EEEEEEE--B-HHHHHHHHHHHHHS..SS-EEEEEEEEEETHHHHHHHTS-T CS
  CLP_protease  44 dpdkdillyinspGGsvtaglaIydtmqyi..kpdvsticlGlaaSmgslllaagek 98 
                    ++k + l+inspGG v a+ a+y++++ +    + +++  G+ aS + + ++a+++
    AHX11339.1  80 PKIKAVILHINSPGGAVAASEALYNALKSVaqVKPLVVVSHGVMASGAYMAAMAADH 136
                   57899**********************99854234457888*******999999986 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.15
                   HHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-SS CS
  CLP_protease 145 khtgqslekiekdldrdtflsaeeAveyGLideviek 181
                   k+   s   + ++++  +++  +eA++  Lide+ ++
    AHX11339.1 211 KRRRISDPAVIEEISTGKVFLGTEAIAISLIDEIGDE 247
                   55555555666677777888899**********9875 PP

>> Succ_CoA_lig  Succinyl-CoA ligase like flavodoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.1   1.8e-06    0.0079      39     106 ..      66     137 ..      56     164 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.8e-06
  Succ_CoA_lig  39 dvdvadlleylaedpetkvillylEsird....grkflsaarraarkkpvvvlksGrseagaraaashtgal 106
                   d+d    ++ +a  p++k+++l++ s +      +++ +a++++a+ kp+vv+  G  ++ga +aa     +
    AHX11339.1  66 DLDRDRRIASFAYNPKIKAVILHINSPGGavaaSEALYNALKSVAQVKPLVVVSHGVMASGAYMAAMAADHI 137
                   66666678889999***********96654444899*********************999988776544333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (308 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2321.19
//
Query:       AHX11340.1  [L=558]
Description: ABC transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-28   98.0   0.0      1e-27   97.3   0.0    1.4  1  ABC_tran        ABC transporter
    2.3e-16   60.3  27.3    3.6e-16   59.6  27.3    1.2  1  ABC_membrane    ABC transporter transmembrane region
    0.00038   20.0   4.4     0.0034   16.9   4.2    2.1  1  SMC_N           RecF/RecN/SMC N terminal domain
     0.0017   18.3   0.0     0.0038   17.1   0.0    1.6  1  RsgA_GTPase     RsgA GTPase
      0.008   15.9   0.1      0.017   14.9   0.1    1.5  1  AAA_29          P-loop containing region of AAA domain
  ------ inclusion threshold ------
      0.027   14.8   0.0      0.052   13.9   0.0    1.5  1  AAA_16          AAA ATPase domain
      0.048   13.9   0.0       0.14   12.5   0.0    1.7  1  AAA_22          AAA domain
      0.072   12.8   0.2       0.39   10.4   0.0    2.0  2  IstB_IS21       IstB-like ATP binding protein
       0.92    8.7  13.8       0.11   11.7   6.2    2.2  2  ABC_membrane_3  ABC transporter transmembrane region
       0.95    8.9   3.7       0.45    9.9   0.1    2.1  2  TMEM215         TMEM215 family


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.3   0.0   5.7e-31     1e-27       2     137 .]     349     489 ..     348     489 .. 0.94

  Alignments for each domain:
  == domain 1  score: 97.3 bits;  conditional E-value: 5.7e-31
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.........HHHTCHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.........esdeeiekalsk 91 
                 +n+s+k+++ge va+vG +G GKSt+l+l++g ++  +G i+++g ++++ ++  +r+ ++++pqe ++ ++  ++en         + d++++++ + 
  AHX11340.1 349 NNLSFKINRGEHVAFVGASGGGKSTILALILGFYSACAGCITINGIPVSNLSRACVRSLFAWVPQELSVISGN-LKENvcmksegnsDNDDHFADICAA 446
                 89****************************************************************9999999.899999999998777788******* PP

                 STTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  92 lglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpta 137
                  ++++l++++   + s LS Gqkqr+ +ara++ +++++llDE+t+
  AHX11340.1 447 ANIHDLPKNT---DISDLSRGQKQRINIARAIFADRQVILLDEATS 489
                 **99977666...36*****************************96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.6  27.3     2e-19   3.6e-16       1     267 [.      17     277 ..      14     286 .. 0.87

  Alignments for each domain:
  == domain 1  score: 59.6 bits;  conditional E-value: 2e-19
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHHSCH CS
  ABC_membrane   1 liliillailagvlsplfplvlgrildtlldkgdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfkkilrqpmsffdtnsv 97 
                   ++l++l+ +l+g+ls++   ++g+ +++++d g   +     ++l+++++ l+ ++++ ++  +   +g r+   l  +l+  +++++++ +++n  
    AHX11340.1  17 VFLAVLTVFLSGFLSIALGKIIGHSVQSISDGGIGGS-----LLLMIVFFSLFLSLIVSFRGIFSGLLGVRIAEGLLFDLYGVLIKANLETINRNAR 108
                   4566666667777777777777777777766666666.....777777777777777888888889************************9998543 PP

                   HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHH CS
  ABC_membrane  98 GellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlvllailpliilvsaviakilkklkkkeqkavakassvaeEslsgirtVk 194
                     + + l +dv  l++++g+   +++++++tf+g+li++fy+   l+l l+  +p+i+l+  +++  +k+l+     + +k++  + Esls+i+ +k
    AHX11340.1 109 -LIPTILGSDVMVLQNFFGSGGPVLLRNIMTFLGSLIILFYTEKTLFLYLILSIPVILLLLLLFGVNVKRLSFIATGKSDKVYLEIKESLSNIQIIK 204
                   .56677******************************************************************************************* PP

                   HTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHH CS
  ABC_membrane 195 afgreeyflekfekaleeakkagikkaianglligitqllgllsyalalwfGttlvisgelsvgdlvvflslf 267
                   af +e++f ++  k ++e+ ++ +++ i+++++igi ++l++l +++ + fG+  v+++ +++ +l  f+ ++
    AHX11340.1 205 AFLKERFFFNRVFKLTKEFSRSFVRYVIIRSVFIGIVMALVFLGVSIFIDFGVGSVLDNRINSATLSEFIFYA 277
                   *******************************************************999987776655444444 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   4.2   1.9e-06    0.0034      27     213 ..     361     533 ..     338     538 .. 0.67

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.9e-06
                 EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSEEEEEET.TEEE-HHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
       SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.skekasvkkaeveitfdnedkklkiekeevsisrrvkrkgeseykin.gkevtkkev 123
                  a vG+ G GKs +l  i   LG+ sa       +   i+      +++++a v  +f    ++l++ + +++ ++ +k++g+s+        +  +++
  AHX11340.1 361 VAFVGASGGGKSTILALI---LGFYSA-------CAGCITInGIPVSNLSRACVRSLFAWVPQELSVISGNLKENVCMKSEGNSDNDDHfADICAAANI 449
                 566777777777777655...775444.......22222211244456667777777755555544444444333333333333322220234555777 PP

                 HHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 124 sellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvgvtk 213
                 ++l ++++is   LS+G+k+ + +a       +  + + llDe  + LD +n k + +++ +   +  +i++++r   ++++dk++ ++k
  AHX11340.1 450 HDLPKNTDIS--DLSRGQKQRINIAR----AIFADRQVILLDEATSSLDRSNEKDIDSIIAAMPRDKTVIMVAHRFSGIKNMDKIIVIKK 533
                 7777777776..6******9877763....2344555799*********************************************99887 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   2.1e-06    0.0038      67     121 ..     325     380 ..     299     392 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 2.1e-06
                  HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCT CS
  RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkd.ktsvlvGqSGvGKStLinallp 121
                  e+ +ele  ++++ + s++++  +++l+ +++  + +++vG SG GKSt++  +l+
   AHX11340.1 325 EQFDELEFKDVQFSYKSSEDNVVINNLSFKINRgEHVAFVGASGGGKSTILALILG 380
                  333445555677777888888999******9988****************988865 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   9.5e-06     0.017      15      41 ..     351     376 ..     346     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 9.5e-06
      AAA_29  15 htieidlkgatlltGpsGsGKSTllDA 41 
                  +++i++ + + ++G+sG GKST+l A
  AHX11340.1 351 LSFKINRGEHVAFVGASGGGKSTIL-A 376
                 5688987779**************9.4 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   2.9e-05     0.052      22     122 ..     356     472 ..     348     515 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.9e-05
      AAA_16  22 grpelvllsGesGvGKsslvrellralekd.ggiflrgkcdqlesaipysalaqalareellrqllde................aesaeleawreklee 103
                 +r+e v ++G+sG GKs+++  +l  +++  g+i+++g  +++        l +a+ r +l++ + +e                + +++ +++ + +++
  AHX11340.1 356 NRGEHVAFVGASGGGKSTILALILGFYSACaGCITINGIPVSN--------LSRACVR-SLFAWVPQElsvisgnlkenvcmksEGNSDNDDHFADICA 445
                 45689*******************6444432355566666665........8888855.8888888886666666666666655333344444444555 PP

      AAA_16 104 ala........avpelagaeasrllel 122
                 a++        ++++l++ +++r++ +
  AHX11340.1 446 AANihdlpkntDISDLSRGQKQRINIA 472
                 444676666665555555555555555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   7.6e-05      0.14       6     104 ..     359     492 ..     355     516 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 7.6e-05
      AAA_22   6 gilvvtGesGtGKTtllrrlleqldeeakaeeerpevv...fvtlpsst..sskdllrellralglelka............................. 70 
                  +++ +G sG GK+t l+ +l  + +       +++++    + +++++    ++l+ ++ ++l +   +                             
  AHX11340.1 359 EHVAFVGASGGGKSTILALILGFYSA-------CAGCItinGIPVSNLSraCVRSLFAWVPQELSVISGNlkenvcmksegnsdnddhfadicaaanih 450
                 67899******************975.......777775464444555566899999999999998777788999999999999999999999988888 PP

      AAA_22  71 ...erlsseell.ealeqalrarav....ielliiDEaqh.lr 104
                    ++ + ++l   + ++   ar +    ++++++DEa   l+
  AHX11340.1 451 dlpKNTDISDLSrGQKQRINIAR-AifadRQVILLDEATSsLD 492
                 88888888888844444444444.45999********988775 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00022      0.39      19      70 ..     332     382 ..     318     401 .. 0.72
   2 ?   -0.5   0.1      0.48   8.7e+02      99     145 ..     469     514 ..     454     525 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00022
   IstB_IS21  19 ledidfraarsldkrkvkeLatlsf.iekkenivllGpsGvGKs.hlaialgve 70 
                 ++d++f+ + s d+  +++L   sf i++ e ++++G sG GKs  la  lg  
  AHX11340.1 332 FKDVQFSYKSSEDNVVINNL---SFkINRGEHVAFVGASGGGKStILALILGFY 382
                 45566666656665555555...55499***************72578888854 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.48
   IstB_IS21  99 laralkrllkvdllilDdlgllpldqaeaellfeviekryerrsiii 145
                 ++ a + ++  ++++lD+ ++  ld+ +++++  +i++    +++i+
  AHX11340.1 469 INIARAIFADRQVILLDE-ATSSLDRSNEKDIDSIIAAMPRDKTVIM 514
                 333344455567788887.5788999999999999988765555554 PP

>> ABC_membrane_3  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   6.2   6.1e-05      0.11      11     164 ..      16     177 ..       6     186 .. 0.80
   2 ?    1.2   0.8       0.1   1.8e+02      18      69 ..     238     289 ..     225     291 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 6.1e-05
  ABC_membrane_3  11 rlavtfllvlaenvlllayPlligfaiddllagkvaqlliyalvv..llliligaarrivDTRaysrIyaelavevvleqrqqdldtSkvaarl. 102
                      +++  l v++  +l +a+  +ig  ++++  g +  +l++++v+  l+l li + r i       rI + l   ++   ++ +l+t +++arl 
      AHX11340.1  16 LVFLAVLTVFLSGFLSIALGKIIGHSVQSISDGGIGGSLLLMIVFfsLFLSLIVSFRGIFSGLLGVRIAEGLLFDLYGVLIKANLETINRNARLi 110
                     344455678899**********************998888887772257789*****************************************94 PP

  ABC_membrane_3 103 .....alsrelvdFlEkhlPtlitavvsivgavvmllvlefslglsallillllllllprFarrner 164
                          + +  l +F+ +  P+l+ ++++ +g++++l   e  l l  +l + ++llll  F    +r
      AHX11340.1 111 ptilgSDVMVLQNFFGSGGPVLLRNIMTFLGSLIILFYTEKTLFLYLILSIPVILLLLLLFGVNVKR 177
                     432221233466************************9999888877777777777777777655555 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.1
  ABC_membrane_3  18 lvlaenvlllayPlligfaiddllagkvaqlliyalvvllliligaarrivD 69 
                     + ++ ++++l + ++i f + ++l +++  + +   ++  l++  ++ ri+D
      AHX11340.1 238 IGIVMALVFLGVSIFIDFGVGSVLDNRINSATLSEFIFYALLASTSIGRIMD 289
                     4455677889999******************999999999999999999998 PP

>> TMEM215  TMEM215 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.7      0.77   1.4e+03      18      40 ..      13      37 ..       5      42 .. 0.86
   2 ?    9.9   0.1   0.00025      0.45     114     200 ..     433     518 ..     411     534 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.77
     TMEM215 18 svflvfGfmftv..sGlkGetlGdi 40
                s+flvf  ++tv  sG+   +lG+i
  AHX11340.1 13 SIFLVFLAVLTVflSGFLSIALGKI 37
                9*****9999987789999999887 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00025
     TMEM215 114 krkgevsvsssitvgeakslikkvdqdevlryldacypsnvlsgvgdvstysvldkkcsardrsayseaedkvllvPrd.siivysyk 200
                 + +++++ +   ++++ + l k++d  +++r  ++    n+  ++    ++  ld+ +s+ drs+ +++++ +  +Prd  +i+++++
  AHX11340.1 433 NSDNDDHFADICAAANIHDLPKNTDISDLSRGQKQR--INIARAIFADRQVILLDEATSSLDRSNEKDIDSIIAAMPRDkTVIMVAHR 518
                 445666677777788888888888888888865554..456677788889999**************************445555665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (558 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       945  (0.0527079); expected 358.6 (0.02)
Passed bias filter:                      467  (0.0260472); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 3932.36
//
Query:       AHX11341.1  [L=581]
Description: ribonucleoside-diphosphate reductase, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.6e-110  370.1   0.0    3.3e-71  240.4   0.0    2.1  2  Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
    6.4e-14   51.7   0.0    1.2e-13   50.8   0.0    1.5  1  Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
  ------ inclusion threshold ------
        0.1   12.7   0.0        0.2   11.8   0.0    1.4  1  IFNGR1           Interferon gamma receptor (IFNGR1)


Domain annotation for each model (and alignments):
>> Ribonuc_red_lgC  Ribonucleotide reductase, barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  240.4   0.0   5.5e-75   3.3e-71       2     344 ..      70     389 ..      69     391 .. 0.91
   2 !  127.6   0.0   8.3e-41   4.9e-37     382     523 ..     399     544 ..     396     545 .. 0.97

  Alignments for each domain:
  == domain 1  score: 240.4 bits;  conditional E-value: 5.5e-75
                      EE.....BSS-EEEE-X..............XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC   2 sCfvlsvedslesIletvkeaallskaggGvGlnlsklRakgslvkgtegaasGpvsfmklidavadvvkqgGkRrGAamvylevwHpDiekfi 95 
                      sCf+ ++edsle+I +  +e + l  +ggGvG ++ +lR+ g+ vk  +g++sG+++f+ + +a + +++qg  RrG+ +vyl v+Hp+i++f+
       AHX11341.1  70 SCFLNETEDSLEGIVNLWNENVWLAAHGGGVGSYWGNLRSIGEKVKC-SGKTSGIIPFIVVQNALTLAISQGSLRRGSSAVYLPVNHPEIMEFL 162
                      9********************************************87.9********************************************* PP

                      XXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.........................XXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC  96 daKekntgeeenrlsnlnisvgvpdlFmeavkedkdwtLfsPrtvvkleklygeefeeeyeeleekakikkkevkakeLfeeiaesawetgePg 189
                      d+++   g+ ++++ nl+ +v+++d+Fm av ++k w+L+sP++                       +   ++v+a++++ +i++++ etgeP+
       AHX11341.1 163 DLRRPTGGDPNRKALNLHHAVVISDDFMDAVIHNKGWNLISPKD-----------------------SAIITTVSARDIWIKILTARLETGEPY 233
                      ***9989999*********************************3.......................222349********************* PP

                      XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.... CS
                      xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
  Ribonuc_red_lgC 190 vlfkDtiNrrnvlekak.ggkIratNlCgEiplleyes......vavCnLasinLakfvkkdeegkkefdwdelkkviqlvvraLdnvid.... 272
                      +l++D+  +r +  ++     ++++NlC+Ei+l++  +      +avC L+s+nL+kf           +w++  + i+ v+ +Ldnv++    
       AHX11341.1 234 ILYIDNTQKRRPEIYKRlNLGVKMSNLCAEITLTTGLDhlnnhrTAVCCLSSLNLEKFD----------EWEHDTHFIRDVMHFLDNVLEdfin 317
                      ************988884558**************999999*****************9..........4555555555555555555542200 PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 273 vnkyplpeiekntkktRriGlGvmgladalaklgipydseealkfarkitelltyyaykaSvelAkergpfp 344
                           + ++++++ ++R+iG+Gvmg++++l k+gip++s  a +++ ki++ +  +a + S e+A  +g++p
       AHX11341.1 318 KAPSSMSKAKYSAVRERSIGMGVMGFHSLLQKKGIPFESAIAKSVNLKIFQKIRSEADRVSREMALTKGACP 389
                      566668999************************************************************987 PP

  == domain 2  score: 127.6 bits;  conditional E-value: 8.3e-41
                      XXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 382 rnamvtalaPTgsiSlia.gtssgiePifalvykksvtvgeflevnpvfeeeLkklglwseellkki...lesvqgleeipeeikrvfktaldi 471
                      r+++ +a+aPT+siS+ia +ts gieP+ a+v+++++ +g+f++ n+++ e L+k+g ++ee  + i   ++svq+l+ + e+ k vf+ta++i
       AHX11341.1 399 RFTHKIAIAPTASISIIAgNTSPGIEPYAANVFIQKTLSGSFIVRNKHLDELLEKKGENNEETWSSIithEGSVQHLDFLTEDEKMVFRTAYEI 492
                      778999***********98999*****************************************9999777777********************* PP

                      XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Ribonuc_red_lgC 472 dqedhikaqaaiqkwidqsiSktinlpneatvedvkelyllAwklGlKgvty 523
                      dq+++i+++a+++++++qs+S++++l+++   +++++++llAwk+GlK+++y
       AHX11341.1 493 DQRWIIEHAADRTPYVCQSQSVNLFLHSDLHKRELHQIHLLAWKKGLKSLYY 544
                      **************************************************99 PP

>> Ribonuc_red_lgN  Ribonucleotide reductase, all-alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.8   0.0   2.1e-17   1.2e-13       3      83 .]       2      66 ..       1      66 [. 0.92

  Alignments for each domain:
  == domain 1  score: 50.8 bits;  conditional E-value: 2.1e-17
  Ribonuc_red_lgN  3 ltynalkvledrYllkdengeivEspqqmfmRvAlalaiaealydkleedkdlaeefydlmssqkflpasPtlmnaGtelg 83
                     lt ++  vl+drYl    ++   Es+q++f+RvA + a          +d  +ae++y+++s+++f+pa+P+l+n Gt++g
       AHX11341.1  2 LTSFGKAVLKDRYLQ---QS---ESYQDLFARVAHYYA----------DDPMHAERLYNYISNLWFMPATPILSNGGTKRG 66
                     5778999*******6...44...8**************..........7999**************************986 PP

>> IFNGR1  Interferon gamma receptor (IFNGR1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.3e-05       0.2      38     123 ..     247     331 ..     228     335 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.3e-05
                 SEEEEEEE--.SEEEEEEEEEETTT--B-----EEEEE-XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      IFNGR1  38 vqCelaiess.envCvsvvgvskvwevrtekskevCvpelvvslvdiyyiKkindlkrkkiilkksleskvksatsetkleskYsli 123
                 +  +l++ ++ +n C +++++++ ++++  +    C+++l++ ++d +       + ++ + l ++le+ +++a s +  + kYs +
  AHX11341.1 247 IYKRLNLGVKmSNLCAEITLTTGLDHLNNHRTAVCCLSSLNLEKFDEWEHDT-HFIRDVMHFLDNVLEDFINKAPS-SMSKAKYSAV 331
                 55578999999*************************************8766.99***************999999.8888999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (581 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       452  (0.0252106); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 4367.87
//
Query:       AHX11342.1  [L=114]
Description: HIT domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      3e-25   88.8   0.0    3.5e-25   88.6   0.0    1.0  1  HIT       HIT domain
    2.2e-15   57.1   0.0    2.7e-15   56.8   0.0    1.1  1  DcpS_C    Scavenger mRNA decapping enzyme C-term binding
  ------ inclusion threshold ------
      0.036   14.2   0.1       0.81    9.8   0.0    2.1  2  PilO      Pilus assembly protein, PilO


Domain annotation for each model (and alignments):
>> HIT  HIT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6   0.0   5.8e-29   3.5e-25       1      97 [.      13     109 ..      13     110 .. 0.96

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 5.8e-29
                 TGCC-CCEEEE-SSEEEEE-SS-SSSSEEEEEESSTGCSGGGCC..HHHHHHHHHHHHHHHHHHHTCTTCCCEEEEEEESGGGT-SSSS-EEEEEEC-T CS
         HIT   1 ekeipstvvyeddlvlafldidpkapghlLvipkkhlselhdlt..eeelakllsavkkvakalqkkfknkglrvvinngahagqsvahlHiHviprre 97 
                 +ke p++++yedd+vlaf+d +p+ap+h+Lvipk + + + d+    ++++ ++s v  va+ l+   +++g+rvv+n g  agq+v+h H+H+++++e
  AHX11342.1  13 RKELPCKKIYEDDEVLAFHDAFPMAPIHVLVIPKGKFTSFADFVasSADVGSFFSKVADVARILEV--EKTGYRVVTNHGSGAGQTVKHFHVHILAGKE 109
                 6899**************************************988899****************99..788*************************986 PP

>> DcpS_C  Scavenger mRNA decapping enzyme C-term binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.8   0.0   4.5e-19   2.7e-15       3     101 ..       7     106 ..       5     113 .. 0.82

  Alignments for each domain:
  == domain 1  score: 56.8 bits;  conditional E-value: 4.5e-19
                 HHHHHHTTSS-B-EEEE-SSEEEEE-SS-SSSEEEEEEESS---SGGG--TTTTT..HHHHHHHHHHHHHHHTT-T-EEEEE--SCCCT--S-S--EEE CS
      DcpS_C   3 vfnilakgkepervvyedekfvvlkDikpkaklhllvipkrdikslrdLtkehlp..llkemrekakkvieekynevdaeelrvgvhyqPsvyhlHlHv 99 
                 +f ++ +++ p + +yed++++++ D+ p a++h+lvipk +++s  d+ ++  +     + + ++  ++e ++ ++++   + g  + ++v+h+H+H+
  AHX11342.1   7 IFARILRKELPCKKIYEDDEVLAFHDAFPMAPIHVLVIPKGKFTSFADFVASSADvgSFFSKVADVARILEVEK-TGYRVVTNHGSGAGQTVKHFHVHI 104
                 7889999999**************************************96665550044444444455565655.47999******************* PP

                 EE CS
      DcpS_C 100 is 101
                 ++
  AHX11342.1 105 LA 106
                 98 PP

>> PilO  Pilus assembly protein, PilO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.012        71      81     108 ..      31      60 ..       6      62 .. 0.74
   2 ?    9.8   0.0   0.00014      0.81      99     120 ..      61      82 ..      58     104 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.012
        PilO  81 kefyaelPikiev..tGsYhdigaFvsava 108
                 ++ +   Pi++ v  +G++ ++++Fv++ a
  AHX11342.1  31 HDAFPMAPIHVLVipKGKFTSFADFVASSA 60 
                 6777788999988446*********98755 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00014
        PilO  99 digaFvsavakLpRIvtledlk 120
                 d+g+F+s+va+  RI+++e+  
  AHX11342.1  61 DVGSFFSKVADVARILEVEKTG 82 
                 89**************998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       323  (0.0180155); expected 358.6 (0.02)
Passed bias filter:                      304  (0.0169558); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.34
# Mc/sec: 995.23
//
Query:       AHX11343.1  [L=264]
Description: exodeoxyribonuclease III [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.2e-17   61.5   0.0      1e-16   61.2   0.0    1.1  1  Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
  ------ inclusion threshold ------
      0.043   13.7   0.6        0.1   12.5   0.0    1.9  2  DUF1409        Protein of unknown function (DUF1409)
       0.16   11.8   0.2       0.32   10.8   0.2    1.4  1  DUF3410        Domain of unknown function (DUF3410)


Domain annotation for each model (and alignments):
>> Exo_endo_phos  Endonuclease/Exonuclease/phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.0   1.7e-20     1e-16       1     233 []      10     255 ..      10     255 .. 0.74

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 1.7e-20
                    EEEEESTG...CHHHHTHHHHHHHHHHHHHHCTTSEEEEEEEBSCTCHHHHHHHHHTTCEEEEECCHECSSSTTSSEEEEEECSTEEEEEEEEEEE CS
                    xxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Exo_endo_phos   1 ltwNvngq...aspalgssrrsdrladlltaydaDvlgLQEvdddelsriplllalggflgasstsptgggggggnggavlsrfpltslfrrtfie 93 
                    +twNvn+     +p          ++  l + + Dvl+LQE++++e+s++ +   +  ++   +       ++ +ng+a+lsrfp+  +       
     AHX11343.1  10 ATWNVNSIrqrVEP----------VQRFLLSEKIDVLLLQELKCQEESFPFQVFQDLSYNVILRC------QKAYNGVAILSRFPIVKV------- 82 
                    7******8444334..........9999999999****************999988444444444......699************555....... PP

                    TSSSSGCEEEEEEEEEEEEEEE............CCCHHGHHHHHHHHHHHHHHHHHHHHHTTSEEEEEE.E-SSSTSGGGBSCGHHHHHHCTTTH CS
                    xxxxxxxxxxxxxxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
  Exo_endo_phos  94 fndlvaalrreplaakleqlni............ashrdhdlvrdlqllalllqvealnadrgapvivaG.DfNarpsdddsrvlrtrglalapap 176
                     + lv  ++ +   +++e++               s+ +++   ++q+ + l +++   + +   ++++G D Na+p   d+ +  +  + +   +
     AHX11343.1  83 SDSLVNDDEARYIEGTVEFPGKrirlisiyvpnaQSPDSPRFEYKMQFHDALTRRITEYLSHANEILLLGgDINAAPENIDVYDHVKLDGCTGFHI 178
                    222333333333333333333355556778****8888888888888888888888887777777777777****999999999888888888777 PP

                    .........H..............SSCESCETTTTTTTTTTTEB-BEEEEEECHHHCCEEEEEEECCHHEEC.......TSSCSSSB CS
                    .........x..............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxx RF
  Exo_endo_phos 177 .........v..............glyllgggptptyvtraggsrlDrilaspalalfrsgvlppplalvrr.......ealtlSDH 233
                                                 ++ ++     ++ g+r+D+il s + a           +lv++       + +++SDH
     AHX11343.1 179 kernklrelLnigmfdtfrmkypdKQEFSWWDYRGGGLQKNEGMRIDHILTSAEGAD----------SLVDCyivkslrYIEKPSDH 255
                    7776666550566778888999******************************73222..........33333555555578999999 PP

>> DUF1409  Protein of unknown function (DUF1409)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   1.7e-05       0.1      12      35 ..      13      36 ..      11      39 .. 0.93
   2 ?   -3.1   0.2       1.3   7.7e+03       7      12 ..      84      89 ..      83      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
     DUF1409 12 dvGsIRsRveeiqdqlpddladvl 35
                +v sIR Rve +q  l+ + +dvl
  AHX11343.1 13 NVNSIRQRVEPVQRFLLSEKIDVL 36
                788*******************98 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 1.3
     DUF1409  7 dsLvnd 12
                dsLvnd
  AHX11343.1 84 DSLVND 89
                99**98 PP

>> DUF3410  Domain of unknown function (DUF3410)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   5.3e-05      0.32      37      62 ..     183     207 ..     178     213 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                 HHHHCTTCCCHHHHHHHT------GG CS
     DUF3410  37 lfRrelekakgFdalRknYpeRREfs 62 
                 ++R+ l + + Fd+ R +Yp++ Efs
  AHX11343.1 183 KLRE-LLNIGMFDTFRMKYPDKQEFS 207
                 5665.56999***************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2281.92
//
Query:       AHX11344.1  [L=93]
Description: phosphoribosyl transferase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-06   25.6   0.1    7.9e-06   25.5   0.1    1.1  1  Pribosyltran  Phosphoribosyl transferase domain
    3.1e-05   23.5   0.1    3.5e-05   23.3   0.1    1.1  1  UPRTase       Uracil phosphoribosyltransferase
    0.00019   21.0   0.1    0.00024   20.7   0.1    1.3  1  PRTase_2      Phosphoribosyl transferase
    0.00081   18.7   0.1    0.00093   18.5   0.1    1.0  1  PRTase_3      PRTase ComF-like


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   0.1   1.8e-09   7.9e-06      52     124 ..      22      88 ..       3      91 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 1.8e-09
                   TT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
  Pribosyltran  52 evplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlv 124
                   ++p a ++++k+r++ ++ ++++      ++  +++  +++ DD+++tG T    +elL+ ++p+++ +++l+
    AHX11344.1  22 TIPQATLSVEKRRENLQNAFSIK------NSVGIRNAFIILLDDVITTGATASSCAELLAQHNPKRIVVITLA 88 
                   56777788888888888888875......677999******************************99999886 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.1   7.8e-09   3.5e-05      95     159 ..      26      87 ..      12      91 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 7.8e-09
     UPRTase  95 ghlglqreeetlepveyynkLPkkiaertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsv 159
                   l ++++ e+l+    ++     i++  ++llD vi TG++a ++ +lL ++  + ++I+v+++
  AHX11344.1  26 ATLSVEKRRENLQNAFSIK-NSVGIRNAFIILLDDVITTGATASSCAELLAQH--NPKRIVVITL 87 
                 4555555665665444433.234457777***********************4..5799*99987 PP

>> PRTase_2  Phosphoribosyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   5.4e-08   0.00024     119     158 ..      49      87 ..       7      91 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 5.4e-08
    PRTase_2 119 aaakelvLvDDEistGktalnliralqeklprkryvvvsl 158
                  +++ ++L DD i+tG ta   ++ l +++p+ r+vv++l
  AHX11344.1  49 IRNAFIILLDDVITTGATASSCAELLAQHNPK-RIVVITL 87 
                 45678****************99999998886.5666666 PP

>> PRTase_3  PRTase ComF-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   2.1e-07   0.00093      94     165 ..       8      79 ..       3      89 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 2.1e-07
    PRTase_3  94 kpvlkvklhraatksedygslsaedreklilndkyhidker.lkgktlifldDiritgshedkirkslkeekl 165
                 k++ ++++++++ ++   ++ls e+r++  l++ + i + + +++  +i ldD+ +tg +++   ++l++++ 
  AHX11344.1   8 KVSVRLDVLSKTRNTIPQATLSVEKRREN-LQNAFSIKNSVgIRNAFIILLDDVITTGATASSCAELLAQHNP 79 
                 5667788888888889999***9998877.7889999877548*******************99999988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      378  (0.0210832); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 715.62
//
Query:       AHX11345.1  [L=295]
Description: protein-export membrane protein SecF [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-53  180.5  11.1    2.2e-53  180.5  11.1    1.7  2  SecD_SecF  Protein export membrane protein
    9.5e-09   34.5   2.9    1.7e-08   33.7   2.9    1.5  1  Sec_GG     SecD/SecF GG Motif


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.2      0.12   1.1e+03     135     171 ..      21      56 ..      19      60 .. 0.69
   2 !  180.5  11.1   2.5e-57   2.2e-53      11     185 ..     114     286 ..     105     290 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.12
                 HHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTT CS
   SecD_SecF 135 tiltslttllvvvallllggdslkdfalallvGlivg 171
                  i+  ++++l+v + ++lg + l +f + ++ Gl++ 
  AHX11345.1  21 KIAFYMSLVLTVTTFFFLGTKGL-NFGIDFTGGLVLE 56 
                 56667788888888888888877.5666666666655 PP

  == domain 2  score: 180.5 bits;  conditional E-value: 2.5e-57
                 S.-EEEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHH CS
   SecD_SecF  11 k.daekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrv 108
                 + ++++ +++ vgp++++ l+ k++la+++++++i+iy+ +rF +++ala +++++hDvi+++ ++s l ie++ ++vaa+LtiiGYS+nd+vv+fd++
  AHX11345.1 114 PyNFQYERIDYVGPQIGHSLIYKSILAIGFSVLGIFIYLLFRFSYSFALAGVVTIIHDVIFLMCIYSSLAIEFNTSSVAAVLTIIGYSINDSVVIFDKL 212
                 34689999******************************************************************************************* PP

                 HHHHHH--SS-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHHHHH CS
   SecD_SecF 109 renlrkkkratlkeiinlslnqtLtrtiltslttllvvvallllggdslkdfalallvGlivgtyssifiaspllll 185
                 ren+     ++l + in s+n+tL+rtilts tt+l+++ + ll ++ ++ fal++l G+++gtyssifi++pl+ll
  AHX11345.1 213 RENIGV---KDLYKRINISVNTTLSRTILTSFTTMLAIAPVALLSNGDIQTFALMILSGVAIGTYSSIFISAPLALL 286
                 ***877...89**************************************************************9875 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   2.9   1.9e-12   1.7e-08       1      25 [.      36      60 ..      36      63 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 1.9e-12
                .HHHHC--EE-TTTS-EEEEEEEE- CS
      Sec_GG  1 islftkGlNLGlDFtGGthielqfd 25
                ++l+tkGlN+G+DFtGG ++e++ +
  AHX11345.1 36 FFLGTKGLNFGIDFTGGLVLEIRSQ 60
                79********************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      411  (0.0229238); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2289.74
//
Query:       AHX11346.1  [L=752]
Description: NADP-dependent malic enzyme [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-68  231.5   0.0    2.5e-68  230.8   0.0    1.4  1  PTA_PTB        Phosphate acetyl/butaryl transferase
      3e-30  105.4   0.6    6.5e-28   97.8   0.1    2.9  2  malic          Malic enzyme, N-terminal domain
    3.6e-13   49.4   0.5    1.9e-12   47.1   0.5    2.1  1  Malic_M        Malic enzyme, NAD binding domain
  ------ inclusion threshold ------
      0.078   12.7   6.7      0.033   13.9   1.9    2.6  2  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
      0.079   12.3   0.1       0.25   10.7   0.0    1.8  2  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,
       0.17   11.2   1.0       0.49    9.7   1.0    1.7  1  ThiF           ThiF family


Domain annotation for each model (and alignments):
>> PTA_PTB  Phosphate acetyl/butaryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  230.8   0.0   8.3e-72   2.5e-68       6     319 .]     437     747 ..     432     747 .. 0.95

  Alignments for each domain:
  == domain 1  score: 230.8 bits;  conditional E-value: 8.3e-72
                 HHHHHCTS--EEEES-TTSHHHHHHHHHHHHTTSSEEEEES-HHHHHHHHHHCTB--TT.-EEE-TTT-CCHHHHHHHHHHHCCCC.S-HCCHHHHTT. CS
     PTA_PTB   6 ivekakkekkrivlpegedervlkAakelleegiadviLigdeaeikakaleldldlsg.ieivdpetsekleeyadelyelrkrkgvtieearevvr. 102
                 i+   +++kkr++++ege+ r ++ a +  ++g +++iL+g ++ i+++ +e +l     iei +++ s+k +ey++ +y+  +rkg   ++  + ++ 
  AHX11346.1 437 ISGMLRENKKRVIFAEGEEIRSIRVAVQWRDMGYGTPILVGRSSLIEERMQEMNLSSRSgIEILNAAVSKKNDEYIEYMYRTLQRKGFLHRRCVRDIKt 535
                 55667899*********************************8888888888888876666****************************99998777777 PP

                 SHHHHHHHHHHTTSSSEEEE-TTS-HHHHHHHHHHCT-B-TT----EEEEEEEETTEEEEEESSSS-SS--HHHHHHHHHHHHHHHHHCCSS--EEEEE CS
     PTA_PTB 103 datyfaamlvklgeaDglvsGavnttadtlrpalqiiktkpgvklvSsvfimlledrlllfaDcavnvnPtaeelaeialesaktakalgeeeprvAlL 201
                 d+++faa l++ g+ D++++G++++++d l++++ ii+  +   +v s++i+++ + ++++ D+ +   P+a++laeia++ a++++ +g   prvA++
  AHX11346.1 536 DRNVFAACLLAAGDGDAMITGLTRSYSDCLNDVVPIIGVTD---TVFSMSIIITDKDTFFVCDAGIDNIPDAQDLAEIAIKGAEVVQGIG-SSPRVAII 630
                 ***************************************99...555778999*************************************.******** PP

                 -SSSTTSS-SHHHHHHHHHHHHHHHH-TTSEEEEEE-HHHHH-HHHHHHH-TTSTTTT--SEEE-SSHHHHHHHHHHHHHCCTEEEEEEEEESBSS-EE CS
     PTA_PTB 202 SyStkgsakgesvekvrealkivkekapdlvvdGelqlDaAlseevaekkapesevaGkAnvlvfPdLeagnigykivqrlakaeaiGPilqGlakPvn 300
                 + S++gs++ges+ ++rea++i++   + ++++Ge+++D Al+e+ ++  +p  +++G Anvlv+P+ ea++   k  +++ + + iGPil+Gl+k+v+
  AHX11346.1 631 ANSNFGSSNGESALRAREAVEILDDLGVSFEYEGEMEVDTALNERSRDI-YPFLRLSGAANVLVMPSAEAASALCKFSREIMGTTVIGPILLGLNKSVQ 728
                 *********************************************9987.************************************************* PP

                 E--TT--HHHHHHHHHHHH CS
     PTA_PTB 301 dlSrgasvedivnvaaita 319
                 ++ ++  v++i+n+a+i+a
  AHX11346.1 729 IVQPSYDVSEILNLALIAA 747
                 *****************97 PP

>> malic  Malic enzyme, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.8   0.1   2.2e-31   6.5e-28       4     181 ..      26     155 ..      23     156 .. 0.95
   2 ?   -3.8   0.0       3.1   9.3e+03      17      47 ..     351     381 ..     342     400 .. 0.70

  Alignments for each domain:
  == domain 1  score: 97.8 bits;  conditional E-value: 2.2e-31
                 ECCCCCCHHCCCHHHHHHHHSTTCHHHHHHHHHHHGGCHHSCCCEGGGETCHHHHHTTSS.SS..EEEEE-SSSBTTTBS-G.HHHHHHHHHHHHHHHH CS
       malic   4 netlfykllkekleellpivYtPtvgeacqeyseeyrkarglylsikdkekikeilknlpeedvkvivvtdgeriLGlGdlG.vagvgimvGKlaLyta 101
                 + +  +k+l ++  e+l+++Y+P+v+++c e+++++ +a+ +y+s+++                 v+v+++g+++LGlG+lG +a++++m+GK++L+++
  AHX11346.1  26 LGVHATKPLLTQ--EDLSLAYSPGVAQPCLEIKNNPLDAY-KYTSKGNL----------------VAVISNGTAVLGLGNLGaAASKPVMEGKAVLFKK 105
                 566778889999..**************************.********................*****************9999************* PP

                 HHS-EGGGEEEEEECS-BS.HHHHC.TT..S.SSB...SHHHHHHHHHHHHHHHHHHGCTSEEEE-S--CCHHHHHHHHH CS
       malic 102 lagidPekvlpvvldvgtnneelledplYlGlrkkRvkgeeydefvdefveavkelfppkaliqfEDfkaknafeilery 181
                 +a+i+    ++++++++                           +v+ef+++vk++++++++i++ED+k++++fei++r+
  AHX11346.1 106 FADIE---SIDIEVNTE---------------------------DVEEFISTVKNIAGTFGGINLEDIKSPECFEIEQRL 155
                 *****...999999998...........................9*********************************97 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 3.1
                 HHHHHHHSTTCHHHHHHHHHHHGGCHHSCCC CS
       malic  17 eellpivYtPtvgeacqeyseeyrkarglyl 47 
                 +  + i+  P  +e++ +ys+++ ++  +y+
  AHX11346.1 351 KAIADIARMPISAEVMAAYSNTHMQYGKDYI 381
                 4555566667777777777777666655665 PP

>> Malic_M  Malic enzyme, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.5   6.2e-16   1.9e-12       3     226 ..     170     358 ..     168     366 .. 0.84

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 6.2e-16
                 HHHHHHHHHHHHHHHHH-S-GGG--EEEEC-SHHHHHHHHHHHHHHHTTTS-HHHHHTTEEEEETTEE-BTT-S--.-TTTGGGSBS--SS--S....S CS
     Malic_M   3 gTaavalagllaalkitgkklseqkivvlGaGsagiGiaeqivealvkeGlseeeakkkiylvDrkGLltedrekl.eeekkpfakkkeelkeakdklt 100
                 gTa+++ agl++a+ +tg+++++  +vv G G+agi     ++e +++ G+      +ki + D++G++ ++re    ++k  +a + +         t
  AHX11346.1 170 GTAIIVCAGLINAADLTGRRVEDLSVVVNGCGAAGIA----CIELMKNIGV------SKIIVCDQSGVIKTSREFApGDRKAAYAVDIN-------ADT 251
                 9*********************************985....5667777785......58***********9996652456666665433.......348 PP

                 HHHHHHHH--SEEEE-SSSSS-S-HHHHHHHHHHSSS-EEEE--SSGGGSSS-HHHHHHHTTT-SEEEESS----EEETSEEE--EE--GGGTHHHHHH CS
     Malic_M 101 LeevvkkvkptvliGlsgvagafteeivremaksterPiilplSNPtskaEataedvlkwtdgkalvasGsPfkpvelngktyeigQaNNayifPglgl 199
                 Le ++k+  ++v +Gls va++++ e + +m      P+i++l NP+ +++    ++ k  + +a+va+G          +  + +Q NN+  fP l  
  AHX11346.1 252 LEGALKN--ADVFVGLS-VANVLKPEWLSKMN---RDPVIFALANPDPEIDP---ELAKKVRPDAIVATG----------RSDYGNQINNVMCFPYLFR 331
                 9***997..69*****9.67899999998885...68*********987654...4556667899***98..........456789************* PP

                 HHHHTT-SS--HHHHHHHHHHHHTT-- CS
     Malic_M 200 gvivarakritdemllaaaealaelvs 226
                 g++ ++a++ + em laa +a+a++++
  AHX11346.1 332 GALDVNASKFNTEMKLAAVKAIADIAR 358
                 ***********************9875 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.2         1     3e+03      35      55 ..      79      98 ..      67     102 .. 0.80
   2 ?   13.9   1.9   1.1e-05     0.033      24      84 ..     184     247 ..     165     382 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1
                   EEEE--SHHHHHHHHHHHHCT CS
  ELFV_dehydrog 35 vaisGsGnvgsyaallltelg 55
                    a+ G Gn+g +a + ++e g
     AHX11346.1 79 TAVLGLGNLGAAASKPVME-G 98
                   6899*******99998876.4 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.1e-05
                    HTTTS-STTEEEEEE--SHHHHHHHHHHHHCT-EEEEEEESSEEEEETTEE...-HHHHHHHHH CS
  ELFV_dehydrog  24 klkldslegkrvaisGsGnvgsyaallltelgakvvavsDssGviydpeGl...dieellelke 84 
                    +l ++++e+ +v++ G G  g ++++l+++ g + + v D+sGvi  +  +   d+++  ++  
     AHX11346.1 184 DLTGRRVEDLSVVVNGCGAAGIACIELMKNIGVSKIIVCDQSGVIKTSREFapgDRKAAYAVDI 247
                    345558999************************************9988887765555444444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       0.9   2.7e+03      40      53 ..      80      93 ..      72     127 .. 0.81
   2 ?   10.7   0.0   8.5e-05      0.25      26      96 ..     182     263 ..     166     280 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 0.9
                  EEES-SHHHHHHHH CS
  2-Hacid_dh_C 40 GiiGlGrIGqavak 53
                  +++GlG++G a+ k
    AHX11346.1 80 AVLGLGNLGAAASK 93
                  799******98776 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 8.5e-05
                   TCCGSBS-GTTSEEEEES-SHHHHHHHHHHHHTT-.EEEEESSSHHHHH..........CHHHHTCEECSHHHHHHH-SEEE CS
  2-Hacid_dh_C  26 ekallgkelsgktvGiiGlGrIGqavakrlkafgm.kviaydrskkkee..........eeeelgvelvsleellaesDivs 96 
                    ++l+g+++++  v + G+G+ G a ++++k +g+ k+i+ d+s   ++          ++ ++ ++ ++le +l+++D+ +
    AHX11346.1 182 AADLTGRRVEDLSVVVNGCGAAGIACIELMKNIGVsKIIVCDQSGVIKTsrefapgdrkAAYAVDINADTLEGALKNADVFV 263
                   678999*****************************99*****9987332233444443345556667888888888888865 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   1.0   0.00016      0.49      14      50 ..     188     224 ..     175     231 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                 HHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEES CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF  14 ekLrdskvllvGaGglGsellknLalsGvgkltlvDn 50 
                 ++++d +v++ G+G+ G  +++++  +Gv+k+ + D+
  AHX11346.1 188 RRVEDLSVVVNGCGAAGIACIELMKNIGVSKIIVCDQ 224
                 57899*******************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (752 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.28s 00:00:00.96 Elapsed: 00:00:00.44
# Mc/sec: 5103.30
//
Query:       AHX11347.1  [L=51]
Description: hypothetical protein NHE_0399 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       161  (0.00897987); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 376.60
//
Query:       AHX11348.1  [L=37]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       683  (0.0380947); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 279.78
//
Query:       AHX11349.1  [L=641]
Description: ATP-dependent metallopeptidase HflB family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-63  213.5   0.4    4.3e-63  212.6   0.4    1.5  1  Peptidase_M41  Peptidase family M41
    2.3e-45  154.3   0.0    5.4e-45  153.1   0.0    1.7  1  AAA            ATPase family associated with various cellular
      4e-14   52.1   0.1      2e-13   49.9   0.0    2.1  2  AAA_lid_3      AAA+ lid domain
    5.5e-09   36.4   1.4    2.5e-08   34.2   0.4    2.2  2  FtsH_ext       FtsH Extracellular
    3.3e-05   23.2   0.0    6.9e-05   22.2   0.0    1.4  1  TIP49          TIP49 P-loop domain
    0.00026   21.0   0.1     0.0039   17.2   0.1    2.7  1  AAA_5          AAA domain (dynein-related subfamily)
    0.00034   21.0   0.0     0.0011   19.3   0.0    2.0  1  AAA_16         AAA ATPase domain
    0.00063   19.5   0.0     0.0047   16.7   0.0    2.5  3  RuvB_N         Holliday junction DNA helicase RuvB P-loop dom
      0.001   19.4   0.3      0.056   13.7   0.1    3.0  3  AAA_22         AAA domain
     0.0029   17.3   0.0     0.0056   16.4   0.0    1.4  1  IstB_IS21      IstB-like ATP binding protein
     0.0041   17.3   0.5       0.12   12.5   0.0    3.2  3  AAA_2          AAA domain (Cdc48 subfamily)
  ------ inclusion threshold ------
      0.021   14.2   1.2      0.042   13.2   0.2    1.9  2  Mg_chelatase   Magnesium chelatase, subunit ChlI
       0.07   12.8   0.0       0.25   11.1   0.0    2.0  1  AAA_24         AAA domain
      0.072   13.5   0.0       0.17   12.3   0.0    1.6  1  AAA_17         AAA domain
      0.081   13.1   0.0       0.17   12.0   0.0    1.6  1  AAA_33         AAA domain
      0.097   12.9   0.1        0.3   11.3   0.0    1.8  2  AAA_28         AAA domain
       0.12   12.9   0.2       0.38   11.3   0.2    1.8  1  ABC_tran       ABC transporter
       0.28   11.1   1.4       0.63    9.9   0.1    2.3  4  NACHT          NACHT domain
        3.3    8.0   4.7        2.1    8.7   0.4    2.6  2  AAA_19         AAA domain


Domain annotation for each model (and alignments):
>> Peptidase_M41  Peptidase family M41
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  212.6   0.4   4.5e-66   4.3e-63       2     190 ..     407     586 ..     406     587 .. 0.97

  Alignments for each domain:
  == domain 1  score: 212.6 bits;  conditional E-value: 4.5e-66
                    X--HHHHHHHHHHHHHHHHHHCCSSS-S-B--EES--TTS-----------TSS--BHHHHHHHHHHHHHHHHHHHHHHH..S-BGGGHHHHHHHH CS
  Peptidase_M41   2 visekekklvAyHEaGHalvglllkeadpveKvtiiPRgqalGltlslPeedklsltkeellarlavllGGraaEelifg..evttGasnDlekat 95 
                    v++++ek l+AyHEaGHa+ +l l+ +dp++K+tiiPRg+alGl++ lPe+d++s+t++++ a l+v++GGraaEe+ifg  +vt+Gas+D+++at
     AHX11349.1 407 VMRDEEKLLTAYHEAGHAITSLKLEASDPIHKATIIPRGRALGLVMRLPEHDRVSFTRARMHADLIVAMGGRAAEEIIFGedKVTSGASSDIKQAT 502
                    7899****************************************************************************99************** PP

                    HHHHHHHHTS---TTT-S--------..----.------SS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHHHHHHHSEE-HHHHHH CS
  Peptidase_M41  96 kiarkmvtefGmsdklGpvsleeeeeeevflgkelkkekelseetaeeideevkelveeayerakeileekreelealaeaLlekEtldaeeiee 190
                     +ar+mvt++Gms+k+Gp+ + +  +           +++ls+e+ + id+evk l+++a e+a++il+e+ ++l+++a+aLle+Etl++ee+++
     AHX11349.1 503 MLARSMVTKWGMSKKVGPLLYGDPTD-----------NHTLSTEMSNLIDSEVKILITDALENATKILNENLDSLHKIANALLEYETLTGEELSA 586
                    ********************999777...........3579**************************************************9976 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.1   0.0   5.7e-48   5.4e-45       2     130 ..     194     324 ..     193     326 .. 0.97

  Alignments for each domain:
  == domain 1  score: 153.1 bits;  conditional E-value: 5.7e-48
                 EEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHHHHHHTT CS
         AAA   2 llyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksr...sgseseeeervvnqLlteldgvk 97 
                 ll+GppGtGKTllaka+a e++v+f++isgs++++++vg +++++r++f++ k++a p+ +fiDEida++++r    g+ ++e+e+++nqLl e+dg++
  AHX11349.1 194 LLIGPPGTGKTLLAKAIAGEAKVPFFSISGSDFVEMFVGVGASRVRDMFDQGKKNA-PCLIFIDEIDAVGRHRgvgFGGGNDEREQTLNQLLVEMDGFE 291
                 9******************************************************9.******************9999******************** PP

                 TSSSTEEEEEEESSGGGSTHHHHS.TTSSEEEET CS
         AAA  98 kkeskvivigatnrpdkldpallr.gRfdrkiei 130
                  +e+ vi+i+atnrpd ldpal+r gRfdr+i i
  AHX11349.1 292 ANEG-VIIIAATNRPDVLDPALVRpGRFDRQITI 324
                 *866.**************************988 PP

>> AAA_lid_3  AAA+ lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.0   2.1e-16     2e-13       1      44 [.     348     391 ..     348     392 .. 0.98
   2 ?   -1.4   0.0       2.2   2.1e+03      12      24 ..     577     589 ..     564     590 .. 0.71

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.1e-16
   AAA_lid_3   1 dvdlkeLAerTeGySGADlaalcreAallAlrrgikeitmedfe 44 
                 +vd++ +A+ T+G+SGADla+l++e+al A rr++k +t edfe
  AHX11349.1 348 NVDVSIVARGTPGFSGADLANLVNESALIAARRNRKVVTNEDFE 391
                 799****************************************8 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 2.2
   AAA_lid_3  12 eGySGADlaalcr 24 
                 e  +G +l+al+r
  AHX11349.1 577 ETLTGEELSALIR 589
                 557999****997 PP

>> FtsH_ext  FtsH Extracellular
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.4   2.6e-11   2.5e-08       3      95 ..      10      88 ..       8      98 .. 0.80
   2 ?    0.3   0.0      0.96   9.1e+02       2      32 ..     112     139 ..     108     163 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 2.6e-11
    FtsH_ext  3 lwlllallllllllslfg.gsgtgstkeisyseFledleqgnvekvvvqestisalirrptgdgvsttkkgnstttystptlgsvesleekLee 95
                lw+ +++++ ll+ + +  + ++g  ++i +seFl+ +e+g+v+++ +++ +is           +  k+g  ++t  t+++ +v    ++L++
  AHX11349.1 10 LWIGIIVFVTLLFGQVALnLGFGGRNEKIQFSEFLNLVEKGEVQRILIDGYNIS-----------GQLKNGVHFYTKATTYPDLV----PFLRK 88
                566666666666666555699999******************************...........***************95444....44444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.96
    FtsH_ext   2 llwlllallllllllslfggsgtgstkeisy 32 
                 ++++ll++++ +++      +++g  k++s+
  AHX11349.1 112 WFPMLLLIGVWIFFMK---QMQSGGNKTMSF 139
                 4555555555555544...777777777776 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   7.3e-08   6.9e-05      26      88 ..     159     226 ..     142     232 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 7.3e-08
                 XXXXXXXXXXXXXXXXXXXX....XXXXX...XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49  26 lvGqkkareaagvivelike....kklaG...ravLlaGpsgtGktalaiaiskelgedvpfvalsgsev 88 
                 + G  +a+e  + iv++++e    +kl+G   ++ Ll Gp+gtGkt la ai+ e  ++vpf ++sgs++
  AHX11349.1 159 VAGIDEAKEELAEIVDFLREpkkfQKLGGkipKGCLLIGPPGTGKTLLAKAIAGE--AKVPFFSISGSDF 226
                 56777888888888888876433357888333589******************98..57*********86 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   4.1e-06    0.0039       2      37 ..     193     228 ..     192     315 .. 0.63

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 4.1e-06
                 EEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT-- CS
       AAA_5   2 vlLvGppGtgKselaerlaaalnreveyvqltrdtt 37 
                  lL+GppGtgK+ la+ +a   + +++ + ++++ +
  AHX11349.1 193 CLLIGPPGTGKTLLAKAIAGEAKVPFFSISGSDFVE 228
                 59*****************99999999888887664 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-06    0.0011      24     107 ..     184     325 ..     166     406 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-06
      AAA_16  24 p......elvllsGesGvGKsslvrellralekd..............ggif..lrgkcdqlesaipysalaqalareellrqlldeaesaeleawrek 100
                          +ll+G++G+GK+ l+++++ +++                g+ +  +r  +dq ++++p +++++ +++ +  r ++    ++e+e+   +
  AHX11349.1 184 KlggkipKGCLLIGPPGTGKTLLAKAIAGEAKVPffsisgsdfvemfvGVGAsrVRDMFDQGKKNAPCLIFIDEIDAVGRHRGVGFGGGNDEREQTLNQ 282
                 333344599******************987777777777778887777433345888888888888888888888777777777777777777777777 PP

      AAA_16 101 leeala....................................a 107
                 l+ ++                                     +
  AHX11349.1 283 LLVEMDgfeanegviiiaatnrpdvldpalvrpgrfdrqitiS 325
                 7777777777777777777766666666666666666666662 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0     5e-06    0.0047      35      67 ..     192     224 ..     154     264 .. 0.75
   2 ?   -1.8   0.0       2.4   2.3e+03      36      66 ..     353     383 ..     333     420 .. 0.65
   3 ?   -3.3   0.0       7.2   6.8e+03      37      73 ..     521     556 ..     520     567 .. 0.64

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 5e-06
      RuvB_N  35 hvllyGpPGlGkttlakiiakelgvklkitsgP 67 
                  +ll+GpPG Gkt lak ia e +v + + sg 
  AHX11349.1 192 GCLLIGPPGTGKTLLAKAIAGEAKVPFFSISGS 224
                 579*********************998887775 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 2.4
      RuvB_N  36 vllyGpPGlGkttlakiiakelgvklkitsg 66 
                 ++  G PG+  + la+++ +   +  +    
  AHX11349.1 353 IVARGTPGFSGADLANLVNESALIAARRNRK 383
                 5667999999999999998776555555444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 7.2
      RuvB_N  37 llyGpPGlGkttlakiiakelgvklkitsgPvlekag 73 
                 llyG P     tl++ +++ +++++ki  + +le+a+
  AHX11349.1 521 LLYGDPTD-NHTLSTEMSNLIDSEVKILITDALENAT 556
                 56777754.4456666677777777766666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.1     6e-05     0.056       8      29 ..     193     214 ..     190     229 .. 0.85
   2 ?    1.8   0.0      0.29   2.8e+02      87     112 ..     243     283 ..     232     304 .. 0.63
   3 ?   -1.6   0.0       3.2     3e+03      71     117 ..     525     571 ..     494     592 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-05
      AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                 ++++G++GtGKT+l++ ++ ++
  AHX11349.1 193 CLLIGPPGTGKTLLAKAIAGEA 214
                 589*************998766 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.29
      AAA_22  87 rarav..ielliiDEaqhlr..s...........eealeeL 112
                 ++ ++  + l+ iDE++ +   +           e+ l++L
  AHX11349.1 243 DQGKKnaPCLIFIDEIDAVGrhRgvgfgggnderEQTLNQL 283
                 333334459********996541444445554445555555 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 3.2
      AAA_22  71 erlsseellealeqalraravielliiDEaqhlrs...eealeeLrslln 117
                  + +++ l + + + +++  +  +li D  ++  +   +e+l  L++++n
  AHX11349.1 525 DPTDNHTLSTEMSNLIDSEVK--ILITDALENA-TkilNENLDSLHKIAN 571
                 566677777777777777777..8888888887.4366777877777777 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0     6e-06    0.0056      49      72 ..     192     215 ..     188     259 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6e-06
   IstB_IS21  49 nivllGpsGvGKshlaialgveav 72 
                 +++l+Gp+G+GK+ la a++ ea 
  AHX11349.1 192 GCLLIGPPGTGKTLLAKAIAGEAK 215
                 689****************98875 PP

>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.0   0.0      0.88   8.3e+02      10      56 ..     129     176 ..     122     184 .. 0.79
   2 !   12.5   0.0   0.00012      0.12       7      84 ..     194     268 ..     191     298 .. 0.80
   3 ?   -0.7   0.2       1.5   1.4e+03      20      79 ..     533     595 ..     504     631 .. 0.56

  Alignments for each domain:
  == domain 1  score: -0.0 bits;  conditional E-value: 0.88
                 --TTSSHHH.HHHHHHHHTT-....-EEEEEGGG---.----THHHHHH CS
       AAA_2  10 gptgvGkte.lakalaellfvkkekkliradaselle.eeevehlvsrl 56 
                  ++g +kt+   k+ a+ll  ++++k++ +d   + e +ee++++v+ l
  AHX11349.1 129 MQSGGNKTMsFGKSKARLLG-DRNNKVTFKDVAGIDEaKEELAEIVDFL 176
                 45666777788899999999.9**********99999888888888765 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 0.00012
                 EEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG-------THHHHHHHHHTTT-HHHHTTS.EEEEETGGG----...- CS
       AAA_2   7 lllgptgvGktelakalaellfvkkekkliradaselleeeevehlvsrligappgyvgaeegG.ivllDEidKihpk...e 84 
                 ll+gp g+Gkt+laka+a   +v    ++  +  s++ e   +   v    +   +++g+++    +++DEid + ++   +
  AHX11349.1 194 LLIGPPGTGKTLLAKAIAGEAKV----PFFSISGSDFVE---MFVGVGASRVRDMFDQGKKNAPcLIFIDEIDAVGRHrgvG 268
                 789******************98....************...77778888888888888888768********998864443 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.5
                 HHHHHHHTT-....-EEEEEGGG---.....----THHHHHHHHHTTT-HHHHTTSEEEEETGGG CS
       AAA_2  20 akalaellfvkkekkliradaselle.....eeevehlvsrligappgyvgaeegGivllDEidK 79 
                 + ++++l+  ++e k+ + da e ++     + ++ h +++ + + +  +g e +  +  +Ei K
  AHX11349.1 533 STEMSNLI--DSEVKILITDALENATkilneNLDSLHKIANALLEYETLTGEELSALIRGEEIIK 595
                 44444444..4677777777777666444333344445555555555555555555555555544 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       1.7   1.6e+03     112     129 ..     162     179 ..     156     185 .. 0.86
   2 ?   13.2   0.2   4.4e-05     0.042      26      43 ..     194     211 ..     190     215 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 1.7
  Mg_chelatase 112 LDElpefkrkvlevLReP 129
                   +DE+ e  +++++ LReP
    AHX11349.1 162 IDEAKEELAEIVDFLREP 179
                   79999999*********9 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.4e-05
  Mg_chelatase  26 llvGppGsGKtmlakrlp 43 
                   ll+GppG+GKt+lak+++
    AHX11349.1 194 LLIGPPGTGKTLLAKAIA 211
                   89*************986 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00026      0.25       5      24 ..     193     214 ..     190     283 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00026
      AAA_24   5 iliyGpsgiGKTtlakel..gp 24 
                 +l++Gp+g+GKT lak +  + 
  AHX11349.1 193 CLLIGPPGTGKTLLAKAIagEA 214
                 79**************986533 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00018      0.17       1      52 [.     196     248 ..     196     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00018
                 EE-TTSSHHHHHHHHHHHHTEEEEEH.HHHHHHHHHTTTSHSSHHHHCTSHHH CS
      AAA_17   1 lGgPGsGKgtqceklvekygfthlsa.Gdllreeakrgglakardemrklple 52 
                 +G+PG GK+ +++ ++ + +++++s  G+ + e+    g+++ rd +++++++
  AHX11349.1 196 IGPPGTGKTLLAKAIAGEAKVPFFSIsGSDFVEMFVGVGASRVRDMFDQGKKN 248
                 69***************999999887667777888888887778877777665 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00018      0.17       3      29 ..     194     222 ..     193     283 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00018
      AAA_33   3 llvGlpGsGKstlaerllkklg..avlls 29 
                 ll+G+pG+GK+ la+ ++ + +  ++ +s
  AHX11349.1 194 LLIGPPGTGKTLLAKAIAGEAKvpFFSIS 222
                 789************99988776555555 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00032       0.3       3      27 ..     194     219 ..     193     243 .. 0.81
   2 ?   -2.9   0.0       7.4     7e+03     108     151 ..     379     424 ..     365     431 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00032
      AAA_28   3 vitGgestGKTtlleaLa.argypvv 27 
                  ++G+++tGKT l++a+a + ++p +
  AHX11349.1 194 LLIGPPGTGKTLLAKAIAgEAKVPFF 219
                 589**************944466655 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 7.4
      AAA_28 108 rydlvfllppapeidddgeR..redleereaiderlrealrelgip 151
                 r ++ +++++++e+ +d+     e+    ++ +e+l+ a++e+g+ 
  AHX11349.1 379 RRNRKVVTNEDFEYARDKILmgMERKSLVMRDEEKLLTAYHEAGHA 424
                 4444455555555544443311233344455556666666666665 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.2   0.00041      0.38      15      36 ..     194     215 ..     187     224 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00041
                 EEEESTTSSHHHHHHHHTTSS- CS
                 xxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  15 aivGenGaGKStLlkllagllk 36 
                  ++G+ G+GK+ L+k++ag+ k
  AHX11349.1 194 LLIGPPGTGKTLLAKAIAGEAK 215
                 599****************976 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   0.00067      0.63       3      25 ..     193     215 ..     191     219 .. 0.89
   2 ?   -3.6   0.0       9.9   9.3e+03      84     109 ..     252     284 ..     248     301 .. 0.60
   3 ?   -2.7   0.0       5.2   4.9e+03      14      28 ..     502     516 ..     502     523 .. 0.87
   4 ?   -2.9   0.0       5.7   5.4e+03      85      99 ..     547     561 ..     520     593 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00067
                 EEEEC-TTTCHHHHHHHHHHHHC CS
       NACHT   3 vilqGeaGsGKTtLlqklalawa 25 
                 ++l G++G GKT L++ +a +++
  AHX11349.1 193 CLLIGPPGTGKTLLAKAIAGEAK 215
                 6899**************98765 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 9.9
                 EEEEE-STT-SS-TCH................H CS
       NACHT  84 LlilDglDelvtdlgq.......kekqpvrtlL 109
                 L+ +D +D + ++ g        +++q +++lL
  AHX11349.1 252 LIFIDEIDAVGRHRGVgfgggndEREQTLNQLL 284
                 566677776666666555555533334344433 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 5.2
                 HHHHHHHHHHHCTS- CS
       NACHT  14 TtLlqklalawaegk 28 
                 T+L+++++++w  +k
  AHX11349.1 502 TMLARSMVTKWGMSK 516
                 9**********8776 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 5.7
                 EEEE-STT-SS-TCH CS
       NACHT  85 lilDglDelvtdlgq 99 
                 li D+l+ + ++l++
  AHX11349.1 547 LITDALENATKILNE 561
                 566777777777766 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.4    0.0022       2.1      13      31 ..     193     211 ..     188     217 .. 0.82
   2 ?   -0.2   0.4       1.2   1.2e+03      37      37 ..     542     542 ..     459     632 .. 0.54

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0022
      AAA_19  13 llvtaGpGtGKTrvlkhiv 31 
                 +l++++pGtGKT + k+i 
  AHX11349.1 193 CLLIGPPGTGKTLLAKAIA 211
                 799*********9877765 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 1.2
      AAA_19  37 l 37 
                  
  AHX11349.1 542 S 542
                 1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (641 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       723  (0.0403257); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        84  (0.00468515); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.65u 0.30s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 4580.07
//
Query:       AHX11350.1  [L=773]
Description: phenylalanine--tRNA ligase, beta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-56  191.1   0.0    1.9e-56  190.5   0.0    1.3  1  B3_4             B3/4 domain
    2.7e-43  147.9   0.0    4.6e-43  147.2   0.0    1.3  1  tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM 
      1e-21   76.8   0.3    1.9e-21   75.9   0.3    1.5  1  tRNA_bind        Putative tRNA binding domain
    3.4e-18   65.7   0.0    5.2e-16   58.7   0.0    2.9  2  B5               tRNA synthetase B5 domain
    6.8e-12   45.6   0.0    1.6e-11   44.4   0.0    1.7  1  FDX-ACB          Ferredoxin-fold anticodon binding domain


Domain annotation for each model (and alignments):
>> B3_4  B3/4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  190.5   0.0   5.2e-60   1.9e-56       1     174 []     205     379 ..     205     379 .. 0.99

  Alignments for each domain:
  == domain 1  score: 190.5 bits;  conditional E-value: 5.2e-60
                 TSSEEEEEEEES--.-----HHHHHHHHHTT-----HHHHHHHHHHHHHT--EEEEEGGGTBT.EEEEEE--TTEEEEBTTS-EEEE-TTSEEEETEEE CS
        B3_4   1 acpryaarvlrgvkktapspewlqrrLrragirpinnvVDitNyvmlelgqPlhafDldkiqg.divvrlakegeklvtldgkereldeedlviadsek 98 
                 ac+++a+  ++gvk + +spewl++rL r+gir+++++VDi Nyvml++g P+h++D+d+i+g ++++  + ++ k  +ldgke+++ ++ +vi d+ +
  AHX11350.1 205 ACSKFAGLSITGVK-NTDSPEWLRKRLNRIGIRSVSALVDIVNYVMLSYGSPMHIYDADEIKGrSLSISVSVGERKCKALDGKEYTIPDGSIVIEDQVS 302
                 699***********.8**********************************************99*********************************** PP

                 EE.EETTTEEBTTTB--TT--EEEEEEEE--HHHHHHHHHHTT---HHHHHHHH---TTTHHHHHHHHHHHHHHHH- CS
        B3_4  99 pv.slagvmggeeskvsedTknvfleaaafdpvsirktarrlglrseaskrfergvdpekleaaldravallselcg 174
                  v ++ag++g e+s+++ +T+n+fleaa+f+ v+i+ t r+l++++e+++rfergvdp  +e al+ a +++ e+cg
  AHX11350.1 303 EVhAIAGIIGAEKSECTLSTTNIFLEAAVFNCVNIALTRRKLKINTESAYRFERGVDPGFTETALRIAGSMIIEVCG 379
                 ***************************************************************************97 PP

>> tRNA_synthFbeta  Phenylalanyl tRNA synthetase beta chain CLM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  147.2   0.0   1.3e-46   4.6e-43      19     197 ..     480     647 ..     475     660 .. 0.94

  Alignments for each domain:
  == domain 1  score: 147.2 bits;  conditional E-value: 1.3e-46
  tRNA_synthFbeta  19 qklrrklrdllagaGlnEvitysfvsekeldklleddderkavelanPlsedqsvlRtsLlpglLevlarNlargnedvrlFEigkvflkdsee 112
                      + l++++r l+++ G++Evit+sf+se + ++       +++v ++nPl+ +++v+R+s++ +lL+v+++N ++g + vr+FEig+v+ k+   
       AHX11350.1 480 ESLEERIRGLMIARGFSEVITWSFMSERKCAEK------DDLVLIQNPLGLEFNVMRPSIIYNLLDVAQKNHNNGTHIVRVFEIGRVYSKN--- 564
                      6799***********************997555......89**************************************************... PP

  tRNA_synthFbeta 113 elpeeerhlaivltgkreeeswsekaravdfydlkgivealleslgiekvefepae.hpalhpgrsAeikvdgkevGvlGelhpev 197
                         +e++ ++++ +g++ +++++eka+ +df+dlk+ +e l++ l++e+++f+++    ++hpg++A +++ ++++G++Ge+hpe+
       AHX11350.1 565 ---AENSVISALKSGQSFQRNVHEKAHSMDFFDLKADLEMLFNYLNLENISFSKEGlPTWYHPGKAAVVSIAKRRIGFMGEIHPEI 647
                      ...9**************************************************6626678***********************98 PP

>> tRNA_bind  Putative tRNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.9   0.3   5.4e-25   1.9e-21       1      95 [.      42     143 ..      42     144 .. 0.94

  Alignments for each domain:
  == domain 1  score: 75.9 bits;  conditional E-value: 5.4e-25
                 EEEEEEEEEEEETTSSTEEEEEEEESSSSEEEEEESCTTTST.HHHHTTEEEEEETTSESE....EETTEEESSEE-EEEC...CESSCEEEEEESST- CS
   tRNA_bind   1 lrvGkvleaeehpnadkLlvlkvdvGeeeprqivsgaknvye.peelvakkvvvvanlkpk....klrGveSeGMilsaee...ldekevgilelpadv 91 
                 ++v++v e+++hp+ad+L+ + v +G++e  qiv+ga+nv++  ++++a +++v+++  +     k+rG eS GM++s+ e   ++e++ gilel +++
  AHX11350.1  42 FVVARVEEVSKHPQADRLRLCRVSDGNQE-FQIVCGAQNVRAgLKVVLACIGAVIPSNSMSikksKIRGCESMGMLCSSRElglSEEDDGGILELGDEY 139
                 58***************************.************9************9766656688******************999999********** PP

                 -TTC CS
   tRNA_bind  92 eaGe 95 
                 e+G+
  AHX11350.1 140 EIGT 143
                 *998 PP

>> B5  tRNA synthetase B5 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.017        61      10      32 ..      10      50 ..       1     173 [. 0.74
   2 !   58.7   0.0   1.4e-19   5.2e-16       1      67 []     397     462 ..     397     462 .. 0.96

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.017
                HHHTS---HHHHHHHHHHTT-E................... CS
                xxxxxxxxxxxxxxxxxxxxxx..................x RF
          B5 10 kllGidlseeeiikiLkrlgce..................r 32
                + l +++s e+ii+ L +lg+e                  +
  AHX11350.1 10 EHLDTSVSLEQIITALISLGFEverchsigsgfvvarveeV 50
                567789999************96665555555555555550 PP

  == domain 2  score: 58.7 bits;  conditional E-value: 1.4e-19
                 EEEEHHHHHHHHTS---HHHHHHHHHHTT-E.EESSTTCEEEE--TT-TT--SHHHHHHHHHHHH-G CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
          B5   1 vslrvekinkllGidlseeeiikiLkrlgceriekdkdlllVtvPswRsDlereeDliEEvaRlyGY 67 
                 v++ ++ +++++Gi+++ +++i+iL++lg+e+ ++++++l+V  PswR+D+  +++++EE +R++GY
  AHX11350.1 397 VKFPISFFSSMTGIEIEISRMIQILTNLGFEV-TQNGKELDVISPSWRNDISTQACIAEEMLRVHGY 462
                 578889999**********************8.999999***************************9 PP

>> FDX-ACB  Ferredoxin-fold anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.0   4.6e-15   1.6e-11       1      94 []     675     769 ..     675     769 .. 0.93

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 4.6e-15
                 -SS--EEEEEEEE..EESSS-HHHHHHHHHHHH-TTEEEEEEEEEEESTTS-SSEEEEEEEEEE--SSS---HHHHHHHHHHHHHHHHTT.T-BES CS
     FDX-ACB   1 SkfPaverDlalv..vdekveaaelleavreaagellesvqlfDvYrgkklaegkkSlalrltlqskertLtdeevnaaiekvvealekklgaelR 94 
                 SkfP verD+++v  +d++  +++l++ vr+ + +l+++v+lfD+Y+g+  + ++ Sla+ +t++++ ++++ ee+  + +k+++ +e+++  +lR
  AHX11350.1 675 SKFPVVERDFSFVfeLDKDPCWEALEKEVRSIS-KLIKDVTLFDRYEGDFNGMKRLSLAFLVTMENDLHSMSSEEIGGLSDKIIQCVEERFFGTLR 769
                 9***********94446777899*******988.9*************99999************************************9988877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (773 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.61u 0.25s 00:00:00.86 Elapsed: 00:00:00.40
# Mc/sec: 5834.73
//
Query:       AHX11351.1  [L=401]
Description: cell division protein FtsA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      2e-19   69.9   1.3    2.7e-16   59.8   0.2    2.3  2  FtsA            Cell division protein FtsA
    3.5e-10   39.2   1.1    8.4e-10   38.0   1.1    1.6  1  MreB_Mbl        MreB/Mbl protein
    2.2e-09   37.6   0.4    6.7e-09   36.0   0.0    2.1  2  SHS2_FTSA       SHS2 domain inserted in FTSA
  ------ inclusion threshold ------
       0.02   14.2   0.0       0.54    9.5   0.0    2.3  2  Hydantoinase_A  Hydantoinase/oxoprolinase


Domain annotation for each model (and alignments):
>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.9   0.1   0.00045         2       2      88 ..      16     190 ..      15     196 .. 0.64
   2 !   59.8   0.2     6e-20   2.7e-16       2     103 .]     209     368 ..     208     368 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00045
                 EEEE-SSSEEEEEEETTEEEEEEEES-...-HHHHHHH.......HHHHHT--HHHHHHHHHHH--S--.....................EEEEEHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxx.....................xxxxxxxxx RF
        FtsA   2 lvDiGagktdvavaedgalvhlrvigv...ggngitkd.......iakalrtaveeAerikikyGsala.....................ekeigrkel 69 
                 ++D+G+ k  ++ ++  +   l+v g+   ++ gi+ +       ++++l   +e+ e+++ + G                         +        
  AHX11351.1  16 ILDLGSDKLRCMNFNLINSSELEVTGFaevPAVGIKGGiainiekAKRSLLGVIEATEKVS-DEGIEDIyiiisdpsitgkqyraklevdN-------- 105
                 79*************9777778888888889999999933333344444444455555555.44443336666666666555555443332........ PP

                 H..........................................................GGGGSTTHHHHHHHH........HT- CS
                 x..........................................................xxxxxxxxxxxxxxx........xxx RF
        FtsA  70 s..........................................................ggsalpnleelaera........lsp 88 
                 +                                                            +++ nle+l++++        +sp
  AHX11351.1 106 KkisevdaellrkkvaekistpiihmvqqeclidgvqevsnpigmygkslsasfyvitgIRTMMLNLENLISQCnlrfagcaFSP 190
                 0333555557777777777788888888888888888888888888777777777777767777777777777765544444455 PP

  == domain 2  score: 59.8 bits;  conditional E-value: 6e-20
                 EEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHHT--HHHHHHHHHHH--S--...................EEEEEHHHHH........... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................xxxxxxxxxx........... RF
        FtsA   2 lvDiGagktdvavaedgalvhlrvigvggngitkdiakalrtaveeAerikikyGsala...................ekeigrkels........... 70 
                 +v++Ga +t++av++ g+++++++i+vgg++++kdia +l++ ++ Ae++k++ +++l                    +++++ +e++           
  AHX11351.1 209 IVEMGAASTSMAVFKSGKVQFISSIPVGGSHVSKDIAFGLNVGISIAESLKKDCAHLLLdrnsesnridisgysdlvhQQDVSIREIAdmavprleeif 307
                 79*************************************************88777777777777777777776666666666666669********** PP

                 ...................GGGGSTTHHHHHHHHHT-..........HH.HT-GGGHHHHH CS
                 ...................xxxxxxxxxxxxxxxxxxx........xxx.xxxxxxxxxxx RF
        FtsA  71 ...................ggsalpnleelaeralspk........lee.vsdpeyasalg 103
                                    ggs++ +++++ae+++  k        +++ v + ey+s+ g
  AHX11351.1 308 emahekvkdsnfstvvltgGGSKITQIRRIAEKIFMKKvrvqgdfrVRDvVYGSEYSSVFG 368
                 **********************************955455667788777799999999876 PP

>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   1.1   1.9e-13   8.4e-10     144     304 ..     204     349 ..     200     365 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.9e-13
                 SS-EEEEEE-SS-EEEEEEETTEEEEEEEES-SHHHHHHHHHHHHHHHHSEE--HHHHHHHHHHH-BSS--HHHH..EEEEEEEETTTTCEEEEEEEHH CS
    MreB_Mbl 144 psgnmvvdiGggttevavislggivtsksvrvaGdeldeaiikyirkkynlliGertaekikieigsavkeeeee..kmeikGrdlvtglpkevevsse 240
                   g ++v++G+ +t++av   g +  ++s+ v+G ++ ++i       + l +G + ae++k++ +++  ++++e  +++i+G    + l ++  vs +
  AHX11351.1 204 EVGAIIVEMGAASTSMAVFKSGKVQFISSIPVGGSHVSKDI------AFGLNVGISIAESLKKDCAHLLLDRNSEsnRIDISGY---SDLVHQQDVSIR 293
                 5799************************************9......59*******************9998888668888885...69999******* PP

                 HHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHHHHHSS-EEE- CS
    MreB_Mbl 241 evrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldkllseetglpvkva 304
                 e++++    +++i e+++e          +d    ++vltGGg+++ +++++ ++ +  +v+v 
  AHX11351.1 294 EIADMAVPRLEEIFEMAHEKV--------KDSNFSTVVLTGGGSKITQIRRIAEKIFMKKVRVQ 349
                 *************99887655........5666789**************99999888888775 PP

>> SHS2_FTSA  SHS2 domain inserted in FTSA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.0   0.0   1.5e-12   6.7e-09       6      79 .]      94     163 ..      90     163 .. 0.79
   2 ?   -2.7   0.1       1.8   8.2e+03      10      27 ..     273     291 ..     270     306 .. 0.70

  Alignments for each domain:
  == domain 1  score: 36.0 bits;  conditional E-value: 1.5e-12
                 EEEEEEEEE-TTS-E--HHHHHHHHHHH....CHTTEEEEEEEEEEEEETTTEEESB-TT-EESEEEEEEEEEE CS
   SHS2_FTSA   6 svnskgvvaisgedeiteedvervleaakavaipedreilhvipqeyivDgqegikdPvGmsGvrLevevhvit 79 
                 +++ +++ ++ ++ +i+e d e + ++    a +  + i+h++ qe  +Dg +++++P+Gm+G++L++++ vit
  AHX11351.1  94 GKQYRAKLEVDNK-KISEVDAELLRKKV---AEKISTPIIHMVQQECLIDGVQEVSNPIGMYGKSLSASFYVIT 163
                 5555566666666.66666666665555...6677899**********************************98 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 1.8
                 EEEEE-TTS-.E--HHHHH CS
   SHS2_FTSA  10 kgvvaisged.eiteedve 27 
                 +++++isg +  + ++dv 
  AHX11351.1 273 SNRIDISGYSdLVHQQDVS 291
                 5667777776688888874 PP

>> Hydantoinase_A  Hydantoinase/oxoprolinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00012      0.54      67     112 ..     193     238 ..     176     246 .. 0.81
   2 ?    2.3   0.0     0.018        81     228     270 ..     305     348 ..     254     353 .. 0.70

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
  Hydantoinase_A  67 vgaaatsklagekkvItfDmGGTstDvslikdgevevsleteiagv 112
                      g++ +s+ ++e  +I ++mG  st ++++k+g+v++ ++  ++g 
      AHX11351.1 193 SGYSVLSEDEREVGAIIVEMGAASTSMAVFKSGKVQFISSIPVGGS 238
                     455566667888889********************99887776665 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.018
  Hydantoinase_A 228 avrklsvergldpkeltlvvfGGaG.aq.haaalaeelgvkkviv 270
                     ++ ++  e+ ++ +++ +vv +G+G ++  + ++ae++ +kkv v
      AHX11351.1 305 EIFEMAHEK-VKDSNFSTVVLTGGGsKItQIRRIAEKIFMKKVRV 348
                     455554444.45555555555555514414678999999998865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (401 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 2846.04
//
Query:       AHX11352.1  [L=53]
Description: hypothetical protein NHE_0404 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       507  (0.0282782); expected 358.6 (0.02)
Passed bias filter:                      337  (0.0187964); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 440.39
//
Query:       AHX11353.1  [L=91]
Description: NADH-ubiquinone/plastoquinone oxidoreductase, chain 3 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-32  111.0   0.6    2.6e-32  110.9   0.6    1.0  1  Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, ch


Domain annotation for each model (and alignments):
>> Oxidored_q4  NADH-ubiquinone/plastoquinone oxidoreductase, chain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.6   1.4e-36   2.6e-32      11      99 .]       2      90 ..       1      90 [. 0.97

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 1.4e-36
                 SS-----HHHHS-SSSS--SS---.--HHCHHHHHHHHHHHHHHHHHHHHHHHHSST..HHHHHHHHHHHHHHHHHHHHHHHHH-S-XX CS
  Oxidored_q4 11 lgpkkpnkeklspYEcGfepvgearlrfsvkfylvallFliFDvevvflfpwavslkelglfgliemllFllillvglvYewkkgaLeW 99
                 ++p+ ++++k ++YEcGf++++++ +rf+v+fy+v +lF+iFD+e+vflfpwa +++elg +g+i+ml+Fl il+vg+vYe+ +gaLeW
   AHX11353.1  2 IAPSVYSRHKGDSYECGFDKLSSTGERFHVRFYIVGILFIIFDLEIVFLFPWAAVARELGPAGFISMLIFLSILTVGFVYELLSGALEW 90
                 567778999******************************************************************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 757.16
//
Query:       AHX11354.1  [L=167]
Description: NADH-quinone oxidoreductase, B subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.9e-23   80.4   0.1    1.2e-22   80.1   0.1    1.1  1  Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit


Domain annotation for each model (and alignments):
>> Oxidored_q6  NADH ubiquinone oxidoreductase, 20 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   80.1   0.1   6.9e-27   1.2e-22       3     129 ..      45     152 ..      44     154 .. 0.90

  Alignments for each domain:
  == domain 1  score: 80.1 bits;  conditional E-value: 6.9e-27
                  HHHHHHT-TTTTHHHHHHTEEEEEETTT-S--HHHHHHTHTTTSEEEEEESBE...EEEHHHHHHHHGGGSSEEEEESHHHHH-TGGGSTT-TEE-HH CS
  Oxidored_q6   3 GcsisllaleedlldllelielryhetlladskeeeieakekeadvlvveGavtrkpkealellkelaekakaviavGtCAafGGipaaannpsvgee 100
                  +c +++++ + + +d+      r+++ +  +++         + dv++v G++t+k+++al++++++++++k+vi++G+CA  GG ++ +   sv   
   AHX11354.1  45 CCAVEMMHFTASRYDM-----DRFGMIFRPSPR---------QSDVMIVAGTLTNKMAPALRRVYDQMAEPKYVISMGSCANGGGYYHYSY--SV--- 123
                  4999999999999999.....899999999999.........9********************************************4433..33... PP

                  HHHHHC.S-E.EEE-SSS--HHHHHHHHH CS
  Oxidored_q6 101 vgellevvpvdinipGCPphpeailetll 129
                  v+++++ +pvd+++pGCPp++ea+l+++l
   AHX11354.1 124 VRGCDRIIPVDVYVPGCPPTAEALLYGVL 152
                  469*********************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1286.76
//
Query:       AHX11355.1  [L=190]
Description: NADH-quinone oxidoreductase, subunit C [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-35  121.8   0.0    3.1e-35  121.5   0.0    1.1  1  Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd s


Domain annotation for each model (and alignments):
>> Complex1_30kDa  Respiratory-chain NADH dehydrogenase, 30 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  121.5   0.0   1.7e-39   3.1e-35       6     121 ..      29     143 ..      24     144 .. 0.95

  Alignments for each domain:
  == domain 1  score: 121.5 bits;  conditional E-value: 1.7e-39
                     HHHHHHHHHHHH...TT--EEEEEEEEETT..SSSEEEEEEEE--S-.-EEEEEE....-S-BEE--TTT-STHHHHHHHHHHHSHHBCTTSSTS CS
  Complex1_30kDa   6 edllevakflkdeeelgfdvlsdltavDek..eerfevvyhllsleknerirvkvevdeeepevpSvtdlfpgadwyEREayDmfGivfeghpdl 98 
                     ++l ev+ ++     lgf++l+d+ +vD++  e+r+e++y+ll +++n+r +vk++vd   ++vp+++ +f++adw+ERE+yDm+G+ f++hp l
      AHX11355.1  29 DSLMEVLGYVSS---LGFTLLVDVFGVDYPerEKRIELIYILLDMKQNRRCHVKLAVDPALEKVPTCCGIFRAADWFEREVYDMYGVIFSDHPRL 120
                     677788888888...*************9999*************************999999******************************** PP

                     S-SSSSTTSSS-TTSTTS----- CS
  Complex1_30kDa  99 rrillpedfeghPLRkdfplsge 121
                     +ril++++feg+P+ kdfpl+g+
      AHX11355.1 121 ERILTDYGFEGFPMLKDFPLTGY 143
                     ********************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (190 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1566.75
//
Query:       AHX11356.1  [L=335]
Description: glyceraldehyde-3-phosphate dehydrogenase, type I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.7e-60  201.3   0.0    8.7e-60  200.9   0.0    1.1  1  Gp_dh_C        Glyceraldehyde 3-phosphate dehydrogenase, C-te
    1.6e-30  105.4   0.0    3.9e-30  104.2   0.0    1.7  1  Gp_dh_N        Glyceraldehyde 3-phosphate dehydrogenase, NAD 
     0.0022   17.9   0.0      0.012   15.6   0.0    2.2  3  ADH_zinc_N     Zinc-binding dehydrogenase
  ------ inclusion threshold ------
      0.084   13.5   0.1       0.87   10.3   0.1    2.2  1  NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
       0.14   11.5   0.1       0.25   10.7   0.1    1.4  1  2-Hacid_dh_C   D-isomer specific 2-hydroxyacid dehydrogenase,


Domain annotation for each model (and alignments):
>> Gp_dh_C  Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.9   0.0   2.4e-63   8.7e-60       1     158 []     157     313 ..     157     313 .. 0.99

  Alignments for each domain:
  == domain 1  score: 200.9 bits;  conditional E-value: 2.4e-63
                 HHHHHHHHHHHHEEEEEEEEEEEECTTTSBSSSS--.SSTTTTSBTTCSSEEEE-THHHHHHHHSGGGTTTEEEEEEEESSSSEEEEEEEEEESSTS-H CS
     Gp_dh_C   1 LaplakvlndkfgikkglmttvhaytndQkllDgpskkdlrraraaaeniiptstgaakavglVlpelkgkldglAvrVPtpnvsvvdlvvelekevtv 99 
                 Lapl+ v+++ fg+ +++mtt+h+ytndQ+++D+ + kdlrrara+a++iipt+tgaak +g+++pel+gk+dg+A+rVPtpnvs+vdl++++e++v+v
  AHX11356.1 157 LAPLIDVIHKGFGVSSAFMTTIHSYTNDQNVVDNNH-KDLRRARACAMSIIPTTTGAAKTIGKIFPELSGKVDGIAMRVPTPNVSMVDLTLNTERDVSV 254
                 8********************************776.************************************************************** PP

                 HHHHHHHHHHHHTTTTTTEEEEHSHHHGGGGTTGCSSEEEEGGGCEEETTTEEEEEEEE CS
     Gp_dh_C 100 eevnaalkeaaegalkgilsyteeelvssDlvgdphssifdaketivveenlvkvvawy 158
                 + vn+a+ +aa ++lkg+ls+++e+lvs D++gdphs+++d + t vv ++++++ awy
  AHX11356.1 255 KVVNNAFINAASSYLKGVLSTCDEPLVSVDFNGDPHSAVVDLTGTYVVCNRMLRLGAWY 313
                 **********************************************************9 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   1.1e-33   3.9e-30       1     100 [.       1     103 [.       1     104 [. 0.95

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 1.1e-33
                 CEEEEESTSHHHHHHHHHHH..HHTTCEEEEEE-TS-HHHHHHHHHEETTTEC-SS-EEEE.TTEEEETTEEEEEE--SSGGGS-CHHHTSSEEEE-SS CS
     Gp_dh_N   1 vkvainGfGRIGrlvlrall..eekelevvaindltdletlayllkyDsvhgrfkgeveae.eealvvngkkikvlaekdpeelpwkelgvdlVvestG 96 
                 ++vainGfGRIGr vlr+l+  ++ ++e+va+n+ +++e++++llkyDsv+grf+  v++  e+ + ++g ++++++e d++ l+w++l+vdlV+e++G
  AHX11356.1   1 MRVAINGFGRIGRAVLRILMgsNRGDVEIVAVNTPGSIENCVHLLKYDSVYGRFPCAVSYAsEDVVLLEGAPVRFSRELDISLLDWGKLNVDLVLECSG 99 
                 79******************86666**********************************996777999******************************* PP

                 S--S CS
     Gp_dh_N  97 vftd 100
                 vf++
  AHX11356.1 100 VFNS 103
                 **86 PP

>> ADH_zinc_N  Zinc-binding dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1   4.1e+03      54      82 ..      20      48 ..      14      54 .. 0.78
   2 !   15.6   0.0   3.3e-06     0.012      55      93 ..      87     127 ..      76     166 .. 0.76
   3 ?   -2.0   0.0       0.9   3.2e+03      77     116 ..     138     177 ..     130     185 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
                TTTSSEEEEEESSCSHHHHHHHHHCEEEE CS
  ADH_zinc_N 54 tggegvdvvfecvGsgatleaalkllkpg 82
                 g +  dv + +v+++ ++e+++ llk++
  AHX11356.1 20 MGSNRGDVEIVAVNTPGSIENCVHLLKYD 48
                55666788888899999999999999876 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 3.3e-06
                 TTSSEEEEEESSCSHHHHHHHHHCEEEEEEEEECSC..TSS CS
  ADH_zinc_N  55 ggegvdvvfecvGsgatleaalkllkpgGrlvvvGg..gkg 93 
                 g+ +vd+v+ec+G+  ++e+a   l+ g ++v+v +  +  
  AHX11356.1  87 GKLNVDLVLECSGVFNSYERASGHLRAGAKFVLVSApvPDA 127
                 5779******************************9964333 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 0.9
                 HCEEEEEEEEECSC.TSSEEEEEHHHHHHTT-EEEEE-SSC CS
  ADH_zinc_N  77 kllkpgGrlvvvGg.gkgeeefdlrnlllkeksilGsllgs 116
                 ++lkp  r+  vG   +++   +l +++ k   +   ++ +
  AHX11356.1 138 DILKPSDRIISVGScTTNCL-APLIDVIHKGFGVSSAFMTT 177
                 57889999999998777776.77777777777777666666 PP

>> NAD_binding_3  Homoserine dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1   0.00024      0.87       1      84 [.       7     115 ..       7     125 .. 0.53

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00024
                    --SHHHHHHHHHHHH---SSEEEEEEEEESSEEE-TT.........................HHHHHT--CB---HHHHHHHH........S-EEE CS
  NAD_binding_3   1 GlGaiGsavleqlkrqqseielelvavadrdsllskd.........................rkallasealtldlddliahl........dpdvv 63 
                    G+G iG+avl++l+ +++  ++e+vav        ++                          + + a+ +   +ld     +        ++d+v
     AHX11356.1   7 GFGRIGRAVLRILMGSNRG-DVEIVAVNTPG--SIENcvhllkydsvygrfpcavsyasedvVLLEGAPVRFSRELD-----IslldwgklNVDLV 94 
                    99*************9995.99999997665..22221234444455555554444433333222222222222222.....02223355456666 PP

                    EE-S--HHHHTTHHHHHHTTE CS
  NAD_binding_3  64 VEcasseavaelvlkaLkagk 84 
                    +Ec ++    e +   L+ag 
     AHX11356.1  95 LECSGVFNSYERASGHLRAGA 115
                    666665555555555555555 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   6.9e-05      0.25      38      58 ..       2      22 ..       1      50 [. 0.77

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 6.9e-05
                  EEEEES-SHHHHHHHHHHHHT CS
  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkaf 58
                  +v+i G+GrIG+av ++l + 
    AHX11356.1  2 RVAINGFGRIGRAVLRILMGS 22
                  799*************99754 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (335 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       479  (0.0267165); expected 358.6 (0.02)
Passed bias filter:                      443  (0.0247086); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 2719.30
//
Query:       AHX11357.1  [L=377]
Description: phosphoglycerate kinase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-97  325.6   0.0    5.3e-97  325.1   0.0    1.1  1  PGK       Phosphoglycerate kinase


Domain annotation for each model (and alignments):
>> PGK  Phosphoglycerate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  325.1   0.0    3e-101   5.3e-97       6     376 ..       7     362 ..       3     364 .. 0.93

  Alignments for each domain:
  == domain 1  score: 325.1 bits;  conditional E-value: 3e-101
                 -TT-EEEEEE-----EECTTEES--HHHHHHHHHHHHHHHTT-EEEEEE--S--TT.S-GGG-SHHHHHHHHHHHTT-EEEESSTTSHHHHHHHHT-TT CS
         PGK   6 lkgkrvlvRvDfNvplkkegkitddtriraalpTikyllekgakvvllsHlgrpkg.ekeklslkpvaerLsellgkeVkfvedvvgeeveeaiaelke 103
                 ++  rv++RvDfNvp++ +g+i+d +ri  alpTi+ ll+++++v llsH+g+p++ +k+++s + ++e+++e    +++++    ++e  ++++ lk 
  AHX11357.1   7 VRSCRVILRVDFNVPVTADGVINDFSRIAVALPTIELLLKNNCSVLLLSHFGKPDSgSKSTFSFNRIIEQIREFSRLDIRLI----QSEYLDNASTLKL 101
                 77889*************************************************765889***************9899998....4556667899*** PP

                 T-EEEES-GGGSTTTTTT-HHHHHHHHHT-SEEEE--GGGTTS--TTTTHHHHCSEEEE-HHHHHHHHHHHHHHHS--SSEEEEEEES-HHHCHHHHHH CS
         PGK 104 gevllLeNvrfykeEekndeelakklasladvyVnDAFgtahrahaStvgiakvlsaaaGllmekElealskvlenperplvailGGakvsdkikvien 202
                 +ev lLeN+rf ++E +nd+e+a++la+++dvy+nDAF+++hr+haS+vgi+++l++  Gl +++E++al+++ +   ++ +ai+GG+k+s+k+ +i+ 
  AHX11357.1 102 REVALLENIRFFDGEVSNDPEFARRLAQYGDVYINDAFSVSHREHASVVGIPNYLPSTTGLAFAQEYSALDSIAS---KDSAAIIGGSKISTKLPLIKG 197
                 *******************************************************88****************95...889****************** PP

                 HTTT-SEEEEETCHHHHHHHHTT-B-TTSS--GGGHHHHHHHHHHHHHHT-EEE--SEEEEESSSSTTS.EEEECCG--TT-EEEEE-HHHHHHHHHHH CS
         PGK 203 LlekvdkliigGgmantFlkaqgleigkslveedklelakellekakkkgvkillpvDvvvakeeaekeakvveveaipedemalDigpktielfaeai 301
                 Ll+kv ++i+gG+++n+ lk +g+eig+sl+e  + ++          + +++++p D+++++  ++++ ++v+++ +p++em+lD+gp+++ ++++++
  AHX11357.1 198 LLKKVGTVILGGALVNVVLKSRGYEIGRSLCEGVHCDI----------SLENLFIPFDFITSSGVEDENYHIVDARFVPKHEMMLDVGPASLIAIKTIL 286
                 ********************************943332..........224699********86444448999************************** PP

                 CC-SEEEEES-SS-TTSGCCCHHHHHHHHHHHHHCH..TSEEEEESHHHHHHHHHTT-GGGSSEEESSSHHHHHHHC CS
         PGK 302 keaktvvwnGpmGvfeiekfakGTkaiakalaeatk..galsivGGgdsaaaveklgladkvshvStGGgAsLelLe 376
                  + k ++wnGp+G fe+++f++GT ++ + ++  t+  g++s++GGgd++aa++ ++ +  +s++St GgA+L++ e
  AHX11357.1 287 GRYKKILWNGPIGAFEVKPFDSGTIELGNYISFLTRnsGVMSVIGGGDTLAAIKLIQ-DPCFSYISTSGGAFLKFQE 362
                 *******************************99887789**************8877.789************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       295  (0.0164538); expected 358.6 (0.02)
Passed bias filter:                      291  (0.0162307); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.22s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 3002.53
//
Query:       AHX11358.1  [L=369]
Description: cell cycle family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-66  222.4  29.9    9.7e-66  222.2  29.9    1.0  1  FTSW_RODA_SPOVE  Cell cycle protein


Domain annotation for each model (and alignments):
>> FTSW_RODA_SPOVE  Cell cycle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  222.2  29.9   5.4e-70   9.7e-66       4     357 ..      18     358 ..      15     360 .. 0.89

  Alignments for each domain:
  == domain 1  score: 222.2 bits;  conditional E-value: 5.4e-70
  FTSW_RODA_SPOVE   4 lllvllllvilGlvmiysaslveslvlfg.dsfvlfirqlvylllglivfvlllriplkfleklakllliislllLvlvkvplgssanGAkrWi 96 
                       ll++++l+i+G+ +i sas + +++    ++  ++    + ++lg  ++v+++ ++ + l k++ ++++ ++++L +v +  ++ ++GAkrWi
       AHX11358.1  18 TLLIVSILIIIGMSLIASASPAIAMKIGFiNHYQFIHNHTLNIILGYSMIVFFSCLSTQEL-KILCTFFLGVMIILTFVTLLKSTNIKGAKRWI 110
                      5677788888*********988777765404577778889999*****9999999977766.677777888888888887768999******** PP

  FTSW_RODA_SPOVE  97 rlggisiqPsEfvkialilflAavlskkkkevksrlrellillvivllilvlillqpdlgtavllliillvvlflsglslklilaivlalilvi 190
                      ++ g+s+qPsEf+k  + +f A++ls+       ++r++l ++ + l i++l+llqpd+g  v + ii++ ++fls   + li + ++  i+ i
       AHX11358.1 111 SIVGFSLQPSEFIKPTFSVFCAWILSN-------NPRNCLYASFCYLGITLLLLLQPDFGMFVTVSIIFFSIIFLSRTTIFLIPVFMS--IFSI 195
                      ***************************.......8899999999999*****************************988877666666..4444 PP

  FTSW_RODA_SPOVE 191 aivllilledyqvkrvtslldpfkdplgsgYqviqsliAigsGGllGkGlgnsqqkleyLPeahtDfIfavigEelGlvGvllllllffllivr 284
                       +++++l+ ++ + rv ++ + + +   + +qv ++  ++++GGllG G +++++k+  LP ahtDfIf+v gEe+Glv  l +++l++lli++
       AHX11358.1 196 IVLTSYLTIPHVKYRVDNFFNSKGE---NNFQVQKATESLARGGLLGVGPSEGKVKM-HLPDAHTDFIFSVAGEEFGLVLTLSIVILYLLLIIT 285
                      4444566666667799999999888...67*************************76.7*********************************** PP

  FTSW_RODA_SPOVE 285 glriarkakdrfgsllavgivllivvqsfinigmvlGllPvtGltlPflSyGGsSllalliligillnisree 357
                       l  ++ ++++f+ l  +gi++ +  q +ini ++l l+P++G+tlPf+SyGGsS+++  ++igi+l + r++
       AHX11358.1 286 NLSKISDLENEFSMLAGMGIISYLGAQCLINISVNLNLIPTKGMTLPFISYGGSSMISSGMAIGIMLALTRKK 358
                      *******************************************************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       956  (0.0533214); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.42
# Mc/sec: 2639.09
//
Query:       AHX11359.1  [L=303]
Description: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.4e-86  289.3   1.1    2.7e-86  289.1   1.1    1.0  1  LYTB      LytB protein
  ------ inclusion threshold ------
      0.055   12.6   0.6      0.079   12.1   0.1    1.5  2  NadA      Quinolinate synthetase A protein


Domain annotation for each model (and alignments):
>> LYTB  LytB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.1   1.1     3e-90   2.7e-86       1     263 [.       3     277 ..       3     278 .. 0.96

  Alignments for each domain:
  == domain 1  score: 289.1 bits;  conditional E-value: 3e-90
                 EEE-TT-SS-HHHHHHHHHHHHHHCCC-S..EEECS-SSS-HHHHHHHHHCTEEEESSSST.....EEEE-TT---HHHHHHHHHTTEEEEE---HHHH CS
        LYTB   1 illaksaGfCfGVerAieiaeealeekke..vyvlgeivHNeqvverLeekgvkfieelee.....vviirAhGvskeveeelkekglevvDatCplVk 92 
                 il+a ++GfC+GVerA+++++ a+++++e  ++v +eivHN++v+++++++gv fie+ +e     v+i+ AhGvs eve+++k+ +l+++Da CplV 
  AHX11359.1   3 ILIAAPRGFCAGVERAVNTVDIAIDRYPEkkIFVHHEIVHNTRVIQDFKARGVVFIENVNEaeansVLILNAHGVSSEVEDHAKSMDLILIDASCPLVL 101
                 6899***********************999**************************88543234468********************99********** PP

                 HHHHHHHHHHHCT-EEEEES-TT-HHHHHHHCCT--TEEEESSCHHHHHG.....CEEEEE-TTS-HHHHHHHHHHHHHHSTCEEEC-S--CHHHHHHH CS
        LYTB  93 kvqkevkklakegyeiviiGkkkHpEvegilgqaeekvvvveeseevekl.....kvalvsQTTlsveefeeivealkkklkelevkdtiCkatqeRqe 186
                 k+++e++ ++ke+++++iiG+++H+Ev g++g  + +++++e+ e++ekl     k+a+v+Q+Tls ++++ +v+alk+k++++  +++iC+atq+Rq+
  AHX11359.1 102 KIHREAQAYEKENFTVLIIGNRNHAEVMGTAGRVKARTYILEKLEDIEKLddlegKLAYVTQSTLSCDHVSVMVNALKRKFPNIVGRSDICYATQNRQD 200
                 *****************************************988888888899********************************************** PP

                 HHHHHHGHSSEEEEES-TT-HHHHHHHHHHHHCSCTEEEESSGGG--HHHHTT-SEEEEEE-TTS-HHHHHHHHHHH CS
        LYTB 187 avkelakevdlvivvGgknSsNtkkLveiakeknkktyliesaeeldeewlegvkkvgitaGaStpeelieeviekl 263
                 avk+lakevdl+++vG+knSsN+++L+++++e ++k++li++ +e + +w+egv+++gi++GaS+p+ l++e +e l
  AHX11359.1 201 AVKALAKEVDLMLIVGSKNSSNSNNLMRVSREICPKAFLIDNYKEAEAHWFEGVNRIGISSGASAPDLLVQELVEFL 277
                 ************************************************************************99987 PP

>> NadA  Quinolinate synthetase A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   8.8e-06     0.079     172     262 ..      18     102 ..       2     119 .. 0.84
   2 ?   -2.9   0.0      0.33     3e+03     103     117 ..     191     210 ..     169     233 .. 0.57

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 8.8e-06
                 -CHHHHHHHHCSTT-EEEE-TTS-HHHHHCSSEE--HHHHCCCCGTTSSSCEEEES-THHHHHHHHH-TTSEEE.....ECSSSSSTTGGG CS
        NadA 172 kaeeveelkeehpdakvlvHPEckeevveaadvvgSTsqiikavkeseakefiigTelglverlkkeapekefialsaeaaeeavCetMkk 262
                  +++v+ + +++p+ k++vH E  ++    +d+       i+ v+e+ea++++i    g+ ++++++a++ ++i ++a      +C+   k
  AHX11359.1  18 AVNTVDIAIDRYPEKKIFVHHEIVHNTRVIQDFKARGVVFIENVNEAEANSVLILNAHGVSSEVEDHAKSMDLILIDA------SCPLVLK 102
                 4677888999*********************************************************99999995533......3665555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.33
                 EEES..SS-HHHHTT-...S CS
        NadA 103 vtYv..NssaevKals...d 117
                 ++Y   N + +vKal+   d
  AHX11359.1 191 ICYAtqNRQDAVKALAkevD 210
                 44433344445555544331 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (303 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       648  (0.0361426); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2304.86
//
Query:       AHX11360.1  [L=98]
Description: hypothetical protein NHE_0413 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.11   12.9   0.0       0.13   12.7   0.0    1.3  1  DciA      Dna[CI] antecedent, DciA


Domain annotation for each model (and alignments):
>> DciA  Dna[CI] antecedent, DciA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   7.1e-06      0.13      47      76 ..      49      83 ..       4      93 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 7.1e-06
        DciA 47 r.....dgtLvvevesgawateLryqkpqllerln 76
                      + t +v++e++ + ++L+y+ ++l+er++
  AHX11360.1 49 LyavggQITVYVCAENPGVSLKLHYRFQELVERVK 83
                2555445689***********************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       487  (0.0271627); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.28s 00:00:00.63 Elapsed: 00:00:00.41
# Mc/sec: 715.76
//
Query:       AHX11361.1  [L=235]
Description: uroporphyrinogen-III synthase HemD family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.1e-12   45.2   0.0    7.9e-12   45.0   0.0    1.1  1  HEM4      Uroporphyrinogen-III synthase HemD


Domain annotation for each model (and alignments):
>> HEM4  Uroporphyrinogen-III synthase HemD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.0   0.0   4.4e-16   7.9e-12      46     231 ..      48     222 ..      13     223 .. 0.88

  Alignments for each domain:
  == domain 1  score: 45.0 bits;  conditional E-value: 4.4e-16
                 EEE--HHHHHHHHHHHHHTT---HHHHHCSEEESSHHHHHHHHHTT---SEE-..SSSHHHHGGGS-..---EEEEEE-SS.S--HHHHHHHHHTTEEE CS
        HEM4  46 liftSanavealfealkreeedvkalaslkvaavGpaTaraLeelglrvdlvpseegtaegLaeelae.slagkrvlllrgeiarddlaegLeergaev 143
                 +++tS+na++a +        +++a+++l ++++ +  a+ +++l++ ++      +t+e+L + + +   ++ r+++l g +  +d++  +++ g++ 
  AHX11361.1  48 IVVTSKNAIRA-LS-------LLDASKDLNIYTMTDNIAKFAKDLEFFNVSSCG-CNTVEELEKHIIStFDKSNRFIYLSGMEITRDIVFICNAYGFTF 137
                 89*********.33.......56699*******************999975555.9******7755552666699************************ PP

                 EEE-SEEEEE-HHHHHHHHHHHHTT--SEEEESSHHHHHHHHHH-S-HHHHHCTSEEEEESHHHHHHHHHTT---SEEETS--HHHHH CS
        HEM4 144 devevYetvpaeeepeelkealkagevdavvftSpstvrnllellkdegdelkevkvaaiGptTaealkklglkvdvvaeeptaeglv 231
                 +++++Y+  ++e+++e l+e+l++ +v ++ ++S +++  + +ll+d+  e + ++++ +++++a  l     +++ v++ pt+++l+
  AHX11361.1 138 ERLICYKMNAREKFSEVLVELLRTARVKCISIFSRRAAVVCRSLLTDYRFEPNLFHYFLMSNRVASVL---DYPNIHVPPFPTQSALI 222
                 ***********************************************997777888888999998888...77777778888888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       486  (0.0271069); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1744.47
//
Query:       AHX11362.1  [L=390]
Description: EAL domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-50  171.9   0.7      3e-50  171.0   0.2    1.6  2  EAL            EAL domain
  ------ inclusion threshold ------
       0.08   13.1   2.7        1.1    9.4   0.2    2.8  2  TetR_C_8       Transcriptional regulator C-terminal region
       0.14   10.6   0.1       0.22    9.9   0.1    1.2  1  Hemagglutinin  Haemagglutinin


Domain annotation for each model (and alignments):
>> EAL  EAL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.26   1.6e+03     165     185 ..      52      73 ..      45      98 .. 0.64
   2 !  171.0   0.2   4.9e-54     3e-50       4     237 ..     155     379 ..     153     380 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.26
                 HHCCC--SEEEE-HHHH.TTTT CS
         EAL 165 ylarlppdiiKldrsll.adle 185
                 +++ l++di+K d++     ++
  AHX11362.1  52 QIRTLKLDIVKYDSENFlLLID 73 
                 4788999999999764424444 PP

  == domain 2  score: 171.0 bits;  conditional E-value: 4.9e-54
                 HHHHCCTT-EEEEEEEEEESSS-SSEEEEEEEEEEECTTCEE-CCCCHHHHHHCTCHHHHHHHHHHHHHHHHHHHHCHTT--EEEEEE--CHHCC-CCH CS
         EAL   4 lrealenkelalyyQPvvdlktgkvvgleallrwqhpdgglispeeflplaerlgllaeldrwvleqalqdlrrlaeqldadiklsinlspasladeef 102
                 l +al+n +l+ ++QP+vd+++++vv  e llr++ ++   i  ++++++ae+++l++ +d++v+++++  l +     ++d+kls+n+s +s+ +  +
  AHX11362.1 155 LYNALRNSNLYGVFQPIVDIQNSEVVFNEFLLRIKGQET--I--QDYITAAEKTNLISIIDEFVFKHVMTLLES-----NPDLKLSFNISMFSINNGRW 244
                 6789******************************99977..3..9*************************8888.....9******************* PP

                 HHHHHHHHHCCT-GCC-EEEEEEHHHHHHTHHHHH.HHHHHHHCTT-EEEEEEETSS.TCCCHHHCCC--SEEEE-HHHHTTTTTSCHHHHHHHHCHHH CS
         EAL 103 leelrellkqsgpspsrLvleitesellarlealqeevlarLralGirialddfgtg.ysslsylarlppdiiKldrslladleedeeaqalvkalial 200
                 ++++++l+ + ++ ++r+v+eite+ +l++l+++  + + +L++ G++ialddfg+  y  + +l +lp+d+iKld+++ ++++++++   ++++++++
  AHX11362.1 245 VDDILRLFVNLPFIAKRVVVEITEEMMLRNLDKVF-DFIFKLKSVGCSIALDDFGRNfYIPFLQLEKLPIDYIKLDKEFAKGITDSKNVPIFMSSILEI 342
                 ******99777888888********9999999995.*******************994579999*********************************** PP

                 HCCCT-EEEE-S--SHHHHHHHHHHT-SEE-STTT-- CS
         EAL 201 akelgikvvaegVeteeqlealrelgcdlvQGyllsk 237
                 ak+l++k++ae+Ve+++ ++a+++lg++++QG++l k
  AHX11362.1 343 AKNLNVKIIAEFVEDSDVFKAFKQLGIRYMQGNYLQK 379
                 **********************************987 PP

>> TetR_C_8  Transcriptional regulator C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.2     0.023   1.4e+02       5      52 ..     166     213 ..     162     237 .. 0.80
   2 ?    9.4   0.2   0.00018       1.1      12      70 ..     314     372 ..     308     378 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.023
                 HHHHHHHHHHHHTHHHHHHHHHH-.THHHHHHHHHHHHHHHHHHHHHH CS
    TetR_C_8   5 egllklfeyikenkdfyknllssngresfekylkelikelilkvieel 52 
                  +++ + ++ + +  f + ll+ +g+e++++y+    k++++ +i+e 
  AHX11362.1 166 GVFQPIVDIQNSEVVFNEFLLRIKGQETIQDYITAAEKTNLISIIDEF 213
                 556666666666666777899************999999999999875 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00018
                 HHHHHTHHHHHHHHHH-.THHHHHHHHHHHHHHHHHHHHHH-TT--S-HHHHHHHHHHH CS
    TetR_C_8  12 eyikenkdfyknllssngresfekylkelikelilkvieelsegkelseedkefiadfy 70 
                 +yik +k+f k +  s++ + f++ + e++k+l  k+i e  e+ ++ ++ k+  ++++
  AHX11362.1 314 DYIKLDKEFAKGITDSKNVPIFMSSILEIAKNLNVKIIAEFVEDSDVFKAFKQLGIRYM 372
                 8*************************************999988888777777766665 PP

>> Hemagglutinin  Haemagglutinin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   0.1   3.7e-05      0.22     395     448 ..      36      90 ..      17     102 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 3.7e-05
                    SSXXTTTTHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHH CS
  Hemagglutinin 395 gkelnelekrieeldkkvddgfldvitynie.llvllenerildfedsnvknlee 448
                    +    + ek++ el++++  ++ld++ y+ e +l+l+++e+ ++    +v +l +
     AHX11362.1  36 SDGKRKYEKELSELERQIRTLKLDIVKYDSEnFLLLIDDEGAIEGIHAKVTELAS 90 
                    55567899*********************9846778899****998888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (390 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      544  (0.0303419); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3023.57
//
Query:       AHX11363.1  [L=384]
Description: 1-deoxy-D-xylulose 5-phosphate reductoisomerase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-28   98.4   0.0    3.8e-28   97.5   0.0    1.5  1  DXP_redisom_C    1-deoxy-D-xylulose 5-phosphate reductoisomer
    6.7e-22   78.6   0.0    1.1e-21   77.9   0.0    1.4  1  DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomer
    2.1e-15   57.0   0.0    4.1e-15   56.1   0.0    1.5  1  DXPR_C           DXP reductoisomerase C-terminal domain
    0.00073   19.3   0.2       0.76    9.7   0.0    2.5  2  Peptidase_C25_C  Peptidase family C25, C terminal ig-like dom


Domain annotation for each model (and alignments):
>> DXP_redisom_C  1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.5   0.0   8.4e-32   3.8e-28       1      84 []     140     220 ..     140     220 .. 0.96

  Alignments for each domain:
  == domain 1  score: 97.5 bits;  conditional E-value: 8.4e-32
                    EEE-SHHHHHHHHHSGCCCCTTEEEEEEEE--GTTTTS-HHHHCT-SHHHHHS-SS----HHHHHHHHHSHHHHHHHHHHHHHC CS
  DXP_redisom_C   1 ilpvDsEhsaifqllkeekkkevekiiltasGGpfrklkleeleevtveealkhPnWsmGkkitvdsatlmNkglEvieakllf 84 
                    i p+DsEh ai +ll++++ k ++ i+ltasGGpf ++k+   + v +++al+hP W+mGkk +vdsatl+Nk lEviea++lf
     AHX11363.1 140 ISPLDSEHYAINELLRSRDPKLLKGITLTASGGPFFRKKK---SGVGIADALSHPVWKMGKKNSVDSATLVNKILEVIEAHYLF 220
                    68*********************************98776...57899***********************************9 PP

>> DXP_reductoisom  1-deoxy-D-xylulose 5-phosphate reductoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.9   0.0   2.4e-25   1.1e-21       1     129 []       4     130 ..       4     130 .. 0.94

  Alignments for each domain:
  == domain 1  score: 77.9 bits;  conditional E-value: 2.4e-25
                      EEEESTTSHHHHHHHHHHHHC.TTTEEEEEEEESSTHHHHHHHHHHHT-SEEEESSHHHHHHHHHHHHHTTSSSEEEESHHHHHHHHCHTT-SE CS
  DXP_reductoisom   1 vviLGsTGSIGtqtLdvieen.pdkfevvalaagsnvellaeqakefkpklvavadeeaaeelkealkekelktevlvGeealkelaeeeeadv 93 
                      ++iLGsTGS+G+q ++v++++ +d++ev al++ s+  lla+qa +++pk v +++e+a+ +lk+ l  +++++ev++++++ +  +   + d+
       AHX11363.1   4 ISILGSTGSVGSQIVEVVSRFyKDTIEVDALSCRSSYLLLAQQALDLSPKRVFISEESAYPKLKQIL--SSTNIEVICDRSGDIGNIF-ADNDM 94 
                      78*****************98799*******************************************..5799999999998665555.478** PP

                      EEE--SSGGGHHHHHHHHHTTSEEEE--SHHHHHHH CS
  DXP_reductoisom  94 vvaaivGaaGLkptlaaikagkriaLANKEsLVvaG 129
                      ++ a +G+ GL p + a++ g  +a +NK  +V++G
       AHX11363.1  95 LIVATSGIEGLLPMYDALSYGIPVATSNKDGIVCGG 130
                      **********************************98 PP

>> DXPR_C  DXP reductoisomerase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.1   0.0   9.1e-19   4.1e-15       2     114 ..     253     367 ..     252     368 .. 0.80

  Alignments for each domain:
  == domain 1  score: 56.1 bits;  conditional E-value: 9.1e-19
                 -SS-THHHHHHHHHTTS-.....------HHHHEE.EEEB---TTTTCHHHHHHHHHHH-TCHHHHHHHHHHHHHHHHHTTSS-TTHHHHHHHHHHH.. CS
      DXPR_C   2 gtpDMrlpIayaLayper.....gverldlaklgs.ltFekpdlerFpclklayealkaggtapavlnAAnEvaveaFlegkisFldIaeiieevle.. 92 
                 ++pDM++ I+ +L+         + +  +++ +g+ ltF + + e+Fp+lk+ +    +g+   +++n An+ av++Fl g+i+F+ I+++i++ +e  
  AHX11363.1 253 SSPDMKIGINSTLSRLVGgsaetTQKYANISLIGKnLTFYPAEIEEFPVLKFLR----TGQ--EITFNVANDLAVSEFLYGRIAFHAIPDFIAAGMEsf 345
                 89************4444443321333444444435**************9864....333..589*******************************76 PP

                 TTT....SSHHHHHHHHHHHHH CS
      DXPR_C  93 seekseaksledileldaeare 114
                 + ++++ ++++d+l++ +ea++
  AHX11363.1 346 HYNENSINNIDDVLATYNEAKQ 367
                 55578899*********99986 PP

>> Peptidase_C25_C  Peptidase family C25, C terminal ig-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.0    0.0011       4.9      13      45 ..      69     102 ..      61     108 .. 0.86
   2 !    9.7   0.0   0.00017      0.76      20      41 ..     357     378 ..     344     382 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0011
                      ETT-SEEEEEESSTT-EEEEEETTEEEEEEE-.B CS
  Peptidase_C25_C  13 plgtnsievscdvdgalvalSannkllGsaiv.a 45 
                      +l+ ++iev cd  g +  + a+n++l +a++  
       AHX11363.1  69 ILSSTNIEVICDRSGDIGNIFADNDMLIVATSgI 102
                      578899********************98887755 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.00017
                      EEEESSTT-EEEEEETTEEEEE CS
  Peptidase_C25_C  20 evscdvdgalvalSannkllGs 41 
                      +v ++++ a  alS+nnkl++ 
       AHX11363.1 357 DVLATYNEAKQALSNNNKLFDR 378
                      5899***************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (384 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       477  (0.0266049); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.19s 00:00:00.65 Elapsed: 00:00:00.35
# Mc/sec: 3294.99
//
Query:       AHX11364.1  [L=223]
Description: short chain dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.1e-23   83.8   0.0    1.3e-23   83.5   0.0    1.0  1  adh_short     short chain dehydrogenase
    9.1e-19   67.9   0.0    1.1e-18   67.7   0.0    1.2  1  adh_short_C2  Enoyl-(Acyl carrier protein) reductase
    1.1e-05   25.5   0.0    1.4e-05   25.1   0.0    1.2  1  KR            KR domain
  ------ inclusion threshold ------
      0.079   13.3   0.0       0.13   12.6   0.0    1.3  1  DUF4709       Domain of unknown function (DUF4709)
      0.092   12.1   0.0       0.12   11.8   0.0    1.2  1  DUF1776       Fungal family of unknown function (DUF1776)
       0.12   11.9   0.0        0.2   11.1   0.0    1.5  1  Epimerase     NAD dependent epimerase/dehydratase family


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.5   0.0   4.3e-27   1.3e-23       1     179 [.       4     184 ..       4     195 .. 0.93

  Alignments for each domain:
  == domain 1  score: 83.5 bits;  conditional E-value: 4.3e-27
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---S.S--SSGGGCSH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGi.tgsgpfselse 98 
                 k+vl+tGa + IG  +a+++a+eGa++v+ +   ++l e+ + ++++g + + +q++++d  ++eal + +    +kld+Lv+     ++++   +++ 
  AHX11364.1   4 KIVLITGAHNKIGASVARRFASEGASLVLPAVDLSDLGELDQDIRKLGGESVLVQTNISDILQIEALAASITGMSKKLDALVAAHFYtSKPNVLVDYEV 102
                 79********************************************************************************87766778888899999 PP

                 HHHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEE..EGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE CS
   adh_short  99 eewervievNltgvflltravlpamlkqssGrIvnvs..SvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaP 179
                 +ew++++e N+     l +++   ++ + sGr++++s  S++gk+p+  +++Y As a++++l++  +++++++gi+vn++a 
  AHX11364.1 103 DEWKKILEENFSLNWYLLKHFDGLLKLSGSGRVIFISveSIVGKNPLY-FSPYVASNAGLVQLMNGYSNDVQTHGIKVNMIAL 184
                 99**********99999999999999********98866888988875.799*****************************97 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.0   3.5e-22   1.1e-18       1     170 [.      10     183 ..      10     218 .. 0.91

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 3.5e-22
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSE.E.EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgae.v.lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreef 95 
                   Ga + IG+ +A+++a+eGa++vl  ++ ++  ++++  ++lg e v ++++++d  q+eal++ ++   +klD lv +  ++ k  + +++ + +e+
    AHX11364.1  10 GAHNKIGASVARRFASEGASLVLPAVDLSDLGELDQDIRKLGGEsVlVQTNISDILQIEALAASITGMSKKLDALVAAHFYTSK-PNVLVDYEVDEW 105
                   78889******************999999966777766667655477*******************************999999.9999******** PP

                   HHHHHHHTHHHHHHHHHHHHHCTSC..CEEEEEEEGGGTSBSTTTT.HHHHHHHHHHHHHHHHHHHHGGGTEEEEEEE CS
  adh_short_C2  96 draldvnlyslfllakaalplmkeg..gsivnlssvgaervvpnyn.aygaaKaalealtrylAvelgpkgiRvNavs 170
                   +++l+ n+   ++l+k++  l+k +  g+++ +s  +     p y   y a+ a+l++l+    +++  +gi+vN ++
    AHX11364.1 106 KKILEENFSLNWYLLKHFDGLLKLSgsGRVIFISVESIVGKNPLYFsPYVASNAGLVQLMNGYSNDVQTHGIKVNMIA 183
                   ********************887554799****99988888999988*****************************98 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0   4.7e-09   1.4e-05       3     162 ..       6     167 ..       4     186 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 4.7e-09
                 EEEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHTT-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE----.-----TTT- CS
          KR   3 ylitGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaelealgaevevvaaDvsdkdavealleeikaeeppikGvihaAgv.lrdklleem 100
                 +litG+  ++G ++ar  a++ga+ lvl + + +   +   l + +++lg e  +v+  +sd  ++eal ++i+   +++   + a    ++ + l + 
  AHX11364.1   6 VLITGAHNKIGASVARRFASEGAS-LVLPAVDLSDLGE---LDQDIRKLGGESVLVQTNISDILQIEALAASITGMSKKLDALVAAHFYtSKPNVLVDY 100
                 79********************95.8888888444444...4455556666666777777777777777777777778889888777651568999*** PP

                 -HHHHHHHHTTTTHHHHHHHHHTTT...S--SEEEEEEEHHHHH--TT-..HHHHHHHHHHHHHHHH CS
          KR 101 taedleqvlapKvkGawnLhelled...esldffvlfSSiagllgsagq..anYaaaNaflDalaey 162
                 + ++++++l+  ++  w L + +      s    v+f S+ +++g++    + Y a Na l +l++ 
  AHX11364.1 101 EVDEWKKILEENFSLNWYLLKHFDGllkLSGSGRVIFISVESIVGKNPLyfSPYVASNAGLVQLMNG 167
                 *******************999987755666678999999999998754227888888877776654 PP

>> DUF4709  Domain of unknown function (DUF4709)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.2e-05      0.13      19      72 ..      57     115 ..      49     129 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.2e-05
     DUF4709  19 tQTdvsEilelkeltevtqkLvkevksl.krdfeflkqllqakye....eklkeealel 72 
                 +QT++s+il++  l++++  + k++++l   +f ++k  + ++ye    +k+ ee ++l
  AHX11364.1  57 VQTNISDILQIEALAASITGMSKKLDALvAAHFYTSKPNVLVDYEvdewKKILEENFSL 115
                 8************************9863679999999******954444566665555 PP

>> DUF1776  Fungal family of unknown function (DUF1776)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   3.9e-05      0.12     112     197 ..     101     184 ..      56     186 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 3.9e-05
     DUF1776 112 plsswaselnerllspiltlqallplltsrakqkakiivvnpsissslnlpfhapEalvssalsalfevLkrelrphnidvtqikL 197
                  +++w++ l+e+++  + +l+ +  ll+   + + ++i+++   +   n+ + +p +     l +l++  +++++ h+i+v +i L
  AHX11364.1 101 EVDEWKKILEENFSLNWYLLKHFDGLLKL--SGSGRVIFISVESIVGKNPLYFSPYVASNAGLVQLMNGYSNDVQTHGIKVNMIAL 184
                 5789************************8..68*********999999***********************************987 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   6.6e-05       0.2       1     123 [.       6     148 ..       6     198 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 6.6e-05
                 EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHHHH..T-SEEEE--S.---HHHHHHSHHH. CS
   Epimerase   1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl........elveldltdrsalerlfkee..qpdavihlAa.vggvaassedpad. 86 
                 +l+tGa+  iG+ ++++++++g   v+    ls+ ++  ++ ++        +    d+++ +al++ +     + da + +    + +++ +++  d 
  AHX11364.1   6 VLITGAHNKIGASVARRFASEGASlVLPAVDLSDLGELDQDIRKlggesvlvQTNISDILQIEALAASITGMskKLDALVAAHFyTSKPNVLVDYEVDe 104
                 79********************99666666665555554444448999977777777777777777666543338888887766677666665555541 PP

                 ...HHHHHTHHHHHHHHHHH....HHTCTEEEEEEEGGGGTSCS CS
   Epimerase  87 ...fieknlqgtlnlleaar....kagvkrllflsSsevYGkda 123
                    ++e+n+ +++ ll+        +g  r++f+s  ++ Gk++
  AHX11364.1 105 wkkILEENFSLNWYLLKHFDgllkLSGSGRVIFISVESIVGKNP 148
                 11155677777777777766333233666888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (223 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 1922.65
//
Query:       AHX11365.1  [L=307]
Description: phage integrase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-34  119.6   0.0    1.9e-34  118.9   0.0    1.3  1  Phage_integrase  Phage integrase family
    3.4e-08   33.7   0.6    2.7e-07   30.8   0.1    2.6  3  Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
  ------ inclusion threshold ------
      0.038   14.1   0.0      0.072   13.2   0.0    1.5  1  Integrase_1      Integrase


Domain annotation for each model (and alignments):
>> Phage_integrase  Phage integrase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.9   0.0   3.1e-38   1.9e-34       3     170 ..     124     290 ..     122     292 .. 0.90

  Alignments for each domain:
  == domain 1  score: 118.9 bits;  conditional E-value: 3.1e-38
                      HHHHHHHHHHHCCGC..HHHHHHHHH..HHHHHHHT--HHHHTT-BGGGEECTTTEEEEEEEECSSSSEEEEECTHHHHHHHHHHHHHHCHCCT CS
  Phage_integrase   3 ltedeverllaalee..slkirdkll..lellyetGlRisEllsLrvkdldlengvilvheregKgskeravplseealellkellskaleeae 92 
                      lt de+ + ++   +  s+ i ++++    lly++GlR+sE+l+Lr+kdl  e++ i+v    gKg+ker + +   + ++l+++l+ +    e
       AHX11365.1 124 LTLDEITEVIEKFSSlkSTWIVQRNIalCYLLYGSGLRVSEALNLRIKDL--EQSSIKV---LGKGNKERMIQILPVVRKALEDYLELCPFPSE 212
                      5666666666666666644444444433889******************9..9******...***************************99999 PP

                      TTSBSSBETTSSB--HHHHHHHHHHHHHHCT-SSC--TTHHHHHHHHHHHHHCTSHHHHHHHHT-SSCCHHHHHHCCC CS
  Phage_integrase  93 ksellfaskrgkplsrqtvrkafkraveeagiekpltpHtlRhsfataLleagvdlrvvqkllGHssisttqiYthva 170
                      ++++lf+ + g++l+r  +  a+ +++++ ++++++tpH lRhsfat+Ll++g+ +r++q+llGHss+++t++Yt+++
       AHX11365.1 213 RENFLFLDRYGNKLCRTVIASAMISLRKKFNLSPNITPHALRHSFATHLLQSGIGIRKIQELLGHSSLASTEVYTKLD 290
                      99*************************************************************************975 PP

>> Phage_int_SAM_1  Phage integrase, N-terminal SAM-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   4.5e-11   2.7e-07       4      80 ..      16      97 ..      13     101 .. 0.81
   2 ?   -2.1   0.0      0.81   4.8e+03      52      75 ..     218     240 ..     211     243 .. 0.78
   3 ?   -0.8   0.0      0.32   1.9e+03      26      57 ..     268     299 ..     266     302 .. 0.85

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 4.5e-11
                     HHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHH.TS-.....-TTT--HHHHHHHHHS----------HHHHHHHHHHHHHHH CS
  Phage_int_SAM_1  4 fleyLikerglspnTlraYrrdLrrflkflaergke.....sleqlttedvraflaeleeeglsatslarrlsalrsFfqfl 80
                     + + L+  +++s nT++aY+ dL ++l+fl   +++     +l+ ++   +r + a +++++ s +  +r+ls++++Ff++l
       AHX11365.1 16 WINWLSGIKNFSSNTVAAYKIDLLSLLDFLCRFHGRpvlvaDLTIINNTTLRGWFADRRRRKISFRANSRALSSVKNFFRYL 97
                     566678889*********************995555012225555666666***********999999999*********98 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.81
                      HHHS----------HHHHHHHHHH CS
  Phage_int_SAM_1  52 flaeleeeglsatslarrlsalrs 75 
                      fl+++ ++ l +t +a ++++lr+
       AHX11365.1 218 FLDRYGNK-LCRTVIASAMISLRK 240
                      77777774.888999999999997 PP

  == domain 3  score: -0.8 bits;  conditional E-value: 0.32
                      HHHHHHHHHH.TS--TTT--HHHHHHHHHS-- CS
  Phage_int_SAM_1  26 Lrrflkflaergkesleqlttedvraflaele 57 
                      +r++++ l ++   s e  t  dv++ +++++
       AHX11365.1 268 IRKIQELLGHSSLASTEVYTKLDVASLVKKYA 299
                      68889999999999999999999999999886 PP

>> Integrase_1  Integrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.2e-05     0.072      36     148 ..     151     259 ..     120     260 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.2e-05
  Integrase_1  36 vlqLarvlGLRseEAvqlakslktWkkaLergeerlrvvfGTKGgrpRevtile..realksavalaikvaeernGkLidkpdlslipd....ryrei 127
                  +  L +  GLR  EA++l        k+Le+  ++++v    KG ++R ++il   r+al+  ++l     e++n   +d+   +l       +  + 
   AHX11365.1 151 LCYLLYGSGLRVSEALNLR------IKDLEQ--SSIKVL--GKGNKERMIQILPvvRKALEDYLELCPFPSERENFLFLDRYGNKLCRTviasAMISL 238
                  334445559*******996......455554..556655..6***********999**********85444555555566544444333333388888 PP

  Integrase_1 128 lrrlgltgessphslRyayaq 148
                  +++  l+ ++ ph+lR+++a 
   AHX11365.1 239 RKKFNLSPNITPHALRHSFAT 259
                  888999*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.34
# Mc/sec: 2665.58
//
Query:       AHX11366.1  [L=240]
Description: cobB/CobQ-like glutamine amidotransferase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    5.9e-53  179.6   0.0    3.1e-52  177.3   0.0    1.9  1  GATase_5   CobB/CobQ-like glutamine amidotransferase domain
    0.00039   20.1   0.0    0.00059   19.5   0.0    1.3  1  GATase_3   CobB/CobQ-like glutamine amidotransferase domain
      0.003   17.4   0.0      0.006   16.4   0.0    1.5  1  DJ-1_PfpI  DJ-1/PfpI family
  ------ inclusion threshold ------
      0.038   13.7   0.0      0.074   12.8   0.0    1.4  1  GATase     Glutamine amidotransferase class-I
      0.074   13.1   0.0       0.15   12.1   0.0    1.4  1  HisKA      His Kinase A (phospho-acceptor) domain


Domain annotation for each model (and alignments):
>> GATase_5  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  177.3   0.0   8.6e-56   3.1e-52       3     260 .]       3     239 ..       1     239 [. 0.91

  Alignments for each domain:
  == domain 1  score: 177.3 bits;  conditional E-value: 8.6e-56
    GATase_5   3 kvailreeGvngeyemaaafekaGfeavdvhmsdllegrvslddfqilalpGGfsygDelgsgkgwakslllneklrealekflnredtlaLGiCnGfq 101
                 k+++l   G+n+e e+ +afe aGf+ +  h+++l+++   l+d+q++a+pGGfs gD+ g+g+++a   +    + e++++fln+ d l++GiCnG q
  AHX11366.1   3 KALVLSGYGINCETETLYAFELAGFSGKILHINELITDPYILEDYQVIAIPGGFSFGDHTGAGNAFACKAR---IVLEQIDNFLNK-DRLVIGICNGAQ 97 
                 789****************************************************************9888...5***********.************ PP

    GATase_5 102 lLvklglvpggeieeaeksptltrNksgrfesrlvsvvvsekspsvflkgmeglslpvahGeGrfvfkseevlkeleangqvalrYvdeegkpteeypl 200
                 +L++l           +  +t++ N s+r+++ + ++ v ++++s++lk++ +++lp+ahGeG++++     l++ e +g++a++Y ++          
  AHX11366.1  98 ILTRLFT---------DIGVTFEANISNRYQCGWYDLSV-ADTESIWLKNIGEIRLPIAHGEGNLQA-----LNTKELKGKIAMQYLED---------- 171
                 ****973.........3458*****************77.899************************.....4455667999****999.......... PP

    GATase_5 201 NPNgSpegiagitspdGRvlalmpHpervveavqksiipe......eeeee......vspwlrlFenavkyv 260
                   NgS + ia+it+ +GR+l++mpHper+v+a+q+  +        +   +       +p++++F+na++y+
  AHX11366.1 172 -VNGSSDRIAAITEYKGRMLITMPHPERAVTATQMDDYYLrreeyrR---KavehpsEGPGMQIFRNAYDYF 239
                 .9********************************9987663444431...144556789************7 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.6e-07   0.00059      38      96 ..      44     107 ..      29     158 .. 0.75

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.6e-07
    GATase_3  38 gedadlvilpGgkdtiqdl....a.llresgldeaikeaaeaggpvlgiCGGlqmLGeeiedpe 96 
                  ed++++ +pGg++  +      a + +++ + e+i +++++++ v+giC G q+L + ++d  
  AHX11366.1  44 LEDYQVIAIPGGFSFGDHTgagnAfACKARIVLEQIDNFLNKDRLVIGICNGAQILTRLFTDIG 107
                 47899999***98865544111131345567789***********************9998854 PP

>> DJ-1_PfpI  DJ-1/PfpI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.7e-06     0.006      59     108 ..      44     100 ..       3     104 .. 0.72

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.7e-06
                 CCG-SEEEE--BHHHHHHHHTSH.......HHHHHHHHHHHTT-EEEEETTTHHHHH CS
   DJ-1_PfpI  59 aaeyDalvlpGGragperlrene.......kvvelvkefaekgklvaaICagpqlLa 108
                  ++y ++ +pGG +  ++  + +        v+e + +f++k++lv  IC g+q+L 
  AHX11366.1  44 LEDYQVIAIPGGFSFGDHTGAGNafackarIVLEQIDNFLNKDRLVIGICNGAQILT 100
                 469*********9977766543323333447899999******************97 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   2.1e-05     0.074      24      90 ..      29     105 ..      15     164 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 2.1e-05
                 EEEEETTSHHHHHHHTHHSTSEEEEEEES..SCTT.........TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTT CS
      GATase  24 vevvpidasaeeilellknpdgilvsgGp..gspg.........vegkieaikearenkiPiLGICLGmQllaiefgr 90 
                  +++ i++ +   + +l++++ i ++gG+  g+ +         +   +e i ++++++  ++GIC G Q+l+  f+ 
  AHX11366.1  29 GKILHINELITDPY-ILEDYQVIAIPGGFsfGDHTgagnafackARIVLEQIDNFLNKDRLVIGICNGAQILTRLFTD 105
                 55666665444443.6999*********83344448888888888888888999999999************988875 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   4.3e-05      0.15      12      56 ..     140     184 ..     140     185 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4.3e-05
                 HHHHHHHHHHHHHHHHHC..T-HSSCHHHHHHHHHHHHHHHHHHH CS
       HisKA  12 ELrtPLsailgnaeaLkregklteelkeyletiesearrldhlve 56 
                 E+r P++   gn++aL  ++      ++yle++  +++r+ ++ e
  AHX11366.1 140 EIRLPIAHGEGNLQALNTKELKGKIAMQYLEDVNGSSDRIAAITE 184
                 8999************555355678999*************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1767.18
//
Query:       AHX11367.1  [L=914]
Description: hypothetical protein NHE_0422 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (914 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       585  (0.0326287); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.69u 0.27s 00:00:00.96 Elapsed: 00:00:00.43
# Mc/sec: 6371.77
//
Query:       AHX11368.1  [L=143]
Description: phosphopantetheine attachment site family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    7.9e-08   32.6   0.2    2.7e-07   30.8   0.1    1.9  2  PP-binding  Phosphopantetheine attachment site


Domain annotation for each model (and alignments):
>> PP-binding  Phosphopantetheine attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1   1.5e-11   2.7e-07      16      67 .]      33      86 ..      17      86 .. 0.84
   2 ?   -0.9   0.0      0.12   2.2e+03       2      18 ..     109     125 ..     108     139 .. 0.73

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.5e-11
  PP-binding 16 eeidpdtdlf.dlGlDSllavellaaleeefgv.eiplsdlfe.hptlaelaayl 67
                +e++++tdl  dlG+DSl+a+e+++++ee  ++ eip +      +t++ +++y+
  AHX11368.1 33 DELKLETDLAsDLGMDSLDAAEIIMRIEEDHDLeEIPEDYA-RkANTVKHIYDYV 86
                46889*****99*******************9956666555.4499999999886 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.12
  PP-binding   2 klrelvaevlgvpleei 18 
                 kl++ +ae  g++++++
  AHX11368.1 109 KLITRIAENAGLEVSDL 125
                 56677777777766664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1164.23
//
Query:       AHX11369.1  [L=416]
Description: beta-ketoacyl-acyl-carrier-protein synthase II [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-47  161.3   0.0    4.4e-47  160.8   0.0    1.2  1  ketoacyl-synt    Beta-ketoacyl synthase, N-terminal domain
    1.1e-33  115.7   0.1    1.7e-33  115.1   0.1    1.3  1  Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain


Domain annotation for each model (and alignments):
>> ketoacyl-synt  Beta-ketoacyl synthase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  160.8   0.0   4.9e-51   4.4e-47       2     253 .]       3     250 ..       2     250 .. 0.90

  Alignments for each domain:
  == domain 1  score: 160.8 bits;  conditional E-value: 4.9e-51
                    --EEEEEEEEEBTTBSSHHHHHHHHHTT---EEES-TTSSCGTTSBTSSTTEEE-BSS.EEE..S.TTEGGTTSTHHHHHHHCTS-HHHHHHHHHH CS
  ketoacyl-synt   2 epvaivGmgarfPggndveefwelLlegrdaiselpadrwdadklydpparaagkiktklggfld.vddfdpeffgispreaeamdpqqrllleaa 96 
                    ++v+++G+g +++ + + ee w+l+l++r++i+++ +  +d+++l   p  ++g++ ++     +   df  + fg  pr   + d+ + +   a+
     AHX11369.1   3 KRVVVTGLGLVTCLSSKREESWKLILSSRSGIRKIST--FDTENL---PVCIGGEVLDS-----EsGGDFVVKEFGD-PR---RHDKYILYGFAAS 84 
                    69**********************************5..888888...89999999884.....4467899999985.44...69*********** PP

                    HHHHHHHTS.-HHTCTTGGEEEEEEESSTHH...HHHHHHHHHTTGGGSCTTHHHHHSTTHHHHHHHHHHT--SSEEEEESGGGHH.HHHHHHHHH CS
  ketoacyl-synt  97 wealedagl.tpeeldgsrvgvfiGvgagdy...aalaaldedgsevkaspkavgavlanviagrisyalglrGpsvtvdtACsSs.lvavhaavq 187
                    +ea+ d+ l +  +ld+srvgv iG+g+g     ++ + l ++g+++k+sp++++a l n ++g++++++g++Gp+ +++tAC+++ + +v+ + +
     AHX11369.1  85 REAVLDSCLlDYPSLDKSRVGVSIGSGIGGLpliEKNSILLHEGGPRKVSPFFIPASLINLTSGNVAIEHGFTGPNDAIVTACATGaHSVVNSY-R 179
                    ***999988677799**************66666445555566779****************************************77777777.* PP

                    HHHTTS-SEEEEEEEE---SHHHHHHHHHTT.BB-TT.SGGGTTBTTB...-SB-BB-EEEEEEEEECHHH CS
  ketoacyl-synt 188 slrsgeadvalaGGvellltpeavagfsaag.llspd.grckafdpka...dGfvlGEGvGavvLkrleda 253
                     + + eadv++aG++e +l+  ++agf++++ l++++ +++ka++p++   dGfv+++G+G+++L+++e+a
     AHX11369.1 180 IICNDEADVMVAGASEGALCRVGIAGFASMKaLSKRNdEPEKASRPWDvnrDGFVMSDGAGILILEEYEHA 250
                    *******************************6666669*****************************9987 PP

>> Ketoacyl-synt_C  Beta-ketoacyl synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.1   0.1   1.9e-37   1.7e-33       1     117 [.     258     371 ..     258     372 .. 0.98

  Alignments for each domain:
  == domain 1  score: 115.1 bits;  conditional E-value: 1.9e-37
                      SEEEEEEEEEE--STSSSTSTTHHHHHHHHHHHHHHHT--GGGEEEEE-SS-SSHHHHHHHHHHHHHHHGGGGGSCTSEEE-THHHH-B-GGGH CS
  Ketoacyl-synt_C   1 yavikgsavnsdgahnsltapngeaqaraiekalaeagvdpedvdyveahgtgtplgDpiElealkkvfgekarkqplavgSvKsniGHleaAa 94 
                      ya++ g+++++d++h+ +++p+g+++ + + +a++++g + e+vdy++ hgt+tp gD +El+alk++fg++    +  v+S+Ks+iGH+++Aa
       AHX11369.1 258 YAELIGFGASGDAYHIAAPHPEGDGAFASMSRAIRMSGKTLEEVDYINTHGTSTPTGDIVELNALKRLFGNSL---RAGVSSTKSSIGHALGAA 348
                      89*********************************************************************87...589*************** PP

                      HHHHHHHHHHHHHHTEE--BTT- CS
  Ketoacyl-synt_C  95 Gvaelikvvlalkhgvipptlnl 117
                      G +e++ ++la+++ v+ppt+nl
       AHX11369.1 349 GGIEAVLCILAMRDSVMPPTINL 371
                      **********************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (416 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       319  (0.0177924); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.20s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3369.31
//
Query:       AHX11370.1  [L=279]
Description: coproporphyrinogen III oxidase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-95  319.3   0.3    1.9e-95  319.0   0.3    1.0  1  Coprogen_oxidas  Coproporphyrinogen III oxidase


Domain annotation for each model (and alignments):
>> Coprogen_oxidas  Coproporphyrinogen III oxidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  319.0   0.3   1.1e-99   1.9e-95       6     271 ..      13     277 ..       9     278 .. 0.91

  Alignments for each domain:
  == domain 1  score: 319.0 bits;  conditional E-value: 1.1e-99
  Coprogen_oxidas   6 lkelqdeivkaleeld......gkakfkedewereeggggisrvledgkvfekagvnvsvvegklpesavkqmraekkeeleeleffaagvslv 93 
                      +++l+d+i +++ +++       ++ f  ++w+r egggg  + l  g+vfek gvn+s+v+g+++ + ++++     + ++e++f a g+slv
       AHX11370.1  13 FRDLRDQIRDEFLSIEkefdpsFQSGFVVESWKR-EGGGGGEMSLMYGSVFEKIGVNISTVHGSFNGEFATKIP---GALKSEKQFWASGISLV 102
                      56667777777666663333333479********.777777788889************************993...3456789********** PP

  Coprogen_oxidas  94 ihprnPlvPtvhlnyryfeaeekkkawWFgGgaDLtPsylfeedavhfHktlkeacdkhdkelypkfKkwcDeyFyikhRkeaRGvGGiffddl 187
                       h ++PlvP+vh+n r++ +    +++WFgGgaDLtP+y +eeda  fH+ +keacdkhd+++y++f kw+DeyF++khR+e RG+GGiffd+l
       AHX11370.1 103 AHMKSPLVPAVHMNTRMIVT----DNYWFGGGADLTPMYYNEEDACIFHSAFKEACDKHDDDYYNRFSKWADEYFFLKHRNEPRGIGGIFFDYL 192
                      ******************99....378******************************************************************* PP

  Coprogen_oxidas 188 kes.aeelfafvksvgeaflpaYlpivekrkdtpyteeerewqllrrgryveFnLvyDrGtkfGLqtegrvesiLmslPptarwe 271
                      +++ +++ faf+++vg+ fl+ Y ++v++++  +yt e+re+qll+rgryveFnL+yDrGt+fGL+t+g + +iLmslPp+a+w+
       AHX11370.1 193 RTDdWQRDFAFTQDVGKCFLSVYPKLVRRNMYLEYTPEQREFQLLKRGRYVEFNLLYDRGTEFGLKTGGNTKAILMSLPPVAQWK 277
                      9665********************************************************************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       290  (0.0161749); expected 358.6 (0.02)
Passed bias filter:                      258  (0.0143901); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2247.73
//
Query:       AHX11371.1  [L=195]
Description: clan AA aspartic protease, TIGR02281 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-19   70.4   0.0      2e-19   69.9   0.0    1.2  1  gag-asp_proteas  gag-polyprotein putative aspartyl protease
    4.5e-14   52.9   0.0    6.4e-14   52.4   0.0    1.2  1  Asp_protease_2   Aspartyl protease
      4e-06   26.6   0.0    1.1e-05   25.2   0.0    1.7  1  Asp_protease     Aspartyl protease
  ------ inclusion threshold ------
      0.042   13.7   0.0      0.067   13.0   0.0    1.4  1  YhcG_C           YhcG PDDEXK nuclease domain
      0.052   13.9   0.0       0.14   12.5   0.0    1.6  2  RVP              Retroviral aspartyl protease
       0.15   12.0   0.0       0.24   11.4   0.0    1.3  1  AUDH_Cupin       Aldos-2-ulose dehydratase/isomerase (AUDH) C


Domain annotation for each model (and alignments):
>> gag-asp_proteas  gag-polyprotein putative aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   69.9   0.0   6.7e-23     2e-19       2      92 .]      87     178 ..      86     178 .. 0.95

  Alignments for each domain:
  == domain 1  score: 69.9 bits;  conditional E-value: 6.7e-23
                      EEEETTEEEEEEEETT-SS-EEEHHHHHHTTGGGGEB..TT--EE-TTSTT-EEEEEEEEEE.EETTEEEEEEEEEES.SSSEEEEHHHHHH CS
  gag-asp_proteas   2 kvkingkpvkflvDTGAsstiiseelaerlglsrkedkgkvevktangeveakrvrldsvkiggielrnvsavvlege.lddlLLGldfLkr 92 
                      ++ +ng +vk lvDTGAs+ti+s+++a+rlg++ +  +++ e++tang++ a++v +d v i+   +  +s++v   e   ++L G++fLk+
       AHX11371.1  87 DLLFNGVRVKCLVDTGASDTILSRKDARRLGINLDALDYTKEYQTANGKINAAPVLFDDVCINRYCIPSLSVSVSVLEnSGTSLVGMSFLKH 178
                      6779******************************************************************9999997735899*******96 PP

>> Asp_protease_2  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.4   0.0   2.1e-17   6.4e-14       1      90 []      86     175 ..      86     175 .. 0.96

  Alignments for each domain:
  == domain 1  score: 52.4 bits;  conditional E-value: 2.1e-17
  Asp_protease_2   1 vpvtinGkpvrfllDTGasttlispelaeklglkvreseltvrvsgaggevkarlvrldslklggltlknvpalvldlgeeidglLGmdf 90 
                     v++ +nG++v++l+DTGas t++s++ a++lg++ +++++t+ +++a+g+  a+ v +d++ +    ++++ ++v  l+++ + l Gm+f
      AHX11371.1  86 VDLLFNGVRVKCLVDTGASDTILSRKDARRLGINLDALDYTKEYQTANGKINAAPVLFDDVCINRYCIPSLSVSVSVLENSGTSLVGMSF 175
                     56779************************************************************9999999999999999*******98 PP

>> Asp_protease  Aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   3.6e-09   1.1e-05       4     120 ..      61     180 ..      58     184 .. 0.60

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 3.6e-09
  Asp_protease   4 veenlekalehtPeafvkvt..mlyinvevngvkvkafvdsGaqksilskkcaercglm.rlld.trfkgiakGvGtkkilGrvhsaevklgdlf.. 94 
                   +++++++  ++t  +f k     +y+++  ngv vk +vd+Ga  +ils+k a r g++   ld t+    a+G  + +    v   +v ++ +   
    AHX11371.1  61 IRDKFRENAQNTEMVFKKARdgHFYVDLLFNGVRVKCLVDTGASDTILSRKDARRLGINlDALDyTKEYQTANG--KIN-AAPVLFDDVCINRYCip 154
                   555555555555555554432268*******************************9996223441232333333..222.22333444444444311 PP

  Asp_protease  95 .lpvalsvledkevdlllGldllkrhq 120
                    l+v++svle++    l+G+  lk++ 
    AHX11371.1 155 sLSVSVSVLENSGTS-LVGMSFLKHFD 180
                   145667777776655.35777777665 PP

>> YhcG_C  YhcG PDDEXK nuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.2e-05     0.067      19     108 ..      48     133 ..      40     161 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.2e-05
      YhcG_C  19 ykErelekalieklkkfllelGkgFafvgrqyrleveekefyidLlfYhlklkcyvvieLKvgefkpedagklnlYlsaldeelkkeedn 108
                 ++Er  +++l+e++++ + e  ++   v ++      + +fy+dLlf  +++kc+v      + ++ +da +l + l+ald +++ ++ n
  AHX11371.1  48 VQERFFQNQLVEQIRDKFRENAQNTEMVFKKA----RDGHFYVDLLFNGVRVKCLVDTGASDTILSRKDARRLGINLDALDYTKEYQTAN 133
                 56777777777777777777766666666654....589*****************9999999999999999999999999887766655 PP

>> RVP  Retroviral aspartyl protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   4.7e-05      0.14      11      33 ..      90     112 ..      82     115 .. 0.85
   2 ?   -3.2   0.0       3.5     1e+04      78      95 ..     161     178 ..     148     181 .. 0.61

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.7e-05
                 ETTEEEEEEE-TTBSSEEEES-- CS
         RVP  11 iggkyieallDtGAdatviseed 33 
                  +g +++ l+DtGA +t++s +d
  AHX11371.1  90 FNGVRVKCLVDTGASDTILSRKD 112
                 5677999************9876 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 3.5
                 EESTTSSSEEE-HHHHCC CS
         RVP  78 lilpalpvnilGrdlLqq 95 
                  +l ++   ++G ++L++
  AHX11371.1 161 SVLENSGTSLVGMSFLKH 178
                 333334444777777765 PP

>> AUDH_Cupin  Aldos-2-ulose dehydratase/isomerase (AUDH) Cupin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.1e-05      0.24      29      60 ..      24      55 ..      12      79 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.1e-05
  AUDH_Cupin 29 ddkeeiaHiqlWtaGlgvdarlHnHsdksFke 60
                +  ++i+Hi +W aG+ v a ++n +++ F++
  AHX11371.1 24 SRARRISHILFWCAGVCVIAFFYNVQERFFQN 55
                44789********************9999975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1048  (0.0584528); expected 358.6 (0.02)
Passed bias filter:                      843  (0.0470188); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1479.49
//
Query:       AHX11372.1  [L=40]
Description: hypothetical protein NHE_0427 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       120  (0.00669307); expected 358.6 (0.02)
Passed bias filter:                      112  (0.00624686); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 332.27
//
Query:       AHX11373.1  [L=665]
Description: hypothetical protein NHE_0428 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-10   41.1   0.1    2.5e-10   40.2   0.1    1.4  1  IAT_beta  Inverse autotransporter, beta-domain


Domain annotation for each model (and alignments):
>> IAT_beta  Inverse autotransporter, beta-domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.2   0.1   1.4e-14   2.5e-10      60     169 ..     209     336 ..     167     352 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.2 bits;  conditional E-value: 1.4e-14
    IAT_beta  60 ssldlLlplydnkesllFsQlglrrk.ddrttvNlGlGlRrfldewml.GaNaFlDydlt.ss.hsRlglGaEawkdylkLsaNyYirlsgwkkskdle 154
                  +  +L+pl  ++++l++   +++   ++ + v +G+ +Rr l++ m+ G+N F D + t ++ ++ +++GaE++ + l++s+N Y++  +    + ++
  AHX11373.1 209 REYGALIPLIGRDKGLAYLDSKVKFYdSKAQEVSAGVVVRRKLGKSMIgGLNLFRDIRNTpEHmYTWYSFGAEMFFKTLSISGNCYFSSKDGYVNE-VK 306
                 566789******************77588889***********65555279*******99733599*********************976532222.21 PP

    IAT_beta 155 dye...............erpanGyDvrae 169
                 +                 + pa+GyDvr+ 
  AHX11373.1 307 KLSldsedqrksrvllneKLPADGYDVRTA 336
                 222233455689999997779******986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (665 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       679  (0.0378716); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.39
# Mc/sec: 5149.02
//
Query:       AHX11374.1  [L=38]
Description: hypothetical protein NHE_0429 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      254  (0.014167); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.38
# Mc/sec: 296.86
//
Query:       AHX11375.1  [L=161]
Description: iron-sulfur cluster assembly accessory family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.6e-09   37.3   0.1    3.1e-07   30.5   0.1    2.2  1  Fe-S_biosyn  Iron-sulphur cluster biosynthesis
  ------ inclusion threshold ------
       0.11   12.6   0.0       0.14   12.2   0.0    1.4  1  DnaJ_C       DnaJ C terminal domain


Domain annotation for each model (and alignments):
>> Fe-S_biosyn  Iron-sulphur cluster biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.5   0.1   3.5e-11   3.1e-07       2     111 .]      40     157 ..      39     157 .. 0.95

  Alignments for each domain:
  == domain 1  score: 30.5 bits;  conditional E-value: 3.5e-11
                  EEEE-HHHHHHHHHHHHCTTECEEEEEECCTSCCGGS.TT.EEEEEEEEESSTS..................TTTEEEEEETTEEEEEEGGGHHHS.T CS
  Fe-S_biosyn   2 kitlteaAaeklkkllaedkkelrLdvddgggpyskggCsiggkyslvlvdeed..................eeydevlesnggkvyvksyslvflde 81 
                  k+ +te+A +++ +  +e++  l ++++ gg       C+ g++y+++  ++++                  +e    l+ + + v ++s sl+++ +
   AHX11375.1  40 KLSITESALKQILAITQEKEC-LKITIEPGG-------CN-GFEYRFETKPSDKipddikvndpngihsatlAEKYYLLKGERVIVEIDSASLELI-K 127
                  799****************99.*********.......**.*****999998878899999999999999998999999999**************.9 PP

                  TEEEEEEEETTEEEEEEETCCEEEEEEEEE CS
  Fe-S_biosyn  82 glvldfvedlgtlgLksdngilddnvglgk 111
                  + ++d+v++l + ++   n++ ++++++g+
   AHX11375.1 128 HSQVDYVKELVGEKFVIRNPNSKSRCSCGN 157
                  ****************************86 PP

>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   1.6e-05      0.14       3      55 ..      25      82 ..      23     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1.6e-05
                EEEEE-HHHHHH-.EEE.EEEE.............TEEEEEE-TT--TT-EEEETT-SS CS
                xxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaJ_C  3 veleisleelykGktkkikikrnvi......kkekktlevkipaGikdgqkirlegeGd 55
                +e+++sl   ++G+t k++i++         ++ek+ l+++i++G  +g + r+e + +
  AHX11375.1 25 AEVNLSLAR-MNGATPKLSITESALkqilaiTQEKECLKITIEPGGCNGFEYRFETKPS 82
                667777776.59********99877999**8888889*****************98865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      486  (0.0271069); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1279.57
//
Query:       AHX11376.1  [L=385]
Description: dGTPase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.8e-25   88.3   0.2    1.8e-24   86.1   0.1    2.1  2  HD_assoc  Phosphohydrolase-associated domain
    3.4e-17   62.8   1.6    1.2e-16   61.1   0.7    2.2  2  HD        HD domain
    0.00061   19.3   0.0     0.0011   18.5   0.0    1.4  1  HDOD      HDOD domain


Domain annotation for each model (and alignments):
>> HD_assoc  Phosphohydrolase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.46   2.7e+03      32      66 ..     122     156 ..     108     169 .. 0.69
   2 !   86.1   0.1   2.9e-28   1.8e-24       2      92 .]     284     374 ..     283     374 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.46
    HD_assoc  32 eekarriireLfealledperllpeefrarleaae 66 
                 +++  ri++eL + ++e    +l  e+ + +++++
  AHX11376.1 122 NAQTIRILTELERQYMEFNGLNLTWETIEGIAKHN 156
                 45566899999999999777788888777776665 PP

  == domain 2  score: 86.1 bits;  conditional E-value: 2.9e-28
    HD_assoc   2 avseevaaeiaeLkkflfenvyrhpevqreeekarriireLfealledperllpeefrarleaaedd.araRvVcDyiAgmTDryalrlyar 92 
                 ++s++v++ i+++k+fl++n+y h++v++ +++ +ri+++Lfe+l edp+  lp+++ +r+++ +++ ++a+v+cD+i+ +TDr+a+r+++r
  AHX11376.1 284 HFSPKVEQDIKKIKAFLYKNLYFHYRVNKNRSRLKRIVKDLFEILFEDPQ-CLPDHWYERVKKSSSTnRKAQVICDFISALTDRSAMREHQR 374
                 79************************************************.**********9999999**********************97 PP

>> HD  HD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.1   0.7   1.9e-20   1.2e-16       1     120 [.      62     195 ..      62     197 .. 0.77
   2 ?    0.7   0.0     0.098   5.8e+02      34      89 ..     198     264 ..     193     324 .. 0.56

  Alignments for each domain:
  == domain 1  score: 61.1 bits;  conditional E-value: 1.9e-20
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTHHHHTS..HHH.....HHHCTCCHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHTTC CS
          HD   1 rleHsleVaklarrlaedlgeeedrellllaaLlHDiGkgpfgdafekk.....eeefekflaHekvgaeilrevekrlgld.....ledvaklirehh 89 
                 rl+HsleV ++ar +a+ ++   +++l++++aL HDiG++pfg+ +e++     +   +   +H   + +il e+e    +      +++ ++ i++h+
  AHX11376.1  62 RLTHSLEVSQIARSIARLVN--VNEDLTETIALAHDIGHPPFGHIGEEAlleviS--EHYKFDHNAQTIRILTELERQYMEFnglnlTWETIEGIAKHN 156
                 789*****************..***************************655532..22223455555556666666665557888************* PP

                 CHHHHHHHH......H....HHHCCTSCHHHHHHHHHHHHH CS
          HD  90 eswegkkrp......r....glaerqlslearivklaDrla 120
                 +++  +  +      +           slea+i ++aD +a
  AHX11376.1 157 GPIKDP--HqiireyNelvsLDLQNYSSLEAQISAIADDIA 195
                 *99744..345765515665777788889999999999876 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.098
                 HTTTTHHHHTS..HHH...........HHH....CTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTC CS
          HD  34 lHDiGkgpfgdafekk...........eee....fekflaHekvgaeilrevekrlgldledvaklirehh 89 
                  HDi  g+++     +             e    fek   ++++++ i +++ k  g+ + dv+++ir++ 
  AHX11376.1 198 SHDIDDGLSSK-L--ItyqdlkdlpiiG-EnitrFEKVFPNTDESRIIYKAIRKMIGFLINDVVAVIRKNI 264
                 68888888664.2..1223433333321.023344444445555555555555555444556666555555 PP

>> HDOD  HDOD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   1.8e-07    0.0011      72     152 ..      35     118 ..      30     144 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 1.8e-07
                 HHHHHHHHHHHHS--.....-SS-HHHHHHHHHHHHHHHHHHHHHTT-S-HHHHHHHHHTTTHHHHHHHHHSHHHHHHHHHHHHH CS
        HDOD  72 lvlalslkrlfkgke....eegadlkklwehslavAlvarelaeelgledpeeaflaGLLhdiGklvllsllpeeleellekvae 152
                 ++ +++++rl+++++      +   ++  +hsl+v+ +ar +a+ ++ ++ +   + +L hdiG   + ++ +e l e+ ++  +
  AHX11376.1  35 IIHSSVFRRLMHKTQvftcHGNEYYRSRLTHSLEVSQIARSIARLVNVNE-DLTETIALAHDIGHPPFGHIGEEALLEVISEHYK 118
                 667777777888877766556677788899******************99.*****************99999999988775444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (385 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3061.01
//
Query:       AHX11377.1  [L=238]
Description: DNA repair protein RecO [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.4e-16   59.1   0.1    6.2e-16   58.6   0.1    1.2  1  RecO_C    Recombination protein O C terminal
    2.2e-05   24.3   0.0    4.9e-05   23.2   0.0    1.7  1  RecO_N    Recombination protein O N terminal
  ------ inclusion threshold ------
       0.22   11.5   0.4         18    5.4   0.1    3.1  3  DUF5522   Family of unknown function (DUF5522)


Domain annotation for each model (and alignments):
>> RecO_C  Recombination protein O C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.6   0.1     1e-19   6.2e-16       3     147 ..      78     217 ..      76     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 58.6 bits;  conditional E-value: 1e-19
                 SHHHHHHHHHHHHHHHHHS-SSS--HHHHHHHHHHHHHHHHSS-HHHHHHH.HHHHHHHHTTS----SB-TTT--BS--EE-TTT.....SSEE-TTT- CS
      RecO_C   3 dlerlaaasylaElldrllpeeepnpeLFdlllatLdaLdeasdaalallv.felrlLallGyapdldsCaacgekialaafspswggllcsecaakap 100
                 d+ +l  + +++ +l+++lpe+e  +e +  +++ L+ L++ +  +   ++ + l +L++lG+++dl++Ca++ge+++l++ sp+      +++a+ ++
  AHX11377.1  78 DYRKLKLLNAVISVLLKVLPENEVKEETYHVFTELLHVLKSVNLCYYRKFIeMDLSILQHLGFQLDLSRCAVSGETENLFYISPK------TGRAVTKA 170
                 889999999*******************************999555555666*********************************......88****** PP

                 SS----HHHHHHHHHTTTS-HHHHHHS---GGGHHHHHHHHHHHHHH CS
      RecO_C 101 agrplspetlallrlllrgdleklgelkvspeelrellrllraylee 147
                  g p+ ++ l l++ll++++ +   e+++s+ee  e+  +++ +l+ 
  AHX11377.1 171 VGDPYKDKLLLLPQLLYKISNNFTFEEPISREEFIECVTVTGFFLRT 217
                 *******************7777788****************99985 PP

>> RecO_N  Recombination protein O N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.2   0.0   8.3e-09   4.9e-05       1      72 [.       1      64 [.       1      74 [. 0.84

  Alignments for each domain:
  == domain 1  score: 23.2 bits;  conditional E-value: 8.3e-09
                X-EEEEEEEEEEEEEETTSEEEEEEEETT.EEEEEEEET-..TTSTTTTTS-TT-EEEEEEE.SSS-SSEEEE CS
      RecO_N  1 MslvkteaiVLksrkygEsdlivtlfTrehGkvsalargarksksrlrallqpftllevqlr.kkgrgLktlk 72
                M  +++e++VL ++ + E+++  tlfT+ +G+ ++l         + +a+l +++ +  +++ + +++L+++k
  AHX11377.1  1 M-HWESEGVVLANKGLMENKIVATLFTKHYGLKRGLY--------SRKAMLDMGNIVYCRWSaRLESQLGYFK 64
                7.59****************************99998........3467899999999999999999999843 PP

>> DUF5522  Family of unknown function (DUF5522)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       0.2   1.2e+03      21      32 ..      23      34 ..      13      35 .. 0.85
   2 ?    5.4   0.1     0.003        18      17      31 ..     103     117 ..      98     119 .. 0.85
   3 ?    2.0   0.0     0.035   2.1e+02       9      23 ..     154     168 ..     150     172 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.2
     DUF5522 21 mVfTelyhlkRg 32
                + fT++y lkRg
  AHX11377.1 23 TLFTKHYGLKRG 34
                679*******98 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.003
     DUF5522  17 etgymVfTelyhlkR 31 
                 e+ y+VfTel h  +
  AHX11377.1 103 EETYHVFTELLHVLK 117
                 788*********876 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.035
     DUF5522   9 gedyyldpetgymVf 23 
                 ++ +y+ p+tg  V 
  AHX11377.1 154 ENLFYISPKTGRAVT 168
                 5689*******9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       467  (0.0260472); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.20s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2054.65
//
Query:       AHX11378.1  [L=155]
Description: stringent starvation B family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.9e-34  116.9   0.0    9.5e-34  116.6   0.0    1.0  1  SspB      Stringent starvation protein B


Domain annotation for each model (and alignments):
>> SspB  Stringent starvation protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.6   0.0   5.3e-38   9.5e-34       2     127 ..       9     131 ..       8     146 .. 0.84

  Alignments for each domain:
  == domain 1  score: 116.6 bits;  conditional E-value: 5.3e-38
                 SHHHHHHHHHHHHHHHHCCCTT-ET..EEEEEETTSTT-BS-HHHHGGGSBTTEEEEECCEEEEEE-SSEEEEEEEETTEEEEEEEEGGGEEEEEETTT CS
        SspB   2 lrpyalRavvrwvldevaeenelpehhFyitvdtdapgVkvperLreeypeemtIvLqhafsdLevtedafevglrFggvpeklvvPfaavlafydpev 100
                 l++ a+ +vvr v++  a+++ +p   F+it++tda+gV +++ Lr++yp+em IvLq++f+dL+v +d+f+v l+F+ v e++ vPf+++l f d+e 
  AHX11378.1   9 LVDAAMLGVVRSVVS-EASTG-TP-INFFITFRTDASGVVLSDALRAKYPSEMSIVLQNQFRDLKVFHDRFTVILSFSRVEERISVPFSSILYFLDREC 104
                 67899**********.45557.78.78************************************************************************ PP

                 TEEEE-.--BGGGCHT.TSXXSSCXXX CS
        SspB 101 gfglqFeeaeeaeeeeeeeeaeeeeea 127
                 +f+l+F++  ++ +++e+++ +  +  
  AHX11378.1 105 NFALEFQNLYNKCDSDESDTYDGGSGL 131
                 ******877776666665554443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (155 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       418  (0.0233142); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.34
# Mc/sec: 1350.88
//
Query:       AHX11379.1  [L=222]
Description: rare lipoA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-22   79.9   0.0    2.1e-22   79.2   0.0    1.3  1  DPBB_1    Lytic transglycolase


Domain annotation for each model (and alignments):
>> DPBB_1  Lytic transglycolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.0   1.1e-26   2.1e-22       2      83 .]     127     216 ..     126     216 .. 0.92

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 1.1e-26
                 EEEEEEE-...CCC...-TTSSB--TTS-EEE-SSS-TT-EEEE..TT.--EEEEEEEE----STTECEEE-HHHHHHHT-TTTS-EEEEE CS
      DPBB_1   2 aagsasly...kdg...tacGecyevkcltaahktlplgtycrv..ls.gksvtVtitDrgpfppgrhiDLSkaAfeklakpraGvipVky 83 
                 ++g as+y   + +   ta+Ge+++   +taahk lpl+++++v  l+ gks +V+++Drgpf+++r iDLS++ ++ l+++++G ++Vk+
  AHX11379.1 127 EVGVASWYggtN-HkkiTASGEVFDKHKITAAHKLLPLPSIVKVtnLEnGKSLIVRVNDRGPFIEDRLIDLSEKGAKLLGFQGKGLARVKV 216
                 5799****8752.3577***************************99667***************************************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       491  (0.0273858); expected 358.6 (0.02)
Passed bias filter:                      314  (0.0175135); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1668.96
//
Query:       AHX11380.1  [L=457]
Description: dihydrolipoyl dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
      3e-66  223.6   0.6    4.7e-66  223.0   0.6    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    1.9e-32  111.8   0.5    3.5e-32  110.9   0.5    1.5  1  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.3e-21   76.1   5.9    2.7e-18   66.3   0.3    3.2  3  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    2.4e-14   53.3   1.0    9.6e-14   51.3   1.0    1.9  1  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    7.5e-10   38.4   0.8    7.5e-10   38.4   0.8    3.1  3  GIDA            Glucose inhibited division protein A
    9.8e-10   37.7   7.5    7.9e-06   24.8   0.3    3.9  4  HI0933_like     HI0933-like protein
    2.6e-09   36.9   0.0    4.6e-09   36.1   0.0    1.5  1  FAD_oxidored    FAD dependent oxidoreductase
    6.1e-08   32.8   0.6     0.0036   17.5   0.1    2.7  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
      3e-07   29.9   2.3      8e-07   28.5   0.6    2.4  2  FAD_binding_2   FAD binding domain
    3.6e-06   27.0   0.1      0.086   12.8   0.0    3.3  3  NAD_binding_9   FAD-NAD(P)-binding
    1.7e-05   24.6   5.0     0.0017   18.0   0.2    3.8  4  DAO             FAD dependent oxidoreductase
    3.4e-05   23.1   1.6     0.0047   16.0   0.3    3.2  3  Lycopene_cycl   Lycopene cyclase protein
    5.4e-05   22.2   0.7    8.2e-05   21.6   0.1    1.7  2  Trp_halogenase  Tryptophan halogenase
    0.00014   21.2   0.2       0.42    9.9   0.0    2.4  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    0.00019   20.8   2.4     0.0015   17.8   0.2    3.0  3  Thi4            Thi4 family
    0.00034   20.0   1.1      0.012   14.9   0.1    2.3  2  FAD_binding_3   FAD binding domain
    0.00087   19.2   3.1      0.016   15.1   0.1    2.8  3  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0054   17.2   0.2        2.8    8.4   0.0    2.7  2  NAD_binding_7   Putative NAD(P)-binding
     0.0097   15.3   1.4      0.027   13.8   0.0    2.4  3  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
  ------ inclusion threshold ------
      0.018   14.2   0.0       0.16   11.1   0.0    2.1  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.065   13.7   0.0        4.6    7.8   0.0    2.4  2  XdhC_C          XdhC Rossmann domain
       0.09   12.3   7.3       0.97    9.0   0.9    3.3  3  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
       0.11   12.7   1.0         20    5.5   0.2    2.7  2  TrkA_N          TrkA-N domain
       0.14   11.5   0.0        0.4    9.9   0.0    1.7  2  Amino_oxidase   Flavin containing amine oxidoreductase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  223.0   0.6   6.2e-69   4.7e-66       1     294 []       2     318 ..       2     318 .. 0.95

  Alignments for each domain:
  == domain 1  score: 223.0 bits;  conditional E-value: 6.2e-69
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEE...TTHCHHHCSHHHHCHHHHHHHHHHHHH.........................HHHHCHHHHCCCC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve...legtclnggcllskallgvaedaeias.........................evvkklnqgiell 70 
                  +d+v+iGgGpAG+ aa++++++g+kv+lve   l+g cln+gc+++kall++ae+++ ++                         e+v+kl  gi +l
   AHX11380.1   2 YDIVIIGGGPAGYPAAIKASKSGLKVALVEkdeLGGVCLNRGCIPTKALLHIAEKYHFIKneastlgivvpdvsmdfhraieysrEKVRKLADGISYL 99 
                  69***************************8888****************************************************99*********** PP

                  HCCTCEEEEESCEEEEETEEEC..TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT- CS
                  xxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  71 lgeevvkidpgkkkvklekkke..gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgk 166
                  ++++++++ + ++++   kk+   + +++i++++++lAtGs++r+l  +G+ e+ +k   ++d  +a+  +++p ++++vG+G+iG+E+A+ ++++g 
   AHX11380.1 100 MNKNKIDVFKSHARILHGKKVVlaDLKKTIDAKNIILATGSRARIL--KGL-EYDHKI--IWDCRDAMMPNNQPGSLLIVGSGAIGIEFACIYNSFGT 192
                  ********99996666656665688889*****************9..999.888888..8888888889999999********************** PP

                  EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTEEEEEEETTSCEEEESEEEE-S-EEES-HHCS..HCCT-EEEETTEEE--T CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 167 evtlveardrllraldkelsaaleealekeGvevklgtsvkeidgngeklevvledgeeidadlvvvavGvrpstelle..eklglelderggivvde 262
                  +vt++e  dr+l + d e+s ++e+a++k+G++++  t v  ++ +++ + v l++g+++ +d ++vavG +++++ ++  + +g++l +rg++ vde
   AHX11380.1 193 KVTVIEIQDRILATEDIEISSMAEDAFKKSGIAIHKSTIVISLEVKEDGALVSLSNGNTLSVDRILVAVGTEANSNDIGleNFSGIKL-DRGFVCVDE 289
                  ***********************************9999988887777667*************************999999******.********* PP

                  TSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 263 flrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                  +++t  pgiyaiGD +   g p la++A+ ++
   AHX11380.1 290 YCQTGEPGIYAIGDLV---GAPCLAHKAIYEA 318
                  ****************...*********9876 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.9   0.5   4.7e-35   3.5e-32       1     108 [.     338     445 ..     338     447 .. 0.98

  Alignments for each domain:
  == domain 1  score: 110.9 bits;  conditional E-value: 4.7e-35
                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHHHHHTTSBHHHHHTSB CS
  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelavaikagltvedladti 96 
                    ip+++++ p +as+Gltee Ak+ g+eik+g+++ + ng++++ ++tkg+vK v+d+ktg++lGah++G++++e+i+++a+a   ++t e l   +
     AHX11380.1 338 IPSCIYSFPSIASIGLTEEAAKKLGYEIKIGRVKSDGNGKSVVLGKTKGLVKTVFDKKTGELLGAHMIGHEVTEMINGYAIAKASEATSETLKTVV 433
                    79********************************************************************************************** PP

                    SSSSSTGGGGHC CS
  Pyr_redox_dim  97 hihPtlsealke 108
                    ++hPt+se++ e
     AHX11380.1 434 FPHPTMSEMMYE 445
                    ********9876 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.3   0.1   0.00053       0.4       2      30 ..       4      32 ..       3      37 .. 0.94
   2 !   66.3   0.3   3.6e-21   2.7e-18       2      77 ..     171     245 ..     170     249 .. 0.94
   3 ?   -1.6   0.1       5.6   4.2e+03      35      67 ..     389     422 ..     373     434 .. 0.56

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00053
                EEEECSSHHHHHHHHHHHHTTSEEEEEES CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvver 30
                +v++GgG  g  +A  +++ g kV +ve 
  AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVEK 32
                8**************************96 PP

  == domain 2  score: 66.3 bits;  conditional E-value: 3.6e-21
                 EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEETTS.EEEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegsedg.vesvk 77 
                 +++vG+G ig+E+A++++ +g kVtv+e +d++l  +D e+s++ ++ ++k gi ++ +t v ++e +edg +  v 
  AHX11380.1 171 LLIVGSGAIGIEFACIYNSFGTKVTVIEIQDRILATEDIEISSMAEDAFKKSGIAIHKSTIVISLEVKEDGaL--VS 245
                 79********************************************************************955..44 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 5.6
                 STTSSHHHHHHHHHHHHHTTE.EEECSEEEEEEE CS
   Pyr_redox  35 lrllDeeaskilqeklekngi.evllntkveeie 67 
                   ++D++++++l  ++  + + e++ +  +++  
  AHX11380.1 389 KTVFDKKTGELLGAHMIGHEVtEMINGYAIAKAS 422
                 4667777777777666555442455555555555 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.3   1.0   1.3e-16   9.6e-14       1     305 []       5     302 ..       5     302 .. 0.75

  Alignments for each domain:
  == domain 1  score: 51.3 bits;  conditional E-value: 1.3e-16
  Pyr_redox_3   1 iIiGaGPaGlaaaielkkagledylilEkgnig...........nsiyrypkemtfispsftsekleipdlnaiseetspafslkeeklsrkealeYl 87 
                  +IiG+GPaG  aai++ k+gl ++  +Ek+++g           +++ +  ++  fi  +  + ++ +pd   +s +   a+ +++ek+  +++++  
   AHX11380.1   5 VIIGGGPAGYPAAIKASKSGL-KVALVEKDELGgvclnrgciptKALLHIAEKYHFIKNEASTLGIVVPD---VSMDFHRAIEYSREKV--RKLADGI 96 
                  7********************.699999998872222222222255666777777777654444444444...5555566677777776..4567788 PP

  Pyr_redox_3  88 revaksfelpiklfeeVesvkkedegfevetsketyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefh..kyagqkvvViGgknSavDaAlel 183
                  + +++++++++ + +   ++ +  ++ ++   k+t+ Ak++i+AtG     +    +G e  +k     ++++  + +   ++++G +  +++ A+  
   AHX11380.1  97 SYLMNKNKIDVFKSH--ARILHG-KKVVLADLKKTIDAKNIILATGS----RARILKGLEYDHKIIWDCRDAMmpNNQPGSLLIVGSGAIGIEFACIY 187
                  888888888775544..566654.5678888999************9....333455655434444444444300445678***************** PP

  Pyr_redox_3 184 vrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkk...sl 278
                   + g +Vtv+  ++ i ++e   +++++ + e+ +++    + i +++ + v +++ ke    v+ ++g++++v d++++a+G + + + +     s+
   AHX11380.1 188 NSFGTKVTVIEIQDRILATE---DIEISSMAEDAFKK----SGIAIHKSTIVISLEVKEDGALVSLSNGNTLSV-DRILVAVGTEANSNDIGLenfSG 277
                  *************9999986...78899999999987....349*************************99887.999999****9999866531444 PP

  Pyr_redox_3 279 feldedgrpvlteeteetnvpglflaG 305
                  +  + d+  v+ +e ++t  pg++ +G
   AHX11380.1 278 I--KLDRGFVCVDEYCQTGEPGIYAIG 302
                  4..4577778888999********998 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.8     1e-12   7.5e-10       1     159 [.       3     147 ..       3     153 .. 0.78
   2 ?    0.7   0.2      0.29   2.2e+02       3      29 ..     172     198 ..     170     215 .. 0.83
   3 ?   -0.7   0.0      0.78   5.8e+02     120     163 ..     234     275 ..     198     281 .. 0.71

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1e-12
                 CEEEE-SSHHHHHHHHHHHHTT--EEEE..ES-GGGTT--SSSSEEE-T...THHH.HHHHHHHHT-SHHHHHHHHEEEEEEESTTS-CCC-EEEEEE- CS
        GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi..thkldtiaelsCnpsiggi...akgl.lvrEidalggliikaadkagiqfrilNrskGpavralraqvd 93 
                 d+++iGgG AG+ AA++a+++G+kv+L+   +  + +++ +C p+   +    k++ +++E   lg ++  +    +            a+++ r +v 
  AHX11380.1   3 DIVIIGGGPAGYPAAIKASKSGLKVALVekDELGGVCLNRGCIPTKALLhiaEKYHfIKNEASTLGIVVPDVSMDFHR-----------AIEYSREKVR 90 
                 79**************************8777788999*********9977645543677777777777666666664...........6666644443 PP

                 HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEET CS
        GIDA  94 relyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihig 159
                 +    ++   +l n++++++++  +  l       k+v+ + ++ti ak++++atG+  +++i  g
  AHX11380.1  91 KL---ADGISYLMNKNKIDVFKSHARILHG----KKVVLADLKKTIDAKNIILATGS--RARILKG 147
                 32...3445678888********9999965....667889999**************..7777665 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.29
                 EEE-SSHHHHHHHHHHHHTT--EEEEE CS
        GIDA   3 iViGgGhAGceAAlaaarlGakvlLit 29 
                  ++G G  G+e A      G kv+ i 
  AHX11380.1 172 LIVGSGAIGIEFACIYNSFGTKVTVIE 198
                 69*********************9993 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.78
                 EEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEE CS
        GIDA 120 eliveekkvkgvvtedgetikakavviatGtflkgkihigekel 163
                 +l+v ++  + v +++g+t++ + + +a Gt  + +  ig +++
  AHX11380.1 234 SLEV-KEDGALVSLSNGNTLSVDRILVAVGT-EANSNDIGLENF 275
                 4434.35556699999***************.666667777666 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.3   1.1e-08   7.9e-06       1      33 [.       2      34 ..       2      38 .. 0.93
   2 ?   -0.4   0.0      0.48   3.6e+02     145     165 ..     121     141 ..      91     144 .. 0.75
   3 ?    4.2   0.1      0.02        15       3      35 ..     171     203 ..     170     209 .. 0.91
   4 !   10.2   0.1    0.0003      0.22     110     166 ..     210     265 ..     204     273 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 1.1e-08
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekak 33
                 +d+++iGgG+AG  aAi+a+k g +V+l+ek +
   AHX11380.1  2 YDIVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                 589***************************974 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.48
                  EEE.TTEEEEESEEEE----S CS
  HI0933_like 145 vktkseeeleadklvlAtGGl 165
                  v ++ ++++ a++++lAtG+ 
   AHX11380.1 121 VLADLKKTIDAKNIILATGSR 141
                  333468999*********986 PP

  == domain 3  score: 4.2 bits;  conditional E-value: 0.02
                  EEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS CS
  HI0933_like   3 viviGgGaAGlmaAisaakrgkrVlllekakkl 35 
                  ++++G Ga G+  A   ++ g +V+++e ++++
   AHX11380.1 171 LLIVGSGAIGIEFACIYNSFGTKVTVIEIQDRI 203
                  589*************************88776 PP

  == domain 4  score: 10.2 bits;  conditional E-value: 0.0003
                  HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----SS CS
  HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGlS 166
                  +i ++ + + k++g+ ++ +t v s+e +edg   v+++++++l+ d++++A+G ++
   AHX11380.1 210 EISSMAEDAFKKSGIAIHKSTIVISLEVKEDG-ALVSLSNGNTLSVDRILVAVGTEA 265
                  5677888999**********************.999999***************875 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   0.0   6.2e-12   4.6e-09       1      68 [.       3      83 ..       3     145 .. 0.71

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.2e-12
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsglvatdig.nkaee.............qvvtgiareflerlr 68
                  D+v++GGgpaG+ AAi A ++G kv+Lve++  lGG   + +  +     +++e              vv  +  +f+++++
    AHX11380.1  3 DIVIIGGGPAGYPAAIKASKSGLKVALVEKD-ELGGVCLNRGCIPTKAlLHIAEkyhfikneastlgIVVPDVSMDFHRAIE 83
                  9***************************985.68998776665443332333333444444445555555556666666655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   4.8e-06    0.0036       1      36 [.       6      40 ..       6      46 .. 0.93
   2 !   12.8   0.0   0.00014      0.11       1      31 [.     173     203 ..     173     217 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 4.8e-06
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                   I+G+G +G  aA  ++k g++v l+ek d lGG + 
     AHX11380.1  6 IIGGGPAGYPAAIKASKSGLKVALVEK-DELGGVCL 40
                   9*************************9.58999875 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00014
                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSS CS
  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrl 31 
                    IvG+G+ G  +A+ +   g +v+++e +dr+
     AHX11380.1 173 IVGSGAIGIEFACIYNSFGTKVTVIEIQDRI 203
                    9***************************997 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.6   1.1e-09     8e-07       1      32 [.       3      34 ..       3      41 .. 0.93
   2 ?   -0.2   0.0      0.55   4.1e+02       2      29 ..     171     198 ..     170     203 .. 0.90

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 1.1e-09
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                   D+++iG+G AG+ AA++a++ Glkva+vek +
     AHX11380.1  3 DIVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                   99****************************87 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.55
                    EEEE--SHHHHHHHHHHHHTTT-EEEEE CS
  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavve 29 
                    ++++GsG+ G   A   +  G kv+v+e
     AHX11380.1 171 LLIVGSGAIGIEFACIYNSFGTKVTVIE 198
                    69************99999999999998 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0     0.004         3       1      44 [.       5      42 ..       5      67 .. 0.79
   2 ?    2.7   0.0      0.15   1.1e+02     133     155 ..     117     140 ..      83     141 .. 0.69
   3 !   12.8   0.0   0.00011     0.086     109     155 ..     216     263 ..     210     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.004
  NAD_binding_9  1 aivGaGprGlavlerLlarakkkspleitlfdpsepgagrvwrt 44
                   +i+G+Gp+G  ++ +  ++      l++ l++++e+g g + ++
     AHX11380.1  5 VIIGGGPAGYPAAIKASKS-----GLKVALVEKDELG-GVCLNR 42
                   7**********99887777.....7**********99.665555 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.15
  NAD_binding_9 133 gqavlladg.aslaadaVvLAlGh 155
                    g +v+lad  ++++a++++LA+G 
     AHX11380.1 117 GKKVVLADLkKTIDAKNIILATGS 140
                    4456665552778*********95 PP

  == domain 3  score: 12.8 bits;  conditional E-value: 0.00011
  NAD_binding_9 109 arlpegvtvevhraevv.dleeradgqavlladgaslaadaVvLAlGh 155
                    +++ ++  + +h++++v +le ++dg+ v l++g++l +d++ +A+G 
     AHX11380.1 216 EDAFKKSGIAIHKSTIViSLEVKEDGALVSLSNGNTLSVDRILVAVGT 263
                    4454566788898765439***************************96 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.2   2.3e-06    0.0017       1      33 [.       3      36 ..       3      42 .. 0.94
   2 ?    2.3   0.0      0.13     1e+02     147     213 ..      91     148 ..      62     162 .. 0.64
   3 ?   -0.0   0.3      0.69   5.2e+02       2      28 ..     171     199 ..     170     206 .. 0.77
   4 ?    3.0   0.0     0.085        64     153     205 ..     215     266 ..     211     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 2.3e-06
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                d+viiGGG +G  +A  +++ g  V+l+ek+ ++g
  AHX11380.1  3 DIVIIGGGPAGYPAAIKASKSGlkVALVEKD-ELG 36
                9*****************************9.777 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.13
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEE..EEE--GGGHHHHHTTCTT CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttp.gendaada..vVnaaGawsdllgllkel 213
                 kl+ ++   + ++ +++++   ++ l  +++kv+      +     ++da  +++a+G  +++l   k l
  AHX11380.1  91 KLADGISYLMNKNKIDVFKS-HARIL--HGKKVVLA----DlKK--TIDAknIILATGSRARIL---KGL 148
                 56666666666666666665.55544..22332222....2222..245555******999987...555 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 0.69
                 EEEECTSHHHHHHHHHHHHTT..EEEEES CS
         DAO   2 vviiGGGiiGlstAyeLarrg..Vtllek 28 
                 ++i+G+G iG+  A      g  Vt++e 
  AHX11380.1 171 LLIVGSGAIGIEFACIYNSFGtkVTVIEI 199
                 58********9888877444677888885 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.085
                 HHH.HHHTT-EEEESECEEEEEEEE.TCEEEEEEECTEEEEEEEEEEE--GGGHH CS
         DAO 153 ara.aealGveilegtevtgleeed.gkvwgverttpgendaadavVnaaGawsd 205
                 a++ +++ G+ i++ t v +le ++ g ++ +   ++g++ ++d + +a G  ++
  AHX11380.1 215 AEDaFKKSGIAIHKSTIVISLEVKEdGALVSL---SNGNTLSVDRILVAVGTEAN 266
                 55538999*************87542554444...23766457******998765 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.3   6.2e-06    0.0047       1      34 [.       3      34 ..       3     150 .. 0.83
   2 ?    2.2   0.0     0.099        74       2      40 ..     171     207 ..     170     218 .. 0.89
   3 ?    2.5   0.0     0.083        62      95     159 ..     216     279 ..     207     283 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 6.2e-06
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieasp 34
                   D+v+iG+GpAg   A +   +k glkv l+e  +
     AHX11380.1  3 DIVIIGGGPAGYPAAIKA--SKSGLKVALVEKDE 34
                   9****************9..**********9755 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.099
  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsllfpn 40 
                    ++++G+G+ g+  A     +  g kv++ie  + +l + 
     AHX11380.1 171 LLIVGSGAIGIEFACIY--NSFGTKVTVIEIQDRILATE 207
                    68************999..***********999887765 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.083
  Lycopene_cycl  95 erlv.engvklleak.vesveeeeageslvvleggrkirarlvvdarglaslkkarrlglQtfyGve 159
                    e+   ++g+  ++++ v s e +e+   lv l++g+++    +++a g   + ++ ++gl  f G+ 
     AHX11380.1 216 EDAFkKSGIAIHKSTiVISLEVKED-GALVSLSNGNTLSVDRILVAVG--TEANSNDIGLENFSGIK 279
                    4434377888888883455555555.889*******************..67788999999999986 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.1   1.1e-07   8.2e-05       1      48 [.       3      47 ..       3      68 .. 0.88
   2 ?   -3.8   0.1       5.8   4.3e+03       3      33 ..     172     199 ..     171     201 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 1.1e-07
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS---SS-EE--TH CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseeigtvgvGeatips 48
                    +ivi+GGG+aG+ aA+  +k +   l+v lve++e+g v   ++ ip+
      AHX11380.1  3 DIVIIGGGPAGYPAAIKASKSG---LKVALVEKDELGGVCLNRGCIPT 47
                    69**************999999...9***********99999999996 PP

  == domain 2  score: -3.8 bits;  conditional E-value: 5.8
                     EEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
  Trp_halogenase   3 vivGGGtaGwlaAaalakalkgklevtlves 33 
                     +ivG G  G   A++ +  +   ++vt++e 
      AHX11380.1 172 LIVGSGAIGIEFACIYNSFG---TKVTVIEI 199
                     79*******99999998888...77888885 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0   0.00057      0.42      31      61 ..       4      34 ..       2      81 .. 0.82
   2 !    9.0   0.0     0.001      0.78      25      64 ..     165     204 ..     161     235 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00057
                 EEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
  AlaDh_PNT_C 31 vlviGgGvaGlqAiatakglgakVtvlDvrp 61
                 +++iGgG aG  A+  a++ g kV ++++++
   AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                 89**********************9998875 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.001
                  CB---EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHH CS
  AlaDh_PNT_C  25 gvepakvlviGgGvaGlqAiatakglgakVtvlDvrparl 64 
                    +p+  l++G G  G++ + + +++g kVtv++++ + l
   AHX11380.1 165 NNQPGSLLIVGSGAIGIEFACIYNSFGTKVTVIEIQDRIL 204
                  5689*****************************9987655 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.2     2e-06    0.0015      19      50 ..       3      33 ..       1      54 [. 0.88
   2 ?    0.3   0.0      0.46   3.5e+02      20      49 ..     171     199 ..     161     204 .. 0.87
   3 ?   -0.4   0.0      0.76   5.7e+02      66     107 ..     389     432 ..     358     452 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2e-06
                EEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
        Thi4 19 DvvivGaGssGLtaayylakkpdlkvailers 50
                D+vi+G+G++G  aa   +k+ +lkva++e+ 
  AHX11380.1  3 DIVIIGGGPAGYPAAIKASKS-GLKVALVEKD 33
                9****************9999.********86 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.46
                 EEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
        Thi4  20 vvivGaGssGLtaayylakkpdlkvailer 49 
                 ++ivG+G+ G+  a +     + kv+++e 
  AHX11380.1 171 LLIVGSGAIGIEFACIYNSF-GTKVTVIEI 199
                 689*********99888777.999999995 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.76
                 EEEEETTTHHHH..HHTT---EEESSEEEESEHHHHHHHHHHHH CS
        Thi4  66 aivvrkpakelL..delgikyedegdyvvvkdaalftstllskv 107
                 + v  k++ elL  + +g + +++ +++ +++a ++ts+ l  v
  AHX11380.1 389 KTVFDKKTGELLgaHMIGHEVTEMINGYAIAKASEATSETLKTV 432
                 556667777777223467788999999******99999876555 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   1.6e-05     0.012       2      34 ..       2      34 ..       1      48 [. 0.92
   2 ?    3.5   0.1     0.047        35       5      32 ..     172     199 ..     170     206 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                   +d++I+G+GpaG  +a   s+ G +v lvek +
     AHX11380.1  2 YDIVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                   5899**************************975 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.047
                    EEE--SHHHHHHHHHHHHTTHHEEEEES CS
  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlvek 32 
                    lIVG+G  G+  a +  + G +v+++e 
     AHX11380.1 172 LIVGSGAIGIEFACIYNSFGTKVTVIEI 199
                    8*************************95 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.1     0.064        48       2      32 ..       4      34 ..       3      43 .. 0.93
   2 ?   -2.1   0.0       4.1   3.1e+03      92     115 ..     117     140 ..     104     146 .. 0.74
   3 !   15.1   0.1   2.1e-05     0.016       4      56 ..     173     225 ..     170     248 .. 0.87

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.064
                EEEE--SCCHHHHHHHHHHTT-EEEEE-S-H CS
     3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdise 32
                + +iG G  G   a  + ++gl+V lv+ +e
  AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                789************************9876 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 4.1
                 HHHHHHHHHHCCS-TTSEEEE--S CS
     3HCDH_N  92 lKrkvfaelekiakpdailasnTS 115
                  K+ v+a+l+k+++++ i+  + S
  AHX11380.1 117 GKKVVLADLKKTIDAKNIILATGS 140
                 578888888888877666655555 PP

  == domain 3  score: 15.1 bits;  conditional E-value: 2.1e-05
                 EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
     3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                 ++G+G +G + a +  s g +V++++i++++l++   +i++  e + +k  + 
  AHX11380.1 173 IVGSGAIGIEFACIYNSFGTKVTVIEIQDRILATEDIEISSMAEDAFKKSGIA 225
                 8***************************************9999988887766 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.4   0.0    0.0038       2.8      10      40 ..       4      34 ..       2     143 .. 0.72
   2 ?    6.1   0.0      0.02        15       9      58 ..     170     222 ..     162     270 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0038
  NAD_binding_7 10 vlvvGgGevAarkvrklleagakvtvvapev 40
                   ++++GgG+ ++  + k  ++g kv +v ++ 
     AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                   79*************************9994 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.02
  NAD_binding_7   9 kvlvvGgGevAarkvrklleagakvtvvapev...keele...elvklaeeelekd 58 
                    + l+vG G ++ + +    ++g kvtv+  +    +       e+ ++ae+ ++k+
     AHX11380.1 170 SLLIVGSGAIGIEFACIYNSFGTKVTVIEIQDrilA---TediEISSMAEDAFKKS 222
                    579************************988742221...22223333455555444 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.1       2.3   1.7e+03      39      66 ..       4      31 ..       3      36 .. 0.88
   2 !   13.8   0.0   3.6e-05     0.027      35      83 ..     167     212 ..     141     229 .. 0.74
   3 ?   -2.5   0.1       3.8   2.8e+03      35      58 ..     393     416 ..     379     431 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2.3
                  EEEES-SHHHHHHHHHHHHTT-EEEEES CS
  2-Hacid_dh_C 39 vGiiGlGrIGqavakrlkafgmkviayd 66
                  + iiG G  G  +a ++++ g+kv  ++
    AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVE 31
                  679********************99876 PP

  == domain 2  score: 13.8 bits;  conditional E-value: 3.6e-05
                   TTSEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTCEEC CS
  2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgvelv 83 
                   +   + i+G G+IG ++a + ++fg kv++++ + +     +++ +e  
    AHX11380.1 167 QPGSLLIVGSGAIGIEFACIYNSFGTKVTVIEIQDRIL---ATEDIEIS 212
                   556789*************************9997633...33334434 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 3.8
                   TTSEEEEES-SHHHHHHHHHHHHT CS
  2-Hacid_dh_C  35 sgktvGiiGlGrIGqavakrlkaf 58 
                    +kt  ++G+  IG++v +++++ 
    AHX11380.1 393 DKKTGELLGAHMIGHEVTEMINGY 416
                   445555888888999998888765 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0       0.3   2.2e+02       2      35 ..       1      32 [.       1      36 [. 0.77
   2 ?   11.1   0.0   0.00022      0.16     100     207 ..      83     184 ..      75     228 .. 0.72

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.3
  K_oxygenase  2 ilDligiGiGpsnLsLailleevkkelkalfler 35
                 ++D+++iG Gp+    ai +++    lk+  +e+
   AHX11380.1  1 MYDIVIIGGGPAGYPAAIKASKSG--LKVALVEK 32
                 59*********9988888887776..66666665 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00022
  K_oxygenase 100 dYlrWvasqleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVv 197
                  +Y r+ +++l + +++ ++ +++++ +++  ++l+ ++   ++ ++++ a+n++l++G+++ i + le  +  + ++   +++  +   +++ ++++v
   AHX11380.1  83 EYSREKVRKLADGISYLMNKNKIDVFKSHA-RILHGKKVVLADLKKTIDAKNIILATGSRARILKGLEYDH--KIIWDCRDAMMPN---NQPGSLLIV 174
                  577788888888899999999999988764.46655555578899*****************988888533..6677777777666...899****** PP

  K_oxygenase 198 GsGqSaaeif 207
                  GsG  + e +
   AHX11380.1 175 GSGAIGIEFA 184
                  ***8887754 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.8   0.0       0.1        76       2      35 ..       5      55 ..       4     144 .. 0.72
   2 ?    7.8   0.0    0.0061       4.6       1      55 [.     171     238 ..     171     268 .. 0.72

  Alignments for each domain:
  == domain 1  score: 3.8 bits;  conditional E-value: 0.1
                EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG.................- CS
      XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa.................t 35
                vi+G+g+ + + a  a++ g++v +v+++e                    +
  AHX11380.1  5 VIIGGGPAGYPAAIKASKSGLKVALVEKDELGGvclnrgciptkallhiaE 55
                89************************9998322456555555554444444 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0061
                 EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG-GGG-TT-SE..............-EEEE--S-HH CS
      XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefatkerfpeade..............tavvvlthdhk 55 
                 l+i+G g ++ + a + +++g +vtv++ ++++ ++e+++   +              +  +v++ + k
  AHX11380.1 171 LLIVGSGAIGIEFACIYNSFGTKVTVIEIQDRILATEDIEIS-SmaedafkksgiaihKSTIVISLEVK 238
                 79*************************999977755554422.12334555556666644444444444 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.1     0.017        13       3      42 ..       4      43 ..       2      53 .. 0.85
   2 ?   -0.8   0.1       1.3   9.7e+02      30      79 ..      83     134 ..      80     141 .. 0.65
   3 ?    9.0   0.9    0.0013      0.97       4      38 ..     172     206 ..     170     271 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.017
                    EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTT CS
  UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsg 42
                    i++iG G  G + a+  ++ g +v +v +de     ln+g
      AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVEKDELGGVCLNRG 43
                    99**************************998655555555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 1.3
                     -S-HHHHHHHCTTS-SS--TTHHHHHHHHCH..TTTEEEES-HHHHHHC-SE CS
  UDPG_MGDP_dh_N  30 DideekvdklnsgkipiyepgLeelvkkave..sgrlsfttdvekaveeadv 79 
                       ++ekv+kl  g +++++++  ++ k++++  +g+     d++k++++ ++
      AHX11380.1  83 EYSREKVRKLADGISYLMNKNKIDVFKSHARilHGKKVVLADLKKTIDAKNI 134
                     5677888888888888888888888776652114445555566666655555 PP

  == domain 3  score: 9.0 bits;  conditional E-value: 0.0013
                     EEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHH CS
  UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeighevigvDideekvdk 38 
                      ++G+G +G+  a ++++ g +v+++ i+++  ++
      AHX11380.1 172 LIVGSGAIGIEFACIYNSFGTKVTVIEIQDRILAT 206
                     59**************************9876555 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0     0.034        25       1      31 [.       4      34 ..       4      36 .. 0.91
   2 ?    5.5   0.2     0.027        20       2      39 ..     172     208 ..     171     268 .. 0.79

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.034
                EEEES-SHHHHHHHHHHHHTTEEEEEEESSH CS
      TrkA_N  1 iiiiGlGrvGrslaeeLseggkdvvvidkde 31
                i+iiG G  G+  a + s++g +v +++kde
  AHX11380.1  4 IVIIGGGPAGYPAAIKASKSGLKVALVEKDE 34
                89*****************6546******97 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.027
                 EEES-SHHHHHHHHHHHH.TTEEEEEEESSHHHHHHHHH CS
      TrkA_N   2 iiiGlGrvGrslaeeLse.ggkdvvvidkdeerveelre 39 
                 +i+G G +G + a   ++ g  +v+vi+ +++ +++ ++
  AHX11380.1 172 LIVGSGAIGIEFACIYNSfGT-KVTVIEIQDRILAT-ED 208
                 79****************777.6******9877665.33 PP

>> Amino_oxidase  Flavin containing amine oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0         2   1.5e+03      12      26 ..     189     203 ..     188     203 .. 0.92
   2 ?    9.9   0.0   0.00054       0.4     215     261 ..     213     262 ..     211     280 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 2
                    HTTEEEEEEESSSSS CS
  Amino_oxidase  12 saGfdVtvlEardrv 26 
                    s+G +Vtv+E +dr+
     AHX11380.1 189 SFGTKVTVIEIQDRI 203
                    789**********97 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00054
                    HHHH...TTTTEEEETSEEEEEEEEETTCEEEEETTSTEEEESEEEE-S- CS
  Amino_oxidase 215 alae...elrgldirlntrVkeikregdgvtvtledgevveaDaVvvTvp 261
                    ++ae   +++g  i+ +t V +++  +dg  v l++g+++++D+++v+v 
     AHX11380.1 213 SMAEdafKKSGIAIHKSTIVISLEVKEDGALVSLSNGNTLSVDRILVAVG 262
                    5666777789999***********************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       431  (0.0240393); expected 358.6 (0.02)
Passed bias filter:                      357  (0.0199119); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        24  (0.00133861); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              24  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 3443.69
//
Query:       AHX11381.1  [L=40]
Description: hypothetical protein NHE_0436 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       157  (0.00875676); expected 358.6 (0.02)
Passed bias filter:                      132  (0.00736237); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.35
# Mc/sec: 344.22
//
Query:       AHX11382.1  [L=437]
Description: magnesium transporter [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.5e-20   71.1   5.6    8.4e-09   35.8   0.9    4.1  4  CBS       CBS domain
      2e-18   67.0  11.0      2e-18   67.0  11.0    2.1  3  MgtE      Divalent cation transporter
    1.5e-14   54.4   2.0    1.5e-14   54.4   2.0    2.5  2  MgtE_N    MgtE intracellular N domain
  ------ inclusion threshold ------
      0.094   12.9   0.0        1.4    9.2   0.0    2.8  2  PMBR      Pseudomurein-binding repeat
      0.099   12.9   0.1          7    7.0   0.2    2.5  2  IF3_N     Translation initiation factor IF-3, N-terminal doma


Domain annotation for each model (and alignments):
>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.078   2.8e+02       8      26 ..      77      95 ..      72     114 .. 0.58
   2 !   32.8   0.0     2e-11   7.1e-08       2      52 ..     126     181 ..     125     185 .. 0.91
   3 !   35.8   0.9   2.3e-12   8.4e-09       1      56 [.     189     244 ..     189     245 .. 0.95
   4 ?   -3.1   0.0       3.1   1.1e+04      41      51 ..     251     262 ..     248     262 .. 0.72

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.078
                SCEEEETTSBHHHHHHHHH CS
         CBS  8 dvvtvppdttleealelmr 26
                +++t+ p++ + ++le +r
  AHX11382.1 77 KIITALPTDEIVDVLENLR 95
                5566666666666655553 PP

  == domain 2  score: 32.8 bits;  conditional E-value: 2e-11
                 HHHSBSSCEEEETTSBHHHHHHHHH.HHT....SSEEEEEETTTBEEEEEEHHHHH CS
         CBS   2 gdimtrdvvtvppdttleealelmr.ekg....vsrlPVVdedgklvGivtlrDll 52 
                 g + ++d++++p d+++e++l+ +r +k+    +s ++VVde++ ++G v+l D+l
  AHX11382.1 126 GRLIHKDFIVIPKDWSIEQVLQFIRiQKKmpkyLSEIFVVDESNSPIGSVSLNDIL 181
                 678899******************8866668888*********************8 PP

  == domain 3  score: 35.8 bits;  conditional E-value: 2.3e-12
                 HHHHSBSSCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHHH CS
         CBS   1 VgdimtrdvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllrall 56 
                 V++im +++ tv   ++ ee+++l+re+ ++++ VVde++k+vG+++  D+++ ++
  AHX11382.1 189 VKSIMQTKIETVGTGQDQEEVARLFREYSLRSVAVVDEEKKIVGVISIDDVVDIIS 244
                 899**********************999999********************98775 PP

  == domain 4  score: -3.1 bits;  conditional E-value: 3.1
                 BEE.EEEEHHHH CS
         CBS  41 klv.GivtlrDl 51 
                  l+ G v+++D+
  AHX11382.1 251 ILHaGKVSESDI 262
                 566699999998 PP

>> MgtE  Divalent cation transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       1.2   4.2e+03       5      28 ..      64      87 ..      62     106 .. 0.73
   2 ?   -2.5   0.1       1.7   6.1e+03      40      57 ..     277     294 ..     252     306 .. 0.48
   3 !   67.0  11.0   5.4e-22     2e-18       1     123 [.     308     429 ..     308     430 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 1.2
                HHHHHHHHHHHHHHHHHHHHTTSS CS
        MgtE  5 lglgGnlgaqlasristalhlgel 28
                + +   lg  + s i+tal ++e+
  AHX11382.1 64 NEIIEMLGVRQFSKIITALPTDEI 87
                555566788899999**9999887 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.7
                 HHHHHHHHHHHHHHHHHH CS
        MgtE  40 lrvvlllgvilgllifll 57 
                 l+v +l + + + +i+++
  AHX11382.1 277 LIVTFLSINFSSYVIGFF 294
                 222333333333333333 PP

  == domain 3  score: 67.0 bits;  conditional E-value: 5.4e-22
                 HHHHHHHHHHHHHHHHHHHHHHHHTTSS-GG.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-.CTSHHHHHHHHHHHHHHHHHH..HHHHHHHHHHT CS
        MgtE   1 iPvilglgGnlgaqlasristalhlgelekk.lkkvllkelrvvlllgvilgllifllalllgwslllalvvglalvlvllaaallilgvllplllwkl 98 
                 +P+ +++gGn+g q++++ ++a+ +++l  + +++++lkel+v+l++gvi+++++++++ + +++l l  ++++a+vlv+++a+ +  g+++p+++ k+
  AHX11382.1 308 MPITAAMGGNAGIQASTVAVRAIITKKLAYNnAFRLFLKELLVGLCNGVIMSAFMVMIIAMRFHNLALESTFTIAIVLVFTLATSV--GAAIPFIIEKC 404
                 8*************************9955559***********************998888888999999***************..*********** PP

                 TS-GGGSHHHHHHHHHHHHHHHHHH CS
        MgtE  99 glDPdnaaiPlltalgDllgtlllv 123
                 g DP+++++ + ++++D+l +++l+
  AHX11382.1 405 GGDPALSSSIITSSFTDILAFVVLL 429
                 *********************9996 PP

>> MgtE_N  MgtE intracellular N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.4   2.0   4.2e-18   1.5e-14      10     102 .]      32     123 ..      23     123 .. 0.88
   2 ?    1.6   0.2      0.12   4.3e+02      55      73 ..     228     246 ..     204     254 .. 0.81

  Alignments for each domain:
  == domain 1  score: 54.4 bits;  conditional E-value: 4.2e-18
                 HCCS.-HHHHHHHHHHS-HHHHHHHHCTS-CCCCCHHHHCS-HHHHHHHHCCS-HHHHHHHHCCCHHHHHHHHHHCS-HHHHHHHHHHCTS-TT CS
      MgtE_N  10 leel.peeeraallrllpkeeaaevleeldedlqeeliealsdeelaelleeldsDdaadlleelpeekveellsaldeeereeieellsYped 102
                 + +  +e++r  + ++l   e+  vl+e++e+l  e+ie+l  ++ +++++ l++D+++d+le+l ++  +e++++l+++  + i+e+l+Ype+
  AHX11382.1  32 FINAkSETKREFIHQHL--SEHPYVLTEISEELINEIIEMLGVRQFSKIITALPTDEIVDVLENLRQDSIKEIIDLLPSKLNRVIKEILAYPEE 123
                 44441556666666666..8899*********************************************************************97 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.12
                 HHHHCCS-HHHHHHHHCCC CS
      MgtE_N  55 aelleeldsDdaadlleel 73 
                 ++++  ++ Dd++d+++e 
  AHX11382.1 228 KKIVGVISIDDVVDIISEE 246
                 678888999*****98764 PP

>> PMBR  Pseudomurein-binding repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   0.0   0.00038       1.4      14      30 ..     142     158 ..     140     160 .. 0.91
   2 ?   -0.1   0.0      0.34   1.2e+03       3      15 ..     232     244 ..     232     245 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00038
        PMBR  14 asrvlafiesngrlPny 30 
                 + +vl+fi+  +++P y
  AHX11382.1 142 IEQVLQFIRIQKKMPKY 158
                 679************99 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.34
        PMBR   3 gkisyeeyldmas 15 
                 g is ++++d++s
  AHX11382.1 232 GVISIDDVVDIIS 244
                 679********98 PP

>> IF3_N  Translation initiation factor IF-3, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.0     0.035   1.3e+02       8      29 ..     160     181 ..     158     188 .. 0.89
   2 ?    7.0   0.2    0.0019         7       8      35 ..     219     246 ..     214     252 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.035
                 SEEEEE-SSS-EEEEEEHHHHH CS
       IF3_N   8 revrlvdedGeqlGvistreAl 29 
                 +e+ +vde +  +G +s++++l
  AHX11382.1 160 SEIFVVDESNSPIGSVSLNDIL 181
                 68****************9987 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0019
                 SEEEEE-SSS-EEEEEEHHHHHHHHHHH CS
       IF3_N   8 revrlvdedGeqlGvistreAlrlaeek 35 
                 r v +vde+ + +Gvis++++++++ e+
  AHX11382.1 219 RSVAVVDEEKKIVGVISIDDVVDIISEE 246
                 899******9999*********998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (437 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1166  (0.0650343); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.42
# Mc/sec: 3134.85
//
Query:       AHX11383.1  [L=272]
Description: phage major capsid protein, HK97 family [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.8e-54  184.9   0.0      2e-54  184.8   0.0    1.0  1  Phage_capsid  Phage capsid family


Domain annotation for each model (and alignments):
>> Phage_capsid  Phage capsid family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  184.8   0.0   1.1e-58     2e-54      17     279 ..       1     268 [.       1     269 [. 0.93

  Alignments for each domain:
  == domain 1  score: 184.8 bits;  conditional E-value: 1.1e-58
  Phage_capsid  17 lrerspirqlatvtrtsasgtvkilvqtgeaeaawvg.eteaipetdsp.tfgqitlsvkklaalvpvsnelLddsavdleayiadelaeafarked 111
                   +++ sp+r++a+v ++s +++++++ +  + ea+wv+ e  + +e+d++ ++ ++ +++++l ++++ ++++Ldd a++ e+++ +++a af + e+
    AHX11383.1   1 MKKLSPMRKIASVDTIS-TDCITYIGNGEALEAQWVSdESSDDTEDDAKdHIITTNITTYELFTQPRNTQKVLDDPAIEAERWLIEQAALAFTQLEN 96 
                   6788***********99.*******************7556669999999*********************************************** PP

  Phage_capsid 112 eaflnGdGdgngqpkGilas.......tgavatgtaaavtatntaddlidliyslkaayranasfvmnpstlaalrklkd.adGnylwqpglqagqp 200
                   eaf++G+  +  + +Gil++       +++ ++ ta ++    ta+d+++l ysl  +++ n +f+mn++ ++ +r lk  ++++y++qp+l++g+p
    AHX11383.1  97 EAFITGNAEN--KSHGILKYndcytdqICKITSSTACKT----TAEDILQLHYSLLREFSVNCTFLMNSASIQIVRGLKYeQTEHYMFQPSLRSGEP 187
                   ******4444..************988777777777765....89***************9999***************77**************** PP

  Phage_capsid 201 .tLlGrpvveseampd....agaksageilfGDf.sayiivdregveikvlrdpysafekdqvafratervdgavvdpeAfkklk 279
                    tL+G+ vve+ +mp     +++     i fGDf + y i+ r  +++  l dpys   k+++ f++t+rv+g v++p+Af++l+
    AHX11383.1 188 dTLMGIAVVECAEMPIiptkSATPRPCPIMFGDFrRSYQIINRNEMRV--LGDPYS--VKPYISFYITKRVGGEVINPNAFALLE 268
                   ****************997533333789********************..******..************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       358  (0.0199677); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2074.44
//
Query:       AHX11384.1  [L=841]
Description: uvrD/REP helicase N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-19   69.2   4.8    5.4e-12   45.8   0.0    3.0  3  UvrD_C         UvrD-like helicase C-terminal domain
    1.1e-17   64.6   3.5    1.1e-17   64.6   3.5    2.9  2  UvrD-helicase  UvrD/REP helicase N-terminal domain
    2.4e-10   40.1   0.9     0.0008   19.2   0.0    2.5  2  UvrD_C_2       UvrD-like helicase C-terminal domain
    2.4e-06   28.0   0.1    3.4e-05   24.2   0.0    2.4  2  AAA_19         AAA domain
    8.8e-06   25.8   0.2    3.1e-05   24.0   0.2    1.9  1  PDDEXK_1       PD-(D/E)XK nuclease superfamily
     0.0003   20.4   0.1     0.0078   15.8   0.0    2.8  2  AAA_12         AAA domain
  ------ inclusion threshold ------
      0.017   14.7   0.0       0.05   13.2   0.0    1.8  1  DUF3884        Protein of unknown function (DUF3884)


Domain annotation for each model (and alignments):
>> UvrD_C  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.2     6e-09   1.5e-05       3     157 ..     272     446 ..     270     470 .. 0.79
   2 !   45.8   0.0   2.1e-15   5.4e-12     283     345 ..     532     620 ..     498     624 .. 0.82
   3 ?   -2.7   0.2       1.1   2.8e+03      83      97 ..     671     694 ..     644     764 .. 0.45

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 6e-09
                 xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxx....xxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxx.........xxxxxxxxxxxxxxx. RF
      UvrD_C   3 LekNyRStksLlkaankflenilnr.ralekek....ktvekge.....kivvleaeteeeEaekiaatikall.........ekneklediavLvRs. 81 
                  ek yRS++ +l+ + ++++ i+   +  e+++    ++  +g       i+  + + e + a  i +ti+++          ++  k  dia+Lv   
  AHX11384.1 272 IEKSYRSSNPILEFVDSVFADITLCaSHTETIQhktnREDAPGYvevrpLIKKSDIDAELQLAISIKNTIQSWIsnkrmikakKRSVKAGDIAILVAHr 370
                 6788***************99988844444333444433334437663333333444555556667777877778888888888999*********996 PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      UvrD_C  82 nkdadkiskaLkkegipfnvvdeekfFkreeikdilaylkllankqdkialkrilkrlvlgigkatveriseelkk 157
                  +  d++ ++L++ +ip+n  ++ +    + +  ++ + k +  k+d+ al  ilk+++lg  ++ + +i  + k+
  AHX11384.1 371 TAFVDHLYTQLNSADIPVNFTGKSSVKTNPIFDLLINLGKFITYKYDEEALVTILKSPILGWCDDEILKIKTSNKD 446
                 78899******************9999999999999999**************************99999444444 PP

  == domain 2  score: 45.8 bits;  conditional E-value: 2.1e-15
                 xx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      UvrD_C 283 kk.ekipiiTiHqAKGlEFdvVflagleegtfP...........................syrskkekrleEEkRlfYVaiTRAkkrLfis 345
                  + + ++i+T+H +KG  +++Vf+a+   + +P                            ++ +k    +E +Rl+YVa+TRA ++L++ 
  AHX11384.1 532 ANeNGVTISTVHGSKGAQYPIVFVAD--SNYVPqnrniflhtedglpilsseknieitdrIKERQKVTIYHEHMRLLYVALTRAEDELYVV 620
                 33589*********************..99***8888888888888888777766666553333447799*******************96 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 1.1
                 xxxxxxxxxxxxxx.........x RF
      UvrD_C  83 kdadkiskaLkkeg.........i 97 
                 + a++is  +++e+         +
  AHX11384.1 671 NTAQEISSLFNSEQrkvdedntlV 694
                 333333333333332222222220 PP

>> UvrD-helicase  UvrD/REP helicase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.6   3.5   4.1e-21   1.1e-17      56     312 ..       1     256 [.       1     259 [. 0.72
   2 ?   -0.2   0.3      0.22   5.7e+02     134     139 ..     659     664 ..     521     825 .. 0.53

  Alignments for each domain:
  == domain 1  score: 64.6 bits;  conditional E-value: 4.1e-21
                    HHHHHHHHHHHH...............HHHHCCHHCTT-H.HHHHHHHHCTT.SEEEEHHHHHHHHHHHHHGGTTSHTTTEEECHHHHHHCCHHHH CS
  UvrD-helicase  56 kAaeElkeRiee...............alkkaeqessdde.rlrlalqnlse.anisTlHsfcqkilkkeanrigldpnfrildeedeedlkqqel 134
                    +Aa+E+ +R+ e                l+++++ + dd   +r+    ++  + i+T+H+fc++ +k+    ++  ++++  ++++  ++  q +
     AHX11384.1   1 MAAAEMYNRVFEalsilstmgnvemrrYLRSELEINTDDFsYIRNLICIADSfLRIQTFHAFCLQSIKECDPGYNS-KEIYEENQHTFCKMLAQFI 95 
                    6999999999999999999996666655555555444444555555554443379************987666654.4444444444112222223 PP

                    HHHHHSCHSHTTTTHHHHHHHHHHHHHHCCCCCHHHHCCCHHHHHCHHHHHHHHHHHTTCCTTHHCHSSTSCSHHHHHHHHHHHHHHHHHHHHTCE CS
  UvrD-helicase 135 lkelleksaddslnldkkkleklikelsksrnikkeelslskskaeelrelvskakekqlspkelkkafekasdlqkkiaeflkeyqeqkkeenal 230
                    ++++    ++ s+ ++++kl +                sl ++   +++e+++k+k++ ++++  +              ++l  + e ++ ++++
     AHX11384.1  96 FEKCR-LPERTSEGITEQKLYEI-------------FSSLLHNFHLDYAEIIKKLKDNPIEQLPVNT------------LDILSAFSEFLDLNRNF 165
                    33322.24444555666655533.............3456677788888888888888888887776............789999999999***** PP

                    EHHHHHHHHHH..HHHHCHHHHHHHHHHSSEEEESSGGG-BHHHHHHHHHHHTTTTT.......EEEEE-GGG--GGGGTB-THHHHHHHH CS
  UvrD-helicase 231 Dfsdllhalle..lleeneelaealrerykeiliDEyQDTnkiQyrilkllasghee.......lfmvGDpkQsIYgFRgAdielflkkkk 312
                      ++++h+++   +  ++ +   ++ ++++++liDE+QD n  Q  i+++ +s+          lf+vGD kQsIYgF+gA ++ fl +++
     AHX11384.1 166 SRKYIAHNAVIetAISKEIWNIYEVASKIDHVLIDEAQDNNLKQLYIISRFCSDFLMddsqdksLFIVGDYKQSIYGFQGASPDAFLAFYN 256
                    *******98752233333445567889***********************99987556777899************************996 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.22
                    HHHHHH CS
  UvrD-helicase 134 llkell 139
                     + e l
     AHX11384.1 659 YFDENL 664
                    111111 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   3.1e-07    0.0008       2      27 ..     537     562 ..     536     568 .. 0.87
   2 !   19.0   0.2   3.6e-07   0.00093      31      52 .]     601     620 ..     594     620 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
    UvrD_C_2   2 ayaltihkaQGsefpaVivfdpdlaa 27 
                 ++++t+h ++G ++p+V+v+d ++  
  AHX11384.1 537 VTISTVHGSKGAQYPIVFVADSNYVP 562
                 6899***************9998875 PP

  == domain 2  score: 19.0 bits;  conditional E-value: 3.6e-07
    UvrD_C_2  31 gelrrrlLYtavTRAreklilv 52 
                 +    rlLY+a+TRA ++l++v
  AHX11384.1 601 E--HMRLLYVALTRAEDELYVV 620
                 3..48***************98 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.0   1.3e-08   3.4e-05      68     146 .]      55     244 ..       3     244 .. 0.73
   2 ?    1.0   0.0      0.19     5e+02      51     114 ..     522     707 ..     509     734 .. 0.58

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 1.3e-08
      AAA_19  68 eatTiHrlal......................................................................................... 77 
                 +++T+H++ l                                                                                         
  AHX11384.1  55 RIQTFHAFCLqsikecdpgynskeiyeenqhtfckmlaqfifekcrlpertsegiteqklyeifssllhnfhldyaeiikklkdnpieqlpvntldils 153
                 478888877688888888888888888888888888888888888888888888888888888888888888888888888888888888877766666 PP

      AAA_19  78 ................ldfddlltealelle...........eaeeekklqeee.llivDEfqdvdelqyrLlkallgek.kk......lllvGDpdQl 141
                                 +                         e  +  ++ ++  ++++DE+qd +  q  ++++ + +  ++      l++vGD +Q+
  AHX11384.1 154 afsefldlnrnfsrkyI-------------AhnavietaiskEIWNIYEVASKIdHVLIDEAQDNNLKQLYIISRFCSDFlMDdsqdksLFIVGDYKQS 239
                 67666666644444331.............0222222444442222233444555***********99999999999654444566778********** PP

      AAA_19 142 iyvfr 146
                 iy f+
  AHX11384.1 240 IYGFQ 244
                 **995 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.19
      AAA_19  51 tgrAakelrerlaalgaeatTiHrlal........................................................................ 77 
                 t  A+ +++++  + g+ ++T+H+                                                                           
  AHX11384.1 522 TDDATIRIKNAN-ENGVTISTVHGSKGaqypivfvadsnyvpqnrniflhtedglpilsseknieitdrikerqkvtiyhehmrllyvaltraedelyv 619
                 566667777666.55777788886643667777777777777777777666666666666666666666666666666666666666666666666666 PP

      AAA_19  78 ...............................................ldfddlltealelle........eaeeekklqeeellivDEfqdv 114
                                                                     +++++++ +         + +e+++l  +e+l +D    +
  AHX11384.1 620 vgtgekikknswhelctnsiikigstkedgsyyhtnehkyfdenltdN----RKQNTAQEISslfnseqrKVDEDNTLVMGETLKIDKKTVL 707
                 666666666666666667777777777777777777776666653321....1222222223343344444455555555555555555555 PP

>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.2   1.2e-08   3.1e-05      37     180 ..     717     828 ..     696     839 .. 0.70

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.2e-08
    PDDEXK_1  37 GtlvHaaleefyewkkldkedleelleeaveelwpellleeeilessarlrylaeklkevleklverlaeeleakrgfrpvalelefggekvrLkGriD 135
                 G+l+H++le ++        + +  +       w + +le++          l++k+++ ++k+v ++ e +  + g+r+v++ ++      rL  r+D
  AHX11384.1 717 GELIHEILEYIFI-------VGKPEI-------WLKGFLENRA-------LALNQKEQDEISKTVLKFVENNSIPSGRREVEVLFAG-----RLI-RMD 788
                 5555555554444.......333333.......5565666655.......7888999999999999999989999998888887322.....344.789 PP

    PDDEXK_1 136 rvddkegelriiDyKtgsappkskelaelkegl..QlllYllalaeg 180
                  v+ k++e++i DyKtg+++       e+ + +  Q++lY+ a++  
  AHX11384.1 789 HVEFKDNEIVIRDYKTGKNR-------EITDTIvqQMRLYQRAMQSI 828
                 99988889**********33.......23344557******999977 PP

>> AAA_12  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0       0.1   2.7e+02      18      55 ..     270     307 ..     254     385 .. 0.64
   2 !   15.8   0.0   3.1e-06    0.0078     139     197 ..     533     622 ..     510     624 .. 0.74

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.1
      AAA_12  18 vlLdtqYRmhpeIsrfpsklfYkgkLkdaesvkkrele 55 
                   ++  YR+ + I++f+ + f + +L ++++ + +++ 
  AHX11384.1 270 LKIEKSYRSSNPILEFVDSVFADITLCASHTETIQHKT 307
                 445678************99999888776643333333 PP

  == domain 2  score: 15.8 bits;  conditional E-value: 3.1e-06
      AAA_12 139 sekeievntvdgfQGrekdviilslVRsnekk..............................eig.flkderrlNValTRAkskliivGn 197
                 +e+ ++++tv g  G +  ++++      +++                              ++    +  r l ValTRA ++l++vG 
  AHX11384.1 533 NENGVTISTVHGSKGAQYPIVFVADSNYVPQNrniflhtedglpilsseknieitdrikerqKVTiYHEHMRLLYVALTRAEDELYVVGT 622
                 233399999999999999999987666643333456666666666666677777777777767774667788899**************7 PP

>> DUF3884  Protein of unknown function (DUF3884)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0     2e-05      0.05       7      38 ..     471     500 ..     466     503 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 2e-05
     DUF3884   7 vkFkkvpdvllldeeilkkLGkWlvttgdeWi 38 
                  +F+   +  lldeei+ +LG+W+ + +d +i
  AHX11384.1 471 TTFQI--YSKLLDEEIVSRLGRWYGSETDYYI 500
                 56655..7789*************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (841 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       926  (0.0516482); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.68u 0.29s 00:00:00.97 Elapsed: 00:00:00.47
# Mc/sec: 5404.02
//
Query:       AHX11385.1  [L=53]
Description: hypothetical protein NHE_0440 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       134  (0.00747392); expected 358.6 (0.02)
Passed bias filter:                      125  (0.00697194); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 400.66
//
Query:       AHX11386.1  [L=149]
Description: hypothetical protein NHE_0441 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       572  (0.0319036); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1133.98
//
Query:       AHX11387.1  [L=369]
Description: tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     9e-113  376.7   0.2     1e-112  376.5   0.2    1.0  1  tRNA_Me_trans    tRNA methyl transferase
    1.4e-06   27.9   0.3    1.1e-05   25.0   0.3    2.2  1  QueC             Queuosine biosynthesis protein QueC
    5.1e-05   23.1   0.0    7.3e-05   22.6   0.0    1.2  1  Asn_synthase     Asparagine synthase
    0.00033   19.9   0.1      0.012   14.8   0.2    2.3  2  NAD_synthase     NAD synthase
      0.003   17.2   0.4      0.013   15.1   0.2    2.0  2  ThiI             Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.024   14.4   0.3       0.35   10.6   0.1    2.1  2  ATP_bind_3       PP-loop family
       0.04   13.2   0.1      0.062   12.6   0.1    1.3  1  Arginosuc_synth  Arginosuccinate synthase


Domain annotation for each model (and alignments):
>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  376.5   0.2    4e-116    1e-112       2     356 .]      17     367 ..      16     367 .. 0.95

  Alignments for each domain:
  == domain 1  score: 376.5 bits;  conditional E-value: 4e-116
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklwee...edeegkeccaeedlkdaervaeklgiplevvdfekeykekvfeefleeyeeGrTPnP 94 
                    kv+va+SgG+DSs +aa l++ gy+vigv+l+l+++   +++ +k+cca +d+ da++va ++g  ++v+++e+++k++v+e+f e+y +G+TP P
     AHX11387.1  17 KVMVAMSGGIDSSTVAAYLHQLGYQVIGVTLQLYSSnevSQTRKKTCCAGSDIFDAKSVAAQFGFLHYVINMEDTFKKEVIEDFAESYLKGETPIP 112
                    8********************************999554444449*************************************************** PP

  tRNA_Me_trans  95 dvlCNkeiKfgallekakeelgadalatGHYarvsleeeknevellrakdkkkDQsyfLsqlskealekllfPlgeltKeevrkiAkeaglavaek 190
                    +v+CN+++Kf+ ll+ ak+ l++dalatGHY+r++    kn+ el++++d+ kDQsyfL++++ke+l+ l fPlg+l+K+e+r++A+e g+++ ek
     AHX11387.1 113 CVKCNQTVKFRDLLKIAKS-LNVDALATGHYVRRVIA--KNSIELHKGVDSLKDQSYFLFNTTKEQLKFLRFPLGNLKKSETRDLARELGITISEK 205
                    ******************8.***************99..79******************************************************* PP

  tRNA_Me_trans 191 kdSqgiCfigkrkfkdflkkyleek..eGkiieietgevlGeheGllsyTiGqrkGlkiagaeeplyVvekdakkntvlvgkgedeealaskklrv 284
                     +Sq+iCf+++r++ d+++k  + +   Gki++++ g+vlG+h+G+l+yT+Gqr+Gl+i+ a+eplyV++++  +nt+ vg    ++al++++l++
     AHX11387.1 206 SESQDICFVKSRSYADIVEKFKPGSqrAGKIVDLQ-GKVLGTHSGILHYTVGQRHGLNIS-ASEPLYVIKIEDVTNTIAVGP---RSALKRDSLYI 296
                    *******************998754449*******.************************.9********************...9********** PP

  tRNA_Me_trans 285 kelnwlaeelkekealelevkvrhkqelvkakvelkedetvevklde.kvravtpGQaavlYkgdevLGggii 356
                    ++lnwl +++    a+e+evk+r+ +e vka++  +e+ +++++l+e ++ a++pGQa+v+Y+g++vLGgg+i
     AHX11387.1 297 RQLNWLDNQELI-PAMEVEVKLRSGSEVVKASLFPQEE-RLKITLHEePKCAIAPGQACVMYRGTKVLGGGWI 367
                    *******65444.68******************99998.999999752788********************98 PP

>> QueC  Queuosine biosynthesis protein QueC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.3   4.4e-09   1.1e-05       1     178 [.      17     203 ..      17     217 .. 0.80

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 4.4e-09
                 EEEEE--SSHHHHHHHHHHHHH-SEEEEEEEESS-TTSHHHHHHHHHHHHT--.-EEEEE-G..GGGGGSCGGG---------..--...--------T CS
        QueC   1 kavvllSGGlDSttvlalakkegkevealtfdYgqrhkkeleaakkiakelgveehkildld..llkelggsaLtdeeievpk..eeleeeelpntfVp 95 
                 k++v +SGG+DS+tv+a+ ++ g++v+ +t++  + +++     k+ ++  ++ + k +  +  +l+ + +   t +++ +++  e++ + e+p   V 
  AHX11387.1  17 KVMVAMSGGIDSSTVAAYLHQLGYQVIGVTLQLYSSNEVSQTRKKTCCAGSDIFDAKSVAAQfgFLHYVINMEDTFKKEVIEDfaESYLKGETPIPCVK 115
                 57899***************************9999999999999999999999888887662268888887777777778877677778999999999 PP

                 THHHHHHHHHHHHHHHHT-SEEEE---S-STT--GGGSHHHHHHHHHHHHHH......HTS--EE.E-TTTT--HHHHHHHHHHTTHHHH CS
        QueC  96 aRNliflslaasyaealgaeaiiiGvneedfsgYPDcrdefvkalnkalnlg......edkkiei.eaPlidlsKaeivklgkelgvple 178
                    ++ +   +  a++l+++a+++G     +     ++ e  k ++++   +      ++++++  + Pl +l+K+e+  l+ elg++++
  AHX11387.1 116 CNQTVKFRDLLKIAKSLNVDALATGHYVRRVI--AKNSIELHKGVDSLKDQSyflfntTKEQLKFlRFPLGNLKKSETRDLARELGITIS 203
                 99999999999999999999999998776644..46677776666666666666677767777754899999999999999999996554 PP

>> Asn_synthase  Asparagine synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.6   0.0   2.8e-08   7.3e-05      16      84 ..      14      91 ..      10     129 .. 0.76

  Alignments for each domain:
  == domain 1  score: 22.6 bits;  conditional E-value: 2.8e-08
  Asn_synthase 16 advpvGalLSGGlDSSliaalaarqsksplktFsigf..........ee..kgsdeakyakevaehlgtehtelvlteeel 84
                   d +v + +SGG+DSS++aa++ +    ++  +++ +          ++   + +++  ak va+++g  h+ + +  e+ 
    AHX11387.1 14 RDTKVMVAMSGGIDSSTVAAYLHQLGY-QVIGVTLQLyssnevsqtrKKtcCAGSDIFDAKSVAAQFGFLHYVINM--EDT 91
                  5889999*****************986.777777777777667655411466788999999999999999955554..444 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2   4.6e-06     0.012      19      59 ..      16      54 ..      10     143 .. 0.66
   2 ?    2.7   0.0     0.023        59     150     168 ..     182     200 ..     179     214 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 4.6e-06
                  SEEEEEE-SSHHHHHHHHHHHHHHTCGEEEEEE--SSSTTH CS
  NAD_synthase 19 kgvvlGlSGGvDSslvaalavkalgkenvlalllPssvsse 59
                  ++v++ +SGG+DSs+vaa   ++    +v+++ l    s+e
    AHX11387.1 16 TKVMVAMSGGIDSSTVAAYLHQLG--YQVIGVTLQLYSSNE 54
                  6899********998876554433..477777774222222 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.023
                   TTTTS-HHHHHHHHHHTT- CS
  NAD_synthase 150 piaellKtevkeLakelnv 168
                   p+++l K+e ++La+el++
    AHX11387.1 182 PLGNLKKSETRDLARELGI 200
                   9****************97 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.2   5.2e-06     0.013       5     116 ..      17     141 ..      14     154 .. 0.54
   2 ?   -1.0   0.0      0.44   1.1e+03     143     174 ..     182     214 ..     169     225 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.2e-06
        ThiI   5 kvlaLlSgGiDSp.VaaylllkRGcrvvlvhlknepgtseeaiekveklaellae.yqt.slevkl....vvvdfkev.lkeilekv.......keklt 88 
                 kv++ +SgGiDS  Vaay l + G +v  v+l  +++ s+e+ + ++k     ++ +++ s+  ++    +v++ +++  ke++e         + +  
  AHX11387.1  17 KVMVAMSGGIDSStVAAY-LHQLGYQVIGVTL--QLYSSNEVSQTRKKTCCAGSDiFDAkSVAAQFgflhYVINMEDTfKKEVIEDFaesylkgETPIP 112
                 89999******8626666.5799********9..57777777666665443332212221122232111134444432122333333222333333334 PP

        ThiI  89 ivllkrkm.lriAekvaeeegakalvtGe 116
                 +v + +++ +r   k+a+  +++al tG 
  AHX11387.1 113 CVKCNQTVkFRDLLKIAKSLNVDALATGH 141
                 45444332134444677777777777776 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.44
        ThiI 143 PLigldKeeiiklAkeigtyeisieke..dkCsv 174
                 PL  l K e  +lA+e+g   is + e  d C v
  AHX11387.1 182 PLGNLKKSETRDLARELGIT-ISEKSEsqDICFV 214
                 89999999999*****9943.4443332377755 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00013      0.35       1      51 [.      17      64 ..      17      99 .. 0.70
   2 ?    1.9   0.0     0.065   1.7e+02      85     165 ..     122     204 ..     115     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00013
                EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHH CS
  ATP_bind_3  1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvk 51
                kv+vA+SgG+DS +    l++l  +    + +    ++  e s+  +++++
  AHX11387.1 17 KVMVAMSGGIDSSTVAAYLHQLGYQ---VIGVTLQLYSSNEVSQTRKKTCC 64
                589************9999998442...22222233444445555555555 PP

  == domain 2  score: 1.9 bits;  conditional E-value: 0.065
                 HHHHHHCHHCCT.CEEE---BHHHHHHHHHHHHCCT--CCHHH-.S-SEEEETTCCEE-.CCCT--HHHHHHHHHHTT---B- CS
  ATP_bind_3  85 YevlkealkkegievlllAhhadDqaEtfllrlargsglaglag.ikeaseiasirlvR.PlLkvskeeleeylkekkikwve 165
                 ++ l +++k+ +++ l+++h     +    ++l +g    + ++ + + ++ ++ +++R Pl +++k+e +++++e +i+  e
  AHX11387.1 122 FRDLLKIAKSLNVDALATGHYVRRVIAKNSIELHKGVDSLKDQSyFLFNTTKEQLKFLRfPLGNLKKSETRDLARELGITISE 204
                 55677889999999999999999999999999988876644444255555556688888799999999999999998887666 PP

>> Arginosuc_synth  Arginosuccinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   2.4e-05     0.062       2      60 ..      20      73 ..      19      97 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.4e-05
  Arginosuc_synth  2 LaysGGlDtsviikllkeklgeeviavavdvGqeeedldevkekalklgavksvvvDak 60
                     +a sGG+D s + ++l++  g++vi v++++    +++ ++++k+  +g+    + Dak
       AHX11387.1 20 VAMSGGIDSSTVAAYLHQL-GYQVIGVTLQLYSS-NEVSQTRKKTCCAGS---DIFDAK 73
                     699************9765.5**********999.888888888765554...445554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (369 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2595.81
//
Query:       AHX11388.1  [L=232]
Description: DNA polymerase III, epsilon subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.1e-37  129.2   0.0      3e-37  128.7   0.0    1.2  1  RNase_T         Exonuclease
    1.5e-08   34.8   0.0    2.7e-08   34.0   0.0    1.4  1  DUF5051         3' exoribonuclease, RNase T-like
    1.3e-06   28.2   0.0    0.00013   21.8   0.0    2.4  2  DNA_pol_A_exo1  3'-5' exonuclease
    0.00025   21.1   0.0     0.0011   18.9   0.0    1.9  1  RNase_H_2       RNase_H superfamily


Domain annotation for each model (and alignments):
>> RNase_T  Exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.7   0.0   6.6e-41     3e-37       1     165 []       7     167 ..       7     167 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.7 bits;  conditional E-value: 6.6e-41
                 EEEEEEESSSTTCTTS-EEEEEEEEEETTCCEEEEEEEEEEEHSSHCSSSHHHHHHHHHCHHHHHTCEBHHHHHHHHHHHHHHHTCCCETTTCEEEESS CS
     RNase_T   1 vviDlEttgldakekdeiieiaaisidggeneigetfhfyvkptelakltdecteftgitqemldeapsfkevleefkellrklallvahnaafdvgfl 99 
                 +v+D+Ettgld k  d++iei+++++  ++  +g+ fh+y +p++   +++e+t+++git ++l++ p+f+e+++ef  +++  a +vahna+fdv fl
  AHX11388.1   7 IVLDTETTGLDIKNGDRVIEIGCVEVIDSFL-TGNVFHVYLNPERE--ISKEATRVHGITLDQLQDSPKFNEIADEFIAFIG-SASVVAHNASFDVRFL 101
                 79**********99****************8.**************..**********************************.99************** PP

                 HHHHHHHHHHHHHHHHHCSEHCECHHHHHHHHHCHHHHHHHHHTTCHSSSS.TSSHHHHHHHHHHHH CS
     RNase_T 100 raadkrilkkevpkrnqfldtlildkatlkelartsldklaeklgleedgr.aHrAldDaeataklf 165
                 + ++ r   +++ k + ++dtl ++++ +++ +  sld+l+++++++  +r  H Al Da+ +a+++
  AHX11388.1 102 NSELMRARCRTIIKPENVIDTLAIARKMFPGSPA-SLDALCRRFRISLEQRtTHGALLDAQLLARVY 167
                 ******9989888********************8.***************************99986 PP

>> DUF5051  3' exoribonuclease, RNase T-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0   5.9e-12   2.7e-08       2     161 ..       6     166 ..       5     170 .. 0.77

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 5.9e-12
     DUF5051   2 klmiDiEtlgne..etaelvsIGaVff...petG.eFyaeidlesdeeagidaetieWWlkqskearaellkdtqeakslkdalqaleeFlekslkvwa 94 
                 k+++D+Et+g +  ++  +++IG V +     tG  F+   ++e + +            k  + +    l++ q+ +++++++ ++ +F+  s  v+a
  AHX11388.1   6 KIVLDTETTGLDikNGDRVIEIGCVEVidsFLTGnVFHVYLNPEREIS------------KEATRVHGITLDQLQDSPKFNEIADEFIAFI-GSASVVA 91 
                 689******999889999*********88766889********88873............34555666667888999**************.6899*** PP

     DUF5051  95 ngasfDlviLraafel.lipwkywndrdvrtlvala......pelekgeekkreipfe.gvkHnALaDAkhqaka 161
                 ++asfD++ L++ + +  +   ++ ++ ++tl   +      p+ +     + +i+ e  + H AL DA+  a++
  AHX11388.1  92 HNASFDVRFLNSELMRaRCRTIIKPENVIDTLAIARkmfpgsPASLDALCRRFRISLEqRTTHGALLDAQLLARV 166
                 **********9765554466666667777777666645565544333333444555557899*******998876 PP

>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.0   0.0    0.0081        36      23      44 ..       7      27 ..       2      47 .. 0.77
   2 !   21.8   0.0   2.8e-08   0.00013      74     128 ..      85     144 ..      51     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.0081
                    EEEEEEEE-SSSTTSSEEEEEE CS
  DNA_pol_A_exo1 23 vavDtEttsldlisatlvlili 44
                    + +DtEtt+ld+ +  +++i i
      AHX11388.1  7 IVLDTETTGLDI-KNGDRVIEI 27
                    779*********.445555555 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 2.8e-08
                     T-TTSEEEESSHHHHHHHHHHH.......HTS--SSEEEH.HHHHHHTTHSTTSSHHHHHHHH CS
  DNA_pol_A_exo1  74 edenitkvghnakfDlevlard.......fgielenlfdt.mlaayvldyershsLdsLaeky 128
                      +   ++v hna+fD+++l  +        +i++en++dt  +a ++  + +  sLd L++++
      AHX11388.1  85 GS--ASVVAHNASFDVRFLNSElmrarcrTIIKPENVIDTlAIARKMF-PGSPASLDALCRRF 144
                     54..479*********************************66665555.55559******998 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   2.5e-07    0.0011       1     126 [.       7     156 ..       7     179 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 2.5e-07
   RNase_H_2   1 lffDiEttGlspkknl.iyliGvldvde..keiekltqllaeepeeekailelf...lellekkka................lvtfngksFDvpflkrl 77 
                 + +D+EttGl+ k++  ++ iG+++v +   + + +  +l++e+e  k++ +     l++l++ ++                +v++n +sFDv+fl++ 
  AHX11388.1   7 IVLDTETTGLDIKNGDrVIEIGCVEVIDsfLTGNVFHVYLNPEREISKEATRVHgitLDQLQDSPKfneiadefiafigsasVVAHN-ASFDVRFLNSE 104
                 579*******98887769******995535556668889999998888888644555444444444444555555555555477777.99********* PP

   RNase_H_2  78 fkkyklde..eefrhiDLlkelrkkkl.esysLksvekelgierreedlsGs 126
                 + + +++   +  + iD l ++rk    +  sL ++ + + i  ++  + G+
  AHX11388.1 105 LMRARCRTiiKPENVIDTLAIARKMFPgSPASLDALCRRFRISLEQRTTHGA 156
                 9888888888899**********98887445999999999998877666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.44u 0.26s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1706.66
//
Query:       AHX11389.1  [L=53]
Description: hypothetical protein NHE_0444 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.35
# Mc/sec: 451.03
//
Query:       AHX11390.1  [L=550]
Description: metallopeptidase M24 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.3e-46  157.3   0.0    6.2e-46  156.7   0.0    1.2  1  Peptidase_M24    Metallopeptidase family M24
    9.6e-26   90.8   0.0    2.1e-23   83.2   0.0    2.3  2  Creatinase_N_2   Creatinase/Prolidase N-terminal domain
    2.7e-11   44.2   0.0    8.5e-10   39.4   0.0    2.5  2  Creatinase_N     Creatinase/Prolidase N-terminal domain
    3.3e-11   43.1   0.1    2.5e-10   40.2   0.0    2.4  2  Peptidase_M24_C  C-terminal region of peptidase_M24


Domain annotation for each model (and alignments):
>> Peptidase_M24  Metallopeptidase family M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.7   0.0   1.4e-49   6.2e-46       6     208 ..     292     495 ..     289     496 .. 0.91

  Alignments for each domain:
  == domain 1  score: 156.7 bits;  conditional E-value: 1.4e-49
                    HHHHHHHHHHHHHHHHH..TTCBHHHHHHHHHHHHHHHTTTCEESSSSEEEEGGGGGSTTTBCSSSB...--TTEEEEEEEEEEETTEEEEEEEEE CS
  Peptidase_M24   6 aariasaaleavleaik..pgvterelaaeieattlkrhgarglafppivasgenaavlhytpndrv...lkegdlvlidagaeydgyasDitrTv 96 
                    a++ ++ a+  +l+++k  + ++e e+++++ +++ ++  +   +fp+i a+g+n+a++hy++++++   ++ g l+l+d+ga+y   ++DitrT+
     AHX11390.1 292 AHKRDAIAFMGFLDWLKnnQDTSEIEAEKVLLKFRKEQDLFYSASFPTISAFGANGAIVHYHATEKSnlnFESGNLYLCDSGAQYLDGTTDITRTI 387
                    7888999999999***9444668888888888885555669999*****************9965555668************************* PP

                    ECSSGSHHHHHHHHHHHHHHHHHHHC-ST.TSBHHHHHHHHHHHHHHTTBCCGBSSCSEEEES..SSSSEEEEEESSSTTCSSB--TTBEEEEEEE CS
  Peptidase_M24  97 lvGkftpeqrelyeavleaqeaaikavkp.GvtlseidaaarevlesaglakffphglGHgvG..levhdegpsvsresndgrkleeGmvftiEpg 189
                    ++Gk+t+eq   y++vl+a+  +   ++p G+t++++da+ar  l++++l  ++ h++GHgvG  l+vh++ p+     +++++l++Gm++++Epg
     AHX11390.1 388 AIGKPTEEQCFHYTLVLKAHISLAMVIFPvGTTGKQLDAIARSKLWKYKL--DYGHSTGHGVGsfLNVHEG-PHSF---GNNVPLQPGMIISNEPG 477
                    ***********************************************988..88*********999***98.*966...469************** PP

                    EEEETTTEEEEEBEEEEEE CS
  Peptidase_M24 190 iyfapgeggvriedtvlvt 208
                    +yf +g++g+rie++++vt
     AHX11390.1 478 LYF-EGKYGIRIENLMYVT 495
                    **6.6999**********9 PP

>> Creatinase_N_2  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0043        19      67     102 ..      53      85 ..      49     132 .. 0.77
   2 !   83.2   0.0   4.7e-27   2.1e-23       3     161 .]     139     285 ..     137     285 .. 0.91

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0043
                     -EEEEEES.S-EEEEE-GGG-..-HHHHHHHTTEEE CS
  Creatinase_N_2  67 lsyaivtkdekatLFvdeeklteevkehleengvei 102
                     ++++ivt+ ek+++F+d++ l  ++k++l+e + +i
      AHX11390.1  53 FAMVIVTQ-EKVYFFTDSRYL-IQAKNELHE-HYTI 85 
                     78999987.6*******9987.455556643.3444 PP

  == domain 2  score: 83.2 bits;  conditional E-value: 4.7e-27
                     --------EE--HHHHSS-HHHHHHHHHHHHHHTT-SEEEE-SHHHHHHHTTEE--SBTTB----EEEEEES.S-EEEEE-GGG-..-HHHHHHH CS
  Creatinase_N_2   3 ParpkepvfvlpeeyaGesvaeKlerlrkelkkkkadalvlsaldeiAWllNlRGsDipynPvflsyaivtkdekatLFvdeeklteevkehlee 97 
                       + k++v+ ++++yaG s++eK++++ +++ +   + +++s+ ++++Wl N+RGsD ++ Pv ++  i+  ++ + +F++ + +  e +  l e
      AHX11390.1 139 DTPIKSEVRSHDIRYAGLSSKEKCSAVLDAIGQ---NRYFFSNSESVCWLANIRGSDLDCIPVLCCRGILYPNGLLKVFTHCK-F--EKSPFL-E 226
                     556799*************************76...68********************************8888999**9965.5..445566.5 PP

                     TTEEEE-GGGHHHHHHHHHHHH----EEE-TTSBHHHHHHH-GGGEEE-S-HHHHHHHC--HHH CS
  Creatinase_N_2  98 ngveikpyeevvsdlkalasaskkkvlldpsktsyalasalkekkvveeespiallKavKNevE 161
                     +++ei + +++  +l++l      +vlld+++ts+++ s + e+k+++ ++p  ll+a+KN++E
      AHX11390.1 227 AHIEILSLDDLEIYLASLD-----SVLLDERNTSVYYLSLIGEEKIIHMTDPSVLLRACKNDTE 285
                     7899*******999**995.....79********999999*9*********************9 PP

>> Creatinase_N  Creatinase/Prolidase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.4   0.0   1.9e-13   8.5e-10       1     103 [.       7     113 ..       7     128 .. 0.80
   2 ?    2.0   0.0     0.069   3.1e+02      22      56 ..     475     522 ..     468     544 .. 0.74

  Alignments for each domain:
  == domain 1  score: 39.4 bits;  conditional E-value: 1.9e-13
                   HHHHHHHHHHHTT-SEEEEECC............HHHHHHHSS...-SSSEEEEEEESSCEEEEEECTTHHHHHHHH.TTSEEEEESTHSSHHHHHH CS
  Creatinase_N   1 Rlerlralmeekgldallvtsp............enlrYltGfatetgsrglalvvtadgalllvdalryteaaeesatveevveyddpvealadll 85 
                   Rl +lr +m++ gl a+l++ +             +l +ltGf   tgs  +++ vt+++ ++++d +ry ++a+ +  ++e ++  d +     ll
    AHX11390.1   7 RLIALRSVMRKLGLKAFLIPINdeflleyplasnNRLAWLTGF---TGSFAMVI-VTQEKVYFFTD-SRYLIQAKNE--LHEHYTILD-AGHTSILL 95 
                   7789****************999********************...********.***********.**********..444444444.22333333 PP

                   HHHHHHT-EEEE-TTSSB CS
  Creatinase_N  86 kellesekrvgveldalt 103
                   + ++ + + +g +++ lt
    AHX11390.1  96 AIRGDNIEEIGYDPKLLT 113
                   333333478888887766 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.069
                   C.............HHHHHHHSS....-SSSEEEEEEESSCEEEEEECT CS
  Creatinase_N  22 p.............enlrYltGfa.tetgsrglalvvtadgalllvdal 56 
                   +             enl Y+tG    + g r l l v+ +++l+l + l
    AHX11390.1 475 EpglyfegkygiriENLMYVTGLGdGFLGFRQLTL-VPFEEKLILSNML 522
                   445555555555559*******9878899999999.9999998887755 PP

>> Peptidase_M24_C  C-terminal region of peptidase_M24
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.1      0.46   2.1e+03       3      19 ..     117     133 ..     115     134 .. 0.84
   2 !   40.2   0.0   5.6e-14   2.5e-10       2      41 ..     501     540 ..     500     548 .. 0.90

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.46
                      EEEEES------STT-- CS
  Peptidase_M24_C   3 leFetlTlvPidrklId 19 
                      l++ + T++P   + Id
       AHX11390.1 117 LKLFPCTMIPVNENPID 133
                      677789*******9998 PP

  == domain 2  score: 40.2 bits;  conditional E-value: 5.6e-14
                      EEEEEES------STT--GGGS-HHHHHHHHHHHHHHHHH CS
  Peptidase_M24_C   2 fleFetlTlvPidrklIdvslLtpeEiawLnaYhakvrek 41 
                      fl+F++lTlvP++ klI  ++L++eE awL +Y   + + 
       AHX11390.1 501 FLGFRQLTLVPFEEKLILSNMLSNEESAWLEEYSDSIKAV 540
                      9********************************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (550 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3949.90
//
Query:       AHX11391.1  [L=244]
Description: prolyl oligopeptidase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.7e-17   61.2   0.0      6e-09   35.5   0.0    2.1  2  Hydrolase_4    Serine aminopeptidase, S33
    4.2e-09   36.4   0.0    1.3e-05   25.0   0.0    2.1  2  Abhydrolase_1  alpha/beta hydrolase fold
    2.8e-05   23.7   0.0    9.9e-05   21.9   0.0    1.8  1  Peptidase_S9   Prolyl oligopeptidase family
    8.7e-05   22.5   0.0    0.00014   21.8   0.0    1.3  1  UPF0227        Uncharacterised protein family (UPF0227)
    0.00052   19.7   0.0       0.88    9.1   0.0    2.2  2  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
     0.0031   18.2   0.0      0.021   15.4   0.0    2.0  1  Abhydrolase_6  Alpha/beta hydrolase family
     0.0071   16.1   0.0      0.036   13.8   0.0    1.9  2  Abhydrolase_5  Alpha/beta hydrolase family
  ------ inclusion threshold ------
      0.029   13.9   0.0       0.99    8.9   0.0    2.2  2  DLH            Dienelactone hydrolase family
      0.095   12.7   0.0       0.71    9.8   0.0    2.0  2  DUF1007        Protein of unknown function (DUF1007)
        0.1   12.4   0.0        1.4    8.6   0.0    2.1  2  Abhydrolase_2  Phospholipase/Carboxylesterase


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.5   0.0   3.3e-12     6e-09       7     116 ..      26     132 ..      20     156 .. 0.81
   2 !   23.8   0.0   1.2e-08   2.2e-05     187     234 ..     178     227 ..     160     229 .. 0.85

  Alignments for each domain:
  == domain 1  score: 35.5 bits;  conditional E-value: 3.3e-12
  Hydrolase_4   7 vvlvHGla.ehsgryae.laeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkva 102
                  v+++ Gla + sgr +e l     ++ +a+  +D+ GhGrseg      +++++++ + +++e+v     + + +l+G Sm G + +++++++p+kv+
   AHX11391.1  26 VLFMTGLAsDMSGRKSErLRSFCENNQVAFTRFDYFGHGRSEGSFL-HGNISKWTENALEVLERVT----TGKQILVGSSMSGWMMFKIAEKHPEKVK 118
                  56666665245677666244444567899**************999.789***********99999....45679*********************** PP

  Hydrolase_4 103 glilsaPalkikak 116
                  gl+ +a+a +  ++
   AHX11391.1 119 GLVGIAAAPDFTED 132
                  *****999776655 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 1.2e-08
  Hydrolase_4 187 aakit..lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHel 234
                  +++i+   P+ llhG aD +v++++s el+e + s+ ++++l++g+ H++
   AHX11391.1 178 TQRIKvpCPVVLLHGLADDIVSYRKSIELAELIESSPVEVRLIKGADHSM 227
                  556663377***************************************86 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     7e-09   1.3e-05      33     114 ..      56     130 ..      26     165 .. 0.78
   2 !    9.6   0.0   0.00037      0.67     200     251 ..     175     226 ..     164     229 .. 0.84

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 7e-09
                    EEEEETTSTTSSSTTTGB.CHHSHHHHHHHHH.HH..HHHCTTSSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESECSSCCHHH CS
  Abhydrolase_1  33 illDlrGvgySspapacinddygtasvaddld.ri..ldalgddkltlvGhSmGGmialayaaeyperVkalvllgaidpaasli 114
                      +D  G+g+S+ +           ++ ++ + ++  l++   +k +lvG Sm G +++  a+++pe+Vk+lv ++a   a+++ 
     AHX11391.1  56 TRFDYFGHGRSEGSFLH-------GNISKWTEnALevLERVTTGKQILVGSSMSGWMMFKIAEKHPEKVKGLVGIAA---APDFT 130
                    56899999999888874.......56888888633559999999999******************************...22222 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00037
                    HHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTS..EEEEEEETCSSS CS
  Abhydrolase_1 200 lllrlrelknvlaptlvisgtsDplvppkaledlaqllpk..krlvvisdagHl 251
                    l+l +r+  +v +p+++++g  D +v+++ + +la+l+ +  ++++ i +a H 
     AHX11391.1 175 LILTQRI--KVPCPVVLLHGLADDIVSYRKSIELAELIESspVEVRLIKGADHS 226
                    5556666..7888************************99988999999999886 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.0   5.5e-08   9.9e-05      61     193 ..      89     232 ..      74     241 .. 0.71

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 5.5e-08
                   --GGGEEEEEETHHHHHHHHHHHH-GGG-SEEEEESE---CCCHHCSTTS......THH.HCCCC--TTTCHHHHHHHHHH-CGGG--......... CS
  Peptidase_S9  61 vdserlaitGgSyGGyltgaalnqrpdlFkaavaevpvvdvlrydsdtdl......lte.eymewgnpeeneegykelspyspldnvk......... 141
                   v++ + ++ G S  G+++  +++++p++ k++v  ++  d + + ++         l++  y  ++ + ++e+   +   +++    k         
    AHX11391.1  89 VTTGKQILVGSSMSGWMMFKIAEKHPEKVKGLVGIAAAPDFTEDFLEGLThetkqaLEKnGYFTFTRN-RDEKLVITKTLLDDG---Kknliltqri 181
                   556677889*********************99888888888877766411222233444333333333.222222222222332...1456899999 PP

                   .---EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEETTS-SSTTSSHH CS
  Peptidase_S9 142 .aypplLlihGlaDdrvppaealklvaaLqkkgknvlllifpdegHgvgkpra 193
                    + +p+ l+hGlaDd v + ++++l++  ++   +v+++  ++++H++++p++
    AHX11391.1 182 kVPCPVVLLHGLADDIVSYRKSIELAELIES--SPVEVRLIKGADHSMSDPTS 232
                   9************************998887..678888899****9998876 PP

>> UPF0227  Uncharacterised protein family (UPF0227)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   7.9e-08   0.00014      51     174 ..      84     229 ..      70     233 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 7.9e-08
     UPF0227  51 klvaelgddnillvGssLGGyyatrlgerfglrq...vllnPalkplenlagklgeeavqstqetyvleeyhiielkalelsr..............lk 132
                 ++++ ++  + +lvGss+ G++   ++e++  +    v ++ a  ++e++ + l +e+ q  +++++++  +  + k + +++              +k
  AHX11391.1  84 EVLERVTTGKQILVGSSMSGWMMFKIAEKHPEKVkglVGIAAAPDFTEDFLEGLTHETKQALEKNGYFTFTRNRDEKLVITKTllddgkknliltqrIK 182
                 455566666789******************8776678889999999***********************999999999888888*************** PP

     UPF0227 133 rperilvllskqDevldyrrava..ef...raaaeiveddgdHafkd 174
                  p ++++l++ +D+++ yr++++  e+   +++  + +++ dH+++d
  AHX11391.1 183 VPCPVVLLHGLADDIVSYRKSIElaELiesSPVEVRLIKGADHSMSD 229
                 ******************99875223222256777888888888876 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.1   0.0   0.00049      0.88      97     155 ..      88     145 ..      54     179 .. 0.75
   2 !    9.0   0.0   0.00055      0.98     221     260 ..     177     219 ..     154     226 .. 0.77

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.00049
                    TTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEEEECE-S-TCCCCSECTTEEBCCHHH CS
  Peptidase_S15  97 pwsnGkVgmtGiSYlGttqllaaatgvpalkaivpeaaisdlyddyyregGlvrapggl 155
                      ++Gk   +G+S +G++   +a+++++++k +v +aa  d+ +  + eg +++ +++l
     AHX11391.1  88 RVTTGKQILVGSSMSGWMMFKIAEKHPEKVKGLVGIAAAPDFTE-DFLEGLTHETKQAL 145
                    5678888899****************************999999.77776666666554 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00055
                    HHHHCT--S-EEEEEECCSSTTC.CHHHHHHHHHCCTT-..EE CS
  Peptidase_S15 221 sedadkvkapvllvgGwnDwnvk.ngaiklyealkapgv..kl 260
                     ++  kv +pv+l++G++D++v  +++i+l e +++ +v  +l
     AHX11391.1 177 LTQRIKVPCPVVLLHGLADDIVSyRKSIELAELIESSPVevRL 219
                    45556899********************999988888775444 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.2e-05     0.021      26      99 ..      51     129 ..      26     233 .. 0.65

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.2e-05
                    T.CEEEEE--TTSTS-GGCS.....--HHHCHHHHHHHCCTT..TTSEEEEEETCHHHHHHH.HHHCC......EEEEES-..-- CS
  Abhydrolase_6  26 g.vhvlapDlpGhGrsdppp.....ldledladlaalldelaagggpvvlvGHSlGGalala.aapla....lvvgvlldpppta 99 
                      v+   +D+ GhGrs+++        +   +  +++l+++   +g+ +lvG S+ G+++   a +++     +vg++ +p   +
     AHX11391.1  51 NqVAFTRFDYFGHGRSEGSFlhgniSKW--TENALEVLERVT--TGKQILVGSSMSGWMMFKiAEKHPekvkGLVGIAAAP--DF 129
                    2556688*******88554433222555..345567777775..7789**********77773333668554334466666..22 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0     2e-05     0.036      45      95 ..      81     132 ..      74     166 .. 0.80
   2 ?   -0.3   0.0      0.46   8.3e+02     102     141 ..     186     226 ..     178     228 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
  Abhydrolase_5  45 kaeeiikeapklekfvvgGhslGGvvasrfaaee.ekiegvvflasYPe.kde 95 
                    +a e+++      k ++ G s+ G ++ ++a+++ ek++g+v +a+ P+  ++
     AHX11391.1  81 NALEVLERVTT-GKQILVGSSMSGWMMFKIAEKHpEKVKGLVGIAAAPDfTED 132
                    56777776664.6678999*************9978************96433 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.46
  Abhydrolase_5 102 kvlsivgteDgvlnvkslekakkfl.pkdtkvvsieGgnha 141
                    +v+ + g  D+++++++  + ++ + +   +v  i+G +h+
     AHX11391.1 186 PVVLLHGLADDIVSYRKSIELAELIeSSPVEVRLIKGADHS 226
                    67788899999999877766666662556788899999997 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0      0.04        71      87     127 ..      81     122 ..      32     133 .. 0.86
   2 ?    8.9   0.0   0.00055      0.99     138     190 ..     178     228 ..     170     237 .. 0.81

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.04
         DLH  87 aylksvpevstkkvgvvGfCmGGalalllaaev.pevdaava 127
                 ++l+  ++v t+k  +vG  m G++ +++a +  ++v++ v+
  AHX11391.1  81 NALEVLERVTTGKQILVGSSMSGWMMFKIAEKHpEKVKGLVG 122
                 4555555666899999***************99888998775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00055
         DLH 138 eeaakikapilalfgeeDefipadevekleealkaanvdlelkvYpgagHaFa 190
                 ++  k+ +p++ l+g +D ++   +  +l+e +  +  ++e+ + +ga+H+  
  AHX11391.1 178 TQRIKVPCPVVLLHGLADDIVSYRKSIELAELI--ESSPVEVRLIKGADHSMS 228
                 445566689***************999999999..67788899999****965 PP

>> DUF1007  Protein of unknown function (DUF1007)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.28     5e+02      52      94 ..      28      69 ..      14      83 .. 0.84
   2 ?    9.8   0.0    0.0004      0.71      63     100 ..     128     165 ..     120     187 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.28
     DUF1007 52 llqgldknkdgvldeeelaelakenvenlkeyeYFtelkaggk 94
                 + gl+++  g  ++e l ++ ++n      ++YF +++++g+
  AHX11391.1 28 FMTGLASDMSG-RKSERLRSFCENNQVAFTRFDYFGHGRSEGS 69
                57788888888.67999******************99998775 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.0004
     DUF1007  63 vldeeelaelakenvenlkeyeYFtelkaggkklkfae 100
                 +++e+ l+ l++e  + l++++YFt+ ++ ++kl +++
  AHX11391.1 128 DFTEDFLEGLTHETKQALEKNGYFTFTRNRDEKLVITK 165
                 478999**********************9999987765 PP

>> Abhydrolase_2  Phospholipase/Carboxylesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0      0.13   2.3e+02     102     155 ..      89     142 ..      70     152 .. 0.76
   2 ?    8.6   0.0   0.00081       1.4     154     201 ..     182     227 ..     173     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.13
                    --GGGEEEEEETHHHHHHHHHHHT-SS--SEEEEES---TTGGGTTTTS-GGGG CS
  Abhydrolase_2 102 ipssriiigGFSqGaalalylaltlpkklggivafsgalplsqklessatavtk 155
                    ++  + i++G S+ + +  + a + p+k++g v++  a    + + +  t+ tk
     AHX11391.1  89 VTTGKQILVGSSMSGWMMFKIAEKHPEKVKGLVGIAAAPDFTEDFLEGLTHETK 142
                    77778899999**9*****************99998887777777666666665 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00081
                    GGG-EEEEEEETT-SSS-HHHHHHHHHHHHTTS-GEEEEEETT--SS- CS
  Abhydrolase_2 154 tkklpilqiHgeeDpvvplalgkaakevlkkllkkvelksyeglaHsi 201
                     +  p++++Hg  D +v ++ + +++e+++++    e + ++g  Hs+
     AHX11391.1 182 KVPCPVVLLHGLADDIVSYRKSIELAELIESSPV--EVRLIKGADHSM 227
                    45589**********************9988755..777788888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       458  (0.0255452); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 1703.97
//
Query:       AHX11392.1  [L=185]
Description: cytochrome c family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.4e-08   33.2   0.2    3.8e-07   31.1   0.2    2.0  1  Cytochrom_C      Cytochrome c
      0.004   17.4   0.9      0.019   15.3   0.9    2.0  1  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III


Domain annotation for each model (and alignments):
>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.2   4.3e-11   3.8e-07       2      91 ..      76     173 ..      75     174 .. 0.69

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 4.3e-11
                  --HHHHHHTTGGGTB-SSSBSSS....--HHHHHHHTTT-HHHHHHHHTTSS--S...........SSHHHHHHHGGGGGGG.TT--HHHHHHHHHHH CS
  Cytochrom_C   2 arGkelftanCaaCHgvegggakqgggptlsgaaerasaasigasvanpaavsap...........rddfekkkltaemparkerlteqeiadlaaYL 88 
                  ++G+++ + +C aCH+ e gg+++  gp+l+g+  ++ a   ++++  +   +++             ++  + ++++m       +++eia+l+ YL
   AHX11392.1  76 EAGQKISK-KCIACHTFENGGHNKV-GPNLWGILGKNKAHLGDRFKYSKGLLEKGgtwdyrsmvqfLYKPSAYIKGTKMAFA-GLSKPEEIANLVVYL 170
                  68999996.9************988.78888888877777777776666666666555555555553333333334443322.46667********** PP

                  HTT CS
  Cytochrom_C  89 ksl 91 
                  +sl
   AHX11392.1 171 RSL 173
                  *98 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.9   2.1e-06     0.019       2      67 .]      74     170 ..      73     170 .. 0.56

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 2.1e-06
  Cytochrome_CBB3   2 aaaaGaalykknCasCHg..kggag..............pslagrdwep........................dalvdiiknGkgaMpafggql 55 
                      +++aG+++  k+C +CH+  +gg +              +        +                        + l++   ++kg   af+g  
       AHX11392.1  74 NLEAGQKI-SKKCIACHTfeNGGHNkvgpnlwgilgknkA--------HlgdrfkyskgllekggtwdyrsmvQFLYKPSAYIKGTKMAFAGLS 158
                      56667776.679******7644333666555555554442........1222222233444444444445555555555555567777888888 PP

  Cytochrome_CBB3  56 sdeelwalvaYl 67 
                      ++ee+++lv Yl
       AHX11392.1 159 KPEEIANLVVYL 170
                      899999999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       424  (0.0236488); expected 358.6 (0.02)
Passed bias filter:                      399  (0.0222544); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1338.19
//
Query:       AHX11393.1  [L=189]
Description: phosphoribosylglycinamide formyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-47  160.8   0.1      6e-47  159.7   0.1    1.5  1  Formyl_trans_N  Formyl transferase


Domain annotation for each model (and alignments):
>> Formyl_trans_N  Formyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.7   0.1   3.4e-51     6e-47       1     181 []       3     175 ..       3     175 .. 0.95

  Alignments for each domain:
  == domain 1  score: 159.7 bits;  conditional E-value: 3.4e-51
                     -EEEEEESESSHHHHHHHHHHHHTTSE.CEEEEEEESCTTEHCHHHHHHCCHCCCECHHCCSCCCCCCCHHHHHHHHCTT-SEEEEES--S---H CS
  Formyl_trans_N   1 kkivvlisgtgsnlqalldalkkgsle.advvlvvsnkdkaaglekaeaasiptkvfeekkleprsqfeeelaeelkelkadlivlagymkllpk 94 
                     k+i++lisg gsn++ lld   +++ +  +v +v+sn+++aag++ a + +i +kv++          e+e+ e l++ k+ li+lag+m++l+ 
      AHX11393.1   3 KRIAILISGRGSNMKSLLDFSLNEGRGiFKVSVVISNNPTAAGIQTASEYGIEVKVCKS---------EKEILETLHNKKVALICLAGFMRVLSA 88 
                     69***************9966666555599***************************75.........679************************ PP

                     HHHHSSTTSEEEEESSSTTTTBSS-HHHHHHHTTSSEEEEEEEE--SSSSTS-EEEEEEEE--TT--HHHHHHHHHHHHHHHHHHHH CS
  Formyl_trans_N  95 elvqavrlkilniHpSLLPrfkGaaaiqraleaGdketGvtihfvdeelDtGailaqkkveiiaedtkeeleqrvadaehkalveal 181
                     e+++ v  ki+niHpSLLP+f+G++a+++al aG+k +G+t+hfv+ ++D G+i++q +v++++ dt+++l++r+ + ehk ++ a+
      AHX11393.1  89 EFISNVGCKIINIHPSLLPSFRGLNAQEQALSAGVKIAGCTVHFVTAKIDAGEIIMQGAVPVLKGDTVDSLSERILKMEHKCFPLAV 175
                     **********************************************************************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       469  (0.0261587); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1398.25
//
Query:       AHX11394.1  [L=506]
Description: cytosol aminopeptidase family, catalytic domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   2.1e-121  405.0   4.3   2.7e-121  404.7   4.3    1.1  1  Peptidase_M17    Cytosol aminopeptidase family, catalytic dom
    2.6e-14   53.2   0.5    9.2e-14   51.4   0.0    2.2  2  Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal do


Domain annotation for each model (and alignments):
>> Peptidase_M17  Cytosol aminopeptidase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  404.7   4.3    3e-125  2.7e-121       2     310 ..     184     494 ..     183     495 .. 0.96

  Alignments for each domain:
  == domain 1  score: 404.7 bits;  conditional E-value: 3e-125
                    HHHHHHHS-TTTS-HHHHHHHHHHHHTCCTEEEEEEEECHHHHHTT-HHHHHHHTTSSSS--EEEEEEEE-SS.TTSEEEEEEEEEEEEEE-TTSS CS
  Peptidase_M17   2 lardlvntpaneltpeklaeeaeelakeagkvevevldeeeleekgmgallaVgkgSeeepprlveleykgak.ekekklalVGKGitfDtGGlsl 96 
                    la++lvn+pan l+p+++a+ +++++k++ +++ve+lde++++++gm+all+Vg+gS+  p++l +++y+g++ +++ ++alVGKG+tfDtGG+sl
     AHX11394.1 184 LAKNLVNEPANTLNPDSYANIVKDINKTSPNLKVEILDEKAMQKLGMNALLGVGQGSA-CPSKLAVVKYNGSSnKDDPTIALVGKGVTFDTGGVSL 278
                    79*********************99888888**************************5.6***********99899999***************** PP

                    --HHHHTTGGGGGHHHHHHHHHHHHHHHHT-SSEEEEEEEEEEE--STTSTTTTEEEE-TTS-EEEES-TTGCHHHHHHHHHHHHHGCT--SEEEE CS
  Peptidase_M17  97 KpsasmeemkaDmgGAAavlgalkavaelklpvnvvavlplaeNmisgkavkpgdvitamnGktvevlnTDaEGRLvLADalayaeekekpdlivd 192
                    Kps++m +m +Dm+G+Aavlga++a+a++++++nvvavl+++eN++sg+a++pgd++++ +G+t+evlnTDaEGRLvLADal+ya+e+ k+++++d
     AHX11394.1 279 KPSRGMWDMISDMAGSAAVLGAISALANQGVKANVVAVLGIVENAVSGNAQRPGDIVKSASGQTIEVLNTDAEGRLVLADALWYAQEHLKAKHVID 374
                    *************************************************************************************9999******* PP

                    EE---THHHHHHTTTSEEEEES-HHHHHHHHHHHHHHS-EEEE----HHHGGGG--SSSSEESS-SSSST.HHHHHHHHHHTTSSE.CGEEEEE-T CS
  Peptidase_M17 193 vATLTgavvvalGkkaaglfsnddelaeelekageeagervwrlpleeeykkqlkskvaDlknvgkkrra.gaitAalFLkefvke.tpWaHlDia 286
                    vATLTga+vvalG+++aglfsn+d+lae+l +ag ++ge++w++p++++y++ ++s+ aD+kn+++k ++ ++itAa+FL++f+k+ t+WaHlDia
     AHX11394.1 375 VATLTGAIVVALGHDHAGLFSNNDALAEKLLQAGGKVGEKLWKMPMSKNYDELINSDAADMKNISTKGHGaDSITAAQFLRRFIKDdTQWAHLDIA 470
                    ***********************************************99*****************98888*************8889******** PP

                    TTTES.BTTB.S..EE--TTHHHH CS
  Peptidase_M17 287 gtalkekealkkekgatGvgvrtL 310
                    g+a+++++++ + kga+++gvr+L
     AHX11394.1 471 GVAWNNSTSHISPKGASAFGVRLL 494
                    ****7655444449********98 PP

>> Peptidase_M17_N  Cytosol aminopeptidase family, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.4   0.0     1e-17   9.2e-14       2     126 .]      20     145 ..      19     145 .. 0.95
   2 ?   -2.3   0.1      0.44   3.9e+03      66      66 ..     330     330 ..     296     369 .. 0.56

  Alignments for each domain:
  == domain 1  score: 51.4 bits;  conditional E-value: 1e-17
  Peptidase_M17_N   2 vgvfeggklspaaekldealagllsellkegdftGkagevlvlralsgek....akrvllVGLGkeeeltaealrkaagaaaralkgakvttia 91 
                      vg++e+  l    + ld+++   +s++lk++ ft+k+ e+l+++  + ++     + ++ VGLGk++++++ + +k++ ++   +k+ k++++ 
       AHX11394.1  20 VGLYENTDLFGRISVLDQQSSSFISKALKSSTFTAKPEESLSIFVNDLVEgypeLRQIIPVGLGKQADFDSLSAEKLGTQITSIMKSYKISKAS 113
                      89999999999999****************************999998888888**************************************** PP

  Peptidase_M17_N  92 valplegknsdekaeaaaegallglYrfdrykskk 126
                      v+l+     +de+a ++a g+    Y fd+yk++k
       AHX11394.1 114 VLLD---GIKDEYAVNIAFGIKAKDYVFDKYKTQK 145
                      ****...4477*********************987 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 0.44
  Peptidase_M17_N  66 l 66 
                       
       AHX11394.1 330 R 330
                      1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       711  (0.0396564); expected 358.6 (0.02)
Passed bias filter:                      498  (0.0277762); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.57u 0.24s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 3720.52
//
Query:       AHX11395.1  [L=600]
Description: aspartate--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-98  328.2   0.0    5.8e-98  327.8   0.0    1.1  1  tRNA-synt_2      tRNA synthetases class II (D, K and N)
    3.8e-14   52.7   0.2    9.9e-14   51.3   0.0    1.8  2  GAD              GAD domain
    8.4e-12   44.9   0.2    2.3e-11   43.5   0.1    1.8  2  tRNA_anti-codon  OB-fold nucleic acid binding domain
  ------ inclusion threshold ------
        0.1   12.6   0.1        1.3    9.0   0.1    2.3  2  tRNA-synt_2b     tRNA synthetase class II core domain (G, H, 


Domain annotation for each model (and alignments):
>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  327.8   0.0  1.3e-101   5.8e-98       2     313 ..     136     572 ..     135     573 .. 0.98

  Alignments for each domain:
  == domain 1  score: 327.8 bits;  conditional E-value: 1.3e-101
                  CCHHHHTHHHHCCSHHHHHHHHHHHHHHHHHHHHHHHTT-EE----SEESS--SSSS--EEEEETTT.TEEE-E-S-SHHHHHHHHHCTHSEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2   2 eelrlknryldlrtekvskvlrlrstvtkavrkyleengfieietPiLsksdteegarlFkvksrekekeffaLtqspqlylellivagidrvfqiar 99 
                  ee+rl++ryldlr+++++k++ lrs++++ +rk++e +gfie++tPiL+ s ++egar+++v+sr ++++f+aL+q+pq++++ll+vag+dr+fqia+
   AHX11395.1 136 EETRLRYRYLDLRRSDLKKNIVLRSHIISEIRKFMEAEGFIEFQTPILTAS-SPEGARDYLVPSRIHKGKFYALPQAPQQFKQLLMVAGFDRYFQIAP 232
                  79*************************************************.********************************************** PP

                  EE--S--BTTB-S-CEEEEEEEEET-SCHHHHHHHHHHHHHHHHHHHHCSCCCCCHTTTTTSEE-SSS-EEEEHHHHHHHHHTS-SS--HHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 100 aFRaEdsrtdrhlaEFtqieaemsfieeedimqvleelikslvkevlessakdiefvirrnskdlkkpfkrltykeaieklneigkdldkaderalvk 197
                  +FR+Edsr+dr + EF+q+++emsf+e+edi+ ++e+l+ +++++  +++              ++++f+r++yk+a+       +++dk+d+r  +k
   AHX11395.1 233 CFRDEDSRADRSPGEFYQLDLEMSFVEQEDIFCLMEKLLIKIFSKY-SDK-------------RIHSEFPRISYKDAMLL-----YGTDKPDLRNPIK 311
                  **********************************************.433.............68889************.....************* PP

                  .................................................................................................. CS
                  .................................................................................................. RF
  tRNA-synt_2 198 .................................................................................................. 197
                                                                                                                    
   AHX11395.1 312 itdfttvfresnfsifrekvekgalvrgipapgcgaksrkffddsinyameelkasglayitfeagipkgpiakflsseqiamivqgaqlkendaiff 409
                  ************************************************************************************************** PP

                  ...........................HS--SEEEEEEEB............GGGSTTCBBBSTTS.......TTBBSEEEEEETTEEEEEEEEB--S CS
                  ...........................xxxxxxxxxxxxx............xxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 198 ...........................keknepvfvtdfP............aelkpFyarkeedd.......kkltesyDllingvElvgGslRied 249
                                              +++++++++dfP             +++pF ++k+          + ++++yD+++ng+El +G++R ++
   AHX11395.1 410 scdarhnverisggvrkklgvelalidPSEFRFCWIVDFPyfeldektgkldFSHNPFSMPKDGVSafegdplEIISQQYDIVCNGIELSSGAVRNHR 507
                  ***************************************************************99999****************************** PP

                  HHHHHHHHHHCCHH.SSSGGGGHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGGGCSSS-XX CS
                  xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 250 peeleeklkskgld.eeaeekfswylealeyGapphgGlglGldRlvmlllgsesIrdviaFPkl 313
                  p+++++ ++  g+d +   ++f+ ++e ++yGapph+G++ G+dR+vml++++e+Ir+viaFP +
   AHX11395.1 508 PDIMYRAFEILGFDkDYVDQSFGALVESFQYGAPPHAGIAPGIDRMVMLIADEENIREVIAFPMN 572
                  **************99999********************************************97 PP

>> GAD  GAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0       3.6   1.6e+04      53      66 ..     162     175 ..     159     178 .. 0.71
   2 !   51.3   0.0   2.2e-17   9.9e-14       1      93 [.     327     419 ..     327     421 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3.6
                 EETTTCCCS-HHHH CS
         GAD  53 ltgpiakflteeev 66 
                 ++++i kf+ +e +
  AHX11395.1 162 IISEIRKFMEAEGF 175
                 67899999776655 PP

  == domain 2  score: 51.3 bits;  conditional E-value: 2.2e-17
                 HHHHHHSTEEEEEEEETTG-TTTSHHHHHHHHHHH.HHTTHSHCEEEEESSGGEETTTCCCS-HHHHHHHHHHCT--TTEEEEEEEEEHHHHHH CS
         GAD   1 fsealksggsvkalrvpggaaklsrkeideleefa.kelgakglawikvegegltgpiakflteeevkklleavgaeegDillfvAdkkktvnk 93 
                 f+e +++g  v+++ +pg     srk +d+  + a +el+a gla+i +e +  +gpiakfl++e++  +++ ++ +e+D+++f  d + +v++
  AHX11395.1 327 FREKVEKGALVRGIPAPG-CGAKSRKFFDDSINYAmEELKASGLAYITFEAGIPKGPIAKFLSSEQIAMIVQGAQLKENDAIFFSCDARHNVER 419
                 899***************.7999******9996651689*************************************************999986 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.5   0.1     5e-15   2.3e-11       2      73 ..      36     115 ..      35     117 .. 0.87
   2 ?   -3.5   0.0       2.3   1.1e+04      35      53 ..     319     338 ..     316     338 .. 0.76

  Alignments for each domain:
  == domain 1  score: 43.5 bits;  conditional E-value: 5e-15
                      EEEEEEEEEEEEEETTEEEEEEEETTEEEEEEEET.HHHHHHHTTS-TTSEEEEEEEEEEC.........TTSSEEEEEEEE CS
  tRNA_anti-codon   2 tvaGrvtsisdrsggkvifidlrDgtgriqvvlfr.eeatklaenlkeGdvvrvtGrvkrr.........pggelelkveei 73 
                      ++ G+v ++  r++g+++fidlrD  g+iq+v+   + ++  +  ++ ++vv ++G vkrr         + g+le+ v+++
       AHX11395.1  36 RLSGWVFRK--RDHGSILFIDLRDAYGTIQLVASEeTRDFHKFTAIPYESVVTIEGLVKRRsaetintslKSGDLEVFVKSW 115
                      678******..************************666666666799**************888777777666999999876 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.3
                      ET.HHHHHHHTTS-TTSEEE CS
  tRNA_anti-codon  35 fr.eeatklaenlkeGdvvr 53 
                      fr ++++ + e++++G +vr
       AHX11395.1 319 FReSNFSIFREKVEKGALVR 338
                      44478888999999999986 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00029       1.3      38      93 ..     226     277 ..     225     287 .. 0.79
   2 ?    0.4   0.0      0.12   5.4e+02      35      48 ..     308     321 ..     291     338 .. 0.85

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00029
                   EEEEEEEEEBTTTS..TBC.TTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHH CS
                   xxxxxxxxxxxxxx..xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  38 klyqiqtkyRdEks..dsr.GLlRvreFhqkdgyvfhaeaslddslrdlikaisrifer 93 
                   +++qi +++RdE s  d + G     eF q d ++   e+  +d++  ++k+  +if++
    AHX11395.1 226 RYFQIAPCFRDEDSraDRSpG-----EFYQLDLEMSFVEQ--EDIFCLMEKLLIKIFSK 277
                   789**********87644446.....******98766655..58888888888888876 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                   SSEEEEEEEEEEBT CS
                   xxxxxxxxxxxxxx RF
  tRNA-synt_2b  35 LPlklyqiqtkyRd 48 
                    P+k+++++t++R+
    AHX11395.1 308 NPIKITDFTTVFRE 321
                   59***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (600 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.28s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 4205.10
//
Query:       AHX11396.1  [L=468]
Description: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.1e-33  113.9   0.0    2.1e-32  112.7   0.0    1.6  1  Mur_ligase_M  Mur ligase middle domain
    7.2e-11   42.2   0.0      2e-10   40.7   0.0    1.8  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain
    3.4e-09   36.9   0.0    8.2e-09   35.7   0.0    1.6  1  Mur_ligase    Mur ligase family, catalytic domain
  ------ inclusion threshold ------
      0.025   14.3   0.1      0.046   13.5   0.1    1.4  1  LpxD          UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyl


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  112.7   0.0   4.7e-36   2.1e-32       1     192 []     112     294 ..     112     294 .. 0.93

  Alignments for each domain:
  == domain 1  score: 112.7 bits;  conditional E-value: 4.7e-36
                   EESSS-HHHHHHHHHHHHHCTEEEEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHC.TTTCCHCBESEEEE---TSTTHHHHSSHHHHHH CS
  Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvgttnneiglpktlaemekkeaeyavlEvsshglge.krlegllkpdvavitnispdHldfhgtlenyae 96 
                   +TG+nGKTT +e++aa+l++ g+++  +g++n+ iglp+++++ +   ++++vlE+++ + g+ + l+ ++ p+v +itni+++H+ f+g+ e++a 
    AHX11396.1 112 ITGSNGKTTSKEFTAALLRNYGETHCNAGNLNSLIGLPLSVLNTDF-PCKFLVLEMGMLHHGDiDLLNRIALPKVTIITNIGSAHIKFLGSQEAIAL 207
                   8*****************************************9999.************************************************** PP

                   HHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEEEEESSCSCHHHHHHHHHHHHH CS
  Mur_ligase_M  97 aKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggeleieipllGkhnvyNalaaiaaa 192
                   +Ka++f++      +v+n   py++ li+++k++++++++fg+ k+  d+  k + +++++++ie+    g +++++ p  G h vy  laai++a
    AHX11396.1 208 EKAKIFQNGC---PVVLNPNAPYSDLLIERAKESNSTILSFGEGKDC-DI--KLLDYSNSRVSIEI---YGARYTYQFPNYGLHFVYDSLAAIGVA 294
                   ******8555...69*****************************987.44..55566556667644...599*********************986 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.7   0.0   4.6e-14     2e-10      11      78 ..     329     396 ..     317     403 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.7 bits;  conditional E-value: 4.6e-14
                   TTTEEEEEE.T--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEE CS
  Mur_ligase_C  11 adgvtvidD.yahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvvl 78 
                   ++++tvidD y++n +s+sa++k ++ +++d r+i + g++g+ ger+++f+  +++   +l +sl+++
    AHX11396.1 329 GKKITVIDDtYNANYESISALIKYVQSTYSDMRVITIIGSIGDMGERAEEFYRKLAERVGSL-ESLILI 396
                   5789*************************************************999988874.444444 PP

>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.7   0.0   1.8e-12   8.2e-09       6      84 ..      32      98 ..      29     100 .. 0.96

  Alignments for each domain:
  == domain 1  score: 35.7 bits;  conditional E-value: 1.8e-12
                STTSCCHHHHHHHHHHTTSEEEEEESSHCHHHTT-EEEES-HGGGGEE-TS-TTCHHHHHHHHTTEEEEEHHHHHHHHH CS
  Mur_ligase  6 gidgrgmsagalflalkGykvdGsdfieslialGaaavvghdaanivvssiskdnpeleaakepgipvesraeaLaela 84
                +id+r++++g  f+a+kG++ d + fies++ +Ga+a+++ +              e+++   p+i+v+++ +a+++la
  AHX11396.1 32 SIDSRTIEKGEIFIAIKGERCDAHTFIESAYLNGASAIITRKHL------------ECPELAIPIIKVDDPVAAMQKLA 98
                79*************************************99888............*********************98 PP

>> LpxD  UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1     1e-05     0.046      30      69 ..      61      99 ..      52     100 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1e-05
                CCC---SEEEEEHHHHCCHTTSCS.EESS-HHHHHHHHHH CS
        LpxD 30 lattkAgavivppdlaealpanaalivvenPylafakllq 69
                ++   A+a+i++++l+  + a   +i v++P +a++kl++
  AHX11396.1 61 AYLNGASAIITRKHLECPELAI-PIIKVDDPVAAMQKLAT 99
                55567*******9998776544.35*************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (468 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       456  (0.0254337); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3557.63
//
Query:       AHX11397.1  [L=397]
Description: phosphate ABC transporter, permease protein PstA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.2e-18   66.7  25.9    4.9e-17   62.3  18.4    2.4  2  BPD_transp_1  Binding-protein-dependent transport system inne
    0.00019   21.7   0.3     0.0011   19.2   0.3    2.1  1  DUF3333       Domain of unknown function (DUF3333)
  ------ inclusion threshold ------
      0.027   14.7   2.3      0.027   14.7   2.3    2.8  3  DUF1430       Protein of unknown function (DUF1430)
        1.7    9.4   8.4       0.87   10.3   0.5    3.4  4  DUF2626       Protein of unknown function (DUF2626)


Domain annotation for each model (and alignments):
>> BPD_transp_1  Binding-protein-dependent transport system inner membrane component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.3   0.00023         1      13      44 ..      13      54 ..       8     101 .. 0.81
   2 !   62.3  18.4   1.1e-20   4.9e-17       5     179 ..     196     388 ..     192     393 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00023
  BPD_transp_1 13 nkkldkllrpliivllslPsfvlaillvlvf..........v 44
                  +++++k+++ + i+   +P+f+l+ +l+ +f          +
    AHX11397.1 13 RGFVNKIFSLFCILCAFVPVFLLFTMLFSIFsgaynglqqtK 54
                  7899************************88876665544440 PP

  == domain 2  score: 62.3 bits;  conditional E-value: 1.1e-20
  BPD_transp_1   5 Gilaa.....lnrnkkldkllrpliivllslPsfvlaillvlvf.vilsilghlilpviillllsaapyvrlirraalrslpkdlveaaralGasrw 95 
                   G+l+a     +  ++ ++++l + ++ l+s+P++++++l + +   +l+   ++ l + ++l+++++p+ ++    a+rs+p+  ++aa alGas+ 
    AHX11397.1 196 GVLTAlwigeYLGKGNITRILEVSVNNLSSTPPIIFGVLGLSFYiNFLGLPRSSPLVGGLTLAFMMFPILVISSLHAIRSVPDTIKQAAFALGASKV 292
                   555555555999999999*****************9999775445888999999999**************************************** PP

  BPD_transp_1  96 qifrkvvlPnalppiitglilafggllggavlleflgswpGlgtllleailgydyseis............nggvlalviavlllnlvadilqrll 179
                   q++ ++vlP+++p i+tg +l +++++g+++ l+++g    +g+    +++  ++ + +               + ++++++lll+++++ ++ l+
    AHX11397.1 293 QVILHHVLPLSVPGIMTGTVLGIARIIGESAPLLMIGMVAFVGNIPSKITEPANVFAVQiyiwatssdiamTEKTSVIILILLLLLFLLNCVVYLI 388
                   *************************************55558888888888888887779***********6666666666666666666555554 PP

>> DUF3333  Domain of unknown function (DUF3333)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.3   2.4e-07    0.0011       3     144 ..       9     131 ..       7     138 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 2.4e-07
     DUF3333   3 rlkrRyaaErrFrlyGiaAialallfLviLlvsIvskGltAFtqteitleveldaeeidpkgkaeeskklatanyeklirdalkaklp.eveerrekre 100
                 +l++R    ++F l++i+  ++ ++ L+++l+sI+s ++++++qt+  + ++ld+  i +k+             ++ ir++l + l+ ++  +++  +
  AHX11397.1   9 KLTKRGFVNKIFSLFCILCAFVPVFLLFTMLFSIFSGAYNGLQQTK--FFIDLDEIGITTKD------------SRYQIREKLIKYLKiQIPWETDIFT 93 
                 588999999************************************7..55677777776666............3445777777777755557788888 PP

     DUF3333 101 laelissgaayqlrdrvladpsligttvtvwllasddvDsllkG 144
                 l++++s+   ++++d + ++++      ++w++ s++ D l+k 
  AHX11397.1  94 LMNFLSNYSTHEVMDAIHKEQK------KIWITISGEGDVLHKY 131
                 8888888888888888887766......6777777777777665 PP

>> DUF1430  Protein of unknown function (DUF1430)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.3      0.71   3.2e+03      66      84 ..      25      43 ..      15      55 .. 0.62
   2 ?   -3.3   0.1       2.6   1.1e+04      64      67 ..     186     189 ..     169     204 .. 0.50
   3 ?   14.7   2.3     6e-06     0.027      39      86 ..     343     390 ..     338     395 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.71
     DUF1430 66 iillvvlvlllielllill 84
                i+  +v v ll+ +l++++
  AHX11397.1 25 ILCAFVPVFLLFTMLFSIF 43
                4444555555555555554 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 2.6
     DUF1430  64 ekii 67 
                    +
  AHX11397.1 186 FVSL 189
                 1111 PP

  == domain 3  score: 14.7 bits;  conditional E-value: 6e-06
     DUF1430  39 rhkeyliiqlivllillvlifiltkekiillvvlvlllielllillvq 86 
                    +++ +q+ ++  +  ++++ + + iil+++l+l+l++++++l+++
  AHX11397.1 343 EPANVFAVQIYIWATSSDIAMTEKTSVIILILLLLLFLLNCVVYLIRK 390
                 557899*************************************99876 PP

>> DUF2626  Protein of unknown function (DUF2626)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   1.3      0.32   1.4e+03      44      62 ..       8      27 ..       2      45 .. 0.56
   2 ?    0.4   1.7      0.25   1.1e+03       5      47 ..      23      65 ..      14      73 .. 0.74
   3 ?   -3.3   0.0       3.5   1.5e+04      12      24 ..      89     101 ..      86     118 .. 0.76
   4 ?   10.3   0.5    0.0002      0.87      13      65 ..     326     382 ..     317     390 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.32
     DUF2626 44 lklsertYvy.ifaayltvf 62
                lkl+ r +v+ if  ++++ 
  AHX11397.1  8 LKLTKRGFVNkIFSLFCILC 27
                57788888754666666553 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.25
     DUF2626  5 fRvlgfwtgiiavlafvGdliemallflaqtaffvalgYlkls 47
                f +l  +  ++ ++ ++ ++ + a   l+qt ff+ l  + ++
  AHX11397.1 23 FCILCAFVPVFLLFTMLFSIFSGAYNGLQQTKFFIDLDEIGIT 65
                6666667777777777777778888888999999988766665 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 3.5
     DUF2626  12 tgiiavlafvGdl 24 
                 t i++++ f+ ++
  AHX11397.1  89 TDIFTLMNFLSNY 101
                 6778888887655 PP

  == domain 4  score: 10.3 bits;  conditional E-value: 0.0002
     DUF2626  13 giiavlafvG....dliemallflaqtaffvalgYlklsertYvyifaayltvffvg 65 
                 ++i+++afvG    +++e a +f  q  ++ + + + ++e+t v i +  l +f++ 
  AHX11397.1 326 LMIGMVAFVGnipsKITEPANVFAVQIYIWATSSDIAMTEKTSVIILILLLLLFLLN 382
                 578999****888788999****************************9999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1094  (0.0610185); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.37
# Mc/sec: 3199.61
//
Query:       AHX11398.1  [L=337]
Description: ABC transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.5e-31  107.7   0.0    9.6e-31  107.1   0.0    1.3  1  ABC_tran     ABC transporter
    5.4e-12   46.1   0.9    4.7e-06   26.6   0.0    2.2  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    1.6e-05   24.4   0.2     0.0002   20.9   0.2    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    9.7e-05   22.7   0.1    0.00051   20.3   0.1    2.0  1  AAA_22       AAA domain
    0.00021   21.0   0.0    0.00046   19.9   0.0    1.5  1  AAA_29       P-loop containing region of AAA domain
    0.00028   20.7   0.9      0.028   14.1   0.3    2.1  2  AAA_15       AAA ATPase domain
     0.0011   18.8   0.0     0.0025   17.8   0.0    1.5  1  RsgA_GTPase  RsgA GTPase
     0.0026   18.3   0.1     0.0044   17.6   0.1    1.3  1  AAA_23       AAA domain
     0.0056   17.1   0.0       0.01   16.2   0.0    1.4  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.014   15.4   0.0      0.029   14.3   0.0    1.6  1  NACHT        NACHT domain
      0.017   15.1   0.2      0.066   13.2   0.1    2.0  2  AAA_5        AAA domain (dynein-related subfamily)
      0.057   13.5   0.1       0.15   12.1   0.0    1.7  2  MMR_HSR1     50S ribosome-binding GTPase
      0.065   13.1   0.0       0.14   12.0   0.0    1.5  1  Rad60-SLD    Ubiquitin-2 like Rad60 SUMO-like
       0.12   12.5   0.1        0.6   10.3   0.1    2.1  1  AAA_33       AAA domain
       0.14   12.7   0.0        0.4   11.2   0.0    1.8  2  AAA_18       AAA domain
       0.14   11.9   0.1       0.28   10.9   0.1    1.5  1  AAA_24       AAA domain
       0.15   10.7   0.0        9.1    4.8   0.0    2.0  2  AAA_13       AAA domain
       0.21   11.8   0.2        1.3    9.4   0.2    2.1  1  SbcCD_C      Putative exonuclease SbcCD, C subunit


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.1   0.0   9.6e-34   9.6e-31       1     136 [.      17     160 ..      17     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 107.1 bits;  conditional E-value: 9.6e-34
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG....B-HHHCCHCEEEE-SS--S-TTSBHHHH........HHHTCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxx........xxxxxxxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke....qeleslrkeigvlpqepqlfpeltvren........esdeeiek 87 
                 lkn+ +++  g++v ++Ge+G+GKStLl+l++gl++p +G+i++ +k + +     +l+  +++i++++q+++lfp++tv +n        + ++ +++
  AHX11398.1  17 LKNICFDCDTGQIVCLIGESGSGKSTLLRLISGLESPIAGSIKILDKMVFHfsdkVSLPPEQRNIAMIFQHSSLFPNKTVFDNvqfavnkgNPRKIASE 115
                 79*******************************************9999888988899999***********************998876555555889 PP

                 HHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  88 alsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +l+ +g+++  ++       ++SgGq+q v lara+++ p +lllDEp+
  AHX11398.1 116 MLELVGMSQYSNSMP----FQISGGQQQLVTLARAFAQFPGILLLDEPF 160
                 999999998777776....*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.2   1.5e-06    0.0015       1      24 [.      29      52 ..      29      98 .. 0.77
   2 !   26.6   0.0   4.7e-09   4.7e-06     234     300 ..     130     194 ..      88     198 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.5e-06
      AAA_21  1 lnvliGpNgsGKSnLLdaldllar 24
                + +liG  gsGKS+LL+++++l +
  AHX11398.1 29 IVCLIGESGSGKSTLLRLISGLES 52
                578*****************9943 PP

  == domain 2  score: 26.6 bits;  conditional E-value: 4.7e-09
      AAA_21 234 arelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrll.ellkelsrngaQviltTHSpl 300
                 ++++S G+++l  l+ a+++ +   ++ll+DEp ++L+  l   +  +++++ +++g   +++TH+p+
  AHX11398.1 130 PFQISGGQQQLVTLARAFAQFP---GILLLDEPFSSLDATLRMNIReKVISLIKEKGLTTVIVTHDPY 194
                 4789*******99999999888...*****************99998888888888***********8 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.2     2e-07    0.0002       8     211 ..      10     206 ..       6     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2e-07
                 ESETTEECEEEEEETTS.SEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--..BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEE CS
                 xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N   8 enFksyagktvilpfsk.sftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk..skekasvkkaeveitfdnedkklkiekeevsisrrv 103
                 +n++++  k++  + ++ ++ +++G+ GSGKs ll  i    G +s  +   + l++++++   k +   ++ +++++f++++      ++ v  +++ 
  AHX11398.1  10 HNYQNFSLKNICFDCDTgQIVCLIGESGSGKSTLLRLI---SGLESPIAGSIKILDKMVFHfsDKVSLPPEQRNIAMIFQHSSLF---PNKTVFDNVQF 102
                 57888888888888876257789************999...46666656677889999999655556677889999999888776...45555555555 PP

                 ETTSEEEEEETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECT....TTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 104 krkgeseykingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDe....idaaLDeknvkkvaellkeksknaQfivislr 198
                   ++ +  ki  +  +   +s+  +s+ +   ++SgG+++Lv la  fA        + llDe    +da L  + ++kv +l+kek      ++++++
  AHX11398.1 103 AVNKGNPRKIASEMLELVGMSQYSNSMPF---QISGGQQQLVTLARAFAQF----PGILLLDEpfssLDATLRMNIREKVISLIKEKG--LTTVIVTHD 192
                 55555566777776666666666666655...68***********999933....457777772222345555666788889999888..555555555 PP

                 .HHHCCC-SCEEEE CS
                 .xxxxxxxxxxxxx RF
       SMC_N 199 .eemlekadklvgv 211
                   e le +dklv +
  AHX11398.1 193 pYEALEVSDKLVVI 206
                 15777888888766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.1   5.1e-07   0.00051       4     122 ..      26     183 ..      23     197 .. 0.72

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 5.1e-07
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee...................................erpevv.fvtlpsst.sskdllrellralg 65 
                 t +i++++GesG+GK+tllr +       a                                       ++++v+  v+ ++ + +++++++e+l+ +g
  AHX11398.1  26 TGQIVCLIGESGSGKSTLLRLISGLESPIA---GsikildkmvfhfsdkvslppeqrniamifqhsslfPNKTVFdNVQFAVNKgNPRKIASEMLELVG 121
                 7899***************99987764322...135589999999999999999888888888877775444444767766666688888888888888 PP

      AAA_22  66 lelkaerlsseell.ealeqalrarav.....ielliiDEaqh.lr...seealeeLrsllnlsrkg 122
                  ++ +   +s  +  +  +q+l + a+     +++l++DE    l+   ++++ e++ sl +  +kg
  AHX11398.1 122 MSQYS---NSMPFQiSGGQQQLVTLARafaqfPGILLLDEPFSsLDatlRMNIREKVISLIK--EKG 183
                 88888...777776788888888888888888889999984444544334555555555555..555 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   4.6e-07   0.00046       8      39 ..      11      44 ..       8      49 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.6e-07
      AAA_29  8 NWgtfdghtieidlkg..atlltGpsGsGKSTll 39
                N + f+ + i +d +   ++ l+G+sGsGKSTll
  AHX11398.1 11 NYQNFSLKNICFDCDTgqIVCLIGESGSGKSTLL 44
                66667666666665544799*************8 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.3   2.8e-05     0.028      10      44 ..      11      48 ..       9      74 .. 0.81
   2 ?    4.7   0.0     0.021        20     323     367 ..     150     194 ..     134     195 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
      AAA_15 10 NFRslkdveidlsee...ltvliGkNnsGKSsileald 44
                N+  ++   i ++ +   + +liG+ +sGKS++l+++ 
  AHX11398.1 11 NYQNFSLKNICFDCDtgqIVCLIGESGSGKSTLLRLIS 48
                6666666667777777789****************996 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.021
      AAA_15 323 knvilliEEPEahLHpqaqkvlikllkelandnktQviitTHSph 367
                  + ill++EP  +L   + + + ++ ++l++++   ++i TH p+
  AHX11398.1 150 FPGILLLDEPFSSLDATLRMNIREKVISLIKEKGLTTVIVTHDPY 194
                 4689*****************************99********98 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0025      91     122 ..      18      50 ..       7      76 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                  HHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT CS
  RsgA_GTPase  91 eelkellkd.ktsvlvGqSGvGKStLinallpe 122
                  +++   ++  ++++l+G+SG GKStL+  + + 
   AHX11398.1  18 KNICFDCDTgQIVCLIGESGSGKSTLLRLISGL 50 
                  55666666559****************998874 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.1   4.4e-06    0.0044       6      39 ..      11      47 ..       2      49 .. 0.82

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 4.4e-06
      AAA_23  6 nfrsfrdqeidF...skgltlItGpNGaGKTTildAi 39
                n++ f+ ++i F      +++++G+ G+GK+T+l+ i
  AHX11398.1 11 NYQNFSLKNICFdcdTGQIVCLIGESGSGKSTLLRLI 47
                666666678999887669****************987 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     1e-05      0.01      24      45 ..      27      48 ..      19      86 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1e-05
      AAA_16 24 pelvllsGesGvGKsslvrell 45
                +++v l+GesG+GKs+l+r + 
  AHX11398.1 27 GQIVCLIGESGSGKSTLLRLIS 48
                479***************9875 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   2.9e-05     0.029       2      20 ..      29      47 ..      28      82 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 2.9e-05
                CEEEEC-TTTCHHHHHHHH CS
       NACHT  2 lvilqGeaGsGKTtLlqkl 20
                +v+l Ge+GsGK+tLl+ +
  AHX11398.1 29 IVCLIGESGSGKSTLLRLI 47
                699*************865 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   6.6e-05     0.066       2      20 ..      30      48 ..      29      51 .. 0.91
   2 ?   -1.2   0.0       1.9   1.9e+03      72      72 ..     218     218 ..     137     261 .. 0.60

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.6e-05
                EEEE--SSSSHHHHHHHGG CS
       AAA_5  2 vlLvGppGtgKselaerla 20
                v+L+G++G+gKs+l + ++
  AHX11398.1 30 VCLIGESGSGKSTLLRLIS 48
                8**************9987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
                 E CS
       AAA_5  72 D 72 
                 D
  AHX11398.1 218 D 218
                 2 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00015      0.15       2      22 ..      30      50 ..      29      68 .. 0.84
   2 ?   -2.6   0.0       5.7   5.7e+03      71      80 ..     176     185 ..     142     214 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00015
                EEEEESTTSSHHHHHHHHHTS CS
    MMR_HSR1  2 vaivGrpNvGKStLinaltge 22
                v+++G + +GKStL++ ++g 
  AHX11398.1 30 VCLIGESGSGKSTLLRLISGL 50
                89**************99884 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
                 HHHHCTSEEE CS
    MMR_HSR1  71 laleeadlil 80 
                  +l++ + + 
  AHX11398.1 176 ISLIKEKGLT 185
                 3333322222 PP

>> Rad60-SLD  Ubiquitin-2 like Rad60 SUMO-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.14      23      59 ..      61      98 ..      59      99 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
                HHHHHHHHHHHHT----.TT-EEEETTEE--TTSBGGG CS
   Rad60-SLD 23 vskLieayrkkkgipee.qkvrLiFDGeeLdpnstved 59
                + k++ ++ +k+++p+e  ++ +iF++  L pn+tv d
  AHX11398.1 61 LDKMVFHFSDKVSLPPEqRNIAMIFQHSSLFPNKTVFD 98
                679999*********99789***************976 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.1    0.0006       0.6       2      18 ..      30      46 ..      29     198 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.0006
      AAA_33  2 vllvGlpGsGKstlaer 18
                v l+G +GsGKstl++ 
  AHX11398.1 30 VCLIGESGSGKSTLLRL 46
                789***********985 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0    0.0004       0.4       1      30 [.      30      57 ..      30     100 .. 0.75
   2 ?   -2.1   0.0       5.2   5.2e+03      58      69 ..     173     184 ..     146     228 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0004
      AAA_18  1 IlltGtpGvGKttlakeLskrlgfgvnlrd 30
                ++l G +G+GK+tl + +s ++  + + ++
  AHX11398.1 30 VCLIGESGSGKSTLLRLISGLE--SPIAGS 57
                79***************98776..444444 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 5.2
      AAA_18  58 dklldaleenss 69 
                 +k++++++e   
  AHX11398.1 173 EKVISLIKEKGL 184
                 344444444332 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00028      0.28       3      22 ..      28      47 ..      26      57 .. 0.83

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
      AAA_24  3 lkiliyGpsgiGKTtlakel 22
                + ++++G+sg+GK+tl++ +
  AHX11398.1 28 QIVCLIGESGSGKSTLLRLI 47
                679*************9866 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.0   0.0     0.016        16      23      41 ..      34      52 ..      25      88 .. 0.86
   2 ?    4.8   0.0    0.0091       9.1     527     570 ..     151     192 ..     140     214 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.0 bits;  conditional E-value: 0.016
      AAA_13 23 GwNGaGKTtLSrllrslel 41
                G  G+GK+tL rl++ le+
  AHX11398.1 34 GESGSGKSTLLRLISGLES 52
                888*************975 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.0091
      AAA_13 527 dkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHn 570
                  +i  +D P SSLD++  + +   + s + k+k    + i TH 
  AHX11398.1 151 PGILLLDEPFSSLDATLRMNIREKVISLI-KEKGLTTV-IVTHD 192
                 68999**********99998877777776.44444444.45776 PP

>> SbcCD_C  Putative exonuclease SbcCD, C subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   0.2    0.0013       1.3      63      81 ..     150     168 ..     121     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0013
     SbcCD_C  63 alrlvfLDEAFsklDeesi 81 
                  +++++LDE Fs+lD++ +
  AHX11398.1 150 FPGILLLDEPFSSLDATLR 168
                 4789***********9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (337 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      609  (0.0339673); expected 358.6 (0.02)
Passed Vit filter:                       113  (0.00630264); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 2378.15
//
Query:       AHX11399.1  [L=51]
Description: twin arginine-targeting translocase, TatA/E family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.2e-14   51.6   0.9    4.4e-14   51.5   0.9    1.0  1  MttA_Hcf106  mttA/Hcf106 family
  ------ inclusion threshold ------
       0.12   11.1   0.0       0.12   11.1   0.0    1.0  1  DUF2206      Predicted membrane protein (DUF2206)


Domain annotation for each model (and alignments):
>> MttA_Hcf106  mttA/Hcf106 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.5   0.9     5e-18   4.4e-14       1      46 [.       3      48 ..       3      51 .] 0.95

  Alignments for each domain:
  == domain 1  score: 51.5 bits;  conditional E-value: 5e-18
                 S-HHHHHHHHHHHHHHS-TTTHHHHHHHHHHHHHHHHHHHHHHHH- CS
  MttA_Hcf106  1 lgapelliIlvValllFGpkkLPEvaraLGktLreFkkavkeleee 46
                 lg++++l++++++l+lFG+ kLP v   LGk+Lr  k+++ke e+ 
   AHX11399.1  3 LGPWQILLVFLIILVLFGAGKLPQVIADLGKGLRSLKEELKESEKK 48
                 69****************************************9985 PP

>> DUF2206  Predicted membrane protein (DUF2206)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   1.3e-05      0.12     217     242 ..       6      31 ..       3      49 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1.3e-05
     DUF2206 217 lkiisvflvvllLfnsGfiyeivkds 242
                 ++i+ vfl++l+Lf +G + ++++d 
  AHX11399.1   6 WQILLVFLIILVLFGAGKLPQVIADL 31 
                 9****************999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      487  (0.0271627); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 414.52
//
Query:       AHX11400.1  [L=258]
Description: thiazole biosynthesis ThiG family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   3.5e-103  344.2   0.4     4e-103  344.0   0.4    1.0  1  ThiG          Thiazole biosynthesis protein ThiG
    0.00029   20.4   0.3      0.003   17.0   0.1    2.0  2  His_biosynth  Histidine biosynthesis protein
      0.003   16.8   0.8       0.27   10.4   0.1    2.4  2  NanE          Putative N-acetylmannosamine-6-phosphate epimer
  ------ inclusion threshold ------
      0.011   14.8   0.1      0.015   14.4   0.1    1.2  1  FMN_dh        FMN-dependent dehydrogenase
       0.17   11.7   0.0       0.33   10.9   0.0    1.4  1  DUF4907       Domain of unknown function (DUF4907)
       0.19   10.8   0.6       0.43    9.6   0.1    1.8  2  Dus           Dihydrouridine synthase (Dus)


Domain annotation for each model (and alignments):
>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  344.0   0.4  1.3e-106    4e-103       1     246 [.       6     250 ..       6     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 344.0 bits;  conditional E-value: 1.3e-106
                 EETTEEES--EEEE-STSSSHHHHHHHHHHHT-SEEEEECCGSTTTS.TTS--CCCCCHCCTSEEEEE-TT-SSHHHHHHHHHHHHHTTS-SEEEE--B CS
        ThiG   1 kiagkefksrlllGtgkykslevlkeaveasgaeivtvalrRvnleekaseeellelleekevtllPntaGaktaeeAvriarlarevletdliklEvi 99 
                 kia+++f srl++Gtgky++++ +++a+easg+eivtval+Rvn++++ ++e+l ++++ +++t+lPnta + +aeeAvr   lare+ +++l+k+E+ 
  AHX11400.1   6 KIANRSFVSRLIVGTGKYADFAETAQAIEASGTEIVTVALKRVNITDR-KRETLQDYIDPRKYTYLPNTAFCFDAEEAVRHLVLAREIGGWNLVKVEIF 103
                 5899*******************************************6.69************************************************ PP

                 CETTTTEB-HHHHHHHHHHHHHTT-EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHHHHHHHH-SS-BEEES---SHHHHHHHHHTT- CS
        ThiG 100 adektLlPdvvetlkaaeiLvkeGFevlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnkealkiiieeakvPvivDAGigspsdaaqamelGa 198
                 +++++L+Pd+  tlka eiLvkeGF+v+pY++dD+v++++le++G+ avmPlaapiGsglG++n  +lk+ii++ ++PvivDAG+g+psda+ ame G+
  AHX11400.1 104 SEKEFLYPDMQATLKAVEILVKEGFAVMPYCNDDPVMCKKLEDMGAVAVMPLAAPIGSGLGIQNLFNLKVIIKQSRIPVIVDAGVGTPSDAVVAMEAGC 202
                 *************************************************************************************************** PP

                 SEEEESHHHHTSSSHHHHHHHHHHHHHHHHHHHHH------SS-XTTS CS
        ThiG 199 davllntavaeakdpvamArafklaveaGrlaylagriekrevasass 246
                 d+vl+nt++a+a+ pv+mA+a+klav++Grl ylagr+e +++asass
  AHX11400.1 203 DGVLINTSIAKARFPVQMAEAMKLAVRSGRLGYLAGRMEIQRFASASS 250
                 ***********************************************9 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0      0.07   2.1e+02      96     129 ..      13      46 ..       5      64 .. 0.83
   2 !   17.0   0.1     1e-06     0.003      65     108 ..     171     214 ..     160     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.07
                   -SEEEESHHHHH-THHHHHHHHHHCGGGEEEEEE CS
  His_biosynth  96 adkviigtaavknpelikelaekfgsqkivvaiD 129
                   ++++i+gt    +     +++e+ g + ++va+ 
    AHX11400.1  13 VSRLIVGTGKYADFAETAQAIEASGTEIVTVALK 46 
                   7899**********99******999999999986 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1e-06
                   HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHHHH- CS
  His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigtaavkn 108
                   ++ i+++ +ipv v+ G+ + +d+  ++eag+d v i+t+ +k 
    AHX11400.1 171 LKVIIKQSRIPVIVDAGVGTPSDAVVAMEAGCDGVLINTSIAKA 214
                   567899999******************************98765 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.8   0.1    0.0048        14      70     171 ..      48     153 ..      10     164 .. 0.70
   2 !   10.4   0.1     9e-05      0.27     134     179 ..     169     214 ..     160     226 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0048
                 EE--SS--T--HHHHHHHHHHH--EEEEE-SSHHHHHHHHHTT-SEEE-TTTTSSTTS-...SS--HH....HHHHHHHTT--EEEES---SHHHHHHH CS
        NanE  70 lDatdrerpvtieelikkikekyqllmaDistleeglvakklGvdivGttlsGytkeeek..aepDfa....lvkalseaglkviaeGrintPekakka 162
                 ++ tdr+r+ t+++ i   k +y+   a +   ee++    l  +i G  l      +ek    pD++     v+ l+++g++v+     + P   kk 
  AHX11400.1  48 VNITDRKRE-TLQDYIDPRKYTYLPNTAFCFDAEEAVRHLVLAREIGGWNLVKVEIFSEKefLYPDMQatlkAVEILVKEGFAVMPYCN-DDPVMCKKL 144
                 456788775.4667777778888888888888888887777777777776665443333323445543211168899999999998765.789999999 PP

                 HTT--SEEE CS
        NanE 163 ieiGvdavv 171
                  ++G++av+
  AHX11400.1 145 EDMGAVAVM 153
                 999999985 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 9e-05
                 HHHHHHHHHTT--EEEES---SHHHHHHHHTT--SEEEE-HHHH-H CS
        NanE 134 falvkalseaglkviaeGrintPekakkaieiGvdavvvGsaitrl 179
                 f+l   ++++ + vi++  + tP  a  a+e G d v + ++i++ 
  AHX11400.1 169 FNLKVIIKQSRIPVIVDAGVGTPSDAVVAMEAGCDGVLINTSIAKA 214
                 55555678999****************************9999875 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.9e-06     0.015     208     243 ..     171     207 ..     114     213 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.9e-06
                 HHHHHHHHSSEEEEE.EE-SHHHHHHHHHTTESEEEE CS
      FMN_dh 208 ikwlreqtklplvvK.GvltaedakraveaGvdgivv 243
                 +k + +q ++p++v  Gv t+ da  a+eaG+dg+++
  AHX11400.1 171 LKVIIKQSRIPVIVDaGVGTPSDAVVAMEAGCDGVLI 207
                 6666777777777744777777777777777777765 PP

>> DUF4907  Domain of unknown function (DUF4907)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00011      0.33       7      31 ..     161     185 ..     157     194 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00011
     DUF4907   7 gGyGYqIllnekvlIkQpfIPaisg 31 
                 +G G q l+n kv+IkQ+ IP+i  
  AHX11400.1 161 SGLGIQNLFNLKVIIKQSRIPVIVD 185
                 67777888999***********975 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.44   1.3e+03     138     157 ..      24      43 ..      18      58 .. 0.85
   2 ?    9.6   0.1   0.00014      0.43     175     213 ..     171     208 ..     162     230 .. 0.87

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.44
                 C.HHHHHHHHHHCT-SEEEE CS
         Dus 138 enalelakiveaaGaqaltv 157
                  +  e a+++ea+G + +tv
  AHX11400.1  24 ADFAETAQAIEASGTEIVTV 43 
                 56778999999999999998 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00014
                 HHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
         Dus 175 IkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                  k + ++ +ipvi+  ++ +++da  ++e  G+dgv+i 
  AHX11400.1 171 LKVIIKQSRIPVIVDAGVGTPSDAVVAMEA-GCDGVLIN 208
                 677889999*******************99.*****995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (258 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       514  (0.0286686); expected 358.6 (0.02)
Passed bias filter:                      470  (0.0262145); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1943.99
//
Query:       AHX11401.1  [L=41]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       268  (0.0149478); expected 358.6 (0.02)
Passed bias filter:                      168  (0.00937029); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 323.47
//
Query:       AHX11402.1  [L=263]
Description: dihydropteroate synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    6.9e-55  186.4   0.0    7.8e-55  186.2   0.0    1.0  1  Pterin_bind  Pterin binding enzyme


Domain annotation for each model (and alignments):
>> Pterin_bind  Pterin binding enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.2   0.0   4.4e-59   7.8e-55       2     244 .]       7     248 ..       6     248 .. 0.93

  Alignments for each domain:
  == domain 1  score: 186.2 bits;  conditional E-value: 4.4e-59
                  EEEETTTTTCHCCHHCTHHHHHHHHHHHHHHTT-SEEEEESS-TSTT--CCHHHHHHHHHHHHHHHHHH..HC.TSEEEEE-S-HHHHHHHHHTTSEE CS
  Pterin_bind   2 gilNvtpdsfsdggkfedldkalaqarkmveeGAdilDiggestrPgaervdeeeelervvpvlealrd..ea.dvpisiDttkaevaeaAlkagadi 96 
                  g+lN+tpdsf+dggkf++ d+a+a+  +m+++GAd++Dig+est+P+   ++++ee++r+  vl+++ +  +  +v+ siD++++e+++ Al++g ++
   AHX11402.1   7 GVLNITPDSFFDGGKFLEKDAAIAHTLSMIQDGADVIDIGAESTKPDGVSISQREEIKRLDGVLQEVIAlcRKhNVLTSIDSYNPETVRFALDSGINL 104
                  9****************************************************************99887744499********************** PP

                  EEETTTTSSSTTHHHHHHHHT-EEEEESECSSTTTHCCCCCCCSSHHHHHHHHHHHHHHHHHHTT--GGGEEEETTTTSSTTHHHHHHHHHTHHHHHH CS
  Pterin_bind  97 vNdvsgeerdpkmlelvaeagaavvvmhmrgtpktmqeeegqyedvveeveaflearveaaeeaGvaperillDpgigfgkteehnlellrrldelre 194
                  +N ++  e+ +++l    +++ ++v+mh+ + p + ++   +  dvve ++a++++++  +e+ G+ +e+i++Dpg+gfgkt+++ + +++ +d + +
   AHX11402.1 105 INPQKNVEKMAEILMEKGRNDIPIVLMHSVTIPVEIDADLPDDIDVVETLKAWFTEKLTILESIGISREKIIIDPGLGFGKTTDQCNTIIKSIDSF-K 201
                  ***9999966666666667889***********99999888*******************************************************.* PP

                  TTSSEBEEEGTTGHHHHHHHCTTCHGHHHHHHHHHHHHHHHTT-SEEEES CS
  Pterin_bind 195 alevpvllGvSrksflgrllelgkaeeRdagtaaflalaaaaGadivrVh 244
                   + +p++lG+S+k+f+ r+ + +   e    t+ ++a+  a+ +d++rVh
   AHX11402.1 202 SFSLPIMLGHSNKRFVRRIESQC---ENVRFTLPISAILFAKKIDYIRVH 248
                  ******************97434...66778899999999999******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (263 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2101.89
//
Query:       AHX11403.1  [L=163]
Description: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-24   86.2   0.0    2.6e-24   85.9   0.0    1.1  1  HPPK      7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase


Domain annotation for each model (and alignments):
>> HPPK  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.0   1.4e-28   2.6e-24       2     112 .]       9     137 ..       8     137 .. 0.90

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 1.4e-28
                 EEEEE-SSSHHHHHHHHHHHHHHEEEEE---EEE--S......S..S-GEEEEEEEEEESS-HHHHHHHHHHHHHHTT--C..STS-BS-EEEEEEET. CS
        HPPK   2 lalGsNlgdreanleealealeekvvkvSslyetepv......d..qpdFlNavvevetelspeellealkeiEkelgrer..rwgpRtlDlDillyg. 89 
                 l+lGsN+g++++n+ ea +++  k   +S++++t+++      +  + d+lNa+v  +  ++p e l+++k+iEk+++r +  +++pRt+D+Dil++g 
  AHX11403.1   9 LGLGSNIGNTRKNIIEARNKIPMKDKILSPIIKTKALltknapSawDIDYLNAIVIGKPLFTPLETLQRVKKIEKQMKRIKigKYSPRTIDIDILFWGd 107
                 89*******************7766778999999999876443133446*******************************8767*************** PP

                 .......EEES-TTGGG-HHHHHHHHHHCT CS
        HPPK  90 .......ltlPhprlaeraFvlvplaelap 112
                        lt Ph+++ +r F l+p+a++ p
  AHX11403.1 108 kliteryLTAPHREVLKRFFTLKPIASVCP 137
                 *************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (163 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       517  (0.028836); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.26s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 1215.01
//
Query:       AHX11404.1  [L=389]
Description: methionine adenosyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-55  186.5   0.0    1.2e-54  184.1   0.0    2.0  2  S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal 
    4.1e-32  111.0   0.0    8.1e-32  110.0   0.0    1.5  1  S-AdoMet_synt_M  S-adenosylmethionine synthetase, central dom
      9e-28   96.9   0.0    2.2e-27   95.6   0.0    1.6  1  S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal 


Domain annotation for each model (and alignments):
>> S-AdoMet_synt_C  S-adenosylmethionine synthetase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.16   9.5e+02      45      70 ..     140     168 ..     128     219 .. 0.54
   2 !  184.1   0.0   1.9e-58   1.2e-54       2     137 ..     228     369 ..     227     370 .. 0.97

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.16
                      HHHHHHHHHHHHTTSB...SEEEEEEEE- CS
  S-AdoMet_synt_C  45 yaaryvaknlvaagla...kkvevqlsYa 70 
                      y+ar + + +v+++l     k +v + Y 
       AHX11404.1 140 YYARRILQAVVQERLFgpdGKSQVTIEYD 168
                      78888888888877652223555555553 PP

  == domain 2  score: 184.1 bits;  conditional E-value: 1.9e-58
                      -TTTTS-EETTS-TTTTTTTTSS---S---TTB-TTSHHHHHHHHHHHHHHHHHHTTSBSEEEEEEEE-TT-SS-SEEEEEE-S-BSS-HHHHH CS
  S-AdoMet_synt_C   2 GgpkgdaGltgrkiivdtYgglaahgggafsgKdptkvDrsaayaaryvaknlvaaglakkvevqlsYaigvaepvsisvetfgtekvseeeia 95 
                      Ggp +d+Gltgrki+vdtYgg+ ++gggafsgKd+tkvDrsaay ary+akn+v +gla+++ vql+Yaig+++p++++v t+gt++++e ++ 
       AHX11404.1 228 GGPISDCGLTGRKIVVDTYGGMLPNGGGAFSGKDSTKVDRSAAYLARYIAKNIVFSGLAHQCGVQLCYAIGIDRPLTLQVATYGTARCKEGDLL 321
                      9********************************************************************************************* PP

                      HHHHHH----HHHHHHHHTTTSS--TGGGSS-SSS--......T-TTS CS
  S-AdoMet_synt_C  96 eivkevfdlrpaaiieeldLkkpiykktaayghfgre......elpwe 137
                      + ++ ++d +p++i e l+L+kpiy kta+ ghfg++      +++we
       AHX11404.1 322 SRIEVNIDSSPRGISELLHLTKPIYLKTASRGHFGNQydpedlSFKWE 369
                      ************************************877776666777 PP

>> S-AdoMet_synt_M  S-adenosylmethionine synthetase, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.0   0.0   1.4e-35   8.1e-32       2     120 .]     115     225 ..     114     225 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.0 bits;  conditional E-value: 1.4e-35
  S-AdoMet_synt_M   2 igAgDqGimfGYAtdeteelmPlpillahklaerlaelrkegeleylrpDaKsqvtveYeeelkpvrvdtvvistqhdeevsqeklredlkekv 95 
                      +gAgDqGimfGYAtdet+  mP+p+++a+++++ + + r       + pD+Ksqvt+eY++ ++p+ v++vv+s+qh e+v+ ++lre + ek+
       AHX11404.1 115 HGAGDQGIMFGYATDETPVGMPAPLYYARRILQAVVQER------LFGPDGKSQVTIEYDHYGNPIGVSNVVVSVQHPESVTLKDLRERILEKI 202
                      7*******************************9998888......59************999******************************** PP

  S-AdoMet_synt_M  96 ikkvlkee.lldekktkllinptGkF 120
                      ++ +  +   ld    +++inp+G+F
       AHX11404.1 203 VAVLP-SAwNLDP--DNIFINPAGSF 225
                      99666.5413444..59*******99 PP

>> S-AdoMet_synt_N  S-adenosylmethionine synthetase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.6   0.0   3.7e-31   2.2e-27       3      98 ..       7     102 ..       6     103 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.6 bits;  conditional E-value: 3.7e-31
  S-AdoMet_synt_N   3 lftsesVseGHPDkvadqisdaildailkedpkarvacetlvttglvvvageittk..akvdiekivrevikeigYekeelgfdaktcevlval 94 
                      +ftse+V  GHPDk+adqisd ild++lk+dp +r+a+e++v+++++++age+     ++++ie+ vr  +k++gY +  + +d+ ++e++++l
       AHX11404.1   7 YFTSEAVLPGHPDKIADQISDLILDMYLKKDPCSRTAIEVMVSHKKIIIAGEVYGPriSNAEIEEEVRLFLKHLGYPS--YLLDWGSVEIVNLL 98 
                      7****************************************************554114579**************76..9************* PP

  S-AdoMet_synt_N  95 eeqs 98 
                      +eqs
       AHX11404.1  99 HEQS 102
                      ***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       354  (0.0197445); expected 358.6 (0.02)
Passed bias filter:                      351  (0.0195772); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2999.41
//
Query:       AHX11405.1  [L=91]
Description: helix-turn-helix domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.8e-05   24.8   0.0    2.3e-05   24.4   0.0    1.1  1  HTH_28          Helix-turn-helix domain
    4.3e-05   22.8   0.0    6.1e-05   22.4   0.0    1.3  1  HTH_Tnp_ISL3    Helix-turn-helix domain of transposase family
    0.00052   19.7   0.0    0.00075   19.2   0.0    1.2  1  HTH_23          Homeodomain-like domain
    0.00064   20.1   0.0    0.00074   19.9   0.0    1.1  1  HTH_40          Helix-turn-helix domain
     0.0015   18.5   0.0     0.0022   18.0   0.0    1.2  1  HTH_29          Winged helix-turn helix
  ------ inclusion threshold ------
       0.01   15.7   0.0      0.016   15.1   0.0    1.3  1  Terminase_5     Putative ATPase subunit of terminase (gpP-lik
      0.011   16.1   0.0      0.015   15.6   0.0    1.4  1  HTH_Tnp_1       Transposase
      0.023   14.9   0.3        3.7    7.8   0.1    2.2  2  Fe_dep_repress  Iron dependent repressor, N-terminal DNA bind
      0.044   13.5   0.0      0.077   12.7   0.0    1.4  1  HTH_Tnp_4       Helix-turn-helix of DDE superfamily endonucle
       0.05   13.2   0.0      0.085   12.5   0.0    1.4  1  CENP-B_N        CENP-B N-terminal DNA-binding domain
      0.054   13.4   0.3      0.081   12.8   0.2    1.3  1  Sec7_N          Guanine nucleotide exchange factor in Golgi t
      0.071   12.9   0.0       0.41   10.4   0.0    2.0  2  HTH_psq         helix-turn-helix, Psq domain
        0.1   12.8   0.0       0.15   12.3   0.0    1.3  1  HTH_17          Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> HTH_28  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.4   0.0   1.7e-08   2.3e-05       4      38 ..       2      36 ..       1      37 [. 0.94

  Alignments for each domain:
  == domain 1  score: 24.4 bits;  conditional E-value: 1.7e-08
      HTH_28  4 eiikllaaGhsvreaArelgisrrtvyrWikryee 38
                ++++l ++G+s + +A+++ +s+ t+ rW++++ e
  AHX11405.1  2 HAVQLFLSGVSMNSVAKLFDLSPPTIMRWVNQLKE 36
                79*****************************9876 PP

>> HTH_Tnp_ISL3  Helix-turn-helix domain of transposase family ISL3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.4e-08   6.1e-05      20      51 ..       3      34 ..       1      35 [. 0.89

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.4e-08
  HTH_Tnp_ISL3 20 ilelllesrsvkavArqlgvSwtTVwrildry 51
                  +++l l++ s+ +vA+++++S+ T++r+++++
    AHX11405.1  3 AVQLFLSGVSMNSVAKLFDLSPPTIMRWVNQL 34
                  567777889*******************9985 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   5.4e-07   0.00075       9      41 ..       2      34 ..       1      37 [. 0.92

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 5.4e-07
      HTH_23  9 rillllaeGlsvreIAreLgvsrrTvyrwlkry 41
                ++++l++ G s   +A++++ s+ T+ rw++  
  AHX11405.1  2 HAVQLFLSGVSMNSVAKLFDLSPPTIMRWVNQL 34
                799**************************9875 PP

>> HTH_40  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.4e-07   0.00074       5      76 ..       3      77 ..       1      86 [. 0.71

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.4e-07
      HTH_40  5 tlelleeglsieeIAkerglkesTIegHLaelieegeeidl.erlvseeeekeIeeaiekvgsek...lkpikeal 76
                + +l+ +g s+  +Ak   l++ TI++ + +l e  +  d+ +++ +++e++++e ++  ++s+    l+ + e+l
  AHX11405.1  3 AVQLFLSGVSMNSVAKLFDLSPPTIMRWVNQLKELMK-DDFpTEFSQSSEKSTLEMIYSTLESSTdvvLTHMSEEL 77
                579***********************99999888864.44434554445555555555554433344488888877 PP

>> HTH_29  Winged helix-turn helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   1.6e-06    0.0022       3      36 ..       2      34 ..       1      37 [. 0.91

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.6e-06
      HTH_29  3 qallllaeGvstvsqiAkllglsrrtvyrwlkrf 36
                +a++l   Gvs    +Akl +ls++t++rw++  
  AHX11405.1  2 HAVQLFLSGVS-MNSVAKLFDLSPPTIMRWVNQL 34
                7999999***8.*******************976 PP

>> Terminase_5  Putative ATPase subunit of terminase (gpP-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.1e-05     0.016       5      36 ..       2      33 ..       1      43 [. 0.93

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.1e-05
  Terminase_5  5 qArlLYwqGyrvaeIAeelglkeatVysWkkr 36
                  A++L++ G +  ++A+  +l++ t+  W++ 
   AHX11405.1  2 HAVQLFLSGVSMNSVAKLFDLSPPTIMRWVNQ 33
                 59***************************986 PP

>> HTH_Tnp_1  Transposase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.1e-05     0.015      20      57 ..       7      43 ..       2      78 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.1e-05
   HTH_Tnp_1 20 lepgksvsevArrhgvspnqLykWrrqyregeeaspae 57
                + +g+s+ +vA+  ++sp +  +W+ q  +++++ ++ 
  AHX11405.1  7 FLSGVSMNSVAKLFDLSPPTIMRWVNQL-KELMKDDFP 43
                4789***********************9.555555544 PP

>> Fe_dep_repress  Iron dependent repressor, N-terminal DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0     0.016        22      23      48 ..      11      36 ..       8      37 .. 0.89
   2 ?    7.8   0.1    0.0027       3.7       9      32 ..      54      77 ..      45      80 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.016
                    B-HHHHHHHHTS-HHHHHHHHHHHHH CS
  Fe_dep_repress 23 vktkdlaerLnvspssVsemlkkLek 48
                    v+   +a+  + sp+++   ++ L++
      AHX11405.1 11 VSMNSVAKLFDLSPPTIMRWVNQLKE 36
                    778899*************9999975 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0027
                    HHHHHHHHHH.HHSSB-HHHHHHHH CS
  Fe_dep_repress  9 YLetIYtlse.ekkvvktkdlaerL 32
                     Le IY+  e + +vv t  ++e+L
      AHX11405.1 54 TLEMIYSTLEsSTDVVLT-HMSEEL 77
                    59********66666665.456665 PP

>> HTH_Tnp_4  Helix-turn-helix of DDE superfamily endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.6e-05     0.077      20      52 ..      11      43 ..       9      44 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.6e-05
   HTH_Tnp_4 20 ltyqdLayrFgvsestvsrifhkwvdlLaerlk 52
                +++  +a +F+ s +t+ r+++ + +l+++ ++
  AHX11405.1 11 VSMNSVAKLFDLSPPTIMRWVNQLKELMKDDFP 43
                66777899*******************998765 PP

>> CENP-B_N  CENP-B N-terminal DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   6.2e-05     0.085      13      49 ..       1      37 [.       1      40 [. 0.89

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 6.2e-05
                HHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCHHHH CS
    CENP-B_N 13 ievIqrleegeSkaelarrfnvpestlsdilknKkkl 49
                ++++q+   g S +++a+ f + + t+ +++++ k+l
  AHX11405.1  1 MHAVQLFLSGVSMNSVAKLFDLSPPTIMRWVNQLKEL 37
                68889999999********************987766 PP

>> Sec7_N  Guanine nucleotide exchange factor in Golgi transport N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   5.9e-05     0.081      19      56 ..      38      74 ..      25      85 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 5.9e-05
      Sec7_N 19 aksk.pkflslaersktfsLeLlesvlsnhgdvfrkhpe 56
                +k++ p+  ++++ s+  +Le+++s l++++dv+ +h +
  AHX11405.1 38 MKDDfPT--EFSQSSEKSTLEMIYSTLESSTDVVLTHMS 74
                3322466..999**********************98764 PP

>> HTH_psq  helix-turn-helix, Psq domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0    0.0003      0.41      10      37 ..       2      31 ..       1      38 [. 0.82
   2 ?    0.0   0.1      0.52   7.2e+02      30      39 ..      52      61 ..      52      66 .. 0.68

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.0003
     HTH_psq 10 eavv...nGkmSirkAArkYgiPrsTLwrrk 37
                +av+   +G +S++  A++++ + +T+ r +
  AHX11405.1  2 HAVQlflSG-VSMNSVAKLFDLSPPTIMRWV 31
                5666666**.****************98654 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.52
     HTH_psq 30 rsTLwrrkrg 39
                +sTL++ +++
  AHX11405.1 52 KSTLEMIYST 61
                5888887765 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   0.00011      0.15       7      24 ..      16      33 ..      11      39 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.00011
      HTH_17  7 aAelLgvsrstvyrlirr 24
                +A+l+++s+ t+ r++++
  AHX11405.1 16 VAKLFDLSPPTIMRWVNQ 33
                9***************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.38u 0.26s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 672.74
//
Query:       AHX11406.1  [L=112]
Description: DNA-binding protein, YbaB/EbfC family [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.7e-22   77.0   1.0    1.2e-21   76.8   1.0    1.1  1  YbaB_DNA_bd  YbaB/EbfC DNA-binding family


Domain annotation for each model (and alignments):
>> YbaB_DNA_bd  YbaB/EbfC DNA-binding family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.8   1.0   6.4e-26   1.2e-21       4      81 ..      16      92 ..      13     102 .. 0.91

  Alignments for each domain:
  == domain 1  score: 76.8 bits;  conditional E-value: 6.4e-26
                 HHHHHHHHHHHHHHHTTSEEEEEETTTTEEEEEETT--EEEEEE-GGGG.GS-HHHHHHHHHHHHHHHHHHHHHHHHH CS
  YbaB_DNA_bd  4 aqkmqkkmeeaqeelaekevegssggglVkVtvngkgevksikIdpslldpedkemLedlivaAvndAlkkaeeeaee 81
                 ++ mqkkm+++qe+ ++++++g++ggglVkVtv+g+ ++++ikId+sl   e+  m++dli+aA+n+A + a+e  + 
   AHX11406.1 16 LKGMQKKMSDIQEKKNAARYSGEAGGGLVKVTVDGNLDLQEIKIDNSLEG-EEMSMIADLIIAAYNNAKEVANEDDQF 92
                 688*********************************************75.569******************998775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (112 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       642  (0.0358079); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 842.97
//
Query:       AHX11407.1  [L=407]
Description: DNA polymerase III, subunit gamma and tau [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.5e-42  142.9   0.2    1.2e-41  142.2   0.2    1.3  1  DNA_pol3_delta2  DNA polymerase III, delta subunit
    1.2e-14   54.5   0.0    4.4e-08   33.1   0.0    2.3  2  DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau do
    6.2e-11   42.8   0.0    2.3e-10   41.0   0.0    2.0  1  AAA              ATPase family associated with various cellul
    2.5e-06   27.3   0.1    0.00021   21.1   0.0    2.4  2  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    2.2e-05   24.7   0.0    0.00022   21.5   0.0    2.5  1  AAA_22           AAA domain
    6.3e-05   22.8   0.1    0.00013   21.8   0.1    1.5  1  DNA_pol3_delta   DNA polymerase III, delta subunit
    6.9e-05   22.9   0.1    0.00051   20.1   0.0    2.4  2  AAA_5            AAA domain (dynein-related subfamily)
    0.00049   20.4   0.2      0.028   14.8   0.2    2.7  1  AAA_assoc_2      AAA C-terminal domain
     0.0015   18.3   0.1      0.007   16.1   0.0    2.1  2  AAA_30           AAA domain
     0.0018   18.7   0.1     0.0067   16.8   0.0    2.1  1  Rep_fac_C        Replication factor C C-terminal domain
     0.0051   17.2   0.1      0.054   13.8   0.1    2.3  1  AAA_19           AAA domain
     0.0078   16.1   1.3      0.083   12.7   1.0    2.3  2  Bac_DnaA         Bacterial dnaA  protein
  ------ inclusion threshold ------
      0.019   14.7   0.0      0.036   13.8   0.0    1.4  1  AAA_24           AAA domain
      0.027   14.5   0.0      0.071   13.1   0.0    1.6  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.027   13.7   1.1        3.1    6.9   0.1    2.3  2  TIP49            TIP49 P-loop domain
       0.03   14.5   0.5       0.11   12.7   0.5    2.1  1  TIP49_C          TIP49 AAA-lid domain
      0.066   12.9   0.1        1.4    8.5   0.0    2.2  2  Sigma54_activat  Sigma-54 interaction domain
      0.083   12.7   0.3        2.7    7.7   0.0    2.5  2  DEAD             DEAD/DEAH box helicase
      0.097   12.7   0.0        3.4    7.7   0.0    2.5  2  ResIII           Type III restriction enzyme, res subunit


Domain annotation for each model (and alignments):
>> DNA_pol3_delta2  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.2   0.2   1.3e-44   1.2e-41       2     162 ..      39     196 ..      38     197 .. 0.97

  Alignments for each domain:
  == domain 1  score: 142.2 bits;  conditional E-value: 1.3e-44
  DNA_pol3_delta2   2 qeealkilskalksgrlahayLfeGdegigkkelalnlakallceeknetkpcgecksckkieqgkhpDvivieteekersikldqirelieel 95 
                      q+  +k ls +++ +++a a+Lf+G+ g+gk ++a ++a +++c++ ++++pc +c sc  +  ++hpD++ i+  ++    +++++r +i+++
       AHX11407.1  39 QDFLVKTLSASIALEKVASALLFSGSYGTGKTTAARAMALSINCSDLESSQPCMQCTSCSAVLRNSHPDILEIDAASN---TSVEDVRVIIDSV 129
                      677899*******************************************************************99887...89*********** PP

  DNA_pol3_delta2  96 srkpreskkkiiiiedaekmtksAaNalLktlEEPsenaifiLitsdtnklLktirSRcqelkfspl 162
                      s +p+ s++ki+ii+++ ++++sA NalLk+lEEP+e++ f+L t++ +k+  ti SRcq++++s+l
       AHX11407.1 130 SYRPILSRYKIYIIDEVHMLSQSAFNALLKILEEPPEHIKFFLATTELQKIPSTIISRCQHFRLSRL 196
                      ****************************************************************987 PP

>> DNA_pol3_gamma3  DNA polymerase III subunits gamma and tau domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   4.7e-11   4.4e-08       7      62 ..     257     312 ..     251     322 .. 0.88
   2 !   19.2   0.0   9.1e-07   0.00086      90     140 ..     321     371 ..     314     373 .. 0.92

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 4.7e-11
  DNA_pol3_gamma3   7 rdmLGladrarlldlleallegdaaaalaelreqyaaGadpvvvlrdLlellhqlt 62 
                      r+ +Gl+d +++++lle +++gd++aa++++++ y++G+dp  +l+dL+ l+++ +
       AHX11407.1 257 RSKMGLVDITEMTSLLESITSGDCRAAIDTFNTFYQKGYDPLTILEDLIKLINRRI 312
                      5668***********************************************98755 PP

  == domain 2  score: 19.2 bits;  conditional E-value: 9.1e-07
  DNA_pol3_gamma3  90 klsleqLqrlWqlllkgieevknapdpraaaEmvLlRlaaaaslptpeeal 140
                      +++++ L+rl + +l++ ee+k  ++ +  +E+ ++R+ ++a+lp+p e++
       AHX11407.1 321 ETQISFLSRLAKCVLSSMEEIKAFNNNHDVIELSIVRMSYLADLPSPTEIA 371
                      5678999****************************************9986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.0   0.0   2.4e-13   2.3e-10       1     127 [.      59     191 ..      59     196 .. 0.77

  Alignments for each domain:
  == domain 1  score: 41.0 bits;  conditional E-value: 2.4e-13
                 EEEESSTTSSHHHHHHHHHHHHTHE................EEEEETTTCSSS...STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTC CS
         AAA   1 vllyGppGtGKTllakavakelgve................fleisgsellsk...yvgesekkirelfkeakeka...kpsilfiDEidalaksrsgs 77 
                 +l++G  GtGKT++a+a+a +++ +                +l+ s +++l +       s +++r ++++++      + +i +iDE++ l +s    
  AHX11407.1  59 LLFSGSYGTGKTTAARAMALSINCSdlessqpcmqctscsaVLRNSHPDIL-EidaASNTSVEDVRVIIDSVSYRPilsRYKIYIIDEVHMLSQSA--- 153
                 699******************853333344455444455554444444444.13445666999999999998666688556***********9999... PP

                 CCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGGGSTHHHHSTTSSEE CS
         AAA  78 eseeeervvnqLlteldgvkkkeskvivigatnrpdkldpallrgRfdrk 127
                          n+Ll+ l++  +   ++ + +at++ +k+++ ++ +R+++ 
  AHX11407.1 154 --------FNALLKILEEPPE---HIKFFLATTELQKIPSTII-SRCQHF 191
                 ........***********99...599****************.9*9875 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   0.0   2.2e-07   0.00021       2      91 ..      29     112 ..      28     124 .. 0.84
   2 ?    3.7   0.1      0.05        47      82     109 ..     135     162 ..     116     169 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.2e-07
      RuvB_N   2 rPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfid 91 
                 rP+sl+e +gq+ + ++l+  i+     e+    +l++G+ G Gktt a+ +a  ++ +   +s P ++ +   +a+l n  + d+l id
  AHX11407.1  29 RPRSLNEIVGQDFLVKTLSASIA----LEKVASALLFSGSYGTGKTTAARAMALSINCSDLESSQPCMQCT-SCSAVLRNS-HPDILEID 112
                 9*************999987765....45566789************************999****99764.577888774.45788777 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.05
      RuvB_N  82 leekdvlfideihrlsraveevlysame 109
                 l++ ++  ide+h ls+++ + l + +e
  AHX11407.1 135 LSRYKIYIIDEVHMLSQSAFNALLKILE 162
                 6778899**********99888887777 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   2.4e-07   0.00022       5     128 ..      56     173 ..      52     180 .. 0.66

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 2.4e-07
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelkaerlsseellealeqalrarav...ielliiDE 99 
                 a+ l+  G  GtGKTt +r ++ + +      + ++++  ++++s +  +++   ++l++      +  ++s e ++ + + ++ r      ++ iiDE
  AHX11407.1  56 ASALLFSGSYGTGKTTAARAMALSIN----CSDLESSQPCMQCTSCSaVLRNSHPDILEIDA---AS--NTSVEDVRVIIDSVSYRPIlsrYKIYIIDE 145
                 7889999****************984....22245555688888877444444445444444...33..344444444444444444445555****** PP

      AAA_22 100 aqhlrseealeeLrsllnlsrkgvqliLv 128
                 ++ l s+ a++ L ++l+    +++++L+
  AHX11407.1 146 VHML-SQSAFNALLKILEEPPEHIKFFLA 173
                 ****.********8888856666666554 PP

>> DNA_pol3_delta  DNA polymerase III, delta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.1   1.3e-07   0.00013      45     164 ..     125     234 ..      99     242 .. 0.84

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.3e-07
                     HTTTSTTTTSSSSEEEEEEE--.....TT-S-TTHHHHHHHHTTT--SSEEEEEEES.S--HHHHHHHHHTTTEEEEEE----TTTHHHHHHHHH CS
  DNA_pol3_delta  45 vleecetlpffsdkrivvlknpklltkesklnekllkeLeeylsnlpedtlLiliapkklderkklvklLkkkatvveaktlkeeelkkwiqkra 139
                     +++++   p +s  +i +++  ++      l+++  ++L ++l+++pe++ ++l ++ +l+   k+  ++ ++   ++ ++l++e +   i+k+a
      AHX11407.1 125 IIDSVSYRPILSRYKIYIIDEVHM------LSQSAFNALLKILEEPPEHIKFFLATT-ELQ---KIPSTIISRCQHFRLSRLSKEIISARIKKIA 209
                     555556667778888888888855......6778999********************.666...6556666667789****************** PP

                     HHTT-EE-HHHHHHHHHHHTT-HHH CS
  DNA_pol3_delta 140 qelglkiekealelLlelvennlsa 164
                     + ++++i+++a++++ e++e++l+ 
      AHX11407.1 210 ELEKINITEDAIDFISEKSEGSLRD 234
                     *********************9985 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.4e-07   0.00051       2      93 ..      59     165 ..      58     193 .. 0.74
   2 ?   -2.9   0.0       6.7   6.4e+03      16      35 ..     301     320 ..     298     330 .. 0.58

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.4e-07
                 EEEE--SSSSHHHHHHHGGGGB.S--EEE.EE--TT--HHHHH--B--.....................--------......G-SEEEEESGGG--HH CS
       AAA_5   2 vlLvGppGtgKselaerlaaal.nrevey.vqltrdtteedlkgrreik............ngttslvdsplvraar......egeilvlDEveraese 80 
                 +l  G  GtgK++ a+ +a  + ++ +e    + + t+ + ++   +++            ++ ++  ds+            + +i+++DEv++++++
  AHX11407.1  59 LLFSGSYGTGKTTAARAMALSInCSDLESsQPCMQCTSCSAVLRNSHPDileidaasntsvEDVRVIIDSV-----SyrpilsRYKIYIIDEVHMLSQS 152
                 6788999************9996333333134666677777777777766666663333334444444444.....255666899************** PP

                 HHHHHHHHHHSSE CS
       AAA_5  81 vlnsLlslleerr 93 
                 ++n+Ll++lee  
  AHX11407.1 153 AFNALLKILEEPP 165
                 **********965 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 6.7
                 HHHGGGGBS--EEEEE--TT CS
       AAA_5  16 aerlaaalnreveyvqltrd 35 
                  e l +++nr++++ ++++d
  AHX11407.1 301 LEDLIKLINRRIHTSLNSKD 320
                 44555555555555555555 PP

>> AAA_assoc_2  AAA C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.2     3e-05     0.028       3      52 ..     212     257 ..     210     334 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 3e-05
                  X.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXX CS
  AAA_assoc_2   3 kklkleddalealaeladGDaRkaLnlLElaaeaaeakegkieitledle 52 
                  +k+++++da++++ e ++G  R  + +LE  a ++++    + itl+ l+
   AHX11407.1 212 EKINITEDAIDFISEKSEGSLRDGISILEQSALQQDE----EIITLQLLR 257
                  5799*************************99988875....444444444 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   7.4e-06     0.007      21     114 ..      59     163 ..      47     209 .. 0.75
   2 ?   -3.1   0.0       5.6   5.3e+03      97     115 ..     260     278 ..     260     283 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.4e-06
      AAA_30  21 avltGpAGtGKttalkalreaweaag.grviglAptgkaAkvLae....elgieastiakllkrlk.......grarlepgtllivDEagmvdtkqlaa 107
                  +  G  GtGKtta +a++  ++ +  ++   +      ++vL++     l+i+a++  ++ +  +        r  l++ +++i+DE+ m++++ ++a
  AHX11407.1  59 LLFSGSYGTGKTTAARAMALSINCSDlESSQPCMQCTSCSAVLRNshpdILEIDAASNTSVEDV-RviidsvsYRPILSRYKIYIIDEVHMLSQSAFNA 156
                 5678999***********9999988545555666666666677742222333444444444422.2355666544456666****************** PP

      AAA_30 108 llkaaek 114
                 llk++e+
  AHX11407.1 157 LLKILEE 163
                 ***9987 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.6
      AAA_30  97 agmvdtkqlaallkaaeka 115
                 +g+vd++++++ll+++++ 
  AHX11407.1 260 MGLVDITEMTSLLESITSG 278
                 5899999999999999874 PP

>> Rep_fac_C  Replication factor C C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   7.1e-06    0.0067       4      66 ..     266     331 ..     263     339 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 7.1e-06
                 HHHHHHHHHHHHT-HHHHHHHHHHHHHHC---HHHHHHHHHHHGCCS......S-HHHHHHHHHHHH CS
   Rep_fac_C   4 teieeileaclngdfeeaykklrellvekGysaediltqlhrvvkeq....eelpeaqkleilellg 66 
                 te++++le++ +gd ++a ++++ + ++kGy +  il+ l +++ +      + ++++++ +l++l+
  AHX11407.1 266 TEMTSLLESITSGDCRAAIDTFN-TFYQKGYDPLTILEDLIKLINRRihtsLNSKDETQISFLSRLA 331
                 789999999999**********6.******************9998755322345566666666555 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.1   5.7e-05     0.054       8     130 ..      54     166 ..      47     173 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 5.7e-05
      AAA_19   8 lkekvllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlalldfddlltealelleeaeeekklqeee.l 105
                   ++ ll  +  GtGKT+  +++   ++    ++ ++++ ++  +   ++ +  + +++a+ +T       d+  ++ +         + +++ +++ +
  AHX11407.1  54 KVASALLFSGSYGTGKTTAARAMALSINCSDLESSQPCMQCTSCSAVLRNSHPDILEIDAASNTSV----EDVRVII-DS-------VSYRPILSRYkI 140
                 556778888999999999988877777766666778888888777666666666633333333332....3333333.22.......23345557777* PP

      AAA_19 106 livDEfqdvd.elqyrLlkallgekk 130
                  i+DE+ +++    ++Llk l ++ +
  AHX11407.1 141 YIIDEVHMLSqSAFNALLKILEEPPE 166
                 **********8889999998876555 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.8   0.0       0.4   3.8e+02      34      59 ..      56      81 ..      42      89 .. 0.78
   2 !   12.7   1.0   8.8e-05     0.083      89     204 ..     129     234 ..     108     248 .. 0.78

  Alignments for each domain:
  == domain 1  score: 0.8 bits;  conditional E-value: 0.4
                S--EEEE-SSSSSHHHHHHHHHHHHH CS
    Bac_DnaA 34 ynPlfiygevGlGktHLlkaignevl 59
                   l++ g++G Gkt   +a++  + 
  AHX11407.1 56 ASALLFSGSYGTGKTTAARAMALSIN 81
                45688999*******99999887765 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 8.8e-05
                 HHHHHHHTT-SEEEEE-GGGGTT-HHHHHHHHHHHHHHHTTT-EEEEEESS-TTT-SS--HHHHHHHHSSEEEE-----HHHHHHHHHHHHHHTT---- CS
    Bac_DnaA  89 eefkeklrkvDvLliDDiqflagkektqeelfhtfnalleegkqvvlssDrsPkeleeledrlrsrfeaGlvvdieppdletrlailkkkieaeklevp 187
                  +++  l +  + +iD+++ l++       +  ++  l e  +++ +    + +el+++ + + sr +      +++  +e+  a +kk +e ek++++
  AHX11407.1 129 VSYRPILSRYKIYIIDEVHMLSQSA-----FNALLKILEEPPEHIKFFL--ATTELQKIPSTIISRCQH---FRLSRLSKEIISARIKKIAELEKINIT 217
                 5666677777888999999887544.....5555666666555554443..357899999999999985...78899999999**************** PP

                 TTHHHHHHHH--S-HHH CS
    Bac_DnaA 188 eevlefiaervtdnvRe 204
                 e+++ fi+e+ + ++R+
  AHX11407.1 218 EDAIDFISEKSEGSLRD 234
                 ***********999997 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.9e-05     0.036       7      85 ..      61     157 ..      56     173 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.9e-05
      AAA_24   7 iyGpsgiGKTtlakelgpkplfidtekGlksldadkfpdie................swedfldevvel..aaeladyktlviDtideleelclaev 85 
                   G+ g+GKTt a+ +  ++ + d+e +   ++ +    +                 s+ed++  ++++  +  l++yk+++iD +  l + +++ +
  AHX11407.1  61 FSGSYGTGKTTAARAMALSINCSDLESSQPCMQCTSCSAVLrnshpdileidaasntSVEDVRVIIDSVsyRPILSRYKIYIIDEVHMLSQSAFNAL 157
                 56999***********88888889999888888888776668988889989998888888888888888999**************99998887665 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   7.5e-05     0.071      17      50 ..      54      87 ..      38      98 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 7.5e-05
                CHTEEEEEEESTTSSHHHHHHHHHHHTT------ CS
        TsaE 17 algdvilLeGdLGaGKTtlvrglakalgveevkS 50
                ++++++l++G  G+GKTt +r++a ++++++ +S
  AHX11407.1 54 KVASALLFSGSYGTGKTTAARAMALSINCSDLES 87
                23567******************99988875554 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.9   0.1    0.0033       3.1      45      75 ..      52      81 ..      19      97 .. 0.76
   2 ?    5.7   0.1    0.0076       7.2     282     305 ..     141     164 ..      84     201 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.0033
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49 45 ekklaGravLlaGpsgtGktalaiaiskelg 75
                 +k+a  a+L++G  gtGkt  a a++ +++
  AHX11407.1 52 LEKVA-SALLFSGSYGTGKTTAARAMALSIN 81
                45666.79************88877776665 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0076
                 XXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49 282 lfiDevhmlDiecfsylnralese 305
                   iDevhml   +f  l + le++
  AHX11407.1 141 YIIDEVHMLSQSAFNALLKILEEP 164
                 569*******************87 PP

>> TIP49_C  TIP49 AAA-lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.5   0.00011      0.11       6      42 ..     209     244 ..     200     258 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00011
     TIP49_C   6 akeEgvkldeeAldlLakigtetSLRYaiqLltpasi 42 
                 a+ E+++++e+A+d++++  +e SLR  i+ l+ + +
  AHX11407.1 209 AELEKINITEDAIDFISEK-SEGSLRDGISILEQSAL 244
                 678************9986.5789**99999987765 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   0.0    0.0015       1.4      17      44 ..      51      78 ..      36     105 .. 0.67
   2 ?    2.0   0.0      0.16   1.5e+02      98     119 ..     142     163 ..     137     178 .. 0.92

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0015
                     HHCTSSS-EEEECSTTSSHHHHHHHHHH CS
  Sigma54_activat 17 kvaktdlsvlitGesGtGKellaraihe 44
                     ++ k  + +l  G  GtGK++ ara+  
       AHX11407.1 51 ALEKVASALLFSGSYGTGKTTAARAMAL 78
                     44556688999*************9965 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.16
                      EEETGGGS-HHHHHHHHHHHHH CS
  Sigma54_activat  98 fLDeigelplelQekLlrvlqe 119
                       +De++ l+ ++ + Ll++l+e
       AHX11407.1 142 IIDEVHMLSQSAFNALLKILEE 163
                      68******************97 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.15   1.4e+02      17      38 ..      59      80 ..      46      94 .. 0.78
   2 ?    7.7   0.0    0.0029       2.7     118     143 ..     134     159 ..     103     180 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.15
                EEEEESTTSSHHHHHHHHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 17 vlvaaeTGsGKTlaflipvlqi 38
                +l ++  G+GKT+a+   +l+i
  AHX11407.1 59 LLFSGSYGTGKTTAARAMALSI 80
                6778889*******99888866 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0029
                 HCTTEEEEEEETHHHHHHTTTHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 118 nlsqvrflVlDEadrlldqgfsdfin 143
                  ls+ ++ ++DE+++l+++ f   ++
  AHX11407.1 134 ILSRYKIYIIDEVHMLSQSAFNALLK 159
                 3999*************998876554 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.2   0.0      0.17   1.6e+02      22      45 ..      54      77 ..      28      87 .. 0.73
   2 ?    7.7   0.0    0.0036       3.4     122     158 ..     127     162 ..     102     176 .. 0.73

  Alignments for each domain:
  == domain 1  score: 2.2 bits;  conditional E-value: 0.17
                .TTSEEEEEESTTSTHHHHHHHHH CS
      ResIII 22 krdkrglikmaTGtGKTlvaakli 45
                k    +l+    GtGKT  a +++
  AHX11407.1 54 KVASALLFSGSYGTGKTTAARAMA 77
                445578899999*****8775554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0036
                 .....HHHTTT-SEEEEETGGGTTS.TTTHHHHHT-- CS
      ResIII 122 eeeseellrdrfdviiiDEaHrlgakkswreilekfk 158
                 ++ s +   +r++++iiDE+H l++ ++++++l+ ++
  AHX11407.1 127 DSVSYRPILSRYKIYIIDEVHMLSQ-SAFNALLKILE 162
                 5666777788999************.88888777664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        83  (0.00462937); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 2905.64
//
Query:       AHX11408.1  [L=219]
Description: folate metabolism, CADD family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      1e-29  103.5   0.0    1.3e-29  103.3   0.0    1.1  1  Haem_oxygenas_2  Iron-containing redox enzyme
    8.6e-27   94.3   0.6    1.1e-26   94.0   0.6    1.0  1  TENA_THI-4       TENA/THI-4/PQQC family
  ------ inclusion threshold ------
      0.012   15.5   0.1      0.025   14.4   0.1    1.6  1  DUF4041          Domain of unknown function (DUF4041)


Domain annotation for each model (and alignments):
>> Haem_oxygenas_2  Iron-containing redox enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  103.3   0.0   2.1e-33   1.3e-29       1     170 [.      31     196 ..      31     203 .. 0.91

  Alignments for each domain:
  == domain 1  score: 103.3 bits;  conditional E-value: 2.1e-33
  Haem_oxygenas_2   1 reflrqrapyklvfgdwlalvhsrltdrevkrallenls.EElGdgdlernHvelyrrllkalGldeeplealpelpetlalinlfeavalsrr 93 
                      +e++ q++ +++ ++++l+ +hs+++d +v++ ll nl  EE G    e+nH++l+ ++ +alGl++e +++++ l +t +l ++f ++  s  
       AHX11408.1  31 QEYACQYFNHVNETPRYLSTIHSKCRDIKVRQVLLDNLVdEERG----EENHPKLWLDFCAALGLTQEKVRNAKLLGATKQLSDTFFKLSSSSV 120
                      689*****************************************....777**********************************987777777 PP

  Haem_oxygenas_2  94 llgallGallalEllvsletlklaeelre.lgldeea.peyfdlHvtiDnaHaamaleaviellateepeeqedvlega 170
                        g  +Gal+a+E + + ++++ +e l++ +g+++++ +++f++H+++D+ H+++   ++++++   e e +++++ ++
       AHX11408.1 121 SEG--IGALYAYERQIPDIARVKIESLKKfYGIEKDEeLKFFSVHIEADEWHSEECE-NLLKRMNLSEIEVAKEAALKL 196
                      777..*****************************9888******************6.******999955555555444 PP

>> TENA_THI-4  TENA/THI-4/PQQC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.0   0.6   1.8e-30   1.1e-26      11     207 ..      11     207 ..       4     209 .. 0.86

  Alignments for each domain:
  == domain 1  score: 94.0 bits;  conditional E-value: 1.8e-30
                 HHCSHHHHHHHTT-S-HHHHHHHHHHHHHHHHHHHHHHHHHHHC-SSHHHHHHHHHHHHHHHHCH...HHHHHHHHHHTT-HHHHHCTTT--HHHHHHH CS
  TENA_THI-4  11 yinHpFvkalakGtlpreqfqayviqdylylknfvrvlaiilskssdlevrrelesrivdhdgee...ielhlrlaealGlsreelsktkpspatkayv 106
                 + +H F+k++ +G+l+re +q y+ q+++++++ +r+l++i+sk+ d++vr+ l +++vd +++e    +l+l ++ alGl++e++ + k + atk+ +
  AHX11408.1  11 ILKHDFYKSWESGNLSREDLQEYACQYFNHVNETPRYLSTIHSKCRDIKVRQVLLDNLVDEERGEenhPKLWLDFCAALGLTQEKVRNAKLLGATKQLS 109
                 567************************************************************99999******************************* PP

                 HHHHHHHCHS-HHHHHHHHHHHHHHHHHHHHHHCCHHHS-TSCHHHHHHHHHCSHHHHHHHH...HHHHHHHHHHHTSHHHHHHHHHHHHHHHHHHHHH CS
  TENA_THI-4 107 rylldlarrgslaeavaallpclfvyqeiaerlkeklralegpeyyewvkeyaseefraave...eakrllerllakvsdeqleelqeiflkalefets 202
                 +++ +l++  s++e + al++++ ++  ia+   e l+      +y   k+++ ++f  ++e   +  +  e ll+ ++ +++e ++e +lk+  +  +
  AHX11408.1 110 DTFFKLSS-SSVSEGIGALYAYERQIPDIARVKIESLK-----KFYGIEKDEELKFFSVHIEadeWHSEECENLLKRMNLSEIEVAKEAALKLASALWK 202
                 ******97.59*******************54444445.....69999999999999988871114556666666666666677777777777777777 PP

                 HHHHH CS
  TENA_THI-4 203 fltma 207
                 fl+ +
  AHX11408.1 203 FLDGM 207
                 77665 PP

>> DUF4041  Domain of unknown function (DUF4041)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.4   0.1   4.2e-06     0.025       9      54 ..     172     218 ..     171     219 .] 0.97

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 4.2e-06
     DUF4041   9 gEcdaaiskVkynnietlekRIeksfeainklgktm.nirItpeYle 54 
                 +Ec++++++++ + ie +++   k+++a+ k+   m ++r+t++Yl+
  AHX11408.1 172 EECENLLKRMNLSEIEVAKEAALKLASALWKFLDGMeQVRLTKNYLN 218
                 6********************************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (219 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       522  (0.0291148); expected 358.6 (0.02)
Passed bias filter:                      354  (0.0197445); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1662.07
//
Query:       AHX11409.1  [L=37]
Description: hypothetical protein NHE_0465 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      170  (0.00948185); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 305.25
//
Query:       AHX11410.1  [L=621]
Description: chaperone protein htpG [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
   1.5e-103  347.5   9.7   7.8e-102  341.8   7.2    2.1  2  HSP90        Hsp90 protein
    3.5e-13   49.5   0.1    8.4e-13   48.3   0.1    1.6  1  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like
    2.2e-11   44.3   0.1    8.5e-11   42.4   0.2    2.0  2  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
     0.0063   16.8   2.2     0.0086   16.4   0.1    2.4  2  Styelin      Styelin


Domain annotation for each model (and alignments):
>> HSP90  Hsp90 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6   0.1   0.00017      0.74       1      32 [.     185     216 ..     185     218 .. 0.92
   2 !  341.8   7.2  1.7e-105  7.8e-102      76     485 ..     214     618 ..     211     621 .] 0.91

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00017
                 GGGSHHHHHHHHHHCCTTSSS-EEEEEEEEXX CS
       HSP90   1 eyleekklkelvkkySeFinfpiyllkekeee 32 
                 e+l++ +++++++  S+ i fpiyll ek e+
  AHX11410.1 185 EFLDKFRIEHVITTNSNHIGFPIYLLDEKGEK 216
                 79*************************99776 PP

  == domain 2  score: 341.8 bits;  conditional E-value: 1.7e-105
                 EEEEEESXXSXGGGSXGGGSXHHHHHHHHHHTTTTTSXXSEEEEEEEXSSSXEEEEEEEXSSXXTTTTTTTTTSXXTTEEEEETTEEEESXXTTSSXGG CS
       HSP90  76 kewellNkqkpiWlrkpkevteeeYkeFYkslskdsedplavkhfsaegevefkaiLfvPkrapsdlfekykkkkknnikLYvrrVfitdefedllPky 174
                  e+e++N   +iW++++ ++teee+++F++ +++    p +v+h + eg +e+  +L++P+ +p+dl++    +++ ++kLY+++Vfit+e   l+P+y
  AHX11410.1 214 GEKEQINAATAIWTKNKGDITEEEHQNFFREVAHVGGRPWMVIHNKNEGSIEYINLLYIPSIKPFDLYNP---DRRASVKLYIKKVFITEENVHLIPQY 309
                 5789*****************************************************************6...77999********************* PP

                 GTTXEEEEEESSSXSSSTHHHHHTCHHHHHHHHHHHHHHHHHHHTSXH.HH..H.HTHHHHHHHHHHHHHHHXGG..GHHHHHTTXEEEETTEEEEEEE CS
       HSP90 175 LsFvkGvvdsddLPLNvsREtlqqnkilkvikkklvrKvlemlkklae.ekeey.kkfykefsknlklGiiedsa..nrkklakLlrfksskseeelts 269
                 L+F+kG+vd+ dLPLN+sREtlq n++l  ikk l  +vl+ l+k ae + e+y ++f+++f+  lk G++e     +r++l  L rf+s ++  +l+s
  AHX11410.1 310 LRFLKGIVDCSDLPLNISRETLQYNNTLMKIKKSLTNRVLNDLRKKAEsDPEKYiSEFWSNFGAVLKEGLCEAMPtdERERLFGLCRFYSLNQ-GKLIS 407
                 ****************************************9887766515677889****************965448***********9985.56*** PP

                 HHHHHHHSXTTXXEEEEEEXSSHHHHHTSGGGHHHHHTTXXEEEEXSTTHHHHHHTXSEETTEEEEETTBSTXXX....X.XXHHHHHHHHHHHHHHHH CS
       HSP90 270 LedYvermkekqksiYyiageskeevekspflerlkkkgyevlylvdpiDeyvvqqlkeyegkklvnvakeglel....e.eeeeekkkkeelkkkfee 363
                 L++Y++ mk +qk+iY + ++s+e++++sp le ++++g++vl++vdp+D++ ++   ey++++++++++ +++l    e e+++e++ +++ +k+++ 
  AHX11410.1 408 LDEYIQTMKPEQKEIYCLGSTSIESAKNSPQLEGFLSRGIDVLLFVDPVDDFWINVSDEYKSHNIKSITRSSINLddfqElEKSSEQEVHQHDDKSIDL 506
                 ***************************************************************************432212333444444557788999 PP

                 HHHHHHHTTTTTESEEEEXSSXSSXSEEEEBXTTSXXHHHHHHHHHHHHHHHSSTSSSSSXEEEEEXTTSHHHHHHHHHHHHTTTXHHHHHHHHHHHHH CS
       HSP90 364 ltkllkevlkdkvekvkvserlvdsPcvlvtseygwsanmerimkaqalrdkskssymsskktleinprhpiikeLkkkveedkedeeakdlaellyet 462
                 l+  ++e+lkd+ve+v+vs++l+dsP++l   +  +  +mer m  q           ++kk+lein +hp+i+++ +++++     e +++++lly++
  AHX11410.1 507 LIAKMQEILKDEVESVRVSKKLKDSPVCLAVPDGAMDIRMERFMIEQKQ------LHSKTKKVLEINITHPVISRIIERLDD----PESEEFIQLLYDQ 595
                 9*******************************************98754......344569****************99865....577899******* PP

                 HHHHTTXXXSXHHHHHHHHHHHH CS
       HSP90 463 allesGfsledpasfakrierll 485
                 a++    ++++p ++ak +++ll
  AHX11410.1 596 ACILQAEEVKNPMRMAKLMNKLL 618
                 ***9999********99999887 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.3   0.1   1.9e-16   8.4e-13       7     100 ..      35     149 ..      28     167 .. 0.82

  Alignments for each domain:
  == domain 1  score: 48.3 bits;  conditional E-value: 1.9e-16
  HATPase_c_3   7 laelvdNsldAdaen..................vkievnknrgktgeivieDdGkGmseeelknal.rlatsskeak......rkstslGkkGiGlkl 79 
                  l el+ N+ dA  +                   + i+++k++   + + i D+G Gms+eel++ l ++a+s +e+       +k + +G++G+G + 
   AHX11410.1  35 LRELISNASDALNKLreesnldqelleddtelsIRISFDKEK---KLLEISDNGIGMSKEELIENLgTVARSGTEKFleslkdKKVDLIGQFGVG-FY 128
                  779*******987778899************88888888875...79****************9774788888874443332224555*******.** PP

  HATPase_c_3  80 Aslslgkkltvitkkegesst 100
                  +++++++k++v+t+k g+++ 
   AHX11410.1 129 SVFMVAEKVEVETRKAGTETG 149
                  ****************99984 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.4   0.2   1.9e-14   8.5e-11       3     109 ..      32     180 ..      30     183 .. 0.69
   2 ?   -2.5   0.0       1.6   7.1e+03      49      63 ..     383     399 ..     381     408 .. 0.82

  Alignments for each domain:
  == domain 1  score: 42.4 bits;  conditional E-value: 1.9e-14
                 HHHHHHHHHHHHHHHHHH..........HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.......GTCS.TTCH..HCSTCHTSTSSSHHHHHH CS
   HATPase_c   3 ekrLrqiisnlvdNavkf..........atkageieveikaseddlvisveDnGiGipkedlk.......klfe.kfsq..ddstkrggggtGlGlsiv 81 
                   +Lr++isn++d++ k             +++e++++i+ +++++ ++++DnGiG++ke+l        ++++ kf +  +d++ +  g++G+G++ v
  AHX11410.1  32 DVFLRELISNASDALNKLreesnldqelLEDDTELSIRISFDKEKKLLEISDNGIGMSKEELIenlgtvaRSGTeKFLEslKDKKVDLIGQFGVGFYSV 130
                 679*************9977766664332255577888888788**************************99999****97555555568888888888 PP

                 HHHHHH.......TT...TEEEE............EEET..TTEEEEEEEEE CS
   HATPase_c  82 kklvel.......mg...Geiwv............esep..grGttftftlp 109
                   ++e+        g   G++w             +      rG +++++l+
  AHX11410.1 131 FMVAEKvevetrkAGtetGHLWTsrgkdnfyidevK--GsvPRGARIRIHLK 180
                 666664122222211222455555555444533332..03356888887776 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.6
                 STTHHHTGTCS..TTCH CS
   HATPase_c  49 ipkedlkklfe..kfsq 63 
                 +p +++++lf+  +f++
  AHX11410.1 383 MPTDERERLFGlcRFYS 399
                 899*******9999998 PP

>> Styelin  Styelin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   1.9e-06    0.0086      18      48 ..     216     246 ..     212     249 .. 0.91
   2 ?   -4.2   0.3         4   1.8e+04      39      49 ..     484     494 ..     483     497 .. 0.55

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.9e-06
     Styelin  18 ktYikaalsiakhlLGDmtDeefqefmkeve 48 
                 k  i+aa  i ++  GD+t+ee q+f +ev 
  AHX11410.1 216 KEQINAATAIWTKNKGDITEEEHQNFFREVA 246
                 7889************************995 PP

  == domain 2  score: -4.2 bits;  conditional E-value: 4
     Styelin  39 efqefmkeveq 49 
                 +fqe  k  eq
  AHX11410.1 484 DFQELEKSSEQ 494
                 46665555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (621 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       891  (0.049696); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.64u 0.25s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 4372.57
//
Query:       AHX11411.1  [L=37]
Description: hypothetical protein NHE_0467 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       181  (0.0100954); expected 358.6 (0.02)
Passed bias filter:                      138  (0.00769703); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 302.70
//
Query:       AHX11412.1  [L=611]
Description: hypothetical protein NHE_0470 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     0.0014   18.8   9.3       0.22   11.8   2.7    2.4  2  Bactofilin    Polymer-forming cytoskeletal
  ------ inclusion threshold ------
      0.013   15.3  13.7         27    4.7   0.0    6.0  6  ScsC_N        Copper resistance protein ScsC N-terminal domai
      0.056   13.6   1.3       0.19   11.9   0.0    2.3  2  TssO          Type VI secretion system, TssO
        1.9    8.5   3.7    3.8e+02    1.2   0.0    4.6  5  BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette 


Domain annotation for each model (and alignments):
>> Bactofilin  Polymer-forming cytoskeletal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   2.7   4.9e-05      0.22       3      92 ..     101     194 ..      99     200 .. 0.77
   2 !   10.7   1.4   0.00011      0.51      24      89 ..     194     261 ..     188     266 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 4.9e-05
  Bactofilin   3 igegtkikGe.leve.gdlridGkveGdieakgklvvgeggkvegnika.ee.vvvaGtvkGnveaeekvelkktakveGdikaksleieegav 92 
                 i++++  kGe l+ + +++  + +v+ +++ + +++ + +g v+g+i+   e ++ a +v+++v+ + +v+ ++++ v+G+i+++  +i e  +
  AHX11412.1 101 IAQEVLAKGEkLQENpEAITEATEVQDEVKLNPEVITEASGIVDGEISTgPEaITEATEVQDEVKLNPEVITEASGIVDGEISTGPEAITEATE 194
                 666666777424444244444558999999999***************98551555567************************98877776655 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 0.00011
  Bactofilin  24 kveGdieakgklvvgeggkvegnika.ee.vvvaGtvkGnveaeekvelkktakveGdikaksleiee 89 
                 +v+ +++ + +++ + +g v+g+i+   e ++ a +v+++v+ + +v+ ++++ v+G+i+++  +i e
  AHX11412.1 194 EVQDEVKLNPEVITEASGIVDGEISTgPEaITEATEVQDEVKLNPEVITEASGIVDGEISTGPEAITE 261
                 5677888888999************98551555567************************98666655 PP

>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.3      0.16   7.2e+02      15      24 ..     114     123 ..     112     125 .. 0.84
   2 ?    4.7   0.0    0.0059        27      16      24 ..     132     140 ..     131     143 .. 0.93
   3 ?    4.7   0.0    0.0059        27      16      24 ..     167     175 ..     166     178 .. 0.93
   4 ?    4.7   0.0    0.0059        27      16      24 ..     202     210 ..     201     213 .. 0.93
   5 ?    4.7   0.0    0.0059        27      16      24 ..     237     245 ..     236     248 .. 0.93
   6 ?   -2.9   0.1       1.4   6.4e+03      14      20 ..     511     517 ..     511     517 .. 0.86

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.16
      ScsC_N  15 eNPEiLvEAl 24 
                 eNPE + EA 
  AHX11412.1 114 ENPEAITEAT 123
                 9******996 PP

  == domain 2  score: 4.7 bits;  conditional E-value: 0.0059
      ScsC_N  16 NPEiLvEAl 24 
                 NPE++ EA+
  AHX11412.1 132 NPEVITEAS 140
                 9*******7 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.0059
      ScsC_N  16 NPEiLvEAl 24 
                 NPE++ EA+
  AHX11412.1 167 NPEVITEAS 175
                 9*******7 PP

  == domain 4  score: 4.7 bits;  conditional E-value: 0.0059
      ScsC_N  16 NPEiLvEAl 24 
                 NPE++ EA+
  AHX11412.1 202 NPEVITEAS 210
                 9*******7 PP

  == domain 5  score: 4.7 bits;  conditional E-value: 0.0059
      ScsC_N  16 NPEiLvEAl 24 
                 NPE++ EA+
  AHX11412.1 237 NPEVITEAS 245
                 9*******7 PP

  == domain 6  score: -2.9 bits;  conditional E-value: 1.4
      ScsC_N  14 leNPEiL 20 
                 ++ PEi+
  AHX11412.1 511 IADPEII 517
                 689***8 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   4.2e-05      0.19       8      61 ..      67     120 ..      65     134 .. 0.78
   2 ?   -1.6   0.0      0.59   2.7e+03      57      80 ..     336     359 ..     326     364 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 4.2e-05
        TssO   8 sgflyflllFlvtvlllflivffffkssplqekeillkelerkkkfeekqkelk 61 
                 ++++ ++++F+vt l +++ +   +k++ + +++i  + l + +k++e  + ++
  AHX11412.1  67 MEIINLIAMFVVTALSISIHLSTLYKDYSERKNQIAQEVLAKGEKLQENPEAIT 120
                 78999******************************9555555566655544443 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.59
        TssO  57 qkelkkkvdsiykkIdsLkpevna 80 
                 + e+k+ + +i ++I+ +++++n 
  AHX11412.1 336 KTEIKNFLAEISANISEIDFGNNS 359
                 556777778888888888888886 PP

>> BCA_ABC_TP_C  Branched-chain amino acid ATP-binding cassette transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.084   3.8e+02       9      18 ..     127     136 ..     127     137 .. 0.91
   2 ?    1.2   0.0     0.084   3.8e+02       9      18 ..     162     171 ..     162     172 .. 0.91
   3 ?    1.2   0.0     0.084   3.8e+02       9      18 ..     197     206 ..     197     207 .. 0.91
   4 ?    1.2   0.0     0.084   3.8e+02       9      18 ..     232     241 ..     232     242 .. 0.91
   5 ?   -2.9   0.0       1.5   6.9e+03      12      17 ..     368     373 ..     366     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.084
  BCA_ABC_TP_C   9 aEvrndPrVi 18 
                   +Ev+ +P+Vi
    AHX11412.1 127 DEVKLNPEVI 136
                   79999****9 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.084
  BCA_ABC_TP_C   9 aEvrndPrVi 18 
                   +Ev+ +P+Vi
    AHX11412.1 162 DEVKLNPEVI 171
                   79999****9 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.084
  BCA_ABC_TP_C   9 aEvrndPrVi 18 
                   +Ev+ +P+Vi
    AHX11412.1 197 DEVKLNPEVI 206
                   79999****9 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.084
  BCA_ABC_TP_C   9 aEvrndPrVi 18 
                   +Ev+ +P+Vi
    AHX11412.1 232 DEVKLNPEVI 241
                   79999****9 PP

  == domain 5  score: -2.9 bits;  conditional E-value: 1.5
  BCA_ABC_TP_C  12 rndPrV 17 
                    ++P+V
    AHX11412.1 368 AKNPAV 373
                   58***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       908  (0.0506442); expected 358.6 (0.02)
Passed bias filter:                      528  (0.0294495); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.62u 0.28s 00:00:00.90 Elapsed: 00:00:00.43
# Mc/sec: 4312.25
//
Query:       AHX11413.1  [L=452]
Description: apolipoprotein N-acyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.7e-25   88.1   0.0    7.9e-25   87.7   0.0    1.2  1  CN_hydrolase  Carbon-nitrogen hydrolase


Domain annotation for each model (and alignments):
>> CN_hydrolase  Carbon-nitrogen hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.7   0.0   4.4e-29   7.9e-25       2     258 ..     201     441 ..     200     444 .. 0.84

  Alignments for each domain:
  == domain 1  score: 87.7 bits;  conditional E-value: 4.4e-29
                   EEEEEBB-.....STTHHHHH.HHHHHHHHHHHHHT.TESEEEEETTTTTBSSSHHHHHHHHBHSSSHHHHHHHHHHHHHTEEEEEEEEEEECCTTE CS
  CN_hydrolase   2 vAvvQlpq.....kaadlean.lqklleliaeAark.gadLivlPElfitgykeeahfleaAeaglgetlallaalarkngiavvigliereltngk 91 
                   v +vQ+++     +++d + + lqk +e++++ ++   +d+ ++PE ++++     h +++++          + ++++ g +v++g  +   +n++
    AHX11413.1 201 VRIVQANIphqqrWSTDYSRTvLQKYVEMSKA-KDFqSIDYFIWPESSVPFL---LHTRKSDI---------TKYISANLGKIVIAGGTRI--ENNN 282
                   78999999999887777766526888888888.5557*************99...99997554.........5666677777888888888..8*** PP

                   EEEEEEEEEEETTSEEEEEEE-SS--E.ECTTSCECCGHHTSCS...........-SS.S-EEEETTEEEEEEEGGGGGSHHHHHHHHHTT-SEEEE CS
  CN_hydrolase  92 lqayntavlldldgklvgkyrKlhLfp.geprpptaverelfep...........gdg.ipvfdtpvgkiGaaiCyeigfpellralalkgaeilvn 175
                   +  yn+++l+ +dg++   y+K++L+p ge+ p + ++                 g++  +   ++++++   iCye +f  +l+ + + + +i + 
    AHX11413.1 283 I--YNSIFLI-KDGQVEDYYDKIKLVPlGEYVPLGNILP---INkivngasnfthGKKrRK--ILEGINAAPTICYESIFTSSLHGNCTADWNINLV 371
                   *..**98888.888889*******************944...4445566666665332211..3445599***************999999999999 PP

                   BH.GCCCTCHHHHHHHHHHHHHHHHHHTSEEEEEEBEEEHCETTEEEE--EEEE-TTS-EEEECCSSSTEEEEEEEEHHHHHH CS
  CN_hydrolase 176 lserapvpksmgppqwellgraralengcfviaanqvggyeqlilwpvghSaiidpdGrilaglgeeeegvliaeidladvra 258
                     ++++++ s++ +q+++++r+ra+e g ++i+++ +g+           Sa+idp Grila+ +  + g+l   i+++  r+
    AHX11413.1 372 --NDSWFGNSTALYQHLQMARMRAIEYGLPIIRSTTTGI-----------SAVIDPYGRILARIPYSSQGILDIPIPRKHSRR 441
                   ..9************************************...........**********************99999887665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (452 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.23s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 3514.86
//
Query:       AHX11414.1  [L=815]
Description: asmA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.4e-12   44.9  17.3    1.1e-10   41.0   3.6    3.8  4  AsmA      AsmA family
    1.2e-08   34.8   8.4    4.6e-07   29.6   3.3    3.1  3  AsmA_2    AsmA-like C-terminal region


Domain annotation for each model (and alignments):
>> AsmA  AsmA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    3.7   1.4    0.0024        21      12     118 ..       7     110 ..       5     269 .. 0.80
   2 !    7.6   0.1   0.00016       1.4     433     498 ..     294     358 ..     289     366 .. 0.93
   3 ?   -3.3   0.0      0.31   2.8e+03     198     228 ..     504     534 ..     467     561 .. 0.64
   4 !   41.0   3.6   1.2e-14   1.1e-10     495     602 ..     625     741 ..     617     745 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.0024
        AsmA  12 livLlLLlv.lliaiialfdpnnykptlqqkvkeatnrplaiegdigrsllPwptlsLsdiklaspegakkpelvsveqveisLsplpLlrkqieiasi 109
                 ++++lLL++ l +    +++ n yk+     ++   + + +++g i   +l    l++  +++ +   +      s+ ++++  s +  l ++ ei++i
  AHX11414.1   7 FLIFLLLVIaLSFFGGIILKINSYKEHYSSEISRLIGGNVEVNGTISINFLDL-ALRATSVNIVQYSSDS---RYSIGKLDLHFSKKSILFGRPEISKI 101
                 44555555558999999****************************99888854.7777777776666333...46777777777777777777777777 PP

        AsmA 110 kldgpslsl 118
                  +   ++ l
  AHX11414.1 102 TMRDGEIIL 110
                 766665555 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.00016
        AsmA 433 llgvwqeieadlsanidkvtyssllisdlkaklrlegGvlqLsrlkaglygGeleakgqldlskks 498
                 +l+++q  e dl + i+ +++++  i+d+ ++l +   +l + +l a ++   +++kg+++ +k++
  AHX11414.1 294 NLQKLQTKETDLLLDIETLKLKDTEIKDVHLSLSSSTELLTIGDLSARIADSTINSKGKIE-KKDP 358
                 5678888899***************************************************.7777 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 0.31
        AsmA 198 lawrkikisGkleqdnqsfgslvnvkvnkge 228
                 + + ++++ Gkl++d+  ++  + v +n+++
  AHX11414.1 504 VDSKNLTFVGKLKFDKIARILEIDVDGNTLK 534
                 5555666666666666666555555555544 PP

  == domain 4  score: 41.0 bits;  conditional E-value: 1.2e-14
        AsmA 495 skksatvrlklnaknlplkrLladlskikkldGlldididltgsGnsvatlinnLnGqlklnlnnGalsGlnlnqilvagiaa.........ltssfgt 584
                 + ++  v +++na+++ lk Ll++ ++ + ++G ++i++d+++ Gn+v+++i n +G+l+ln++   ++G n++ +  a+             +  f t
  AHX11414.1 625 NRQPNSVVASINASGIDLKTLLKENFDVNYISGKANIQADVSSKGNTVKQMISNIEGKLALNSAKINIQGGNIDMLSSAIPKVkspkdldeiTRIKFFT 723
                 689999*******************************************************************99888776665556655544444555 PP

        AsmA 585 kstpfknlavslnlkkGv 602
                 ++t +   + s+n+++G+
  AHX11414.1 724 GDTTLLSVTGSSNISNGI 741
                 555555666666666665 PP

>> AsmA_2  AsmA-like C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.1   0.00058       5.2       2      38 ..     320     356 ..     273     397 .. 0.64
   2 !   29.6   3.3   5.1e-11   4.6e-07       5     149 ..     592     744 ..     589     756 .. 0.86
   3 ?   -3.0   0.0      0.46   4.1e+03     213     229 .]     781     797 ..     778     797 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.00058
      AsmA_2   2 gnvsgklrlkdeglrldnlrlrspggklsgsgswstk 38 
                 ++v+++l++  e l++ +l++r+ + +++ +g +  k
  AHX11414.1 320 KDVHLSLSSSTELLTIGDLSARIADSTINSKGKIEKK 356
                 4566666666666666666666666666666666666 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 5.1e-11
      AsmA_2   5 sgklrlkdeglrldnlrlrspggklsgsgswstkggaartnldlkldgvdlgallkrlglaevlgGkgslelnlswqgaplspdlssLsGdlsleledg 103
                 ++  +++++ l++  l+l+  g  l++  + + + + +++  + + +g dl++llk+  +  ++ Gk+++++++s +g++   + s++ G+l l+ +++
  AHX11414.1 592 KLASEINNNILKISGLSLKREGFLLELVSNFTFNRQPNSVVASINASGIDLKTLLKENFDVNYISGKANIQADVSSKGNTVKQMISNIEGKLALNSAKI 690
                 56667788888888899998888888877777766668999*****************************************99*************** PP

      AsmA_2 104 qilgvs...........ll.rdlgllkltldfrdlfgeglafddikgtftienGvvtt 149
                  i+g +           ++  dl+     +   + f +++ + +++g+ +i nG++ t
  AHX11414.1 691 NIQGGNidmlssaipkvKSpKDLD----EITRIKFFTGDTTLLSVTGSSNISNGILGT 744
                 ****88888666665543344444....678899********************9866 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 0.46
      AsmA_2 213 kiaaleyrvtGswdsPk 229
                 ++++++++++G++++Pk
  AHX11414.1 781 EAIPVDITIEGNIWNPK 797
                 67899**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (815 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       781  (0.0435607); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.63u 0.25s 00:00:00.88 Elapsed: 00:00:00.37
# Mc/sec: 6546.23
//
Query:       AHX11415.1  [L=391]
Description: riboflavin biosynthesis protein RibD [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-33  115.9   0.0    2.7e-33  115.5   0.0    1.1  1  RibD_C           RibD C-terminal domain
    4.5e-19   68.2   0.0    8.6e-19   67.3   0.0    1.5  1  dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-
    1.3e-10   41.2   0.8    4.3e-10   39.5   0.1    2.2  3  Inv-AAD          Invertebrate-AID/APOBEC-deaminase
    9.7e-08   31.9   0.0    1.8e-07   31.0   0.0    1.4  1  MafB19-deam      MafB19-like deaminase
  ------ inclusion threshold ------
      0.013   15.5   0.1      0.029   14.3   0.1    1.5  1  DUF655           Protein of unknown function (DUF655)


Domain annotation for each model (and alignments):
>> RibD_C  RibD C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.5   0.0   7.5e-37   2.7e-33       1     193 [.     173     367 ..     173     373 .. 0.88

  Alignments for each domain:
  == domain 1  score: 115.5 bits;  conditional E-value: 7.5e-37
                 -EEEEEEEEETTSBSSCTTSSGCTSS-HHHHHHHHHHHHTSSEEEEEHHHHHHHT--SS--SSCHSCHHHTT.GSS-EEEEEETTS-S-TTSH.HHHSS CS
      RibD_C   1 pyvilklavSlDGklaaaggeskwitgeearadvhelraeadailvGrgtvladnpsltvrwvkkreaeadaearqpvrvVvdstlrvpldak.vltdd 98 
                 p+vilk+a++lDGk+a  +g+s+wit+ ++r+++h+lra  +a +v+  tv+ dnp+l +r+++ +        ++ v++++ds+ ++      +++ +
  AHX11415.1 173 PFVILKVATTLDGKIACSNGKSAWITSAKMRRIAHKLRAMTTATMVSYSTVKCDNPQLDCRLPGLE--------KESVKIILDSRAEIGSAELnLFKNG 263
                 89***************************************************************8........99**********9765444588888 PP

                 S-EEEEESSCSCHHHHHHCC......E..SE-HHHHHHHHHHTT--EEEEEETHHHHHHHHHTTT-SEEEEEEESCE--TTSBCSSSSST-SS....EE CS
      RibD_C  99 aptlvatteeadkekveklk......v..rvdlkelleeLkergirsllveGGatLagsllraglvDelrlyiaPkllGgagktlfdgegfka....lk 185
                    +v +  + ++ k +++       v  rvdl ++l eL ++gi+sllve+G +L  s+l+++l+D++  + a k+ G+++ +l+++ +f+     +k
  AHX11415.1 264 ---IVWSFGRKNSFKYRNFFnfecetVedRVDLLKILHELGDMGINSLLVECGRKLFTSFLKENLFDQIAWFRANKIAGDDAVSLCGDLDFSDpsafIK 359
                 ...66666665555555555555664399**************************************************************99887777 PP

                 EEEEEEEE CS
      RibD_C 186 lklvksea 193
                 l+ ++  +
  AHX11415.1 360 LQKTHEIK 367
                 77666555 PP

>> dCMP_cyt_deam_1  Cytidine and deoxycytidylate deaminase zinc-binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.3   0.0   2.4e-22   8.6e-19       6     100 ..      31     125 ..      26     126 .. 0.93

  Alignments for each domain:
  == domain 1  score: 67.3 bits;  conditional E-value: 2.4e-22
                      HHHHHHHHHHHHHH..TTTSCSEEEEEEETTEEEEEEESBHHCCTGTTB-HHHHHHHHHHHHTSSCETTEEEEEEE--BHH......HHHHHHH CS
  dCMP_cyt_deam_1   6 kllelalkaakeaq..kcsnfkVGavivkngeiistgyngepaggsktiHAEvnAilkaaknggsklegatlyvtlePCsm......Cakaiiq 91 
                      +++++a++++++    + sn++VG+v+vk+ge++++g+ g +     ++HAE +A+++a+k     + g  ly+tlePC++      C + iiq
       AHX11415.1  31 YYMRIAVNTSRTGLafTSSNPSVGCVVVKDGEVVGRGVTGLN----GIPHAEEIALRAAGKS---AI-GGDLYTTLEPCTHygktapCVDKIIQ 116
                      89*********99999************************98....678**********965...45.899*********************** PP

                      HT-SEEEEE CS
  dCMP_cyt_deam_1  92 sgikkvvvg 100
                      sgik+v++g
       AHX11415.1 117 SGIKRVYIG 125
                      ******986 PP

>> Inv-AAD  Invertebrate-AID/APOBEC-deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.5   0.1   1.2e-13   4.3e-10      56     116 ..      94     150 ..      55     160 .. 0.89
   2 ?   -3.5   0.0       2.5   8.8e+03      44      62 ..     207     225 ..     194     247 .. 0.67
   3 ?   -3.7   0.0       2.7   9.8e+03      30      42 ..     355     367 ..     352     374 .. 0.70

  Alignments for each domain:
  == domain 1  score: 39.5 bits;  conditional E-value: 1.2e-13
     Inv-AAD  56 lYttmepCskRlsGnlpCveRilklkeaiktvyvGvkePekfvaenkgrkkleeagievvh 116
                 lYtt+epC++      pCv++i++  + ik+vy+G+++P++ v+  +g +kl+e+gi+vv 
  AHX11415.1  94 LYTTLEPCTHY-GKTAPCVDKIIQ--SGIKRVYIGINDPDERVS-GRGIEKLRENGIKVVS 150
                 9*******975.5578******96..68**************97.58***********875 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.5
     Inv-AAD  44 eklaevlpkntvlYttmep 62 
                 +kl+++ ++++v Y t+  
  AHX11415.1 207 HKLRAMTTATMVSYSTVKC 225
                 5666677777777887764 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 2.7
     Inv-AAD  30 ccliklaekheva 42 
                 +++ikl ++he++
  AHX11415.1 355 SAFIKLQKTHEIK 367
                 6788888888776 PP

>> MafB19-deam  MafB19-like deaminase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   5.1e-11   1.8e-07      17     111 ..      45     142 ..      31     167 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 5.1e-11
  MafB19-deam  17 atkikedkigavivkdkkviargsnekelnakataHaEiaalqqAakklkskrlddatlyvtlepCd......mCagaivqaglkklvygagnpks.. 106
                  a+  ++  +g+v+vkd++v++rg +  +       HaE  al+ A k  ++       ly+tlepC       +C   i+q+g+k++  g ++p+   
   AHX11415.1  45 AFTSSNPSVGCVVVKDGEVVGRGVTGLN----GIPHAEEIALRAAGKSAIGG-----DLYTTLEPCThygktaPCVDKIIQSGIKRVYIGINDPDErv 133
                  566677789****************555....789*******9995555544.....79*******64444447********************9988 PP

  MafB19-deam 107 ....lnkLk 111
                      ++kL 
   AHX11415.1 134 sgrgIEKLR 142
                  888877765 PP

>> DUF655  Protein of unknown function (DUF655)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.1   8.1e-06     0.029      95     144 ..     270     320 ..     253     332 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 8.1e-06
                 HTTHHHHHHHH-.----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SH CS
      DUF655  95 kekEdrfveffn.eaepitiRlHaLelLpgvgkklarkileeRerrrFesF 144
                 +++  ++ +ffn e+e ++ R+  L++L ++g   ++++l e  r+ F+sF
  AHX11415.1 270 RKNSFKYRNFFNfECETVEDRVDLLKILHELGDMGINSLLVECGRKLFTSF 320
                 556668999***88************************************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (391 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      424  (0.0236488); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2877.28
//
Query:       AHX11416.1  [L=664]
Description: DNA ligase, NAD-dependent [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-91  305.8   0.0    4.4e-91  305.3   0.0    1.3  1  DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
    2.3e-30  104.3   2.3    3.1e-30  103.9   0.8    2.0  2  DNA_ligase_OB    NAD-dependent DNA ligase OB-fold domain
    5.2e-13   49.2   0.1    8.7e-12   45.3   0.0    2.9  3  BRCT             BRCA1 C Terminus (BRCT) domain
    2.8e-08   33.6   0.9    5.7e-08   32.6   0.9    1.6  1  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger doma
    3.4e-08   33.5   0.1    2.3e-07   30.8   0.1    2.4  1  HHH_2            Helix-hairpin-helix motif
    4.7e-05   23.9   0.0      0.019   15.6   0.0    2.8  2  HHH_5            Helix-hairpin-helix domain
     0.0006   19.7   0.0      0.002   18.0   0.0    1.9  2  PTCB-BRCT        twin BRCT domain
     0.0024   18.4   0.9       0.13   12.9   0.0    3.1  3  5_3_exonuc       5'-3' exonuclease, C-terminal SAM fold


Domain annotation for each model (and alignments):
>> DNA_ligase_aden  NAD-dependent DNA ligase adenylation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  305.3   0.0     2e-94   4.4e-91       2     317 ..       2     298 ..       1     299 [. 0.97

  Alignments for each domain:
  == domain 1  score: 305.3 bits;  conditional E-value: 2e-94
                      HHHHHHHHHHHHHHHHHHHHHCTT-SSC-HCHHHHHHHHHHHHHHHSGGG--TTSCCG-SSSS--CTS-EEE-SS-----EEE-SHHHHHHHHH CS
  DNA_ligase_aden   2 eakkeleelrellrkydyeYyvldePlvsDaeyDrllkelkelEekfPelitpdSPtqrvgaeleaefkkveHeapllSLdnafdedelkafle 95 
                      e++k++e+l ++l  ++ +Yy++d+P++ DaeyD+  ++  el +++Pel     Pt  +g+ ++ +f+kveH  p+lSL n+f+e e+ ++++
       AHX11416.1   2 EVEKKIESLYKKLLLHNEKYYQDDNPEITDAEYDAIKSQYLELIKENPELEF---PT-IIGHPPSEKFSKVEHLSPMLSLRNVFSEGEFIEYIQ 91 
                      7899*********************************************965...66.59********************************** PP

                      HHHHHSSS--S-EEEEEEEESSEEEEEEEETTEEEEEEE-TTSSEEEB-HHHHCT-TTS-SB-SSSS--SEEEEEEEEE--HHHHHHHHHHHHH CS
  DNA_ligase_aden  96 rieealgnkekvayvvelKiDGlavsllYengvlvraatRGdGttGedvtaNvktiksiPlklkvdnlpeelevRGEvylrkedFeklNeerle 189
                      + +++l++ke++++++e+KiDG++ s  + +g+l + atRGdG tGe++t+N+ +i+  P++++    p+ levRGEv++++e+F++l      
       AHX11416.1  92 KTKRFLNTKENFEFLCEPKIDGVSFSACFIDGKLHSCATRGDGYTGENITENINVISGFPTRIENA--PKVLEVRGEVFIDHETFRRLE----- 178
                      ***************************************************************987..********************9..... PP

                      CT----SSHHHHHHHHHT-SSHHHHHTS--EEEEEEEEEEESS---.SBHHHHHHHHHHCT--B-TT-EEECSHHHHHHHHHHHHHHGGGSSS- CS
  DNA_ligase_aden 190 egeklfaNpRNaAaGslRqldpkitakrkLkliayglglvekeelevktqsealkvlkklglkvseelklvksieevleyieelekkRdeleye 283
                           f+NpRNaAaGslRqldp+it++r+Lk +ay+ ++      +v++q+e+l+ l   g+++++   l ++iee++++++++ +kR++l y+
       AHX11416.1 179 ----GFSNPRNAAAGSLRQLDPEITKQRNLKYFAYSANE--L--PTVRSQKEVLESLAANGFSTNSIKLLSSNIEEIMDFYQSIYDKRADLTYD 264
                      ....8*******************************994..3..5689*******************99************************* PP

                      EEEEEEEESBHHHHHHH-EETSCESSEEEEE--- CS
  DNA_ligase_aden 284 iDGvVvkvdelalqeeLGftakaPrwAiAyKfpa 317
                      iDG+V+k++++ lq++LG +a aPrwA+A+Kfp+
       AHX11416.1 265 IDGLVYKINDIGLQKRLGISADAPRWAVAHKFPS 298
                      ********************************95 PP

>> DNA_ligase_OB  NAD-dependent DNA ligase OB-fold domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0         2   4.6e+03      37      53 ..      15      31 ..      12      32 .. 0.82
   2 !  103.9   0.8   1.4e-33   3.1e-30       2      78 ..     303     379 ..     302     380 .. 0.97

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2
                   XXXXXXXXXXXXXXXXX CS
  DNA_ligase_OB 37 tLhnedeierkdirigd 53
                    Lhne++ ++ + +i d
     AHX11416.1 15 LLHNEKYYQDDNPEITD 31
                   59*****9999888877 PP

  == domain 2  score: 103.9 bits;  conditional E-value: 1.4e-33
                    --XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
  DNA_ligase_OB   2 tkledievqVGRtGaltpvAeLepvelaGttVsratLhnedeierkdirigdtVvvekaGdvIPevvgvvlekreee 78 
                    t+le+ie++VGRtG +tpv  L+pv+++G++Vsra+L nede++rkdir gd V++e+aGdvIP++++v++  r+++
     AHX11416.1 303 TVLEKIELSVGRTGIITPVGLLKPVTIGGVVVSRASLYNEDELKRKDIREGDLVTIERAGDVIPKILAVDKAYRDKQ 379
                    99**********************************************************************99986 PP

>> BRCT  BRCA1 C Terminus (BRCT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.3     3e+03      54      72 ..     201     219 ..     194     221 .. 0.86
   2 ?   -1.6   0.0       1.6   3.7e+03      39      63 ..     501     523 ..     485     535 .. 0.75
   3 !   45.3   0.0   3.9e-15   8.7e-12       6      78 ..     584     654 ..     581     655 .. 0.95

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.3
                 SHHHHHHHHHHTTSEEEET CS
        BRCT  54 srslkylealklnipivhe 72 
                  r+lky+++ ++  p+v+ 
  AHX11416.1 201 QRNLKYFAYSANELPTVRS 219
                 4899***********9985 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.6
                 SCSTTSSEEEESSSHSHHHHHHHHH CS
        BRCT  39 evskktthlvvgepesrslkyleal 63 
                  + +kt ++++ e+   s k++ ++
  AHX11416.1 501 GIGEKTAYILAREY--VSFKKWFSK 523
                 4789999****999..777766544 PP

  == domain 3  score: 45.3 bits;  conditional E-value: 3.9e-15
                 TTTEEEEEEESTSSHHHHHHHHHHHHTTCEEESSCSTTSSEEEESSSHSHHHHHHHHHHTTSEEEETHHHHHH CS
        BRCT   6 fhgckfvitgvldnftrdeleelikehGGkvttevskktthlvvgepesrslkylealklnipivheewlldc 78 
                 ++++ fv+tg+l ++trde++e++k+ GG v +++sk+ ++lv+ge    ++k++ a +l+i+i++e+ ++ +
  AHX11416.1 584 LNNKRFVFTGTLLSITRDEAKEIVKNAGGIVLNAISKNADYLVAGEK--AGSKLSRARELGITIIDEDDFKSL 654
                 689********************************************..88****************987765 PP

>> DNA_ligase_ZBD  NAD-dependent DNA ligase C4 zinc finger domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   0.9   2.6e-11   5.7e-08       2      26 ..     388     413 ..     387     413 .. 0.98

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 2.6e-11
  DNA_ligase_ZBD   2 CPvCGsavvReegeaiyRCtn.lsCp 26 
                     CP+C s++ R+ +ea++RC n  +Cp
      AHX11416.1 388 CPSCSSKLLRKNNEAAIRCMNhKKCP 413
                     *************************9 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   0.1     1e-10   2.3e-07       1      64 []     492     564 ..     492     564 .. 0.81

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1e-10
       HHH_2   1 rllfaLGIrhVGektAklLakrFks.......ldaLkka..sleeLlevddiGeeiAqsivefFeneknreli 64 
                 r++f+LGI+ +GektA +La+++ s       + aL+    ++ e+ ++++ G    +s +efF++++n++++
  AHX11416.1 492 RFIFSLGIKGIGEKTAYILAREYVSfkkwfskMSALEGNieTETEIKNLEGLGGSAYDSLKEFFADPDNQDIV 564
                 79******************9975511122226677653337889*************************986 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   8.4e-06     0.019       6      57 .]     430     484 ..     426     484 .. 0.89
   2 ?    5.3   0.0     0.014        31       5      20 ..     497     512 ..     493     553 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 8.4e-06
                 TSTT--HHHHHHHHTTT.--SHHHHHHS-..HHHHHTSTTS-HHHHHHHHHHHHH CS
       HHH_5   6 svsGiGpktAlallsaG.iesvedlaaad..veeLakipGiGkktAeriilelkd 57 
                 +++GiG++ +   +++G ++ ++d+ +++  +e++ k  G G+k +e++i+ +k+
  AHX11416.1 430 DIEGIGESHISFFINNGfVSELADIFRLEryKEAIKKYEGWGEKSVENLIQNIKK 484
                 69***************6777****999844599****************98875 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.014
                 HTSTT--HHHHHHHHT CS
       HHH_5   5 lsvsGiGpktAlalls 20 
                 l+++GiG+ktA  l++
  AHX11416.1 497 LGIKGIGEKTAYILAR 512
                 5788888888866665 PP

>> PTCB-BRCT  twin BRCT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       3.3   7.5e+03      27      41 ..     412     426 ..     411     428 .. 0.78
   2 !   18.0   0.0     9e-07     0.002      13      59 ..     600     646 ..     590     649 .. 0.93

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 3.3
                 EESSEETT-SEEEEC CS
   PTCB-BRCT  27 yskdltksvTHLick 41 
                 + ++l ++v HL++ 
  AHX11416.1 412 CPDQLVQQVKHLVSS 426
                 667888999999986 PP

  == domain 2  score: 18.0 bits;  conditional E-value: 9e-07
                 HHHHHHHHHHTT-EEESSEETT-SEEEECSS-CHHHHHHHHCT-EEE CS
   PTCB-BRCT  13 rkslqklieamGaeyskdltksvTHLicksgeGekyekAkkwgipvV 59 
                 r++++++++  G+ +    +k+  +L++ +  G+k  +A++ gi+++
  AHX11416.1 600 RDEAKEIVKNAGGIVLNAISKNADYLVAGEKAGSKLSRARELGITII 646
                 8999*****************************************98 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0      0.11   2.4e+02      20      45 ..     464     489 ..     461     492 .. 0.85
   2 !   12.9   0.0   5.6e-05      0.13      22      53 ..     498     529 ..     497     569 .. 0.80
   3 ?   -3.7   0.0         8   1.8e+04      41      64 ..     615     639 ..     598     641 .. 0.61

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.11
  5_3_exonuc  20 ipGvpgiGektAakLlkeygsleeil 45 
                 i+  +g+Gek   +L++++++  +i 
  AHX11416.1 464 IKKYEGWGEKSVENLIQNIKKARNIT 489
                 677789************99988875 PP

  == domain 2  score: 12.9 bits;  conditional E-value: 5.6e-05
  5_3_exonuc  22 GvpgiGektAakLlkeygsleeilenldelke 53 
                 G++giGektA  L +ey s ++ +++++ l++
  AHX11416.1 498 GIKGIGEKTAYILAREYVSFKKWFSKMSALEG 529
                 9*********************9998875443 PP

  == domain 3  score: -3.7 bits;  conditional E-value: 8
  5_3_exonuc  41 leeilenld.elkekklkekLeenk 64 
                 l++i +n+d  ++++k+  kL +++
  AHX11416.1 615 LNAISKNADyLVAGEKAGSKLSRAR 639
                 5677777775566677778877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (664 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      699  (0.0389871); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.66u 0.23s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 5005.59
//
Query:       AHX11417.1  [L=95]
Description: dihydroneopterin aldolase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-09   36.9   0.1      5e-09   36.7   0.1    1.0  1  FolB      Dihydroneopterin aldolase
  ------ inclusion threshold ------
      0.011   15.2   1.8      0.017   14.5   1.7    1.4  1  HSM3_N    DNA mismatch repair protein HSM3, N terminal domain


Domain annotation for each model (and alignments):
>> FolB  Dihydroneopterin aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.7   0.1   5.5e-13     5e-09      12     110 ..       3      89 ..       1      91 [. 0.88

  Alignments for each domain:
  == domain 1  score: 36.7 bits;  conditional E-value: 5.5e-13
                 ESSSHHHHHC-EEEEEEEEEEE-CHHHHHHTTGGGSS-HHHHHHHHHHHHHSSEES-HHHHHHHHHHHHHCHSTESEEEEEEEETTSSSTCESEEEEEE CS
        FolB  12 iGvnpeErelkQrvvvdleleldlskaaesddledtvdYaelakavkelvesssfkllEalaeriaealleefpvekvevrveKpnapigaadavgvei 110
                  Gv ++E+ lk  v ++l++           + ed vdY  +++ +k+  ++++f+ +E lae +++ l++ef+  +++++v K +   + ++++++++
  AHX11417.1   3 LGVRDWEKVLKRLVWINLSI-----------SSEDLVDYNLVIDLLKNTSSTTKFDYIEELAETLLSDLVKEFSPLEISLEVIKHSLS-RLLEHASIQV 89 
                 7*******************...........44566***************99*******************9999999999999954.4477777766 PP

>> HSM3_N  DNA mismatch repair protein HSM3, N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   1.7   1.9e-06     0.017      41     116 ..       7      79 ..       2      91 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.9e-06
      HSM3_N  41 dakrllanikrllvenksedkldydlllelldklvkvssfedvlevysvddlvkalkseidslvvaackvieksyP 116
                 d +++l  +  + ++ +sed +dy+l+++ll++  ++++f+ + e+  ++ l++ l  e ++l   + +vi++s  
  AHX11417.1   7 DWEKVLKRLVWINLSISSEDLVDYNLVIDLLKNTSSTTKFDYIEEL--AETLLSDLVKEFSPLEI-SLEVIKHSLS 79 
                 6777888888889999*************************98776..45566666666666643.4566666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       684  (0.0381505); expected 358.6 (0.02)
Passed bias filter:                      374  (0.0208601); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 714.08
//
Query:       AHX11418.1  [L=367]
Description: carbamoyl-phosphate synthase, small subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-39  133.3   0.0    7.4e-39  132.5   0.0    1.4  1  CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CP
    6.4e-36  123.9   0.1    9.7e-36  123.3   0.1    1.3  1  GATase           Glutamine amidotransferase class-I
    3.1e-07   30.4   0.6    0.00011   22.1   0.6    2.3  1  Peptidase_C26    Peptidase C26


Domain annotation for each model (and alignments):
>> CPSase_sm_chain  Carbamoyl-phosphate synthase small chain, CPSase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  132.5   0.0   1.2e-42   7.4e-39       2     128 .]       9     136 ..       8     136 .. 0.98

  Alignments for each domain:
  == domain 1  score: 132.5 bits;  conditional E-value: 1.2e-42
  CPSase_sm_chain   2 avLvLedGtvfeGksfg.akeavGEvvfnTgmtGYqeiltDpsYagqilvltypliGnyGvneedvesekikvaglvvrelseepsnwraeesL 94 
                      ++L++ dG+ f G s+g ++ av+Ev+f+T+  GYq ++tDps+ gqi+++t p+iGn+G+n++d+e +k+ ++g+v+re   + s++   e++
       AHX11418.1   9 TCLAFTDGSLFFGFSCGkKGVAVAEVCFTTSPLGYQHVITDPSFFGQIILFTSPHIGNIGINSQDNECHKVFARGVVLREDPVDFSHHYRIEHF 102
                      5899*************66899************************************************************************ PP

  CPSase_sm_chain  95 sewlkeekipgisgvDTRaLtkklrekgamkgvi 128
                      s+wl +++++gi+gvDTRa+t+ + ++g+++g+i
       AHX11418.1 103 SDWLVRNQVVGICGVDTRAITRLICRTGSKNGII 136
                      ********************************98 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.3   0.1   1.6e-39   9.7e-36       2     188 ..     185     361 ..     184     363 .. 0.88

  Alignments for each domain:
  == domain 1  score: 123.3 bits;  conditional E-value: 1.6e-39
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT..TTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEEEEECE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg..vegkieaikearenkiPiLGICLGmQllaiefgrkvvkekek 98 
                 +iD++  +++ ++++l +    v +      +     l +++dgi++s+Gpg+p+  +e   e  +++++++iPiLGICLG+Q+++++fg  + k+   
  AHX11418.1 185 IIDFG--IKHGIIRNLQKYFTVVVIAGKR-GFADVV-LSSSFDGIVLSNGPGDPSatYEYLYEDFTKIFSSDIPILGICLGHQIIVLAFGCRTKKML-V 278
                 57777..8888888888776444444433.333332.5799**************999999999*********************************.* PP

                 EEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHH CS
      GATase  99 ehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfli 188
                 +h+g+++++ +        ++++ i++++H++++++ +++ +++ +t++s  d++++++  k+++++++Q+HPE +++p++++++f+ ++
  AHX11418.1 279 GHRGANHPVMN------LITGKVEITSQNHGFVLDE-STLTRDVGITHRSLFDNSVEGVKIKNKKIHSIQYHPEGSPGPHDSHYIFEDFF 361
                 ***********......5566799***********9.****************999999999999*********************9986 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.1   0.6   1.8e-08   0.00011     101     216 .]     248     345 ..     240     345 .. 0.74

  Alignments for each domain:
  == domain 1  score: 22.1 bits;  conditional E-value: 1.8e-08
  Peptidase_C26 101 alergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievns.lHhqaike..laeelrveAvae. 192
                    + ++++PilgiC+G+q++  a+G ++ + +        hr +     +h v         +l+   ++e++s  H + ++e  l  ++ ++ ++  
     AHX11418.1 248 IFSSDIPILGICLGHQIIVLAFGCRTKKMLVG------HRGA-----NHPVM--------NLIT-GKVEITSqNHGFVLDEstLTRDVGITHRSLf 323
                    66789******************999988884......4332.....34442........3333.3555555147777776668888888888888 PP

  Peptidase_C26 193 DgviEaieseeakafvlgvQwHPE 216
                    D+ +E ++++++k  + ++Q+HPE
     AHX11418.1 324 DNSVEGVKIKNKK--IHSIQYHPE 345
                    9999999999966..889999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (367 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       337  (0.0187964); expected 358.6 (0.02)
Passed bias filter:                      321  (0.017904); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2871.21
//
Query:       AHX11419.1  [L=78]
Description: ribosomal protein L31 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-15   55.5   0.1    5.7e-15   55.3   0.1    1.1  1  Ribosomal_L31  Ribosomal protein L31
  ------ inclusion threshold ------
      0.058   13.5   0.0      0.064   13.4   0.0    1.1  1  CBM65_1        Carbohydrate binding module 65 domain 1


Domain annotation for each model (and alignments):
>> Ribosomal_L31  Ribosomal protein L31
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.3   0.1   6.4e-19   5.7e-15       1      67 []       1      72 [.       1      72 [. 0.88

  Alignments for each domain:
  == domain 1  score: 55.3 bits;  conditional E-value: 6.4e-19
  Ribosomal_L31  1 mKkgiHPeyrevvvkcacgeefltrStl.kekpeik...vdvcsksHPfYt.GkqklvdtaGrvekFkkryg 67
                   mKk+iHPe++++ + +++g ++++rStl k+ +++     d+  ++H ++t   ++ v+++++v++Fk+r+g
     AHX11419.1  1 MKKNIHPEVHDIILAFTNGMKIKVRSTLgKKGELVVynaGDWPPETHQAWTkSASTNVKATSKVNRFKDRFG 72
                   9***************************7555554334479**********55789***************7 PP

>> CBM65_1  Carbohydrate binding module 65 domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   7.2e-06     0.064      30      78 ..      16      67 ..       4      74 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 7.2e-06
     CBM65_1 30 ltknseiaVdYtseeeveLilqs...wspdagagWakvapaevdaedgtakf 78
                +t+++ i+V  t ++++eL++++   w p++ + W+k a ++v+a++++  f
  AHX11419.1 16 FTNGMKIKVRSTLGKKGELVVYNagdWPPETHQAWTKSASTNVKATSKVNRF 67
                7999****************9862226677**************77777666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (78 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       474  (0.0264376); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.20s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 658.67
//
Query:       AHX11420.1  [L=247]
Description: hydroxyacylglutathione hydrolase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-21   76.9   0.7    1.9e-21   76.3   0.7    1.3  1  HAGH_C         Hydroxyacylglutathione hydrolase C-terminus
    1.4e-14   54.6   3.9    7.6e-14   52.2   3.9    1.9  1  Lactamase_B    Metallo-beta-lactamase superfamily
    5.9e-05   23.0   0.0    9.4e-05   22.4   0.0    1.2  1  Lactamase_B_3  Beta-lactamase superfamily domain
    0.00014   21.4   0.9    0.00029   20.4   0.7    1.7  1  Lactamase_B_2  Beta-lactamase superfamily domain
    0.00036   20.1   0.0    0.00047   19.7   0.0    1.2  1  Lactamase_B_5  Metallo-beta-lactamase superfamily
  ------ inclusion threshold ------
       0.23   10.3   0.0       0.34    9.7   0.0    1.1  1  Dak1           Dak1 domain


Domain annotation for each model (and alignments):
>> HAGH_C  Hydroxyacylglutathione hydrolase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   76.3   0.7   6.5e-25   1.9e-21       1      80 []     168     245 ..     168     245 .. 0.87

  Alignments for each domain:
  == domain 1  score: 76.3 bits;  conditional E-value: 6.5e-25
      HAGH_C   1 EYtlsNlkFalsvepdnealkkrlkevkelrakgeptvpstladEkktNpFLRldepevqkavgee...vevfaaLRelKdnF 80 
                 EYt +Nl+Fa+s+ep+n a+k++++++k +r     t+p+tl++Ek++NpFLR++e + ++    e   +e+fa LR++Kd+F
  AHX11420.1 168 EYTRDNLRFAMSIEPENIAIKNYWNSIKGHR---YSTIPTTLEQEKNINPFLRIKEYQKNQFP--ElteAEIFAILRKRKDSF 245
                 9*****************************5...79******************872222222..1346************99 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.2   3.9   2.5e-17   7.6e-14       8     197 .]      14     167 ..      12     167 .. 0.93

  Alignments for each domain:
  == domain 1  score: 52.2 bits;  conditional E-value: 2.5e-17
                  EEEEE.ETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHHTTCHCGC CS
  Lactamase_B   8 sylie.gdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkglllagvsad 104
                   ++i   +  ++++D+G + +  +       + + ++ v +v++TH+H+DH++g   +++++  ++++v++ ++ l++ +                  
   AHX11420.1  14 YVFIGnIGSLAFVVDPGDGDSVLDH------VSKYGLSVGWVLVTHHHADHTSGISQIKKRFSDAQVIVPLSEKDLLPCWD----------------- 88 
                  566666677789************9......5899**********************************************................. PP

                  CEEEEETTTEECCCTEEEEEHECTTSTSCCEEEEEETTCCEEEECTTTSSHHCCCCCC.TTCEEE-SHCHHHHHHHHHHHHHHHCHSEEEE.SS CS
  Lactamase_B 105 kpdvdeeeldgnaggrralyvtggpghghghgvveygggkvlftGDallagetgridltlrgaevrdpsdaekyldsllklaglkaevlvp.gH 197
                        +  d++ + +  ++v   +gh+ gh+ +++ ++k+lf+GD+l+++  gr+ +          + + +  +s++k+a l+ ++ ++ +H
   AHX11420.1  89 -----SLAVDEIYLCGTHVKVLELHGHTLGHVGYFFTEEKLLFCGDVLFSAGCGRVFE----------GTHLQMFESIEKIASLPGDTTIYcAH 167
                  .....7778888888888999*************************************..........********************888788 PP

>> Lactamase_B_3  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   3.2e-08   9.4e-05      18     108 ..      24     126 ..      13     135 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 3.2e-08
  Lactamase_B_3  18 rilvDPfka.nlgyeppa..eeaDlvlisqaledHah.letlkqlaenvkvlee.........geslevggleiravatshdavggsergenngfl 100
                      +vDP+++ ++    ++   ++  vl++++++dH   + ++k+ +++++v+ +         ++sl+v+++++ +++ +  + +g++ g  +g+ 
     AHX11420.1  24 AFVVDPGDGdSVLDHVSKygLSVGWVLVTHHHADHTSgISQIKKRFSDAQVIVPlsekdllpcWDSLAVDEIYLCGTHVKVLELHGHTLG-HVGYF 118
                    568999987744444444449999***********8647888888999999999999999999***************************.59999 PP

  Lactamase_B_3 101 leqdglti 108
                    +++++l +
     AHX11420.1 119 FTEEKLLF 126
                    99977654 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.7   9.7e-08   0.00029      32      94 ..      47     109 ..      26     151 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 9.7e-08
                    EEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTT.TTEEEEEE-TTS CS
  Lactamase_B_2  32 daVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleee.pavnvheldwge 94 
                      Vl+th H+DH+ g+  +++ r +++++++p++  + l  + + +++e   ++++v+ l++++
     AHX11420.1  47 GWVLVTHHHADHTSGISQIKK-RFSDAQVIVPLSEKDLLPCWDSLAVDEIYlCGTHVKVLELHG 109
                    579******************.445589999999999998887766666668777777776665 PP

>> Lactamase_B_5  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   1.6e-07   0.00047      47     145 ..      36     138 ..      14     163 .. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 1.6e-07
  Lactamase_B_5  47 wnhleslg.gvawivltn..sdhlraakeiael.tyakiagpaaeketfpiacdrwlsdgdelvsg..lkvlelkgsktpgelal.lleettlitg 135
                     +h+  +g  v w+++t   +dh     +i ++ + a++  p++ek+ +p      l+  +  + g  +kvlel+g  t+g +   + ee+ l  g
     AHX11420.1  36 LDHVSKYGlSVGWVLVTHhhADHTSGISQIKKRfSDAQVIVPLSEKDLLPC--WDSLAVDEIYLCGthVKVLELHGH-TLGHVGYfFTEEKLLFCG 128
                    677888874588**9996337999999999865378*************94..444554455555533799***995.7788765167899999** PP

  Lactamase_B_5 136 dlvrakkags 145
                    d++ +  +g 
     AHX11420.1 129 DVLFSAGCGR 138
                    *998776665 PP

>> Dak1  Dak1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0   0.00011      0.34      52     103 ..     130     182 ..     125     190 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00011
                 SBSEEEEEEETS---HHHHHHHHHHH--S..S-EEEEEESSHHHHHHHHHHHHH CS
        Dak1  52 mldaavaGevFaSPsakqilaaikavdsg..kGvllivkNYtGDvlnfglAaek 103
                 +l  a +G+vF   +  q+++ i++++s   + ++++ + Yt D+l f +++e 
  AHX11420.1 130 VLFSAGCGRVFEG-THLQMFESIEKIASLpgDTTIYCAHEYTRDNLRFAMSIEP 182
                 5667889****97.778999***99977444899****************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       435  (0.0242624); expected 358.6 (0.02)
Passed bias filter:                      395  (0.0220313); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.36
# Mc/sec: 2067.16
//
Query:       AHX11421.1  [L=189]
Description: hypothetical protein NHE_0479 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.3e-50  168.8   0.1    9.5e-50  168.3   0.1    1.2  1  DUF1013   Protein of unknown function (DUF1013)
  ------ inclusion threshold ------
      0.095   12.8   0.4       0.91    9.7   0.0    2.3  2  DUF2773   Protein of unknown function (DUF2773)


Domain annotation for each model (and alignments):
>> DUF1013  Protein of unknown function (DUF1013)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.3   0.1   1.1e-53   9.5e-50       1     137 [.      35     168 ..      35     170 .. 0.95

  Alignments for each domain:
  == domain 1  score: 168.3 bits;  conditional E-value: 1.1e-53
     DUF1013   1 LEvkaiAdgevakgikgldpiangqltreeiercekdekaklklkksklellekkkkgkrytpvskRqdkpdaiawllknhpelkdaqiakLvgtTket 99 
                 LEv++iAdg+va+g+ g+dp  +g++++ +ie+ce+d++++l + ks   + +kkkkg+ ytpv kR+ k+da +wl++n+pel+d+qi+ L+gtT ++
  AHX11421.1  35 LEVEGIADGTVAQGLIGCDPRITGEVEQRDIEECENDPNKRLII-KS--IVDKKKKKGRGYTPVVKRRVKSDASLWLINNYPELSDSQIVSLIGTTAKI 130
                 8******************************************9.33..3344899******************************************* PP

     DUF1013 100 ieairdrthwnsanikpkdPvtlgLcsqkdLdaaveka 137
                 +++ir++t+wn+ n+kp+dP++++Lcsq+dLd a+ k+
  AHX11421.1 131 VKSIREKTYWNYDNLKPRDPLLFNLCSQEDLDDALLKV 168
                 *********************************99886 PP

>> DUF2773  Protein of unknown function (DUF2773)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.0    0.0001      0.91      34      76 ..      95     137 ..      90     145 .. 0.88
   2 ?    0.6   0.1     0.068   6.1e+02      41      71 ..     148     180 ..     141     187 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.0001
     DUF2773  34 vkkarlkedPllllelvqPeldllrdlvktGktrkireearrk 76 
                 v k r+k d +l l  + Pel+  + + + G t ki +  r k
  AHX11421.1  95 VVKRRVKSDASLWLINNYPELSDSQIVSLIGTTAKIVKSIREK 137
                 7899******************99999999*999997766655 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.068
     DUF2773  41 edPllllelvqPeld..llrdlvktGktrkire 71 
                 +dPll     q +ld  ll+  + +   r +re
  AHX11421.1 148 RDPLLFNLCSQEDLDdaLLKVKISEQSERHLRE 180
                 899999888999887446666555666666664 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (189 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       623  (0.0347482); expected 358.6 (0.02)
Passed bias filter:                      449  (0.0250432); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.34
# Mc/sec: 1667.91
//
Query:       AHX11422.1  [L=808]
Description: leucine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-65  221.1   0.1    4.8e-20   71.3   0.2    6.0  5  tRNA-synt_1      tRNA synthetases class I (I, L, M and V)
    1.4e-51  174.7   0.0      9e-51  172.0   0.0    2.1  1  tRNA-synt_1_2    Leucyl-tRNA synthetase, Domain 2
    7.6e-32  110.5   0.0    2.7e-21   75.8   0.0    4.1  4  tRNA-synt_1g     tRNA synthetases class I (M)
      7e-09   35.8   0.4    3.2e-08   33.7   0.2    2.2  2  Anticodon_1      Anticodon-binding domain of tRNA
    1.6e-08   34.3   0.1     0.0056   16.1   0.0    2.7  3  tRNA-synt_1e     tRNA synthetases class I (C) catalytic domai
    1.6e-05   24.0   0.0      0.036   13.0   0.1    3.2  4  tRNA-synt_1f     tRNA synthetases class I (K)
     0.0018   17.3   0.0     0.0034   16.4   0.0    1.4  1  tRNA-synt_1d     tRNA synthetases class I (R)
  ------ inclusion threshold ------
       0.15   12.5   1.0         14    6.1   0.5    2.6  2  Lar_restr_allev  Restriction alleviation protein Lar


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.3   0.2   2.2e-23   4.8e-20      19     178 ..      23     165 ..      13     169 .. 0.89
   2 !   14.6   0.0   3.4e-06    0.0075     365     414 ..     170     219 ..     167     226 .. 0.94
   3 !   51.4   0.0   2.3e-17   5.2e-14     198     351 ..     234     389 ..     220     399 .. 0.76
   4 !   45.1   0.0   1.9e-15   4.3e-12     417     559 ..     399     552 ..     395     556 .. 0.62
   5 !   28.1   0.0   2.6e-10   5.9e-07     562     593 ..     583     615 ..     577     624 .. 0.84

  Alignments for each domain:
  == domain 1  score: 71.3 bits;  conditional E-value: 2.2e-23
  tRNA-synt_1  19 ekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvrewkaeyaeeir 116
                  + ++k++ +    Py  G+lH+Gh  + ++ d++ r+k+ +G++vl+ +GwD  Gl+ e++     ++ +            + + r+w +e ++++r
   AHX11422.1  23 TYKEKKYYVLSMFPYPSGKLHMGHLRNYVIGDVLARFKKANGYNVLHPIGWDAFGLPAEKA-----AIAG------------NVHPRKWTEENISKMR 103
                  33456666777789*******************************************9854.....2333............245699********** PP

  tRNA-synt_1 117 kqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEv 178
                   ++k++G s+D++re  T ++e+ +  ++ f  +   gl y+ +  vnw++  kt+l++  v
   AHX11422.1 104 TTLKNIGLSYDWSREISTCSPEYCKHEQRFFLDFLRAGLAYKKESEVNWDPVDKTVLANEQV 165
                  **********************************************************9766 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 3.4e-06
  tRNA-synt_1 365 cerskkpiiyrateqWfvrvkeladaalkavekvqfvpkskekryaswle 414
                  ++rs++ i+ r  +qWf r++++a+++l+ +++    p++ +++ a+w+ 
   AHX11422.1 170 GWRSGALIEKRKIPQWFLRITDFAEELLQDLDSLPGWPEKVKTMQANWIG 219
                  7**********************************99*******99*986 PP

  == domain 3  score: 51.4 bits;  conditional E-value: 2.3e-17
  tRNA-synt_1 198 eevklviaTTtPeTllgdtavavnpeldyvitkeklilaeallkslvkke.sekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVki 294
                   +  +++  T+PeT++g    a+  +        + i+ e   + + +++ +e + l +++    + +ev +p+ + k+p+   ++v ++ GtG++  
   AHX11422.1 234 GSKFVEVFSTRPETIFGASFCAISID--------HPIVREL--DLVKQEKiEELRTLFNKKLGIPTNLEVVHPFSKAKLPLYLANFVLMDYGTGAIFG 321
                  3335789***********99999999........3333332..22222221222334444455557899***************************** PP

  tRNA-synt_1 295 aPahdedDyevgkkynlevinildedgtlteea...........aef.eglkvfdarkkvveelkekgl 351
                   Pah+e D+e ++kynl++ +++ ++g+ ++ +           ++f +g++v +ark +++ ++  g 
   AHX11422.1 322 CPAHNERDFEFAQKYNLKI-TPVIKKGDTDTALpycdlegemynSDFlDGMEVIEARKRIIQVIESLGI 389
                  *****************85.6777889988888999*******966549*************9999886 PP

  == domain 4  score: 45.1 bits;  conditional E-value: 1.9e-15
  tRNA-synt_1 417 qdWciSRqrwWGhriplfvsketeevvvr.eelkel..vagreeeeaekkalekeakdkl...kkekgelekdedvlDvWFsSgswpfstlgypee.. 506
                  +dW iSRqr+WG +ip+ + ++     v+ e+l  +  +   + ++++  + + + k       k  g   +d+d++D+ F+S+  + +  + p+   
   AHX11422.1 399 KDWGISRQRYWGCPIPVVYCEKCSMQPVKvEDLPITlpEDVDFSKQGNPLESHPKWK--HtncPKCGGPALRDTDTFDTFFESSWYFAAFCN-PSAgi 493
                  8***************98887765333320232222002222233333323232222..1334333466779**********9655555555.87767 PP

  tRNA-synt_1 507 dteelkkffpadmlleGlDiirgWv..arlillsla....ltgsePfkevlvhglvrde 559
                  d+e  k+f p dm++ G+      +  +r  + +l+    lt +ePf++++++g+v  e
   AHX11422.1 494 DKEACKHFLPVDMYIGGVEHAILHLlySRFFVRALQkcgyLTIKEPFTHLVTQGMVCHE 552
                  999***************975443300223333332111166678**********9866 PP

  == domain 5  score: 28.1 bits;  conditional E-value: 2.6e-10
  tRNA-synt_1 562 rKmSKslgNvidpldvikkygadalRltli.ls 593
                   KmSKs++N++d ++vi+kygada R++++  +
   AHX11422.1 583 EKMSKSKKNIVDLEEVITKYGADAARFFILsDN 615
                  6***************************99444 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.0   0.0     4e-54     9e-51       2     184 ..     216     384 ..     215     385 .. 0.89

  Alignments for each domain:
  == domain 1  score: 172.0 bits;  conditional E-value: 4e-54
  tRNA-synt_1_2   2 nWIGrseGleiefkvees.eeklevfttrpdtlfGvtfvalapehplvekl.aekkkelaafieevkkksesereletkekeGvftglkaihPitg 95 
                    nWIG+seG++i+++++++ ++ +evf trp+t+fG++f a++ +hp+v++l   k++++            +e ++  ++k G+ t+l+++hP+++
     AHX11422.1 216 NWIGKSEGASIKLRLSGHgSKFVEVFSTRPETIFGASFCAISIDHPIVRELdLVKQEKI------------EELRTLFNKKLGIPTNLEVVHPFSK 299
                    9*****************77889**************************9943444444............44444556799************** PP

  tRNA-synt_1_2  96 ekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpedeekkleeseeayte.egilvnsgefdglkskeakekiakkl 184
                     k+p+++an+vlm+ygtga++++Pah++rDfeFa+kynl+i++vik+ d++++l      y + eg ++ns+++dg+++ ea+++i++ +
     AHX11422.1 300 AKLPLYLANFVLMDYGTGAIFGCPAHNERDFEFAQKYNLKITPVIKKGDTDTAL-----PYCDlEGEMYNSDFLDGMEVIEARKRIIQVI 384
                    **********************************************98877544.....57777**********************9865 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   75.8   0.0   1.2e-24   2.7e-21       2     135 ..      30     165 ..      29     173 .. 0.95
   2 !    4.4   0.0    0.0057        13     163     219 ..     164     219 ..     162     226 .. 0.87
   3 !    3.8   0.0    0.0087        20     221     238 ..     397     414 ..     389     423 .. 0.87
   4 !   22.2   0.0   2.3e-08   5.1e-05     326     369 ..     583     626 ..     575     644 .. 0.88

  Alignments for each domain:
  == domain 1  score: 75.8 bits;  conditional E-value: 1.2e-24
                   EEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEE..EETTSHHH CS
  tRNA-synt_1g   2 lvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdky..grttseeh 96 
                   +v + +pY++gklH+Ghl++++++D++aR+k+++g++vl+  g D++G p e +A + +v+p++ +e++ +++++++k++++s+d    ++t s e 
    AHX11422.1  30 YVLSMFPYPSGKLHMGHLRNYVIGDVLARFKKANGYNVLHPIGWDAFGLPAEKAAIAGNVHPRKWTEENISKMRTTLKNIGLSYDWSreISTCSPEY 126
                   788999******************************************************************************9652278999*** PP

                   HHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
  tRNA-synt_1g  97 kelvqeifkklkekgliyekeieqlycpkderflpdryv 135
                    +  q++f  + + gl y+ke+e+ ++p d++ l++++v
    AHX11422.1 127 CKHEQRFFLDFLRAGLAYKKESEVNWDPVDKTVLANEQV 165
                   **********************************99986 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.0057
                   ..............EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHH CS
  tRNA-synt_1g 163 elinpksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlk 219
                   ++i+ +   sg+  e ++  ++f+++ +f+++l + +  + + ++e+vk++  +w+ 
    AHX11422.1 164 QVIDGRGWRSGALIEKRKIPQWFLRITDFAEELLQDL-DSLPGWPEKVKTMQANWIG 219
                   56777777788888999999*****************.88889************96 PP

  == domain 3  score: 3.8 bits;  conditional E-value: 0.0087
                   ----EE-ESS-SSS-EET CS
  tRNA-synt_1g 221 gLkdlaisrdldwGipvP 238
                    Lkd+ isr+  wG p+P
    AHX11422.1 397 RLKDWGISRQRYWGCPIP 414
                   59***************9 PP

  == domain 4  score: 22.2 bits;  conditional E-value: 2.3e-08
                   ------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HH CS
  tRNA-synt_1g 326 kKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswe 369
                   +K+SkS++++v+ +e+++++ ad+ R+++++++p ++ +++s +
    AHX11422.1 583 EKMSKSKKNIVDLEEVITKYGADAARFFILSDNPPENTFEWSDK 626
                   8******************************9999887776655 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0       5.9   1.3e+04     121     136 ..     372     387 ..     356     393 .. 0.77
   2 !   33.7   0.2   1.4e-11   3.2e-08       2     145 ..     658     770 ..     657     777 .. 0.80

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 5.9
  Anticodon_1 121 eevellkeivkairkl 136
                  e +e +k+i+++i++l
   AHX11422.1 372 EVIEARKRIIQVIESL 387
                  5788899999999875 PP

  == domain 2  score: 33.7 bits;  conditional E-value: 1.4e-11
  Anticodon_1   2 rwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitEelwqreeeelgkk 99 
                  +++  +++k+++++t+++ee ++n a+++++e+ +n l       +k               ev + ++ tllr+l+Pf+P+++E+l      elg+ 
   AHX11422.1 658 KEFNVKMHKILRDITKYIEEIKLNCAVAKIHEL-VNLL-----STSK---------------EVDRNAIYTLLRVLEPFAPHLSEYLS----AELGNT 730
                  5667799*************************6.6644.....3333...............45578999******************....99**** PP

  Anticodon_1 100 esimlaewpe.kaeelekeleeeevellkeivkairklrselkikps 145
                  + +  ++w + +++ l++      +++   +v+ ++k+ ++++++++
   AHX11422.1 731 NKLYGSPWVSyDESILQD----DTIKI---AVQKNGKFLKTIEVPRN 770
                  ********9755544432....24556...99999998888888766 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.7e-06     0.011      21      49 ..      40      68 ..      21     158 .. 0.86
   2 !   16.1   0.0   2.5e-06    0.0056     251     297 ..     582     629 ..     575     633 .. 0.81
   3 ?   -1.3   0.0      0.47   1.1e+03      58     109 ..     624     679 ..     618     694 .. 0.72

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.7e-06
                  S--BHHHHHHHHHHHHHHHHHHHTT-EEE CS
  tRNA-synt_1e 21 dashlGhaRslvafDilrrilqalgYdvq 49
                   + h+Gh R++v+ D+l+r+ +a gY+v 
    AHX11422.1 40 GKLHMGHLRNYVIGDVLARFKKANGYNVL 68
                  578************************96 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 2.5e-06
                   TBE--TTTT---BHHHHHTTS-HHHHHHHHHSS-.TTS-EEE-HHHHH CS
  tRNA-synt_1e 251 gekmsksLknfitikdvlkkfdprqlRllllsah.yrsqldfkeelle 297
                    ekmsks kn++ +++v++k+ + + R+++ls +  +++++++++ +e
    AHX11422.1 582 VEKMSKSKKNIVDLEEVITKYGADAARFFILSDNpPENTFEWSDKGIE 629
                   59***************************9987513556666666665 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.47
                   SHHHHHHHHHTTS-HHHHHHHH...HHHHHHHHH.HTT----SB--BGGGGHHHHH CS
  tRNA-synt_1e  58 dDkiikrareeeksvkelaekf...ieefkkdle.aLnvlkptleprvsekvdeii 109
                    Dk i+ a +  + +k+laek+   ++e ++ ++ + nv+  ++   ++++++ei 
    AHX11422.1 624 SDKGIEAAFKFLRRIKNLAEKYlavEDEIQSPMNkEFNVKMHKILRDITKYIEEIK 679
                   68888888888888888888763325677777752588888888888888888874 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.8   0.0    0.0012       2.7      20      68 ..      25      73 ..       9      78 .. 0.77
   2 ?   -2.1   0.0      0.62   1.4e+03     105     131 ..      92     118 ..      85     131 .. 0.87
   3 ?   -1.6   0.0      0.43   9.6e+02     132     190 ..     360     430 ..     313     449 .. 0.66
   4 !   13.0   0.1   1.6e-05     0.036     272     317 ..     575     620 ..     570     669 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.0012
  tRNA-synt_1f 20 aekdevvvesGispSGliHiGnlrevltadlvaralrkrgeevrlilis 68
                  +ek+++v++    pSG++H+G lr+ + +d++ar  ++ g +v + + +
    AHX11422.1 25 KEKKYYVLSMFPYPSGKLHMGHLRNYVIGDVLARFKKANGYNVLHPIGW 73
                  3566777777778******************999888877776665555 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.62
  tRNA-synt_1f 105 esyaehfnaelvesLdelgievefisa 131
                    ++ e + ++++ +L+++g  +++ ++
    AHX11422.1  92 RKWTEENISKMRTTLKNIGLSYDWSRE 118
                   589999****************99765 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.43
  tRNA-synt_1f 132 telYksglydeaikealenrekikeilekyrgeereet...............yspylpvcekcgrvdttevve 190
                    e+Y+s  +d    e++e r++i +++e+    e + +                 +  ++cekc+  + ++v++
    AHX11422.1 360 GEMYNSDFLDG--MEVIEARKRIIQVIESLGIGEAKTSyrlkdwgisrqrywgCPIPVVYCEKCSM-QPVKVED 430
                   46777777765..47888899999998887665544444555666666665432223567888876.7777766 PP

  == domain 4  score: 13.0 bits;  conditional E-value: 1.6e-05
  tRNA-synt_1f 272 elillkggekmssSkGnvltledwlevaepevlrflilrrkPkkak 317
                   e i++ + ekms+Sk n++ le++++ +  +  rf+il+ +P ++ 
    AHX11422.1 575 ESISVGKVEKMSKSKKNIVDLEEVITKYGADAARFFILSDNPPENT 620
                   678888999*****************************99886542 PP

>> tRNA-synt_1d  tRNA synthetases class I (R)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   1.5e-06    0.0034      32      62 ..      39      69 ..      17     131 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 1.5e-06
                  TS--BHHHHHHHHHHHHHHHHHHHCT-EEEE CS
  tRNA-synt_1d 32 akemhvGhLrstiiGdavsrlleflGydvir 62
                  + ++h+GhLr  +iGd+++r   + Gy+v+ 
    AHX11422.1 39 SGKLHMGHLRNYVIGDVLARFKKANGYNVLH 69
                  5679*************************84 PP

>> Lar_restr_allev  Restriction alleviation protein Lar
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.031        68      27      36 ..     405     423 ..     372     442 .. 0.76
   2 ?    6.1   0.5    0.0064        14       4      34 ..     457     487 ..     454     500 .. 0.69

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.031
  Lar_restr_allev  27 q.........cvyCadCga 36 
                                +vyC++C +
       AHX11422.1 405 RqrywgcpipVVYCEKCSM 423
                      14455556779******** PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0064
  Lar_restr_allev   4 kpCPfCggravlersqrvvaeigqcvyCadC 34 
                        CP Cgg+a   +++  +   + + + a C
       AHX11422.1 457 TNCPKCGGPALRDTDTFDTFFESSWYFAAFC 487
                      68*******9877776665555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (808 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       772  (0.0430587); expected 358.6 (0.02)
Passed bias filter:                      659  (0.0367561); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.73u 0.25s 00:00:00.98 Elapsed: 00:00:00.44
# Mc/sec: 5477.12
//
Query:       AHX11423.1  [L=72]
Description: hypothetical protein NHE_0481 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       480  (0.0267723); expected 358.6 (0.02)
Passed bias filter:                      182  (0.0101512); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.41
# Mc/sec: 524.49
//
Query:       AHX11424.1  [L=207]
Description: helix-turn-helix family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-11   43.4   0.2    3.9e-11   42.8   0.2    1.3  1  HTH_3           Helix-turn-helix
    2.5e-10   40.2   0.1    5.3e-10   39.2   0.1    1.5  1  HTH_19          Helix-turn-helix domain
      2e-09   37.8   0.0    2.9e-09   37.2   0.0    1.3  1  HTH_26          Cro/C1-type HTH DNA-binding domain
    2.3e-05   24.4   0.0    3.8e-05   23.7   0.0    1.3  1  Phage_CI_repr   Bacteriophage CI repressor helix-turn-helix d
    0.00015   22.0   0.0    0.00023   21.4   0.0    1.2  1  HTH_31          Helix-turn-helix domain
    0.00078   19.4   0.0     0.0013   18.6   0.0    1.3  1  HTH_37          Helix-turn-helix domain
  ------ inclusion threshold ------
      0.028   14.3   0.0       0.13   12.2   0.0    2.1  2  TrmB            Sugar-specific transcriptional regulator TrmB
      0.074   12.9   0.0       0.12   12.2   0.0    1.4  1  YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitox
        0.1   12.6   0.2       0.24   11.4   0.2    1.7  1  Peptidase_S24   Peptidase S24-like
        0.1   12.4   0.1        7.4    6.5   0.0    2.3  2  HTH_10          HTH DNA binding domain
       0.15   11.9   0.0        5.3    7.0   0.0    2.5  2  HTH_23          Homeodomain-like domain


Domain annotation for each model (and alignments):
>> HTH_3  Helix-turn-helix
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.8   0.2   2.4e-14   3.9e-11       1      55 []      18      73 ..      18      73 .. 0.98

  Alignments for each domain:
  == domain 1  score: 42.8 bits;  conditional E-value: 2.4e-14
                HHHHHHHTTHHHHHHHHHHTSSHHHHHHHHTT.SSCSBHHHHHHHHHHHTSEHHHH CS
       HTH_3  1 lkelRkqlglsqeeLAeklGvsrstisriEnG.ernPsletlkklakaLgvsldel 55
                +++++++lg+  +eLAek+Gv +s +++i nG   nP+ ++l  +++ Lg+s+++l
  AHX11424.1 18 IRKRMEELGINARELAEKAGVGKSFVYDILNGkSKNPTSKKLDSISRELGISISYL 73
                8999*************************************************997 PP

>> HTH_19  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.2   0.1   3.3e-13   5.3e-10       4      61 ..      18      75 ..      15      78 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.2 bits;  conditional E-value: 3.3e-13
      HTH_19  4 LkeaReelgltqeelaerlgisrskisaiEngkkdvpsaelllkiaealgidleyllq 61
                +++  eelg++ +elae++g+ +s+ + i ngk+++p++++l +i+++lgi++ yl++
  AHX11424.1 18 IRKRMEELGINARELAEKAGVGKSFVYDILNGKSKNPTSKKLDSISRELGISISYLIN 75
                566669**************************999*********************97 PP

>> HTH_26  Cro/C1-type HTH DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.2   0.0   1.8e-12   2.9e-09       1      63 []      17      79 ..      17      79 .. 0.98

  Alignments for each domain:
  == domain 1  score: 37.2 bits;  conditional E-value: 1.8e-12
      HTH_26  1 kLrelmadrgitkseLargtgisaatlsrlvkgkpervsldtLdkiCdaLgctpgDLleyepd 63
                k+r+ m + gi++ eLa+++g+ ++ ++ +++gk ++++ + Ld i + Lg++++ L+   pd
  AHX11424.1 17 KIRKRMEELGINARELAEKAGVGKSFVYDILNGKSKNPTSKKLDSISRELGISISYLINASPD 79
                79********************************************************99987 PP

>> Phage_CI_repr  Bacteriophage CI repressor helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   2.4e-08   3.8e-05       3      58 ..      18      74 ..      17      79 .. 0.93

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 2.4e-08
                   HHHHHHHHT-SSCHHHHCCTT--HHHHH.HHHHSSS--.HHHHHHHHHHH---HHHHH CS
  Phage_CI_repr  3 leRlmsaygvkmqkeLAdlLgiakssvs.twvrRdffP.gdvvvtcaletdtsLewLa 58
                   +++ m+ +g++++ eLA+ +g++ks+v+ +++ ++++P ++++  ++ e+++s+ +L 
     AHX11424.1 18 IRKRMEELGINAR-ELAEKAGVGKSFVYdILNGKSKNPtSKKLDSISRELGISISYLI 74
                   67889********.*************98899******999999************96 PP

>> HTH_31  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.0   1.4e-07   0.00023       7      56 ..      19      68 ..      16      73 .. 0.94

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 1.4e-07
      HTH_31  7 ralReraGLsqeevAerlgvsestlsrlEqGrrgrpspavlealaralgl 56
                r + e+ G+  +e+Ae +gv +s + ++ +G+  +p+   l+++ r lg 
  AHX11424.1 19 RKRMEELGINARELAEKAGVGKSFVYDILNGKSKNPTSKKLDSISRELGI 68
                7899999************************************9999986 PP

>> HTH_37  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   8.2e-07    0.0013      18      75 ..      13      70 ..       2      74 .. 0.90

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 8.2e-07
                HHHHHHHHHHHHCT--HHHHHHHHT--HHHHHHHHTT--TT--HHHHHHHHHHTTEEE CS
      HTH_37 18 qlalaiaeliekrelsqseaaqllgiaqPkvsrllrgklsrfsldkLlnlltalGqkv 75
                 +a++i++ +e++++  +e+a++ g+ ++ v ++l+gk ++ + +kL+++   lG  +
  AHX11424.1 13 MMAYKIRKRMEELGINARELAEKAGVGKSFVYDILNGKSKNPTSKKLDSISRELGISI 70
                57888*******************************************9999988765 PP

>> TrmB  Sugar-specific transcriptional regulator TrmB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.7e-05      0.13      23      44 ..      27      48 ..      14      49 .. 0.92
   2 ?   -1.9   0.0       1.9   3.1e+03      24      36 ..      58      70 ..      55      72 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.7e-05
                CHHCHHCCCTTSSCHCHHHHHH CS
        TrmB 23 atadeiaeelgvprskvYevLr 44
                 +a+e+ae++gv +s vY++L+
  AHX11424.1 27 INARELAEKAGVGKSFVYDILN 48
                68******************97 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.9
                HHCHHCCCTTSSC CS
        TrmB 24 tadeiaeelgvpr 36
                + d i++elg++ 
  AHX11424.1 58 KLDSISRELGISI 70
                67899****9985 PP

>> YdaS_antitoxin  Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   7.4e-05      0.12      10      37 ..      28      55 ..      18      71 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
  YdaS_antitoxin 10 gqkaLAealgvsqqaVsqWlkgkkqvpa 37
                    ++++LAe+ gv ++ V++ l+gk++ p+
      AHX11424.1 28 NARELAEKAGVGKSFVYDILNGKSKNPT 55
                    7899******************998665 PP

>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   0.00015      0.24       4      26 ..     124     149 ..     122     195 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
                    SSTTCCTXXTTXEEEEECTS...--- CS
  Peptidase_S24   4 GdSMeptlldGdlilVdkfs...epk 26 
                    +dSM+p+++++++++++ f+   ++k
     AHX11424.1 124 DDSMAPSIMPNETLIIREFDqnsKIK 149
                    69***************887444333 PP

>> HTH_10  HTH DNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0045       7.4      24      45 ..      27      48 ..      25      53 .. 0.89
   2 ?    3.7   0.0     0.034        55      21      37 ..      54      70 ..      52      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0045
      HTH_10 24 vtlkeLAkelGIskstlsehLr 45
                ++++eLA++ G+ ks ++++L+
  AHX11424.1 27 INARELAEKAGVGKSFVYDILN 48
                789************9999886 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.034
      HTH_10 21 PRrvtlkeLAkelGIsk 37
                P   +l++++ elGIs 
  AHX11424.1 54 PTSKKLDSISRELGISI 70
                567799*********96 PP

>> HTH_23  Homeodomain-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.0    0.0033       5.3      16      39 ..      23      48 ..       9      52 .. 0.86
   2 ?    2.2   0.0       0.1   1.7e+02      23      33 ..      62      72 ..      57      75 .. 0.84

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0033
      HTH_23 16 e..GlsvreIAreLgvsrrTvyrwlk 39
                e  G++ re A++ gv ++ vy +l+
  AHX11424.1 23 EelGINARELAEKAGVGKSFVYDILN 48
                457999****************9986 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
      HTH_23 23 IAreLgvsrrT 33
                I+reLg+s + 
  AHX11424.1 62 ISRELGISISY 72
                9*******875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       733  (0.0408835); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1591.96
//
Query:       AHX11425.1  [L=233]
Description: heme exporter CcmC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.6e-25   88.6  21.0    4.6e-25   88.6  21.0    2.0  2  Cytochrom_C_asm  Cytochrome C assembly protein


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.6  21.0   2.6e-29   4.6e-25      36     214 .]      14     173 ..       4     173 .. 0.86
   2 !    1.8   0.2    0.0098   1.8e+02      70     100 ..     182     212 ..     174     231 .. 0.73

  Alignments for each domain:
  == domain 1  score: 88.6 bits;  conditional E-value: 2.6e-29
  Cytochrom_C_asm  36 avaliaalillgfalflllaelqesadlnpalqspilmiHvplallsYatliigallsialliierqlkkkkklklsanlkllkqldrlsyrii 129
                      ++++++++++l+++l+    ++ ++ d  +++  +i+++Hvp+a+l+  ++++  ll i++l              s ++++l     ++y+++
       AHX11425.1  14 NILALTIVLTLLYSLAF-YFVFSSPVDQLHGEFVRIMYVHVPAAWLAVLLYSVIGLLNIIYL--------------SFSVPVLGI---VAYALA 89 
                      33344444444444442.3446677777789999****************************..............778888888...99**** PP

  Cytochrom_C_asm 130 liGfvlltigiilGsvWaeeaWGsywsWDpketaslitWlvfaallhsriekgwrgkkaailailgflllllayfgvrllgeglh 214
                      +iG+ ++ i +i+Gs+W+++ WG++w+WD+++t+ ++++++++++  ++ +k+++ k a+i++++g++++++++f+v l+  +lh
       AHX11425.1  90 PIGMTFTMICLITGSLWGKPIWGTFWVWDARLTSMFVLFFLYLGYYLIWDYKEFNIKLASIVNLIGLVNIPIIKFSVYLWA-TLH 173
                      *************************************************999***************************98.776 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.0098
  Cytochrom_C_asm  70 pilmiHvplallsYatliigallsialliie 100
                      +++ iH++++   + ++   ++l+++l++++
       AHX11425.1 182 EGISIHPSMLTPLLLMFFSSFVLTLLLWYFN 212
                      5778888888888888888888888877544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       865  (0.0482459); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.30s 00:00:00.74 Elapsed: 00:00:00.44
# Mc/sec: 1606.00
//
Query:       AHX11426.1  [L=290]
Description: aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.7e-32  111.4   0.0    5.8e-32  110.8   0.0    1.3  1  OTCace_N        Aspartate/ornithine carbamoyltransferase, car
    1.4e-22   80.4   0.0    3.4e-22   79.2   0.0    1.6  1  OTCace          Aspartate/ornithine carbamoyltransferase, Asp
  ------ inclusion threshold ------
       0.02   14.8   0.2      0.057   13.3   0.2    1.7  1  DUF1622         Protein of unknown function (DUF1622)
      0.056   13.9   0.0      0.097   13.1   0.0    1.4  1  UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family,


Domain annotation for each model (and alignments):
>> OTCace_N  Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   1.3e-35   5.8e-32       1     147 [.       2     139 ..       2     140 .. 0.91

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.3e-35
                 S-BSSGGGS-HHHHHHHHHHHHHHHHHHHTTT-STTTTT-EEEEEESS--HHHHHHHHHHHHHTTSEEEEEESTTTSCTTTGGSTTSSCHHHHHHHHHH CS
    OTCace_N   1 rhllsledlskeeieelldlaaelkekvkkekkekllkgktlallFeepStRTrvSfevAakrlGgkvlslseaediqlssvskgrkEsleDtarvlsr 99 
                 r+lls +d+s +ei++++dlaa + ++      e+ l+gk l+ +F+e+StRT +Sf+vAa+rlG+ v + +  +++ +    kg  E+l D +++l++
  AHX11426.1   2 RSLLSNRDVSVDEIYQIFDLAAFYLKN----GIESNLSGKLLFSIFFESSTRTETSFSVAASRLGCIVEKAN-VSNLATR---KG--EHLVDLISTLNA 90 
                 789*****************8877655....36799*****************************9999999.4344444...66..************ PP

                 HT.SEEEEEESSHHHHHHHHHHHSSEEEEEEETSSB-HHHHHHHHHHHH CS
    OTCace_N 100 yv.daiviRhpgaeeleelakyasvpviNagdgdgeHPtQaLaDlltir 147
                 ++ d++viRh+++  l+ l+ y ++ +iNagdg++eHPtQ L+D++ti 
  AHX11426.1  91 FSpDLFVIRHSESGVLHLLKGYIDCGIINAGDGTNEHPTQGLIDAFTIL 139
                 ***********777799999999************************95 PP

>> OTCace  Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   79.2   0.0   7.5e-26   3.4e-22       1     156 [.     146     286 ..     146     287 .. 0.93

  Alignments for each domain:
  == domain 1  score: 79.2 bits;  conditional E-value: 7.5e-26
                 CC.EEEEESS.TTSHHHHHHHHHHHHCT-EEEEES-TTSSH-HHHHHHHHHHHHHHT-EEEEESSCHHHHTT-SEEEE--SSETTCCGGHHHHHHHHCC CS
      OTCace   1 kglkiafvGd.kknnvanslikllarlgmdvvlvaPkglepdkevleeakknakksggsititedleeavkgaDvvytdvwvsmgeekereerlkklkd 98 
                 +gl+i ++Gd  +++va+s i +l rlg+ +++ +P +l p  ++l           + i ++ +  +a++gaDvv++ + +    ++   +++ +  d
  AHX11426.1 146 EGLNILICGDiLRSRVAHSTIPILQRLGAVISISGPLALMP--KIL----------DEGIRYSPNFHDALSGADVVIMLRTQ----NERASQDIDNGID 228
                 599********99*************************766..566..........346899999*****************....45566******** PP

                 CSB-HHHHHHS-TT-EEEE-S---BTTTB-HHHHTSTTBHHHHHHHHHHHHHHHHHHH CS
      OTCace  99 yqvteellklakkdaivlHcLPakrgeEvtdeVfdsprsvvfeqaeNrlhtikAllvl 156
                 + ++++ l+ ak+d++++H+ P++r++E++d V ++ r+ +  q++N++++++A++ +
  AHX11426.1 229 FCLNKAALAVAKPDILIMHPGPVNRNREISDAVLNDSRNGILTQVRNGQYIRAAVISF 286
                 *******************************************************976 PP

>> DUF1622  Protein of unknown function (DUF1622)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.3e-05     0.057      36      66 ..     147     178 ..     145     185 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
     DUF1622  36 gLeflvaadIlkTvva.ptledigvLaaivli 66 
                 gL++l+++dIl++ va  t+  +  L+a++ i
  AHX11426.1 147 GLNILICGDILRSRVAhSTIPILQRLGAVISI 178
                 9************999788888999*****98 PP

>> UDPG_MGDP_dh_C  UDP-glucose/GDP-mannose dehydrogenase family, UDP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   2.2e-05     0.097      19      91 ..     162     230 ..     153     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 2.2e-05
                     HHHHHHHHHHCTSEEEEE-SSTHHCCCCHHGGBTCCEEES-CHHHHTT-SEEEE-S--GGGGGS-HHHHHHCC CS
  UDPG_MGDP_dh_C  19 aldiieeLleegaevkiyDPkvkeeaveaeleekgvevvdsleealkgadaiviltehdefkeldlaklkelm 91 
                     a   i  L++ ga ++i  P +   ++      +g+++  ++ +al+gad++++l  ++e  ++d+++  + +
      AHX11426.1 162 AHSTIPILQRLGAVISISGPLALMPKILD----EGIRYSPNFHDALSGADVVIMLRTQNERASQDIDNGIDFC 230
                     56677888888*********988877766....69************************99998888766655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (290 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       276  (0.0153941); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.40
# Mc/sec: 2195.13
//
Query:       AHX11427.1  [L=212]
Description: hypothetical protein NHE_0485 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (212 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1142  (0.0636957); expected 358.6 (0.02)
Passed bias filter:                      353  (0.0196888); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 1622.12
//
Query:       AHX11428.1  [L=596]
Description: glutamine-fructose-6-phosphate transaminase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-40  138.4   0.6    3.1e-20   72.4   0.1    2.4  2  SIS             SIS domain
    3.1e-18   66.2   0.0    5.5e-18   65.5   0.0    1.4  1  GATase_6        Glutamine amidotransferase domain
    1.6e-12   47.4   0.1      4e-12   46.1   0.0    1.7  2  GATase_7        Glutamine amidotransferase domain
      0.002   17.1   0.0     0.0038   16.2   0.0    1.4  1  GATase_4        Glutamine amidotransferases class-II
  ------ inclusion threshold ------
      0.028   14.4   0.1        0.2   11.7   0.1    2.3  2  CspB_prodomain  Csp protease B prodomain


Domain annotation for each model (and alignments):
>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.1   8.5e-24   3.1e-20       2     129 ..     283     409 ..     282     411 .. 0.94
   2 !   64.0   0.0   3.3e-21   1.2e-17       2     129 ..     448     577 ..     447     578 .. 0.87

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 8.5e-24
                 HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHHHHHHTTSEE..EEEESSTTSHHHHHS CS
         SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaaelakergaki..iaITdskgsplarea 98 
                 L +ak+i ++++G+s++++  +++++e+   + v ve ase+  +      +d l+i+is+sget+d++++++ +++       i++ + ++s++ar +
  AHX11428.1 283 LKSAKNINIVACGSSFFAGCIARAWIEKYLDVRVNVEVASEFTWR---DFMKDELFIFISQSGETADTLLVLKTVRNYSIGSyiISVVNVPESSIARLS 378
                 7799*************************************8888...677899**********************99866667*************** PP

                 SEEEEEEEECHCSSSHCHHHHHHHHHHHHHH CS
         SIS  99 dlalyinaepetlvastksltaqlaaldala 129
                 d ++y+na+pe  va+tks+t+qla l  l+
  AHX11428.1 379 DFHIYTNAGPELSVAATKSFTSQLATLLHLV 409
                 *************************987765 PP

  == domain 2  score: 64.0 bits;  conditional E-value: 3.3e-21
                 HCTSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEEEEHHHHHHTGGGG-STTCEEEEEESSSHHHHHHHHHH.HHHHTTSEEEEEESSTTSHHHHHSS CS
         SIS   2 LakakriyvlGaGtsyaiakelalkleeiggivvevedaselkhgvlalideddlvilisfsgetkdlvaaae.lakergakiiaITdskgsplaread 99 
                 ++ ++ri+++G+G  y++a e+alkl+ei++i +e+ +++elkhg +ali+++ +vil+++s  ++ +v++   +   r++k+ ++Td++g       +
  AHX11428.1 448 IYRSDRIFYVGKGLGYFVAVEGALKLKEISYIMAEGIQSGELKHGSIALIEKGFPVILLAPSSLSFAKVLSSIqEIYTRNGKLFIFTDKDGVKR--LEH 544
                 8999********************************************************88888877777666*************9988655..555 PP

                 EEEEEEEECHC...SSSHCHHHHHHHHHHHHHH CS
         SIS 100 lalyinaepet...lvastksltaqlaaldala 129
                 l +++ + p t     ++++++  q +a+ +++
  AHX11428.1 545 LDVEVVVLPDTselTMPFVYTVAMQILAYRVAV 577
                 556666666665589999999999999998876 PP

>> GATase_6  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.5   0.0   1.5e-21   5.5e-18      13     133 ..      67     191 ..      52     192 .. 0.80

  Alignments for each domain:
  == domain 1  score: 65.5 bits;  conditional E-value: 1.5e-21
    GATase_6  13 evalaHvRlaivglaeeegaqPfpsedgrlllvhNGeiynykelreelpalkglafrsrsDtevllall....eelG.......eevlerlrGmfafai 100
                 +v+++H+R+a++g  + e a+P   +d+ ++++hNG ++n+ elr+ l++ + l+f++++Dtev+l+l+    +  +       ++v+ ++ G fa+++
  AHX11428.1  67 KVGMGHTRWATHGQINLENAHPH--YDSDVAIIHNGIVENATELRKILQE-ESLEFKTDTDTEVILKLIvrhsQ--DhrkidvlQRVMGQIHGSFAIVV 160
                 69************866666***..*************************.****************9977662..14454577888889999999998 PP

    GATase_6 101 wdk.rentlilardrlgvkplyyavdesglafas 133
                 + +  +n+++ ++   g   l+ a++++  ++as
  AHX11428.1 161 IFQnNPNEIFAMK--RG-ISLIAASNGNISVVAS 191
                 8887888888873..23.3355555555555555 PP

>> GATase_7  Glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.0   1.1e-15     4e-12      16     119 ..      89     194 ..      72     197 .. 0.79
   2 ?   -3.6   0.0       2.8     1e+04      86     102 ..     526     542 ..     523     548 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 1.1e-15
    GATase_7  16 mvssedgrlvivfnGeiyNykelreeLeakghrfrtksDtevllallea........ewgeealerlnGmfAfaiwdeeek.rlllaRDrlGikPLyyg 105
                  +   d +++i++nG + N +elr+ L+++ ++f+t++Dtev+l+l+ +        + +++++ +++G+fA++++ +++  ++++++   Gi +L+ +
  AHX11428.1  89 HY---DSDVAIIHNGIVENATELRKILQEESLEFKTDTDTEVILKLIVRhsqdhrkiDVLQRVMGQIHGSFAIVVIFQNNPnEIFAMKR--GI-SLIAA 181
                 44...6789*************************************98889****9999*************99887666515555443..43.45555 PP

    GATase_7 106 edkgdallfaSelk 119
                  + g+  ++aS l+
  AHX11428.1 182 SN-GNISVVASDLS 194
                 55.45666666665 PP

  == domain 2  score: -3.6 bits;  conditional E-value: 2.8
    GATase_7  86 eekrlllaRDrlGikPL 102
                 ++++l++  D+ G+k L
  AHX11428.1 526 RNGKLFIFTDKDGVKRL 542
                 56699999999999876 PP

>> GATase_4  Glutamine amidotransferases class-II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-06    0.0038      62     142 ..      58     137 ..      40     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-06
    GATase_4  62 elvreypiksknvvaHiRkatqGevklenthpFvRelwgrewifAHnGdlkeykpkl....egrfePvGsTDsElafCelleela 142
                  +++++p+ sk+ + H R at+G+++len+hp      + +  + HnG +++ ++ +    e++ e   +TD+E+++  ++++ +
  AHX11428.1  58 DILNKNPF-SKVGMGHTRWATHGQINLENAHPHY----DSDVAIIHNGIVENATELRkilqEESLEFKTDTDTEVILKLIVRHSQ 137
                 55566565.778889*****************74....6788899***9988544434557677788899****99877766544 PP

>> CspB_prodomain  Csp protease B prodomain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   5.7e-05       0.2      12      76 ..     107     169 ..     100     176 .. 0.84
   2 ?   -1.0   0.0      0.52   1.9e+03      65      79 ..     366     380 ..     360     381 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 5.7e-05
  CspB_prodomain  12 dateeerekseelsvgydeeentwelivkysgdleeleeelgieveeLlngYAivtipeskieel 76 
                     ++ +  +e+s+e+++  d +e  ++liv+ s+d  ++   l+  + ++ + +Aiv i +++ +e+
      AHX11428.1 107 ELRKILQEESLEFKTDTD-TEVILKLIVRHSQDHRKID-VLQRVMGQIHGSFAIVVIFQNNPNEI 169
                     555666788888888777.88999**************.999***************99876665 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.52
  CspB_prodomain  65 ivtipeskieelaal 79 
                     +v++pes i +l+++
      AHX11428.1 366 VVNVPESSIARLSDF 380
                     89*********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      493  (0.0274974); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.39
# Mc/sec: 4545.38
//
Query:       AHX11429.1  [L=456]
Description: response regulator [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.7e-46  156.0   0.3      2e-45  154.4   0.2    1.9  2  GGDEF         Diguanylate cyclase, GGDEF domain
    8.8e-33  112.8   6.4    3.2e-27   94.9   0.3    2.9  3  Response_reg  Response regulator receiver domain
  ------ inclusion threshold ------
      0.048   13.4   1.6        1.2    8.9   0.0    2.9  3  NOG1          Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> GGDEF  Diguanylate cyclase, GGDEF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.53   3.2e+03     106     139 ..      14      46 ..       9      53 .. 0.71
   2 !  154.4   0.2   3.4e-49     2e-45       1     161 []     289     448 ..     289     448 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.53
                 HHHCS-EEETTCCEEE---EEEEEEEE..-TTS- CS
       GGDEF 106 llaklkepvelsgeelyvtisiGialappeeged 139
                 +++ l+++++++  ++ +t+s Gi +++  + ++
  AHX11429.1  14 NVKILEIKLTAKYYQV-ITASSGIEAIELAKRNQ 46 
                 5677788888776665.99999999987555544 PP

  == domain 2  score: 154.4 bits;  conditional E-value: 3.4e-49
                 HSB-CCCGSEEHHHHHHHHHHHHHCC.HHCTSEEEEEEEEETTHHHHHHHH-HHHHHHHHHHHHHHHHCCS-TTSEEEEESSSEEEEEEECSSHHHHHH CS
       GGDEF   1 aahDslTgLpNRrlleeeleqelqra.rreqkslavllldldnFkkindtyGhsvGDevLqevakrLssslrksdlvaRlggdeFaillpetsseeaae 98 
                 a +D+lT L+NR ++e++++++l  + ++++k ++++++d+d+Fkkind+yGh +GD +L+++a  L+s+lr +dl++++gg+e +++l +++++ea +
  AHX11429.1 289 AFIDPLTSLYNRYYFEKYVDELLVTVrKSKSKTFSMMMIDIDYFKKINDAYGHLSGDLILKQLALCLKSCLRLNDLIVKFGGEEVVVVLVDATLQEAYD 387
                 679***********************98999******************************************************************** PP

                 HHHHHHHHHHCS-EEETTCCEEE---EEEEEEEE..-TTS-HHHHHHHHHHHHHHHHHCTSSC CS
       GGDEF  99 laerirrllaklkepvelsgeelyvtisiGialappeegedleellkeAdealyeaKkagrnr 161
                 +aer+r  ++++k  + +++ ++++t+siG+a ++  + ++l++ll +Ad++ly aK++grn+
  AHX11429.1 388 AAERVRLVIEQQKFDTINEDVKVNLTVSIGVAEYQ--DRDTLKTLLGRADTNLYVAKERGRNT 448
                 **********************************5..************************95 PP

>> Response_reg  Response regulator receiver domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.9   0.3   5.3e-31   3.2e-27       1     111 [.       5     116 ..       5     117 .. 0.96
   2 !   20.7   0.1     6e-08   0.00036      37     111 ..     189     265 ..     159     266 .. 0.76
   3 ?   -2.9   0.1       1.3   7.6e+03      28      51 ..     384     408 ..     377     410 .. 0.62

  Alignments for each domain:
  == domain 1  score: 94.9 bits;  conditional E-value: 5.3e-31
                   EEEESSSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEESSTSHHHHHHHHHCTES CS
  Response_reg   1 vlivdDdplvrellrqlleeegyeevaeaedgkealellkeekvdlillDinmpgmdGlellkeireed..pelpviiltahseeedavealkagad 95 
                   +l+vdD p ++++l+  l+ + y +v +a++g ea+el+k++++d+illD++mp+mdG+e++++++ +    ++pvii+ta +++e++ve+l+agad
    AHX11429.1   5 ILVVDDIPSNVKILEIKLTAKYY-QVITASSGIEAIELAKRNQPDVILLDVMMPQMDGFETCRRLKSDYstMHIPVIIVTALNDMENKVEGLSAGAD 100
                   89*****************8888.999**************************************99997788************************ PP

                   EEEESSG-HHHHHHHH CS
  Response_reg  96 dflsKpfdpeeLlkal 111
                   +fl+Kp++  +L +++
    AHX11429.1 101 EFLVKPVRDFALFTRI 116
                   *******999988887 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 6e-08
                   HHHHHHHESEEEEESSCSSSEHHHHHHHHHHCT..TTSEEEEEE.SSTSHHHHHHHHHCTESEEEESSG-HHHHHHHH CS
  Response_reg  37 ellkeekvdlillDinmpgmdGlellkeireed..pelpviilt.ahseeedavealkagaddflsKpfdpeeLlkal 111
                     ++++++d+++++i +++ d l+++++++ ++  +++p+i++   +++e ++ e  ++g++d++  p++++e ++++
    AHX11429.1 189 GEIEQHNFDVLIVNITLSK-DLLRVCSTVKSRPksRSIPIILIInDEDDEGVISEITELGISDYVDMPINRSEFIARV 265
                   4689*************98.55*******9999777899999884666688999999****************99987 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 1.3
                   EESSHHHHHHHH.HHHHESEEEEES CS
  Response_reg  28 eaedgkealell.keekvdlillDi 51 
                   ea d++e ++l+ +++k+d i  D+
    AHX11429.1 384 EAYDAAERVRLViEQQKFDTINEDV 408
                   5555555555544777788776665 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       1.3   7.6e+03      36      51 ..     111     126 ..     110     128 .. 0.81
   2 ?    8.9   0.0   0.00021       1.2      15      49 ..     146     178 ..     144     184 .. 0.89
   3 ?    2.2   0.1     0.025   1.5e+02      15      38 ..     372     395 ..     371     403 .. 0.87

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.3
        NOG1  36 sLleeikelfankpvi 51 
                 +L+  ik+l++ k ++
  AHX11429.1 111 ALFTRIKSLLRFKTIL 126
                 69999**999987776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00021
        NOG1  15 davlFllDpseecgysleeQlsLleeikelfankp 49 
                 ++v ++ D+s      +++Q sL+e i+++++  p
  AHX11429.1 146 EIVSYVGDVSSGVIAVVDQQRSLFEPIEKMLK--P 178
                 6899************************9986..4 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.025
        NOG1  15 davlFllDpseecgysleeQlsLl 38 
                 ++v+ l+D++ +  y+ +e ++L+
  AHX11429.1 372 EVVVVLVDATLQEAYDAAERVRLV 395
                 689************999988886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (456 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       609  (0.0339673); expected 358.6 (0.02)
Passed bias filter:                      397  (0.0221429); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.22s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3608.59
//
Query:       AHX11430.1  [L=95]
Description: hypothetical protein NHE_0488 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (95 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       765  (0.0426683); expected 358.6 (0.02)
Passed bias filter:                      418  (0.0233142); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 797.64
//
Query:       AHX11431.1  [L=1591]
Description: bacterial NAD-glutamate dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
          0 1779.0   0.1          0 1778.8   0.1    1.0  1  Bac_GDH        Bacterial NAD-glutamate dehydrogenase
    5.8e-05   22.9   0.1    0.00019   21.3   0.0    1.9  2  ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydro
  ------ inclusion threshold ------
      0.066   12.6   1.4        1.7    8.0   0.1    3.0  3  Chalcone       Chalcone-flavanone isomerase


Domain annotation for each model (and alignments):
>> Bac_GDH  Bacterial NAD-glutamate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1778.8   0.1         0         0       1    1530 [.      68    1584 ..      68    1585 .. 0.97

  Alignments for each domain:
  == domain 1  score: 1778.8 bits;  conditional E-value: 0
     Bac_GDH    1 vrvfnpeleedgwesehtvveivtddmpFlvdsvtaelnrqgltvhlvvhpvleverdkegklleveeekeeaekaekeslilieidrqsdaeelee 97  
                  +++fn++ e +g + ++ vv+i++ dmpFlvds t e++++g+t++  ++ vl +erd++g+l++++++++  e + +esl+++ id++ d+++++ 
  AHX11431.1   68 IKIFNSKKEYKGSKGKYVVVQILNPDMPFLVDSFTEEIKANGFTIYKRLNVVLPIERDENGNLIKIHSRRDPGEGK-NESLLYFLIDET-DQNRISI 162 
                  689******************************************************************9998875.6**********9.9999*** PP

     Bac_GDH   98 leeelekvledvraaveDwkkmreklkelaeele..........kekakvekeeleeaaefLewladdhftfLgyreyeleeeeeeeeleaveesgl 184 
                  l+++le+v + v a+v+Dwkkm + l++ +++++           e+++++  +++e+++fLewl++++f+fLgy+ey+l++e    +le++++s l
  AHX11431.1  163 LRSKLEEVSNLVVAVVSDWKKMVTVLESEISKIKscdlsnqtclLEQKNHNCLSASEIIAFLEWLNEHNFIFLGYEEYSLDKE----KLEKKSSSLL 255 
                  *********************************99999876655333334457889************************998....6999****** PP

     Bac_GDH  185 GilrkeeekeksrelaelpeearkelkekellvltkansrstvhrpayldyvgvkkfdekgkvvgerrflGlftsaaykesvkeiPllrrkveevle 281 
                  Gi+r e++  +s++          + + + ll++ ++   s+vhr++++d++ +k +++kg+v+ge+rflGlfts++y ++v+ iP+lr+k+e+v +
  AHX11431.1  256 GICRLERNLGNSNQ----------FKEYTALLYVGRSGYVSRVHRRVNVDCIRIKCLSDKGEVIGEKRFLGLFTSTVYYQDVRLIPILRKKIENVEK 342 
                  *****993333333..........3445689****************************************************************** PP

     Bac_GDH  282 ragleeeshsgkalleiletyprdeLfqiseeeLleialgilklqerkrvrlflrrdkfgrfvsvlvyvprdryntelrekiqelleealegesvef 378 
                  +a + +++h++kall i++ +pr eLf++s+eeL+e+++g+++l+ ++++rlf+rrdk+g f++++v+vp ++++++lr k+++++++ l+g+ ++ 
  AHX11431.1  343 MASFVKGGHNHKALLAIIQGLPRGELFHTSSEELYETCTGMISLAIKPTLRLFIRRDKVGMFIYCVVFVPNEQFSMKLRYKMRKFIAQILNGTVSDE 439 
                  ************************************************************************************************* PP

     Bac_GDH  379 ttllsesvlarlhfvvrvekkeapevdveelearlaeaarsWedelaealleelgeekakellkryaeafpeaYkedfsaeeavaDierlekleeee 475 
                  + +++es l+rl++v++v++ ea++ + ee+e+ l+++ar+W++el++++++e + +++k+ + +y  +fpe+Yke+f+a ++++Di+++ k+++e+
  AHX11431.1  440 YLIIGESGLVRLQLVLKVDSFEASS-SDEEIEKILISMARDWDEELTDVICKESKAKDNKNGYLEYVGKFPESYKESFDALSGYRDIRKILKVTTEN 535 
                  ********************99965.5689******************************************************************* PP

     Bac_GDH  476 elalslyrpleaeeeelrlklyraeeplsLsdvlpvlenlGlrvlderpyeieaedekevwihdfelelekeeeldldevkerfeeafaavwrgeae 572 
                  +l+++ly++    +++++lk+y +e +l+L++++pv+en++++v+++++y+++++   +v+ih+f l++ +e  +++d+++e+fe a+++++++e+e
  AHX11431.1  536 PLSVKLYEE----SSKYHLKIYFVEGTLELHHLIPVIENMSMKVMEHNCYKVKCSP--TVMIHHFCLQSVAEMLFSVDKIREKFEGALTRIVKNELE 626 
                  *******98....799**************************************96..9************************************** PP

     Bac_GDH  573 nDgfnrLvleagltwrevavlrayakYlrQigltfsqeyieetllkhpeiarllvelFearfdpaleeeeeeeeeekleeeieeaLdevasldedri 669 
                  nD++n+L++ agl+wre+ +lr++  Yl+Qi+++++ +yi+++l++hp+ a l+++lF+arf+p+ +ee+++e+ e l+ + ++ L++v+++  d+i
  AHX11431.1  627 NDQYNALIVLAGLDWREILLLRMFGSYLKQISFKYNPSYIQAALSHHPDAAVLIIRLFHARFSPDIKEESRQEKVEILKGKSKKILSSVTNVMYDNI 723 
                  ***********************************************************************9999********************** PP

     Bac_GDH  670 lrrllelieatlRtnfyqkdedgeakeyislKldpskipelPePrPlfEifVysprvegvHLRggkvARGGlRWSDRreDfRtEvLGLvKaQqvKNa 766 
                  +r+++el+ ++lRtn+y +      keyis+K+++++i+++P P+P++E+fVy +++e++HLRggk+ARGG+RWSDR +DfRtE+LGL+KaQ+ KN+
  AHX11431.1  724 IRTCIELCLSILRTNYYMN------KEYISVKISSKDITDMPLPKPFVEVFVYHNKFEAIHLRGGKIARGGIRWSDRLQDFRTEILGLMKAQMAKNT 814 
                  *****************99......99********************************************************************** PP

     Bac_GDH  767 vIVPvGaKGGFvvkrlpkaadreallaegiacYktfirgLLditDnlvdgevvppedvvrhDedDpYLVVAADKGTAtFSDiANevsaeygFWLgDA 863 
                   I+PvG+KGGF++k++   +dr+ l++++i+ Yk f+rg+Ld+tDn+v+g++ +++d++++D dD+YLVVAADKGTA+FS++ANevsaey+FWLgDA
  AHX11431.1  815 AIIPVGSKGGFILKEQI--EDRQLLTETAIRYYKDFLRGILDLTDNIVNGKCEKAKDILTYDRDDSYLVVAADKGTAKFSNYANEVSAEYNFWLGDA 909 
                  ***************99..9***************************************************************************** PP

     Bac_GDH  864 FASGGsvGYDHKkmGITArGAWesvkrhFrelgvdiqtedftvvGiGDmsGDVFGNGmLlsehirLvaAFdHrhiFiDPnPdaaasfaErkRLFelp 960 
                  FASGGs GYDHKk+GITArGAW s++  F+e   d++++  +++GiGDmsGDVFGNGmLls++i+LvaAF+H+hiFiDPnPd++ sf+Er+R+F+lp
  AHX11431.1  910 FASGGSSGYDHKKLGITARGAWISMQMAFWERFNDLERKGSSIIGIGDMSGDVFGNGMLLSNKIKLVAAFNHMHIFIDPNPDPEISFQERQRMFNLP 1006
                  ************************************************************************************************* PP

     Bac_GDH  961 rssWadYdksliSkGGgvfsRsaKsiklspevrellgieeeeltPneLikaiLkapvdLlwnGGiGTYvkaseeshadvgDkandalRvngkelrak 1057
                   s+W dY++sliSkGGgvf R++K i++s+e++++++i ee+ltPneLik iL+++vd++wnGGiGTYvk+see+++ vgDkand++Rv+gk++rak
  AHX11431.1 1007 SSTWMDYNHSLISKGGGVFLRNEKLIPISSEMKKVFDIYEEKLTPNELIKYILQSDVDVIWNGGIGTYVKSSEETNEVVGDKANDSIRVDGKNVRAK 1103
                  ************************************************************************************************* PP

     Bac_GDH 1058 vvgEGgNLGltQlgRiEyalkggrintDaiDNsaGVdcSDhEVNiKilLnklvaegeltlkqRnklLaemtdeVaelVL.rdnyrqtqalslaeaqa 1153
                  v+ EGgNLG+tQlgRiEy+ +gg +ntD+iDN+aGV cSD EVNiKi+++k++++g++tl++R+ lL++m  eV el+L + n+ q+ +++++++++
  AHX11431.1 1104 VIVEGGNLGCTQLGRIEYSGNGGIVNTDFIDNCAGVSCSDIEVNIKIAFSKAIKSGKITLRERDILLKAMEPEVVELILlHINKIQSLMMAMETMRS 1200
                  *****************************************************************************98578*************** PP

     Bac_GDH 1154 aeeleeqarliraLekegkLdralefLPsdeelaerkaagkgltrPelavLlaYakivlkeellasdlpddpylakelaeyFPkalrerfaeeiekH 1250
                   ++le++++l+ +L k g Ld+++efLPs+ee+++  a+g++++rP++avL aY+k+ ++e++++s+lpd+++l ++l +yFP+ +rerf ++i +H
  AHX11431.1 1201 PRRLEQYQNLVGKLVKVGLLDKKVEFLPSNEEVKRLFAEGRSFERPQIAVLAAYSKMYIYEKIITSELPDSEILYHYLINYFPSLMRERFLSDILDH 1297
                  ************************************************************************************************* PP

     Bac_GDH 1251 rLrreiiatalaNelvnrlGitfvlrlaeetgasvaevvrayvvarevfdleelweeiealdnkvsaevqlelllevrrlleratrWllrnrrkeld 1347
                  +Lrreiiat+laN++vnr G+tf++++ ++tg s++ev+r +v ++e++dl++l+ee+++l ++++ +  +++ + v ++l+++++Wllrn +++++
  AHX11431.1 1298 PLRREIIATKLANNIVNRFGCTFIQNAVQNTGFSSKEVIRVVVTVMEIYDLPALFEELDHLIGQIDIQFFYRINVLVIQFLDQSVYWLLRNYPQPIN 1394
                  ************************************************************************************************* PP

     Bac_GDH 1348 iaaeverfkekvealkakleelleeeelealearaeelveagvpeelakrvaslealasaldivevaeetkrdv......eevaevyfalgerlelk 1438
                  ++++ve+f++kv+++++kl ++l++++l++++++ +++++ g++ el++++a l+++ +al i++++++  +          v+++yf+lg++l+l+
  AHX11431.1 1395 LTSAVEEFSDKVREISTKLVDVLDSNSLSEYRESLQSFEKFGLSPELSNKLAGLQFVSAALGIAQTSKNLCEAEgfeidhMVVSRIYFELGAALSLA 1491
                  *****************************************************************998865544444454899************** PP

     Bac_GDH 1439 wlleqi.selevedrwqalarealrddlaaaqraltaevlkkseeeesaeeaveawlekneealerakallaelkasekldlaklsvalrelr 1530
                  +l+e + +++e++++wq+++   l d+l ++q a+t+e+ k  +++ +  +a+++w+ k++++ler+k++++++++s++ld++k+++++++lr
  AHX11431.1 1492 SLREIVyKKFENSSYWQRISAYCLSDELCDEQLAFTREIAKYIRKDVNYFTAIKQWEGKHSAKLERYKTFYNDIMSSGELDINKFMMLVKRLR 1584
                  ****9834679*******************************************************************************998 PP

>> ELFV_dehydrog  Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       1.1   6.5e+03       4      43 ..     920     958 ..     917     973 .. 0.78
   2 !   21.3   0.0   3.2e-08   0.00019      76     185 ..    1028    1148 ..    1009    1166 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 1.1
                    TTTTTHHHHHHHHHHHHHHHHTTTS-STTEEEEEE--SHH CS
  ELFV_dehydrog   4 ldrpeaTglGvvyyveemlkklkldslegkrvaisGsGnv 43 
                    + + + T++G+ + ++ ++ + ++++le k   i G G++
     AHX11431.1 920 HKKLGITARGAWISMQMAFWE-RFNDLERKGSSIIGIGDM 958
                    666778888888888888888.777788888888888876 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 3.2e-08
                     HHHHHHHHHCSSS.STTHSHH..STSTSEEESHHSHH...HHSS-SEEEE-.SSTTSB-HHHHTHTH.....HTT-SEEE-SSSS-B-HHHHHH CS
  ELFV_dehydrog   76 ieellelkeerks.vkeykks..sekkaeyieneeel...lelkvdilvPc.Atqneideenakali.....kngvklvvEgANlpttqeAkei 157 
                      e+l+ +  e k+ ++ y+++   ++ ++yi ++ ++   ++  + + v +    ne+ +++a+  i     + ++k++vEg Nl++tq  +  
     AHX11431.1 1028 NEKLIPISSEMKKvFDIYEEKltPNELIKYILQS-DVdviWNGGIGTYVKSsEETNEVVGDKANDSIrvdgkNVRAKVIVEGGNLGCTQLGRIE 1120
                     5666666555555355555445433344444332.2222366667777777556688888888888888885448******************* PP

                     HHHTT-EEE-HHHHTTHHHHHHHHHHHH CS
  ELFV_dehydrog  158 leeagvlvvpdkaaNaGGVtvSslEmlq 185 
                     ++ +g +v  d++ N+ GV +S +E+  
     AHX11431.1 1121 YSGNGGIVNTDFIDNCAGVSCSDIEVNI 1148
                     *************************975 PP

>> Chalcone  Chalcone-flavanone isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       0.5     3e+03     148     186 ..     157     195 ..     142     205 .. 0.82
   2 ?    2.1   0.0     0.019   1.1e+02     125     178 ..     524     575 ..     490     594 .. 0.71
   3 ?    8.0   0.1   0.00028       1.7      41      84 ..    1530    1577 ..    1518    1591 .] 0.69

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.5
                 TSEEEEEEESSS---SS-SEEEE-HHHHHHHHHHHHSTT CS
    Chalcone 148 kgsLtvsfskdesipekesavienkllseavLesmiGkn 186
                 +  +++  sk e++++   av+ + +    vLes i k 
  AHX11431.1 157 QNRISILRSKLEEVSNLVVAVVSDWKKMVTVLESEISKI 195
                 5566777799999***999999999999999**999886 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.019
                 HHHHHHTT-EE-TT-EEEEEE-TTSEEEEEEESSS---SS-SEEEE-HHHHHHH CS
    Chalcone 125 kflevfkdetfpPGssilfavspkgsLtvsfskdesipekesavienkllseav 178
                 + ++++k +t +P s  l++ s+k  L + f +     ++   vien  +   v
  AHX11431.1 524 DIRKILKVTTENPLSVKLYEESSKYHLKIYFVEGTLELHHLIPVIENMSM--KV 575
                 457899999999********************999888999999999755..35 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00028
                  EEEEE-TTHHHHHHHH.HTT--HHHHHH-HHHHHHHHHS...SS-EEE CS
    Chalcone   41 igvyledkalkslsak.WkgksaeeLtesvdffrdivtg...pfekli 84  
                  i+ y+ +++  + + k W+gk +++L+    f++di+++   + +k++
  AHX11431.1 1530 IAKYIRKDVNYFTAIKqWEGKHSAKLERYKTFYNDIMSSgelDINKFM 1577
                  67777777666666555*******************986222234544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1591 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       746  (0.0416086); expected 358.6 (0.02)
Passed bias filter:                      511  (0.0285013); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.96u 0.32s 00:00:01.28 Elapsed: 00:00:00.43
# Mc/sec: 11064.26
//
Query:       AHX11432.1  [L=91]
Description: putative glutamyl-tRNA(Gln) amidotransferase, C subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       369  (0.0205812); expected 358.6 (0.02)
Passed bias filter:                      251  (0.0139997); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 747.89
//
Query:       AHX11433.1  [L=311]
Description: hypothetical protein NHE_0491 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       820  (0.045736); expected 358.6 (0.02)
Passed bias filter:                      573  (0.0319594); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2521.10
//
Query:       AHX11434.1  [L=436]
Description: glutamate--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-60  204.8   0.0    2.4e-60  204.1   0.0    1.3  1  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.1   0.0   1.3e-64   2.4e-60       4     291 ..       3     277 ..       1     295 [. 0.87

  Alignments for each domain:
  == domain 1  score: 204.1 bits;  conditional E-value: 1.3e-64
                   EEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE-ST CS
  tRNA-synt_1c   4 tRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvcect 100
                   tRfaP+PtG LH+G+ ++a++++l A++ +GkfilRi+DTd++r  ee++e+i  dlkwlgi+  +   +qs+rf  +++ +e+Li+ G  Y c++t
    AHX11434.1   3 TRFAPSPTGLLHLGNMRTAIISFLCARSSGGKFILRIDDTDKTRVREEYIEKIFIDLKWLGIES-DLCFRQSERFSLYDEAMEQLIQTGRVYACYET 98 
                   9***************************************************************.569***************************** PP

                   HHHHHHHHCCSSHSS-TTTTS-HHHHHHHHHHHHHTTHSTTTS-EEEESSBTTSSGGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHH CS
  tRNA-synt_1c 101 keeleeereeqeklgskerdrydeenlklfeeemkkgkaegekavvRlkideessvefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDal 197
                   +eele er++    g    + y    +       k+ k+++++   R+ +d +  + ++D++rg+i+++  +  d +i++ +++ tY f  vidD++
    AHX11434.1  99 PEELEMERRSLLSRG--LPPVYR--RR-------KEIKNSERSPYYRFELDSSDIISWDDKLRGKIAIDLRSTSDPIIRRENGIYTYMFPSVIDDID 184
                   ********9966666..222222..22.......233467788899*******99****************************************** PP

                   TT-SEEEEEGGGGCCHHHHHHHHHHTT-S..-EEEEEE--EEETTSB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-H.HHHHHHHHHHCC CS
  tRNA-synt_1c 198 eeithvlrteefldntpkyiwllealglev.ppfiheylrlnlekkklSKRklsllvdekqvkewddlreallnflrrlGwtp.ekerelftreel 291
                    +i  ++r+e++++nt+ +i +l+alg +  p f+h++l+  ++  k+SKR +     ++ +++    +e++  +l  lG    ++ +++ + +e+
    AHX11434.1 185 YGIDTIIRGEDHISNTAVQIQMLKALGCNRiPDFAHMPLL-KMQSGKISKRVGGYE--IESLRNAHIEPEVICAYLLNLGGRSsADFKNFKEYKEF 277
                   ***************************9865999999875.688899******999..*****************999886641344444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.23s 00:00:00.70 Elapsed: 00:00:00.37
# Mc/sec: 3500.84
//
Query:       AHX11435.1  [L=41]
Description: na+/H+ ion antiporter subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    0.00055   19.7   0.0    0.00055   19.7   0.0    1.0  1  MNHE      Na+/H+ ion antiporter subunit


Domain annotation for each model (and alignments):
>> MNHE  Na+/H+ ion antiporter subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.7   0.0   3.1e-08   0.00055     101     134 ..       1      30 [.       1      40 [. 0.74

  Alignments for each domain:
  == domain 1  score: 19.7 bits;  conditional E-value: 3.1e-08
        MNHE 101 ltPGTltvdvdedrrvlyvHvldvedeeeearee 134
                 +tPGT+tv ++e+r  +y H++d +   ++ + +
  AHX11435.1   1 MTPGTVTVSISENR--IYFHCFDNSF--KAGIPD 30 
                 69*******99888..******8643..444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       226  (0.0126053); expected 358.6 (0.02)
Passed bias filter:                      181  (0.0100954); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 341.11
//
Query:       AHX11436.1  [L=71]
Description: hypothetical protein NHE_0494 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.056   13.4   2.1       0.06   13.3   0.3    1.8  2  KIX_2     KIX domain


Domain annotation for each model (and alignments):
>> KIX_2  KIX domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.1     0.065   1.2e+03      49      61 ..       7      20 ..       4      28 .. 0.63
   2 ?   13.3   0.3   3.4e-06      0.06      55      69 ..      50      64 ..      32      68 .. 0.86

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.065
       KIX_2 49 kiFsk.AtskedYl 61
                k+F++ +++k++  
  AHX11436.1  7 KVFETsSANKSEKE 20
                67766356666655 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 3.4e-06
       KIX_2 55 tskedYlrkislKml 69
                ts+++Ylrk+s+Km+
  AHX11436.1 50 TSQDKYLRKCSEKMA 64
                7999**********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (71 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.20s 00:00:00.54 Elapsed: 00:00:00.33
# Mc/sec: 636.81
//
Query:       AHX11437.1  [L=284]
Description: ribonucleotide reductase, small chain family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-57  195.1   6.3    1.9e-57  194.9   6.3    1.1  1  Ribonuc_red_sm  Ribonucleotide reductase, small chain


Domain annotation for each model (and alignments):
>> Ribonuc_red_sm  Ribonucleotide reductase, small chain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.9   6.3   1.1e-61   1.9e-57      31     279 .]       1     244 [.       1     244 [. 0.96

  Alignments for each domain:
  == domain 1  score: 194.9 bits;  conditional E-value: 1.1e-61
                     GHHHHHHHHSTS-HHHHHHHHHHHHHHHHHHHHHHHCHHHCHHCCBSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHT.-HHHHHHHHCHHHH-HH CS
  Ribonuc_red_sm  31 lskDlkdwkekLsedekefikkvlaflalldtivnenlverllsevqipearafygfqaamEniHaesYsllletlvkdekekdelfnaieenpa 125
                     + +D++dw++k+s++ek++++++++f++++d+ v + ++++++  ++ pe+ ++++ +a mE+iH  +Y++ll+t+++++ e    + a++++++
      AHX11437.1   1 MADDVQDWHNKISKAEKNLLTQIFRFFTQADVEVHNCYMNHYAGIFKPPEVCMMLTAFANMETIHIAAYAHLLDTVGMPDIE----YLAFTKYQE 91 
                     789**************************************************************************99999....9******** PP

                     HHHHHHHHHHHHCTTTSCHHHHHHHHHHH.HHHHCCCHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSHHHHHHHHHH CS
  Ribonuc_red_sm 126 lqkkaewikkwyeskkdeekfaerlvafa.llegilfysgFaailwlkkrgllpglaeiielilrDeglHtdfagllfkelkeenelenkeleee 219
                     +++k e++  +    +++ ++a++l+++  ++eg++++++Fa++l++ + ++++g+++ii++ +rDe+lH + ++ lf++++ en +++++le+e
      AHX11437.1  92 MKEKCEYLRAFKM--TSPIEIAKTLAVYGaFTEGLQLFASFAILLNFPRFNKMKGMGQIIAYSVRDETLHSNSIIKLFRTFLIENGINKADLEKE 184
                     ********65543..35799********99*******************************************************999******* PP

                     HHHHHHHHHHHHHHHHHHHTTT..BTTCHHHHHHHHHHHHHHHHHHCTT---SS-TT---C CS
  Ribonuc_red_sm 220 veelikeavelEkefitdalpv.ellglnkedvkqYieyvadrllmnlgyeklYnveeenP 279
                     ++e+++ +v  E++fi+ a+++ ++ gl++ +vk+Yi+y+a+ +l++lg+e++Y++ + nP
      AHX11437.1 185 IHEICDAMVLHEDAFIDLAFEMgDVEGLKASEVKEYIRYIANLRLKQLGFEEIYKE-KLNP 244
                     ********************99999******************************8.4666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.34
# Mc/sec: 2490.97
//
Query:       AHX11438.1  [L=37]
Description: hypothetical protein NHE_0496 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       192  (0.0107089); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 296.65
//
Query:       AHX11439.1  [L=538]
Description: transcription termination factor NusA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.8e-27   93.4   7.0    2.4e-25   88.4   0.2    3.5  4  KH_5        NusA-like KH domain
    1.9e-18   67.0   1.1    4.5e-18   65.8   0.3    2.1  2  NusA_N      NusA N-terminal domain
    2.2e-08   33.8   1.6    4.2e-06   26.5   0.2    3.2  2  KH_2        KH domain
    3.3e-06   27.6   2.7     0.0035   17.9   0.0    3.5  5  HHH_5       Helix-hairpin-helix domain
      1e-05   25.2   0.1       0.26   11.1   0.0    2.8  2  KH_1        KH domain
    0.00014   22.1   0.1       0.25   11.6   0.0    3.1  3  DUF4332     Domain of unknown function (DUF4332)
     0.0015   18.3   0.1     0.0087   15.9   0.0    2.3  2  KH_4        KH domain
       0.01   16.0   0.1      0.032   14.4   0.1    2.0  1  Sep15_SelM  Sep15/SelM redox domain
  ------ inclusion threshold ------
      0.061   13.7   0.2       0.22   11.9   0.2    2.0  1  S1          S1 RNA binding domain
          8    6.2   7.2        1.6    8.4   0.1    3.5  4  FlbD        Flagellar and Swarming motility proteins


Domain annotation for each model (and alignments):
>> KH_5  NusA-like KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       5.8     1e+04      26      36 ..     218     228 ..     217     230 .. 0.77
   2 !   88.4   0.2   1.3e-28   2.4e-25       1      68 [.     273     340 ..     273     341 .. 0.97
   3 !    7.1   0.1    0.0032       5.7       4      51 ..     347     388 ..     345     400 .. 0.80
   4 ?   -1.6   0.1       1.7     3e+03      44      62 ..     453     471 ..     444     476 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 5.8
        KH_5  26 kGsrikavsse 36 
                  G+r++ v+++
  AHX11439.1 218 AGDRVRCVIQK 228
                 68899999887 PP

  == domain 2  score: 88.4 bits;  conditional E-value: 1.3e-28
        KH_5   1 aGertkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDlaefianalsPaevlsVk 68 
                 +G+r+kvaV s++ nvdpvGa++g++Gsri+av +eL+gekidvve+s+D + f  nal+P +  ++ 
  AHX11439.1 273 PGSRAKVAVFSSDRNVDPVGACIGMGGSRINAVANELNGEKIDVVEYSSDTTVFLVNALKPIKPVKIM 340
                 79************************************************************998886 PP

  == domain 3  score: 7.1 bits;  conditional E-value: 0.0032
        KH_5   4 rtkvaVkshnpnvdpvGaivgkkGsrikavsseLkgekidvvewseDl 51 
                 r+ ++V ++n     +  ++g++G++i+ +ss   g +i+v    e  
  AHX11439.1 347 RIELVVGDDN-----LSMVIGRSGQNIHLLSSLV-GYRIEVLSDAEVS 388
                 6667788888.....999**********999998.*****99877764 PP

  == domain 4  score: -1.6 bits;  conditional E-value: 1.7
        KH_5  44 vvewseDlaefianalsPa 62 
                  ve+++D  + ++ +l ++
  AHX11439.1 453 AVEYVNDQPKRVKALLEKY 471
                 5788888777777777765 PP

>> NusA_N  NusA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.8   0.3   2.5e-21   4.5e-18       2     121 .]      13     163 ..      12     163 .. 0.80
   2 ?   -3.3   0.0       6.2   1.1e+04      41      55 ..     336     350 ..     316     354 .. 0.75

  Alignments for each domain:
  == domain 1  score: 65.8 bits;  conditional E-value: 2.5e-21
                 CHCCCCCCCCCS---HHHHHHHHHHHHHHHHHCC.T-SSS-EEEEE-TTT--EEEEEEEEEESS-S.............................-TTT CS
      NusA_N   2 llealeelakekgiskevviealeeaLakaykkn.ygedenveveidretgeikvyskktVveeve.............................dpek 70 
                 ++e+++++a+++g+++e++++a+ ++La ++ k+ y  d  ++veidr++gei++ +++ Vve+ e                             + ++
  AHX11439.1  13 IVESINSVAEKEGLNPENLFQAIGAELAYEIGKRqY-GDPRISVEIDRKSGEITISKRLLVVEDSEkdkmmaqlpqetqggvveekalpiihetqEYDD 110
                 799****************************99835.5567*********************7654445555555555666666666666665534446 PP

                 EEEHHHHH.CC.STT--TTBEEEEE----SSCCHCHHHHHHHHHHHHHHHCCH CS
      NusA_N  71 eIsleeak.ki.dpkikvGdtveeevtpkdfgriaaqtakqvivqkireaere 121
                  I+l++ak k+   + k Gd+v e + + + g ++a+ +k +i++ i+++ re
  AHX11439.1 111 IIALSTAKlKYpASEPKPGDVVVERLPSFSSGYLIAKVMKPKIERLINSLVRE 163
                 6******8444544457*******997688888**************999885 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 6.2
                 -EEEEE-TTT--EEE CS
      NusA_N  41 nveveidretgeikv 55 
                  v++ id+e + i++
  AHX11439.1 336 PVKIMIDEEAKRIEL 350
                 378888888887765 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.1     0.012        22      37      62 ..     292     318 ..     288     336 .. 0.78
   2 !   26.5   0.2   2.3e-09   4.2e-06      17      69 ..     338     390 ..     322     397 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.012
                 HHHHTGGGHHHHHHHHHHH.HHHHHHH CS
        KH_2  37 givIGkgGsnikkigkelr.kdiekle 62 
                 g  IG gGs+i+++  el+ ++i+++e
  AHX11439.1 292 GACIGMGGSRINAVANELNgEKIDVVE 318
                 778**********99988525555555 PP

  == domain 2  score: 26.5 bits;  conditional E-value: 2.3e-09
                 EEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEE CS
        KH_2  17 kveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVkln 69 
                 k+ I+++a+r+++v+ + +  +vIG+ G+ni  + + ++++ie+l + +V+ +
  AHX11439.1 338 KIMIDEEAKRIELVVGDDNLSMVIGRSGQNIHLLSSLVGYRIEVLSDAEVSKK 390
                 78899999*****************************************9876 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       5.8     1e+04      18      48 ..      13      40 ..      11      43 .. 0.67
   2 ?   -2.4   0.0       4.2   7.6e+03      24      37 ..     106     119 ..      98     120 .. 0.80
   3 !   17.9   0.0   1.9e-06    0.0035      11      53 ..     409     451 ..     407     455 .. 0.90
   4 ?   -3.4   0.0       8.7   1.6e+04      12      21 ..     461     470 ..     461     472 .. 0.86
   5 !    7.9   0.0    0.0025       4.6       3      56 ..     476     532 ..     475     533 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 5.8
                HHTTT--SHHHHHHS-HHHHHTSTTS-HHHH CS
       HHH_5 18 llsaGiesvedlaaadveeLakipGiGkktA 48
                +++  i+sv++   +++e L ++  iG+++A
  AHX11439.1 13 IVES-INSVAEKEGLNPENLFQA--IGAELA 40
                6666.777776666678888877..777766 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 4.2
                 -SHHHHHHS-HHHH CS
       HHH_5  24 esvedlaaadveeL 37 
                   ++d++a+++++L
  AHX11439.1 106 QEYDDIIALSTAKL 119
                 5689****999988 PP

  == domain 3  score: 17.9 bits;  conditional E-value: 1.9e-06
                 -HHHHHHHHTTT--SHHHHHHS-HHHHHTSTTS-HHHHHHHHH CS
       HHH_5  11 GpktAlallsaGiesvedlaaadveeLakipGiGkktAeriil 53 
                  +++A  l+  G+++v ++a+++v +La i G+  + Ae i+ 
  AHX11439.1 409 EEVIAQLLVTEGFSTVKEIAECEVSRLAFIEGFDTDIAEEIKN 451
                 56789999999****************************9975 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 8.7
                 HHHHHHHHTT CS
       HHH_5  12 pktAlallsa 21 
                 pk+++all++
  AHX11439.1 461 PKRVKALLEK 470
                 8999999987 PP

  == domain 5  score: 7.9 bits;  conditional E-value: 0.0025
                 HHHTSTT--HHHHHHHHTTT--SHHHHHHS-HHHHHTSTT...S-HHHHHHHHHHHH CS
       HHH_5   3 eLlsvsGiGpktAlallsaGiesvedlaaadveeLakipG...iGkktAeriilelk 56 
                 ++ls+s +  ++   lls   +s+e++a+++ +eL +i G   +   t+e++i  ++
  AHX11439.1 476 DMLSLSHLEHEMLEVLLSSKLTSLEKVAELSCDELREIIGenhFDTNTVEQLIIKAR 532
                 568888889999999999999*****************8877788888888888777 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   0.0   0.00014      0.26      11      47 ..     291     324 ..     279     343 .. 0.83
   2 !   11.1   0.0   0.00015      0.26      12      46 ..     358     394 ..     347     406 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
                 HHHHHTGGGHHHHHHHHHH.T-EEEEES.STT...T.-E CS
        KH_1  11 vgriIGkgGsnIkeIreet.gakIkvpk.sedegsdere 47 
                 vg+ IG gGs+I+   +e  g kI+v++ s+d     ++
  AHX11439.1 291 VGACIGMGGSRINAVANELnGEKIDVVEySSD-----TT 324
                 8999************9999******965554.....34 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00015
                 HHHHTGGGHHHHHHHHHHT-EEEEESSTT......T.- CS
        KH_1  12 griIGkgGsnIkeIreetgakIkvpksedeg...sder 46 
                 + +IG+ G+nI+ + +  g +I v  s++e    ++e+
  AHX11439.1 358 SMVIGRSGQNIHLLSSLVGYRIEVL-SDAEVskkKMEE 394
                 579*************66******9.555444443333 PP

>> DUF4332  Domain of unknown function (DUF4332)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.92   1.6e+03      74      94 ..      17      37 ..      14      48 .. 0.81
   2 !   11.6   0.0   0.00014      0.25      54      88 ..     401     435 ..     376     437 .. 0.82
   3 !    6.4   0.1    0.0057        10      48     115 ..     470     537 ..     445     538 .] 0.85

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.92
     DUF4332 74 vdsvaeLaqrnpanLhqklkr 94
                + svae    np+nL+q++++
  AHX11439.1 17 INSVAEKEGLNPENLFQAIGA 37
                6788888889*******9976 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00014
     DUF4332  54 dLarikgigeeyaeLLeaaGvdsvaeLaqrnpanL 88 
                 +++  + ++e  a+LL+  G ++v+e+a++++++L
  AHX11439.1 401 RFVEALNVEEVIAQLLVTEGFSTVKEIAECEVSRL 435
                 46688899**********************99998 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0057
     DUF4332  48 klanlAdLarikgigeeyaeLLeaaGvdsvaeLaqrnpanLhqklkrlnrskklkrqlvptleqvkeW 115
                 k  +  d+     +++e+ e+L+ + ++s +++a+ + ++L + +++   ++++++ql+++ +++  W
  AHX11439.1 470 KYDANMDMLSLSHLEHEMLEVLLSSKLTSLEKVAELSCDELREIIGENHFDTNTVEQLIIKAREALGW 537
                 5556667788889999*******************************999999999999988877666 PP

>> KH_4  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0         2   3.6e+03      39      53 ..     290     304 ..     258     305 .. 0.73
   2 !   15.9   0.0   4.9e-06    0.0087      20      52 ..     337     369 ..     325     376 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 2
        KH_4  39 dlGrvIGkrGrtldA 53 
                  +G  IG  G  ++A
  AHX11439.1 290 PVGACIGMGGSRINA 304
                 378889999999888 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.9e-06
        KH_4  20 vteeeeeeeveielnvegedlGrvIGkrGrtld 52 
                 v+++++ee ++iel v  ++l  vIG+ G+++ 
  AHX11439.1 337 VKIMIDEEAKRIELVVGDDNLSMVIGRSGQNIH 369
                 5555667799********************986 PP

>> Sep15_SelM  Sep15/SelM redox domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.8e-05     0.032       2      75 ..     423     496 ..     422     497 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-05
                 EEEEETT---STTHHHHHHTTTHH.HHBTTEEEEEESS---EEEEE.-SSS---EEEE-SSS-HHHHHHHHHHHT CS
  Sep15_SelM   2 avlevcgcklnrlpevkaFvkedaaakfpnlevkyvrgapPkLill.dedgeeverislekwdrdeieelleekg 75 
                 +v e+ +c++ rl  ++ F ++ a ++ +n +v+yv+ +p +++ l ++ +   + +sl++++ + +e ll++k+
  AHX11439.1 423 TVKEIAECEVSRLAFIEGFDTDIA-EEIKNRAVEYVNDQPKRVKALlEKYDANMDMLSLSHLEHEMLEVLLSSKL 496
                 6889***************88877.******************9663777789999****************996 PP

>> S1  S1 RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   0.00012      0.22      20      65 ..     194     231 ..     170     239 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
                 EEEEETTTEEEEEEGGGSSSSCEESCHHHCEETTEEEEEEEEEEET CS
          S1  20 afVelgngvegfvpaselsrdarvedpdevlkvGdevkvkvlkvdk 65 
                 +++++g g+eg +p s+l        ++e ++ Gd+v+ +++kv++
  AHX11439.1 194 MIIDVG-GAEGILPFSSLI-------KGESFRAGDRVRCVIQKVEY 231
                 6899**.************.......79****************97 PP

>> FlbD  Flagellar and Swarming motility proteins
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0         1   1.8e+03      39      55 ..      93     109 ..      91     112 .. 0.89
   2 ?   -1.6   0.1       1.2   2.1e+03      43      56 ..     255     268 ..     252     269 .. 0.84
   3 ?    8.4   0.1   0.00087       1.6       8      35 ..     303     330 ..     300     348 .. 0.84
   4 ?   -2.9   0.1       2.9   5.2e+03      44      55 ..     446     457 ..     444     459 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 1
        FlbD  39 vVkEsvdeviervieyr 55 
                 vV+E++  +i++  ey 
  AHX11439.1  93 VVEEKALPIIHETQEYD 109
                 89**********99996 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.2
        FlbD  43 svdeviervieyrr 56 
                 +v ev +rv+e ++
  AHX11439.1 255 QVPEVYDRVVEVKK 268
                 6889*****99986 PP

  == domain 3  score: 8.4 bits;  conditional E-value: 0.00087
        FlbD   8 ngeefvlNadlIetieetPDTvItLtnG 35 
                 n     lN + I  +e   DT++ L+n 
  AHX11439.1 303 NAVANELNGEKIDVVEYSSDTTVFLVNA 330
                 5555669*******************96 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 2.9
        FlbD  44 vdeviervieyr 55 
                 ++e+ +r +ey 
  AHX11439.1 446 AEEIKNRAVEYV 457
                 689****99995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (538 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       855  (0.0476881); expected 358.6 (0.02)
Passed bias filter:                      643  (0.0358637); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.40
# Mc/sec: 4054.19
//
Query:       AHX11440.1  [L=795]
Description: translation initiation factor IF-2 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.6e-32  111.5  15.5    6.7e-31  107.3   9.9    3.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    1.2e-24   86.4   2.1    4.4e-24   84.6   2.1    2.1  1  IF-2          Translation-initiation factor 2
    5.3e-11   42.6   0.5    1.5e-10   41.2   0.5    1.8  1  MMR_HSR1      50S ribosome-binding GTPase
    1.4e-09   38.1   1.3    8.3e-07   29.3   0.1    3.1  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    1.3e-06   28.0   0.6    8.1e-06   25.4   0.6    2.2  1  SRPRB         Signal recognition particle receptor beta subun
      7e-05   22.4   2.5    0.00027   20.5   2.5    2.1  1  FeoB_N        Ferrous iron transport protein B
    7.2e-05   22.3   1.4     0.0002   20.9   0.3    2.1  2  Arf           ADP-ribosylation factor family
    0.00096   19.1   1.2     0.0032   17.4   0.4    2.3  2  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0014   18.8   0.1     0.0036   17.5   0.1    1.7  1  Roc           Ras of Complex, Roc, domain of DAPkinase
     0.0022   17.7   0.7     0.0067   16.2   0.7    1.8  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
     0.0051   16.7   6.6       0.15   11.9   1.0    2.6  2  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
      0.053   13.5   0.2       0.13   12.2   0.2    1.7  1  SIS_2         SIS domain
       0.39   10.8   7.5        0.6   10.2   0.0    3.4  4  Dynamin_N     Dynamin family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.3   9.9   4.9e-34   6.7e-31       5     189 ..     315     472 ..     311     476 .. 0.90
   2 ?    2.4   0.3     0.072        99      48     106 ..     580     639 ..     566     736 .. 0.71

  Alignments for each domain:
  == domain 1  score: 107.3 bits;  conditional E-value: 4.9e-34
                 EEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEEEEET CS
    GTP_EFTU   5 nigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavlvvda 103
                  ++++gh+DhGKtTL+d+L +++ + s                  +  giT ++ a +++ +++ + i++iDtPGH+ F++   rg++v+D++vl+v+a
  AHX11440.1 315 VVTVMGHIDHGKTTLLDTLRHTHVTAS------------------ESGGITQHIGAYQVQ-TKDGRSITFIDTPGHAAFTSMRMRGAEVTDIVVLLVAA 394
                 689****************95444433..................468************.8999********************************** PP

                 TTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
    GTP_EFTU 104 veGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealv 189
                 ++Gv++qt e +++a++ +vpiiv+iNK+D+ +a+  ++ +++ q+       + + +++g  +v  v +Sa++g ++++l e + 
  AHX11440.1 395 DDGVNEQTIEAIKHAKAAKVPIIVAINKIDKEGANPLKVMTDLLQHG------VVVEEMQG--DVMSVNISAKNGTNIDKLEELIL 472
                 ****************************************9999888......66666666..6999************9988765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.072
                 HHHHHTSCSSCEEEEEETTCSSEEEEEE...EESSSGGGHHHHHHHHHT-SEEEEEEETTTB CS
    GTP_EFTU  48 eErergiTiksaaisleketkkylinli...DtPGHvdFskevirglrvlDgavlvvdaveG 106
                 +Er +     s   s+e   +k+++n+i   D  G v+ + e i+gl+  D+ + ++  + G
  AHX11440.1 580 QERDKVDNTRSLRDSFE--NEKKKLNFIikaDVNGSVEAITESIKGLSHPDIEISIIHTSVG 639
                 55555555666667778..666666666566***********************99998876 PP

>> IF-2  Translation-initiation factor 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.6   2.1   3.2e-27   4.4e-24       5     104 ..     592     686 ..     588     687 .. 0.93

  Alignments for each domain:
  == domain 1  score: 84.6 bits;  conditional E-value: 3.2e-27
                 HHCCCSCSSCCEEEEEESSHHHHHHHHHHHHCTT.SSTEEEECEEEESSB-HHHHHHHHHSTEEEEEESSSCTHHHHHCCCCCTSEEEEESSHHHHHHH CS
        IF-2   5 feeikeegkelnviikaDvqGsleAlkeaLekleseevkvkvihsgvGaitesDvelasasnaiiigFnvkvskkakklaekegvkirlynvIYklidd 103
                  +++++e+k+ln+iikaDv+Gs+eA++e+++ l++ ++++++ih++vG+i++sD  la++s++ iigF vk+++++k+        i  +++IY++i++
  AHX11440.1 592 RDSFENEKKKLNFIIKADVNGSVEAITESIKGLSHPDIEISIIHTSVGDINDSDLLLAEVSDSYIIGFRVKAERTVKEH-----SAILFHSIIYDVIKH 685
                 56788889*************************77*************************************9999765.....56***********98 PP

                 H CS
        IF-2 104 v 104
                 v
  AHX11440.1 686 V 686
                 7 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.2   0.5   1.1e-13   1.5e-10       2     114 .]     316     422 ..     315     422 .. 0.81

  Alignments for each domain:
  == domain 1  score: 41.2 bits;  conditional E-value: 1.1e-13
                 EEEEESTTSSHHHHHHHHHTSTEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltgekaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeelee 99 
                 v ++G+   GK+tL+ +l  +++ +s+  g T++i  ++v++k+ ++i+++DtpG  +        + +++  e +d+++l+v a  ++++++  e  +
  AHX11440.1 316 VTVMGHIDHGKTTLLDTLRHTHVTASESGGITQHIGAYQVQTKDgRSITFIDTPG--H----AAFTSMRMRGAEVTDIVVLLVAAD-DGVNEQTIEAIK 407
                 7899************************************97766**********..3....112222333333479999999866.779888778788 PP

                 HHHHTTSEEEEEEES CS
    MMR_HSR1 100 lleeakkplilvlnk 114
                   + ak p+i+++nk
  AHX11440.1 408 HAKAAKVPIIVAINK 422
                 87789********98 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.2   0.1    0.0095        13       1      65 [.     502     556 ..     502     562 .. 0.68
   2 !   29.3   0.1     6e-10   8.3e-07       3      73 ..     720     785 ..     719     786 .. 0.93

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0095
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCS CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgled 65 
                  G  a+++v +G+lk+G+ ++   +++      ++++s+  +       v+ a+aGv v + gl++
   AHX11440.1 502 GAFATIIVKEGELKTGELIVA--SGS-----YGKVKSMTDS---SNKKVKKAPAGVPVEVLGLNK 556
                  566899**************9..432.....2444444444...446677777777776666666 PP

  == domain 2  score: 29.3 bits;  conditional E-value: 6e-10
                  EEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   3 valgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  va++ v sG++kk  ++ri++  +  k+     i+sl +f+ +++e+ +g  +G+++++  ++d  +vGd+l
   AHX11440.1 720 VAGCQVKSGVIKKSARIRIVRdGQILKD---LSIKSLKRFKDEVKEVKPGYECGILLNG--YSD-FKVGDIL 785
                  89999**************997777777...***************************8..***.8****98 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.4   0.6   5.8e-09   8.1e-06       2     137 ..     312     438 ..     311     454 .. 0.74

  Alignments for each domain:
  == domain 1  score: 25.4 bits;  conditional E-value: 5.8e-09
                 ---EEEEE-STTSSHHHHHHHHHHSS---B---S..S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS-HHHHHHHHHH CS
       SRPRB   2 skpavllvGlsdsGKTslftrLttdsvkktvtSq..essaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDStidpkevkevAEl 98 
                 ++p v ++G  d GKT+l+  L   +v+ +      +   a++v++++g ++t+iD PGh  + +  +    + + +  l+   D  ++++ ++     
  AHX11440.1 312 RAPVVTVMGHIDHGKTTLLDTLRHTHVTASESGGitQHIGAYQVQTKDGRSITFIDTPGHAAFTSMRMRG-AEVTDIVVLLVAADDGVNEQTIE----- 404
                 5788999***************9998887776543567779999*****************998766655.33334444444455555544433..... PP

                 HHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHHHH CS
       SRPRB  99 lyeilliteklkdavdiliACnKqelflakspklikdaL 137
                       i+  +  +v+i++A nK +   a + k++ d L
  AHX11440.1 405 -----AIKHAKAAKVPIIVAINKIDKEGANPLKVMTDLL 438
                 .....3444556778888888888887777777776665 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   2.5     2e-07   0.00027       3     154 ..     316     469 ..     314     471 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2e-07
                 EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHHHH CS
      FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardflleeepdvvvnvvdatnlernLyLtlq 100
                 v+++G  + Gkttl+++l  ++ + +   G+t      ++++k+ ++++++D PG  +++++ +    ++d+++      ++  +d    e+++  +  
  AHX11440.1 316 VTVMGHIDHGKTTLLDTLRHTHVTASESGGITQHIGAYQVQTKDgRSITFIDTPGHAAFTSMRMRGAEVTDIVV------LLVAADDGVNEQTIEAIKH 408
                 7899****************************9999999988877***********999988776655555553......4444555566999999999 PP

                 HHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHH.......TS-EEEEBTTTTBTHHHHHH CS
      FeoB_N 101 llelgvpvvlalnmideaekkgieidlkkLsekL.......gvpvvktsakkkegieellk 154
                     +vp+++a+n+id+  ++ +++ ++ L++ +       +v  v++sak++++i++l +
  AHX11440.1 409 AKAAKVPIIVAINKIDKEGANPLKVMTDLLQHGVvveemqgDVMSVNISAKNGTNIDKLEE 469
                 *************************999998654111112234457889999999999876 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.3   1.4e-07    0.0002      16     163 ..     315     461 ..     302     472 .. 0.78
   2 ?   -1.0   0.0      0.76     1e+03     117     150 ..     563     596 ..     554     621 .. 0.70

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 1.4e-07
                 EEEEEESTTSSHHHHHHHHHHSSCEECSS...SSSEEEEEEEETT.EEEEEEEE-SSGGGGGGGGGGCTTESEEEEEEETT-CTTHHHHHHHHHHHCTS CS
         Arf  16 rilllGLDnaGKtTilkklkleelvttvP...Tigfnveeleikn.lkftvwDvGGqeklRplWknYfektdavifvvDsadreRleeakeeLkallee 110
                  + ++G    GKtT+l  l++ +++       T++    ++++k+  ++t+ D  G+    ++  +  e td v+ +v + d       +e+  + +++
  AHX11440.1 315 VVTVMGHIDHGKTTLLDTLRHTHVTASESggiTQHIGAYQVQTKDgRSITFIDTPGHAAFTSMRMRGAEVTDIVVLLVAADDG-----VNEQTIEAIKH 408
                 4567787788**********99998754333399999999*99872579999***********************99987764.....34444556899 PP

                 GCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSSEEEEEEBTTTTBT CS
         Arf 111 eelkevallvlaNKqDlpealseeelrellgleelkgkrkleiqkcsavkgeg 163
                  + ++v+++v  NK+D ++a   + +++ll+   +  + +  ++++++  ++g
  AHX11440.1 409 AKAAKVPIIVAINKIDKEGANPLKVMTDLLQHGVVVEEMQGDVMSVNISAKNG 461
                 99******************999999999988877656666665555544444 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.76
                 EEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSSS CS
         Arf 117 allvlaNKqDlpealseeelrellgleelkgkrk 150
                  + v+ N +D++  l+++e  +  + ++l+ + +
  AHX11440.1 563 YFFVVKNEKDAKAMLDSQERDKVDNTRSLRDSFE 596
                 6789999999999999999998888888874444 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       3.9   5.4e+03      27      78 ..     289     335 ..     287     343 .. 0.59
   2 !   17.4   0.4   2.3e-06    0.0032      42     100 ..     399     471 ..     382     476 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 3.9
  MMR_HSR1_Xtn  27 ykihnaevliredvtvDdlidviegnrvYipclyvlNKiDlisleeldelar 78 
                   yk+  ae+l +e+ +vD+     ++nr   p+++v+  iD  + + ld+l++
    AHX11440.1 289 YKLSAAELLTKERENVDN---SSMKNR--APVVTVMGHIDHGKTTLLDTLRH 335
                   666666666666655553...234444..46777777777777777766655 PP

  == domain 2  score: 17.4 bits;  conditional E-value: 2.3e-06
  MMR_HSR1_Xtn  42 vDdlidvieg.nrvYipclyvlNKiDlisleeldelare.............pnsvviSaekelnldeLkeki 100
                    ++ i++i++ +   +p ++++NKiD+   + l+ ++                 sv iSa++++n+d+L e i
    AHX11440.1 399 NEQTIEAIKHaKAAKVPIIVAINKIDKEGANPLKVMTDLlqhgvvveemqgdVMSVNISAKNGTNIDKLEELI 471
                   6788999977466899***********888888888875566778877776558888************9987 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   2.6e-06    0.0036       3     120 .]     317     425 ..     315     425 .. 0.74

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 2.6e-06
                 EEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEEGHHHHCHHHHHHH CS
         Roc   3 vlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalailvydsrssenlkeWlke 101
                  ++G    GKt+ll+ + + +++ +e+  i   +   +v   ++    k+ +  ++ + Dt G+  f s++    +  ++++l++ +++  n ++ ++ 
  AHX11440.1 317 TVMGHIDHGKTTLLDTLRHTHVTASESGGITQHIGAYQV---QT----KDGR--SITFIDTPGHAAFTSMRMRGAEVTDIVVLLVAADDGVN-EQTIEA 405
                 6789999************99999888777666666554...22....2334..57789*********998777777777777665544433.456777 PP

                 HHHH.CSSS-EEEEEE-TTT CS
         Roc 102 lkkv.agkspvilvgnkiDl 120
                 +k+  a k p+i+ +nkiD+
  AHX11440.1 406 IKHAkAAKVPIIVAINKIDK 425
                 77652667899999****95 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.7   4.9e-06    0.0067       4     137 ..     316     467 ..     314     472 .. 0.63

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 4.9e-06
   PduV-EutP   4 illiGkvgsGKttLtqalkg............eelkYkktqaiefsd.eviDtPGeylenrklysalivtsae.advialvqdate...eesvfppgfa 85 
                 + ++G+++ GKttL  +l++            +++   + q+ +  + ++iDtPG  +    + +++++  ae +d+++l+++a++   e+++ + + a
  AHX11440.1 316 VTVMGHIDHGKTTLLDTLRHthvtasesggitQHIGAYQVQTKDGRSiTFIDTPGHAA----F-TSMRMRGAEvTDIVVLLVAADDgvnEQTIEAIKHA 409
                 679*****************666666666666555555555555544245*****643....3.44555544426899998888752215555667888 PP

   PduV-EutP  86 svfnkeviGiitkidlaedeenieaveelLks.......aGaekifevsavekegieel 137
                 +  + ++i  i kid+    + +++  +lL++        G     ++sa + ++i++l
  AHX11440.1 410 KAAKVPIIVAINKIDKE-GANPLKVMTDLLQHgvvveemQGDVMSVNISAKNGTNIDKL 467
                 89999**********98.66667766666653100000022223355666666666666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.5    0.0035       4.8      84     160 ..     298     370 ..     268     376 .. 0.61
   2 !   11.9   1.0   0.00011      0.15      10      96 ..     378     470 ..     374     477 .. 0.75

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0035
                  TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEESS-S CS
  RsgA_GTPase  84 aktkegleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliDtPG 160
                  +k++e++++ + + +  +++++G+   GK+tL+++l+ ++ ++    se+ g  +h    +   +  ++ + iDtPG
   AHX11440.1 298 TKERENVDNSSMKNRAPVVTVMGHIDHGKTTLLDTLRHTHVTA----SESGGITQHIGAYQVQTKDGRSITFIDTPG 370
                  34556666666666778999****************9973222....222233333332222222222444556666 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00011
                  TTTEES--EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHH.....HHHHHHHHHHHTTSEEE..E--TTTHTTHHHHHHH CS
  RsgA_GTPase  10 rpkvaNvdqllivvslkepelslnlldrfLvlaeekgiepvivlnKiDlleeee.....eleelkeelealgyevl..lvsaktkegleelkel 96 
                  r + a v+ +++++ ++++ +++++++ ++ +a+++++++++++nKiD    +      +l +    +e+++ +v+   +sak+++++++l+el
   AHX11440.1 378 RMRGAEVTDIVVLLVAADDGVNEQTIE-AIKHAKAAKVPIIVAINKIDKEGANPlkvmtDLLQHGVVVEEMQGDVMsvNISAKNGTNIDKLEEL 470
                  5567889999988888889****9998.789*****************9887776666645555555555554544115667777888888775 PP

>> SIS_2  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   9.7e-05      0.13     106     135 ..     389     418 ..     368     421 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                 EEEEE-SS--SHHHHHHHHHHHHHT-EEEE CS
       SIS_2 106 vLlviSnsGnnavvveaaeaakergmkviA 135
                 vLlv+ ++G+n+  +ea+++ak+  +++i+
  AHX11440.1 389 VLLVAADDGVNEQTIEAIKHAKAAKVPIIV 418
                 89************************9985 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.4       4.1   5.7e+03      78      78 ..     180     180 ..     128     230 .. 0.49
   2 ?   10.2   0.0   0.00043       0.6       1      35 [.     316     350 ..     316     360 .. 0.90
   3 ?    4.6   0.1     0.022        30      93     157 ..     353     413 ..     346     424 .. 0.70
   4 ?   -2.7   0.1       3.8   5.3e+03      58      80 ..     580     603 ..     565     632 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.1
                 H CS
   Dynamin_N  78 k 78 
                  
  AHX11440.1 180 S 180
                 2 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00043
                 EEEEEBTTTTHHHHHHHHHTS--S---SSS---S- CS
   Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTrrp 35 
                 ++v+G+  +GK+++l+ L + ++  ++++ +T+ +
  AHX11440.1 316 VTVMGHIDHGKTTLLDTLRHTHVTASESGGITQHI 350
                 789**************************999876 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.022
                 EEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTT CS
   Dynamin_N  93 lkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnsealflarevdpk 157
                 +++++ +   +t++D+PG        +++ ++ ++  di++++++a+  + ++  + ++++   k
  AHX11440.1 353 YQVQTKDGRSITFIDTPGHAA----FTSMRMRGAEVTDIVVLLVAADDGVNEQTIEAIKHAKAAK 413
                 6777888899********877....4456677788888888888888877777777776665544 PP

  == domain 4  score: -2.7 bits;  conditional E-value: 3.8
                 E.T-EB--CHHHHHHHHHHHHHHH CS
   Dynamin_N  58 k.ekkledfsevreeieketekia 80 
                 + ++k ++   +r+ +e+e++k++
  AHX11440.1 580 QeRDKVDNTRSLRDSFENEKKKLN 603
                 346777788888888888888776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (795 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1461  (0.0814881); expected 358.6 (0.02)
Passed bias filter:                      503  (0.0280551); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.71u 0.34s 00:00:01.05 Elapsed: 00:00:00.45
# Mc/sec: 5298.81
//
Query:       AHX11441.1  [L=91]
Description: ribosome-binding factor A family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-07   31.6   0.4    2.1e-07   31.3   0.4    1.1  1  RBFA      Ribosome-binding factor A
  ------ inclusion threshold ------
      0.039   13.8   0.5      0.043   13.7   0.5    1.0  1  DUF4906   Domain of unknown function (DUF4906)


Domain annotation for each model (and alignments):
>> RBFA  Ribosome-binding factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.4   2.3e-11   2.1e-07       1      91 [.       5      83 ..       5      90 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 2.3e-11
                TCHHHHHHHHHHHHHHHHHCT-HCCTGHHCEEEEEEESTTSSEEEEEEEESS-HHHHHHHHHHHHHTHHHHHHHHHHHC-SSSG-EEEEES CS
        RBFA  1 RqervaeliqrelseilqeelkdprlgklvtiteVkvsrDlskakVyvsvlgseeekeevlkaLkkaagflrrelakrlklrktPeLkFvl 91
                R+ r+++ + + ++ei+     +  +g   t+ +V v +D + a V + +l+ +     +  + ++ +  +r +++k+l+lr+tP+L+Fv 
  AHX11441.1  5 RKLRIESVLLKSITEII-----NRTFGMIATVANVTVADDSKSAVVSLYLLDAS-----L--NARDVEAAIRVRIGKSLTLRNTPKLSFVT 83
                789**************.....55666699*****************9988833.....2..3577899********************96 PP

>> DUF4906  Domain of unknown function (DUF4906)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.5   4.8e-06     0.043      39     103 ..      22      86 ..       3      90 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.8e-06
     DUF4906  39 gknlpmtgvkenvivagtt.tvavpltRlvakvdfrvtvassagtftiksirlvsvprkaklfasd 103
                 ++++ m +   nv+va ++ ++ v+l  l+a ++ r  +a  +++   ks+ l++ p+ + +++++
  AHX11441.1  22 NRTFGMIATVANVTVADDSkSAVVSLYLLDASLNARDVEAA-IRVRIGKSLTLRNTPKLSFVTTRK 86 
                 689****************55559***********988885.444459**********99999886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (91 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      307  (0.0171231); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 722.67
//
Query:       AHX11442.1  [L=784]
Description: PD-(D/E)XK nuclease superfamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      6e-19   68.9   0.0    1.2e-18   68.0   0.0    1.5  1  PDDEXK_1  PD-(D/E)XK nuclease superfamily
  ------ inclusion threshold ------
        1.4    9.0   4.2         12    5.9   0.0    3.5  4  AAA_14    AAA domain


Domain annotation for each model (and alignments):
>> PDDEXK_1  PD-(D/E)XK nuclease superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.0   0.0   1.3e-22   1.2e-18       1     240 [.     548     774 ..     548     778 .. 0.72

  Alignments for each domain:
  == domain 1  score: 68.0 bits;  conditional E-value: 1.3e-22
    PDDEXK_1   1 rlSvsrletfleCplrfflryllglre..eeelea..pdlGtlvHaaleefyewkkldkedleelleeaveelwpellleeeilessarlrylaeklke 95 
                 +lS++ +e + + p++f++ry+lg++e  +  +++   +lG ++H ++++  + +k +ke+ +++l +++++++ + ++ ++  +  +r   + e+   
  AHX11442.1 548 KLSPTMIELLISSPYKFYMRYILGIKEvnPIGIKPgyKELGCVLHNVFRRAAN-EKFSKEEYKQILLDELQKYATQYPYVKN--LWLPRGLKILEQFSL 643
                 59***********************88885555555359**********9999.7777777777776666666666333332..233333333333333 PP

    PDDEXK_1  96 vleklverlaeeleakrgfrpvalelefggekvrLkGriDrvd.dkegelriiDyKtgsappkskelaelkegl..QlllYllalaegeelkeegepag 191
                    + ++r+++   ++++   +++e ef g  v+++ r+Dr++  ++g++ i+++Ktg  p+ +    ++ke +  Qll+  l+l++   +  e   ++
  AHX11442.1 644 FHNDRLNRIST--LENEKEVSISFE-EFKG--VEIRCRFDRIEfLDDGTVSIVEFKTGIVPTLK----QIKEFIkpQLLIQGLVLQRS--QHME--ISE 729
                 33333333333..222223444444.4445..9**********877779*********955333....45555555************..4433..677 PP

    PDDEXK_1 192 alylrleepkvkdeevvkkmalteeeleallqeleelaeeilagefpar 240
                 +ly++       d+ v++++a++++e+e+ + +l+el++++l+g+f + 
  AHX11442.1 730 LLYCKP----SVDKIVLRQIAAPMQEIESCQYKLKELLRHYLSGNFNFC 774
                 888877....55899*****************************99875 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.1      0.44   3.9e+03      28      46 ..      71      89 ..      62     140 .. 0.68
   2 ?    2.3   0.1     0.018   1.7e+02      22      76 ..     292     345 ..     289     391 .. 0.74
   3 ?   -2.6   0.0      0.59   5.3e+03      28      71 ..     418     463 ..     388     466 .. 0.55
   4 ?    5.9   0.0    0.0014        12      56      87 ..     599     630 ..     585     640 .. 0.76

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.44
      AAA_14 28 vkkesilyinldderdkkl 46
                 +++++ yin+ ++   ++
  AHX11442.1 71 LEQQNFEYINFRTKAIIAI 89
                5677888888877665433 PP

  == domain 2  score: 2.3 bits;  conditional E-value: 0.018
      AAA_14  22 likell.vkkesilyinldderdkkladpekllelileklkeekktylflDEiqev 76 
                 +++e++ v+++ i+ ++l d  +  ++d+ +++ l++ ++   k +  + DEi ++
  AHX11442.1 292 FFREKYkVHPDGIFLLKLIDLALLGSTDE-NIIALLKHRYIY-KYNSSIVDEIEKS 345
                 788888999**************998877.477777776444.4566899***986 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 0.59
      AAA_14  28 vkkesilyinldderdkkladpekllelileklke..ekktylflD 71 
                  + +++l + l+++ ++  +++e+ +e++  +  +  ++k++l+lD
  AHX11442.1 418 NDYKEVLTFFLENHYFYPCEKNENSIEVFSPREASflNHKNVLLLD 463
                 3445555555555555555544444455544422234456666665 PP

  == domain 4  score: 5.9 bits;  conditional E-value: 0.0014
      AAA_14  56 ileklkeekktylflDEiqevpewekalkslv 87 
                   ek+++e+ + ++lDE q++ + + ++k+l 
  AHX11442.1 599 ANEKFSKEEYKQILLDELQKYATQYPYVKNLW 630
                 344444456667***********999999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (784 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      437  (0.0243739); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.62u 0.33s 00:00:00.95 Elapsed: 00:00:00.46
# Mc/sec: 5074.76
//
Query:       AHX11443.1  [L=436]
Description: inosine-5'-monophosphate dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     2e-138  461.1   5.9   2.2e-138  461.0   5.9    1.0  1  IMPDH            IMP dehydrogenase / GMP reductase domain
    1.2e-21   76.9   2.2    2.8e-10   40.5   0.0    3.3  3  CBS              CBS domain
    8.3e-14   51.4   3.2    9.5e-14   51.2   2.4    1.5  2  FMN_dh           FMN-dependent dehydrogenase
    4.6e-11   42.7   2.9      4e-08   33.0   2.5    2.2  2  NMO              Nitronate monooxygenase
      3e-07   30.1   2.1    0.00041   19.9   0.1    2.4  2  His_biosynth     Histidine biosynthesis protein
    4.3e-06   26.1   3.8    8.1e-06   25.2   3.8    1.4  1  Glu_synthase     Conserved region in glutamate synthase
    2.2e-05   23.7   1.4       0.04   13.0   0.1    2.2  2  Dus              Dihydrouridine synthase (Dus)
    4.9e-05   22.6   2.3    0.00012   21.4   2.3    1.6  1  NanE             Putative N-acetylmannosamine-6-phosphate epi
    0.00044   19.7   1.6       0.21   11.0   0.1    2.6  2  G3P_antiterm     Glycerol-3-phosphate responsive antiterminat
  ------ inclusion threshold ------
      0.014   14.8   0.2      0.041   13.3   0.2    1.8  1  Ribul_P_3_epim   Ribulose-phosphate 3 epimerase family
      0.016   14.5   0.4      0.016   14.5   0.4    2.1  2  DHO_dh           Dihydroorotate dehydrogenase
      0.016   13.9   0.0      0.029   13.0   0.0    1.3  1  UDPGP            UTP--glucose-1-phosphate uridylyltransferase
      0.019   15.9   0.1       0.04   14.9   0.1    1.5  1  Methyltransf_24  Methyltransferase domain
      0.028   13.7   2.7      0.042   13.2   0.3    2.2  2  ThiG             Thiazole biosynthesis protein ThiG


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  461.0   5.9  1.7e-141  2.2e-138      42     345 .]       1     422 [.       1     422 [. 0.99

  Alignments for each domain:
  == domain 1  score: 461.0 bits;  conditional E-value: 1.7e-141
                 STTT-SHHHHHHHHHTTSEEEE-SSS-HHHHHHHHHHHHTS.......................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......................................................... RF
       IMPDH  42 mdtvtesemAialareGgigvihknlsieeqaeevkkvkrs.......................................................... 82 
                 md+vt+s +Ai+la++Ggigvih+n+s+++qa e++kvk++                                                          
  AHX11443.1   1 MDMVTGSALAIELAKHGGIGVIHRNMSPKKQALEIRKVKKYeswivsnpitispddtiqrilelkklhgysglpvvdegnrligiltnrdirfieetsi 99 
                 9************************************************************************************************** PP

                 ...........................................................TTSXBXTTSXB-EEEEE-SSTTHHHHHHHHHHTT-SEEEE CS
                 ...........................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH  83 ...........................................................pnaakdekgrllvgaavgvkedalervkalveagvdvlvv 122
                                                                            pna+kd+k rl+vgaa+g+++d ler++ lv+++vdvlv+
  AHX11443.1 100 kvsdlmttknlitvregvsyseaqlllhknrierlivvddefkcvglitvkditnfaahPNASKDSKSRLRVGAAIGATQDFLERAEVLVKEDVDVLVI 198
                 *************************************************************************************************** PP

                 E-STSSSHHHHHHHHHHHHHTTTSEEEEEEE-SHHHHHHHHHTT-SEEEE-SS-STTBHHHHHCSB---HHHHHHHHHHHHCTCT-EEEEES---SHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 123 dsahghsekvleavkeikkkveeveviaGnvataegakaLieagadavkvGiGpGsiCttrvvagvGvpqltAvaevaeaakkagvpviaDGGikysgd 221
                 d+ah+h++ v +a+++ik+++ ++ +iaGn+atae+a+ Li+ag+d++kvGiGpGsiCttrvv+gvGvpq+tA+++va+a+k+++++viaDGGi+ysgd
  AHX11443.1 199 DTAHAHTRIVGDAIRQIKNNFIDIPLIAGNIATAEAAEYLIKAGVDGIKVGIGPGSICTTRVVTGVGVPQFTAILDVANACKNTEIKVIADGGIRYSGD 297
                 *************************************************************************************************** PP

                 HHHHHHTT-SEEEESCCCTTBTTSSSEEEEETTEEEEEEEETTSHHHHHH-SS-TTS-...--SS-SBEEEEEE--B-HHHHHHHHHHHHHHHHHHHT- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 222 ivkAlaaGadavmlGsllagteEspgeviliegrkyKeyrGmgslgamkkgskdryfqk.keklvpeGvegrvpykgsvkevveqlvgglrsgmgylGa 319
                 i+kA+aaGad+vm+Gsl+agteEspgev+l++gr+yK+yrGmgs+gam+ gs+dryfq+ + klvpeGveg vp+kg + +vv+ql+gg++s+mgy+G 
  AHX11443.1 298 IAKAIAAGADCVMIGSLFAGTEESPGEVVLYQGRSYKSYRGMGSVGAMSIGSADRYFQNsSMKLVPEGVEGLVPFKGALGDVVYQLIGGVKSSMGYTGN 396
                 ************************************************99********6367************************************* PP

                 SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 320 ktieelkekakfvritaaglkeshvH 345
                 k+iee+k++ +f++itaa+ +e+h+H
  AHX11443.1 397 KSIEEMKNNCNFINITAASNNEGHPH 422
                 *************************9 PP

>> CBS  CBS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.5   0.0   2.2e-13   2.8e-10       7      52 ..      47      92 ..      38      95 .. 0.90
   2 !   34.2   0.1     2e-11   2.6e-08       1      55 [.     101     156 ..     101     158 .. 0.89
   3 ?   -0.9   0.0       1.8   2.3e+03      11      30 ..     200     220 ..     189     228 .. 0.69

  Alignments for each domain:
  == domain 1  score: 40.5 bits;  conditional E-value: 2.2e-13
                SSCEEEETTSBHHHHH..HHHHHHTSSEEEEEETTTBEEEEEEHHHHH CS
         CBS  7 rdvvtvppdttleeal..elmrekgvsrlPVVdedgklvGivtlrDll 52
                ++++t++pd+t+  +l  +++  +g+s+lPVVde ++l+Gi+t rD+ 
  AHX11443.1 47 SNPITISPDDTIQRILelKKL--HGYSGLPVVDEGNRLIGILTNRDIR 92
                699*************66667..99*******9999**********96 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 2e-11
                 HHHHSBS.SCEEEETTSBHHHHHHHHHHHTSSEEEEEETTTBEEEEEEHHHHHHHH CS
         CBS   1 Vgdimtr.dvvtvppdttleealelmrekgvsrlPVVdedgklvGivtlrDllral 55 
                 V+d+mt+ +++tv++  + +ea  l+ ++++ rl VVd++ k+vG++t +D+ ++ 
  AHX11443.1 101 VSDLMTTkNLITVREGVSYSEAQLLLHKNRIERLIVVDDEFKCVGLITVKDITNFA 156
                 8999888799****************5555****9999999***********9875 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 1.8
                 EEETTSB.HHHHHHHHHHHT.S CS
         CBS  11 tvppdtt.leealelmrekg.v 30 
                 t++  t  +++a++++ +++ +
  AHX11443.1 200 TAHAHTRiVGDAIRQI-KNNfI 220
                 5555566699999999.55555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.2   2.4   7.4e-17   9.5e-14     194     303 ..     198     315 ..     132     324 .. 0.77
   2 ?   -3.5   0.0       3.2   4.1e+03     324     344 ..     385     405 ..     378     406 .. 0.79

  Alignments for each domain:
  == domain 1  score: 51.2 bits;  conditional E-value: 7.4e-17
                 HCCCHB-TC--HHHHHHHHHH.HSSEEEEEEE-SHHHHHHHHHTTESEEEE--GGG.....TSSTT-.--HHHCHHHHHHHH...SS-EEEESS--SHH CS
      FMN_dh 194 fvgkqldpsltwddikwlreq.tklplvvKGvltaedakraveaGvdgivvSNHGG.....Rqldga.patidvLpeiveavgg.rievlvDgGirrGs 284
                 + + + ++++  d i++++++  ++pl+   + tae a+ +++aGvdgi v    G     R + g+ ++ + ++ ++++a+++ +i+v++DgGir   
  AHX11443.1 198 IDTAHAHTRIVGDAIRQIKNNfIDIPLIAGNIATAEAAEYLIKAGVDGIKVGIGPGsicttRVVTGVgVPQFTAILDVANACKNtEIKVIADGGIRYSG 296
                 4444455666677899999862579**************************888888888898887636779999********857************* PP

                 HHHHHHHTT-SEEEESHHH CS
      FMN_dh 285 DvlkAlalGAdavllGRpf 303
                 D++kA+a GAd+v++G  f
  AHX11443.1 297 DIAKAIAAGADCVMIGSLF 315
                 ****************766 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.2
                 HHHHHHHHHHT-SBHHHHHCG CS
      FMN_dh 324 aelertmallGvksvaeldrs 344
                   ++++m  +G ks++e++++
  AHX11443.1 385 GGVKSSMGYTGNKSIEEMKNN 405
                 567899*********999865 PP

>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.1   0.0    0.0012       1.6      19      59 ..       1      40 [.       1      53 [. 0.86
   2 !   33.0   2.5   3.1e-11     4e-08      89     236 ..     168     326 ..     136     373 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0012
         NMO 19 mggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvka 59
                m ++++ +La   ++ Gg+Gv+    +++ + a eirkvk+
  AHX11443.1  1 MDMVTGSALAIELAKHGGIGVIH-RNMSPKKQALEIRKVKK 40
                66899******************.899999*********97 PP

  == domain 2  score: 33.0 bits;  conditional E-value: 3.1e-11
         NMO  89 eaalelnieegvrfyrkvevvldekvevvsfgfglpteevv......arlkeagvvli.ptissvkearkvearGaDalivqGpeaGGhqGtpevgd.. 178
                    ++++i   + f ++ ev+ +e v+v  +  +      v      ++ ++ ++ li + i+++++a  ++++G D + v G   G    t+ v +  
  AHX11443.1 168 RLRVGAAIGATQDFLERAEVLVKEDVDVLVIDTAHAHTRIVgdairqIKNNFIDIPLIaGNIATAEAAEYLIKAGVDGIKV-GIGPGSICTTRVVTGvg 265
                 444666666777799999999999888877766665554442221112344455544315689**************8644.77777766656655556 PP

         NMO 179 kglfaLvpqvldavd...iPviAaGGiidrrgvaaaLalGAsgvqigtrfLltkesdakda 236
                 + +f+ +  v++a +   i viA GGi    ++a a+a+GA  v ig+ f +t+es+ +++
  AHX11443.1 266 VPQFTAILDVANACKnteIKVIADGGIRYSGDIAKAIAAGADCVMIGSLFAGTEESPGEVV 326
                 667777777887777788**************************************98776 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.4   0.00046      0.59      30     102 ..     180     249 ..     173     264 .. 0.80
   2 !   19.9   0.1   3.2e-07   0.00041      65     105 ..     275     315 ..     265     331 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00046
                   SHHHHHHHHHHHT-SEEEEEEHHHHCTTHHHHHHHHHHHHHH-SSEEEEESS.SSSHHHHHHHHHCT-SEEEES CS
  His_biosynth  30 dpvelakryeeegadelhvvDldaakegreanldlveeiaeevfipvqvGGG.Irsledveelleagadkviig 102
                   d +e a+ + +e++d l+   +d a++++++  d++++i ++ fi++ +  G I + e++e l++ag+d + +g
    AHX11443.1 180 DFLERAEVLVKEDVDVLV---IDTAHAHTRIVGDAIRQIKNN-FIDIPLIAGnIATAEAAEYLIKAGVDGIKVG 249
                   667777777777777665...688999**************9.7777655555****************55443 PP

  == domain 2  score: 19.9 bits;  conditional E-value: 3.2e-07
                   HHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEEEESHHH CS
  His_biosynth  65 veeiaeevfipvqvGGGIrsledveelleagadkviigtaa 105
                   v++ +++++i+v  +GGIr   d+++++ agad v+ig+  
    AHX11443.1 275 VANACKNTEIKVIADGGIRYSGDIAKAIAAGADCVMIGSLF 315
                   66778888899999999999999999999999999999864 PP

>> Glu_synthase  Conserved region in glutamate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   3.8   6.4e-09   8.1e-06     208     304 ..     222     313 ..     208     316 .. 0.72

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 6.4e-09
                   EEEE-STTHHH.HHHHHHHTT-SEEEEE-TT---SSEEHHHHHHB---HHHHHHHHHHHHHHTT-GGG-EEEEESS--SHHHHHHHHHHT-SEEE-S CS
  Glu_synthase 208 vKlvaeagvet.iaagvakanadiilidGleGGTGAspkssikhaGlPlelalaevdqtlkeeglrdrvsliadGglktgadvvkalalGAdavgig 303
                   + l a++ + +  a  + ka++d i++ G+  G     + ++  +G+P  +a+  v ++ k++    ++++iadGg++ + d++ka+a GAd v ig
    AHX11443.1 222 IPLIAGNIATAeAAEYLIKAGVDGIKV-GIGPGS-ICTTRVVTGVGVPQFTAILDVANACKNT----EIKVIADGGIRYSGDIAKAIAAGADCVMIG 312
                   555555443330233366666666666.333332.345678889************9998875....689**************************9 PP

                   H CS
  Glu_synthase 304 t 304
                   +
    AHX11443.1 313 S 313
                   7 PP

>> Dus  Dihydrouridine synthase (Dus)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.2   0.00036      0.46     173     213 ..     210     249 ..     199     254 .. 0.88
   2 !   13.0   0.1   3.1e-05      0.04     174     213 ..     274     312 ..     266     324 .. 0.88

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00036
                 HHHHHHHHH-S.S-EEEESS--SHHHHHHHHHHH--SEEEES CS
         Dus 173 eaIkevkqavs.ipviaNGdIkdaedaqaileetGadgvmig 213
                 +aI+++k+++  ip+ia G+I +ae+a+  ++  G+dg+ +g
  AHX11443.1 210 DAIRQIKNNFIdIPLIA-GNIATAEAAEYLIKA-GVDGIKVG 249
                 79********99***99.******999988887.****9887 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.1e-05
                 HHHHHHHH-SS-EEEESS--SHHHHHHHHHHH--SEEEES CS
         Dus 174 aIkevkqavsipviaNGdIkdaedaqaileetGadgvmig 213
                 ++++ +++ +i via G+I++  d+ ++++  Gad vmig
  AHX11443.1 274 DVANACKNTEIKVIADGGIRYSGDIAKAIAA-GADCVMIG 312
                 4667788888********************9.*******9 PP

>> NanE  Putative N-acetylmannosamine-6-phosphate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   2.3   9.1e-08   0.00012      53     176 ..     181     315 ..     174     321 .. 0.77

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 9.1e-08
                 SHHHHHHHHTTT-SEEEEE--SS--T--HHHHHHHHHHH-...-EEEEE-SSHHHHHHHHHTT-SEEE-TT....TTSSTTS-...SS--HHHHHHH.. CS
        NanE  53 tlkdideLaaagadiialDatdrerpvtieelikkikeky...qllmaDistleeglvakklGvdivGttl....sGytkeeek..aepDfalvkal.. 140
                 +l+  + L+++++d++ +D+++ +    + + i++ik+++    l+  +i+t e + +  k+Gvd +   +       t         p f+ + ++  
  AHX11443.1 181 FLERAEVLVKEDVDVLVIDTAHAH-TRIVGDAIRQIKNNFidiPLIAGNIATAEAAEYLIKAGVDGIKVGIgpgsICTTRVV-TgvGVPQFTAILDVan 277
                 6788899************77654.4567899*******9886788889****************86554421102233333.3467888887655511 PP

                 ..HHTT--EEEES---SHHHHHHHHTT--SEEEE-HHH CS
        NanE 141 ..seaglkviaeGrintPekakkaieiGvdavvvGsai 176
                   +++++kvia+G i      +kai  G+d+v++Gs  
  AHX11443.1 278 acKNTEIKVIADGGIRYSGDIAKAIAAGADCVMIGSLF 315
                 11567899***************************965 PP

>> G3P_antiterm  Glycerol-3-phosphate responsive antiterminator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.2    0.0025       3.2      34      75 ..     206     246 ..     175     249 .. 0.67
   2 !   11.0   0.1   0.00016      0.21     133     167 ..     277     311 ..     267     314 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0025
                   HHHHHHHHTT-EEEEEGGGEET--SSHHHHHHHHH.TT-SEE CS
  G3P_antiterm  34 eiveklkkagkkvfvhiDlieGlskdeaaveflkkeikvdGi 75 
                   +iv  + ++ k  f++i li G  +  +a e+l k ++vdGi
    AHX11443.1 206 RIVGDAIRQIKNNFIDIPLIAGNIATAEAAEYLIK-AGVDGI 246
                   55666666667778888888888888888888877.777777 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00016
                   TSTTS...EEEEESS--SHHHHHHHCTT.SSEEEE CS
  G3P_antiterm 133 eikkelkipiiaGGLietkedveealkaGaiavst 167
                   + +k+++i++ia G i+ + d+ +a++aGa++v+ 
    AHX11443.1 277 NACKNTEIKVIADGGIRYSGDIAKAIAAGADCVMI 311
                   567899**************************986 PP

>> Ribul_P_3_epim  Ribulose-phosphate 3 epimerase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.2e-05     0.041     156     196 ..     275     314 ..     266     316 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.2e-05
                     HHHHHHHHT---EEEEESS--TT.TCHHHHHHT--EEEESHH CS
  Ribul_P_3_epim 156 vrklidekeldlkievDGGvkld.nieqiaeagadvlVagsa 196
                     v +++++  +++k+ +DGG++    i+++++agad++ +gs 
      AHX11443.1 275 VANACKN--TEIKVIADGGIRYSgDIAKAIAAGADCVMIGSL 314
                     5555554..899********975379999***********95 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6      0.69   8.9e+02     233     272 ..     211     248 ..     206     255 .. 0.83
   2 ?   14.5   0.4   1.2e-05     0.016     241     276 ..     280     315 ..     267     321 .. 0.82

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.69
                 HHHHHHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEE CS
      DHO_dh 233 virelykrlkkeipiIgvGGiesgeDalekieaGAslvqv 272
                  ir++++++  +ip+I+ G i ++e a   i+aG   ++v
  AHX11443.1 211 AIRQIKNNFI-DIPLIA-GNIATAEAAEYLIKAGVDGIKV 248
                 6899999998.9****7.99****9998889999766655 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.2e-05
                 TTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHH CS
      DHO_dh 241 lkkeipiIgvGGiesgeDalekieaGAslvqvytal 276
                  + ei++I+ GGi  + D    i aGA  v +++ +
  AHX11443.1 280 KNTEIKVIADGGIRYSGDIAKAIAAGADCVMIGSLF 315
                 3567****************************9965 PP

>> UDPGP  UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.3e-05     0.029      55      90 ..     379     414 ..     377     423 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.3e-05
       UDPGP  55 avlkLnGglGtsmGckgpKslieVrdgktfLdlivq 90 
                 +v +L Gg+ +smG +g Ks+ e +++ +f+++++ 
  AHX11443.1 379 VVYQLIGGVKSSMGYTGNKSIEEMKNNCNFINITAA 414
                 68899****************************986 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   3.1e-05      0.04       7      87 ..     115     210 ..     112     217 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.1e-05
  Methyltransf_24   7 sGvstlwllralrrngagrlvavdhdpg......aeeaaalare..aglddrvrlikadseealasla.......agsiDllfiDgghaaeavl 85 
                      +Gvs+     +l++n+  rl++vd + +       ++ +++a+   a  d+  rl+++ +  a +++        ++++D+l+iD  ha+++  
       AHX11443.1 115 EGVSYSEAQLLLHKNRIERLIVVDDEFKcvglitVKDITNFAAHpnASKDSKSRLRVGAAIGATQDFLeraevlvKEDVDVLVIDTAHAHTRIV 208
                      677777777788999999999999988888888844444444444444555566666666444444444444889**************99877 PP

  Methyltransf_24  86 ed 87 
                       d
       AHX11443.1 209 GD 210
                      65 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.41   5.3e+02     167     201 ..     212     246 ..     203     251 .. 0.65
   2 ?   13.2   0.3   3.3e-05     0.042     170     211 ..     278     319 ..     253     324 .. 0.82

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.41
                 HHHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEE CS
        ThiG 167 lkiiieea.kvPvivDAGigspsdaaqamelGadav 201
                 ++ i +++ ++P+i    i +++ a   ++ G+d++
  AHX11443.1 212 IRQIKNNFiDIPLIA-GNIATAEAAEYLIKAGVDGI 246
                 555666655777663.33666666666667777766 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 3.3e-05
                 HHHH-SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSS CS
        ThiG 170 iieeakvPvivDAGigspsdaaqamelGadavllntavaeak 211
                  ++++++ vi D Gi+ + d+a+a+  Gad v++ +  a ++
  AHX11443.1 278 ACKNTEIKVIADGGIRYSGDIAKAIAAGADCVMIGSLFAGTE 319
                 467889****************************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       414  (0.0230911); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.39
# Mc/sec: 3357.17
//
Query:       AHX11444.1  [L=321]
Description: hypothetical protein NHE_0502 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
     0.0057   17.1   0.1       0.65   10.5   0.0    2.6  2  CSTF2_hinge  Hinge domain of cleavage stimulation factor subu
  ------ inclusion threshold ------
       0.07   13.4   0.6       0.65   10.3   0.1    2.7  3  DUF948       Bacterial protein of unknown function (DUF948)


Domain annotation for each model (and alignments):
>> CSTF2_hinge  Hinge domain of cleavage stimulation factor subunit 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1      0.01        90       9      36 ..      23      49 ..      18      52 .. 0.86
   2 !   10.5   0.0   7.2e-05      0.65      23      58 ..     184     219 ..     180     224 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.01
  CSTF2_hinge  9 ppglsapdaIsktLsslppeqllellsq 36
                 +p ++ +++I   ++ +p eq++ell++
   AHX11444.1 23 NP-IEEANPIEGLVNHVPDEQVVELLAD 49
                 44.88999*****************986 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 7.2e-05
  CSTF2_hinge  23 sslppeqllellsqlKalaqqnpsqarelLkqnpqL 58 
                  +s +++++++++s+ K+ ++  ++ a +lL+++ + 
   AHX11444.1 184 ASATQSKMVDVMSEIKSTLNRVSNAASALLDKAEDV 219
                  678899*************************99875 PP

>> DUF948  Bacterial protein of unknown function (DUF948)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.26   2.4e+03      27      59 ..     125     157 ..     110     166 .. 0.72
   2 ?   10.3   0.1   7.3e-05      0.65      22      81 ..     189     247 ..     165     254 .. 0.59
   3 ?   -1.9   0.0      0.46   4.1e+03      59      71 ..     296     308 ..     272     316 .. 0.50

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.26
      DUF948  27 tldeaaatieelekqvdpilkevedllakvnel 59 
                 +ld++ +++ +++k +++++  ++d+++ v   
  AHX11444.1 125 MLDRVGKAMPGIQKGAKSTVVWAADTVSSVGSA 157
                 467777777777777777777777777766554 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 7.3e-05
      DUF948  22 lklkktldeaaatieelekqvdpilkevedllakvnelledvneklekvdplteavadlg 81 
                  k+ ++++e+++t++ + + + ++l+++ed+  kv +  +  ++++++   l+++++++g
  AHX11444.1 189 SKMVDVMSEIKSTLNRVSNAASALLDKAEDVAPKVSK-PQHATKESQTPSGLMYSAGNVG 247
                 3444555566666666666666666666666666655.5555555555555555555555 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.46
      DUF948  59 lledvneklekvd 71 
                 + ++v+++l++++
  AHX11444.1 296 VHNEVRSRLQQIN 308
                 2222444444443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       704  (0.039266); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.27s 00:00:00.74 Elapsed: 00:00:00.41
# Mc/sec: 2354.07
//
Query:       AHX11445.1  [L=57]
Description: IMP dehydrogenase / GMP reductase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.9e-11   41.9   0.0    6.5e-11   41.8   0.0    1.0  1  IMPDH     IMP dehydrogenase / GMP reductase domain
     0.0028   16.4   0.0     0.0028   16.4   0.0    1.0  1  UDPGP     UTP--glucose-1-phosphate uridylyltransferase
  ------ inclusion threshold ------
      0.057   13.4   0.0       0.06   13.4   0.0    1.1  1  DUF1307   Protein of unknown function (DUF1307)


Domain annotation for each model (and alignments):
>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.8   0.0   1.1e-14   6.5e-11     303     345 .]       1      43 [.       1      43 [. 0.98

  Alignments for each domain:
  == domain 1  score: 41.8 bits;  conditional E-value: 1.1e-14
                 HHHHHHHHHHHHHHHT-SSHHHHHHH-EEEEE-HHHHHHHS-- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 303 veqlvgglrsgmgylGaktieelkekakfvritaaglkeshvH 345
                 ++ql+gg++s+mgy+G k+iee+k++ +f++itaa+ +e+h+H
  AHX11445.1   1 MYQLIGGVKSSMGYTGNKSIEEMKNNCNFINITAASNNEGHPH 43 
                 589***************************************9 PP

>> UDPGP  UTP--glucose-1-phosphate uridylyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.0   4.7e-07    0.0028      58      91 ..       3      36 ..       1      47 [. 0.90

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 4.7e-07
       UDPGP 58 kLnGglGtsmGckgpKslieVrdgktfLdlivqq 91
                +L Gg+ +smG +g Ks+ e +++ +f+++++  
  AHX11445.1  3 QLIGGVKSSMGYTGNKSIEEMKNNCNFINITAAS 36
                588***************************9875 PP

>> DUF1307  Protein of unknown function (DUF1307)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0     1e-05      0.06      58      96 ..       2      40 ..       1      51 [. 0.91

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 1e-05
                TTTSSS-EEEEEE-SSEEEEEEEEETTS--HHHHTTTT- CS
     DUF1307 58 YkgikGvsekltykddkliekvtidyekadldelkkldg 96
                Y+ i Gv+ ++ y+++k ie+++ + + +++ ++++++g
  AHX11445.1  2 YQLIGGVKSSMGYTGNKSIEEMKNNCNFINITAASNNEG 40
                9****************************9999998877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 460.61
//
Query:       AHX11446.1  [L=518]
Description: hypothetical protein NHE_0504 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.37   10.8   6.5        1.8    8.6   3.2    2.5  2  Baculo_PEP_C   Baculovirus polyhedron envelope protein, PEP, 
       0.85   10.1   3.5         31    5.1   0.2    2.8  2  T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX d


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   3.2    0.0002       1.8      49     118 ..      45     118 ..      40     140 .. 0.67
   2 ?    2.8   0.2     0.013   1.1e+02      43      96 ..     134     189 ..     124     224 .. 0.49

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0002
  Baculo_PEP_C  49 alsedlksllaeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvtNinstLn....nllqalnnl 118
                   +++  +ks +a +++ ++tl t+L  a ++    l n+  +l+s lt+ +s v  i st++    nl++++ ++
    AHX11446.1  45 TITGGIKSGSAWIANTISTLPTTLLGAAQNTGSVLINAVGALKSGLTSVASAVSTIPSTVQnaesNLVNTVVGI 118
                   66677777777777777777777777777777777777777777777777777777777751222466666555 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.013
  Baculo_PEP_C  43 ietqLnalsedlksllaeldtrldtlltnLtdalnalq...dtlrneLtnlnsiltn 96 
                   + tqLn+ s+ ++   + + + + ++++ +++a n ++   d +++  t++n  +  
    AHX11446.1 134 LSTQLNEASTLFNT-GERVLESVGKAAEGVEKAANDITeaaDLMQELVTGVNRWVRA 189
                   44444443333322.333333444444444444444443322222333333333333 PP

>> T7SS_ESX_EspC  Excreted virulence factor EspC, type VII ESX diderm
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3    0.0041        37       6      72 ..      77     141 ..      74     148 .. 0.69
   2 ?    5.1   0.2    0.0035        31      11      41 ..     154     184 ..     151     226 .. 0.80

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.0041
  T7SS_ESX_EspC   6 sVdpdhlrelaakhdevaaeiasavaaaagasaavldshGpicaatndavaaaeaarraagealaaa 72 
                    sV   ++ +l + +++va+ +++ ++++++a ++++++  +++  ++   + ++  r+a  ++l++a
     AHX11446.1  77 SVLINAVGALKSGLTSVASAVSTIPSTVQNAESNLVNT--VVGIGHTVESSGVRIIRDALSTQLNEA 141
                    5888999*********************6665555555..555555555555555555555555554 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0035
  T7SS_ESX_EspC  11 hlrelaakhdevaaeiasavaaaagasaavl 41 
                     + ++a+ ++++a +i+ a++ +++ ++ v+
     AHX11446.1 154 SVGKAAEGVEKAANDITEAADLMQELVTGVN 184
                    6889999999999999999999988777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       990  (0.0552178); expected 358.6 (0.02)
Passed bias filter:                      591  (0.0329634); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.32s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 3520.12
//
Query:       AHX11447.1  [L=151]
Description: mce related family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-18   64.7   0.1    9.3e-18   64.3   0.1    1.2  1  MlaD      MlaD protein
  ------ inclusion threshold ------
          3    7.8   5.6         22    5.0   5.6    2.0  1  YajC      Preprotein translocase subunit


Domain annotation for each model (and alignments):
>> MlaD  MlaD protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   64.3   0.1     1e-21   9.3e-18       3      81 .]      40     116 ..      38     116 .. 0.95

  Alignments for each domain:
  == domain 1  score: 64.3 bits;  conditional E-value: 1e-21
        MlaD   3 ytvtaqfdnangLkvgapVryrGvtvGrVtsitldpdtrrvtvtvdldkksetsipedsraqvstggll.gekyialdpg 81 
                 y++ a f++++gL+ g+++  +Gv++G+Vt+i l +d+ rv v++ +d  +++ +p ds a++st +ll g+++i++d g
  AHX11447.1  40 YELSASFNDVSGLTLGSDILLSGVKIGSVTKIGL-DDSSRVLVKMCID--KSVQLPVDSVATISTKNLLvGARFIDIDVG 116
                 8999******************************.6777789******..***************************965 PP

>> YajC  Preprotein translocase subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.0   5.6    0.0025        22      32      74 ..      49      94 ..       9      99 .. 0.64

  Alignments for each domain:
  == domain 1  score: 5.0 bits;  conditional E-value: 0.0025
        YajC 32 lasLkkGdeVvtigGivGkvvkvd.dde..vtveigesagvkikve 74
                ++ L+ G+ ++++g  +G v+k+  dd+  v v++  +++v++ v+
  AHX11447.1 49 VSGLTLGSDILLSGVKIGSVTKIGlDDSsrVLVKMCIDKSVQLPVD 94
                456999******************8654678888877777888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.41
# Mc/sec: 1095.93
//
Query:       AHX11448.1  [L=86]
Description: hypothetical protein NHE_0506 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-11   44.3   0.0    2.7e-11   44.2   0.0    1.2  1  NDUFA12   NADH ubiquinone oxidoreductase subunit NDUFA12
  ------ inclusion threshold ------
       0.12   12.7   0.0       0.15   12.4   0.0    1.2  1  DUF3085   Protein of unknown function (DUF3085)


Domain annotation for each model (and alignments):
>> NDUFA12  NADH ubiquinone oxidoreductase subunit NDUFA12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0     3e-15   2.7e-11       2      59 ..       6      58 ..       5      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 3e-15
     NDUFA12  2 tlvGeDefGNkYyenkeelegrrrwveyaekakdasqvppeWhgWlhhitdkppteek 59
                t+vG+D +GN+Yy++       +r+v ya+k  d +++  +W  Wlh  +d  pt ++
  AHX11448.1  6 TFVGKDASGNRYYKKG-----TKRFVVYASKDCDPTTISTKWYLWLHNASDLLPTVSQ 58
                68************85.....68******9966******************9999654 PP

>> DUF3085  Protein of unknown function (DUF3085)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   1.6e-05      0.15      19      44 ..      17      43 ..       4      50 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1.6e-05
     DUF3085 19 kladgqkklvaYa.eecdPktnpedww 44
                 +++g+k++v+Ya ++cdP+t   +w+
  AHX11448.1 17 YYKKGTKRFVVYAsKDCDPTTISTKWY 43
                6899********9358****9998888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      231  (0.0128842); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 634.19
//
Query:       AHX11449.1  [L=207]
Description: 3'-5' exonuclease family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-34  119.5   0.0    1.5e-34  119.2   0.0    1.1  1  DNA_pol_A_exo1  3'-5' exonuclease


Domain annotation for each model (and alignments):
>> DNA_pol_A_exo1  3'-5' exonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  119.2   0.0   8.4e-39   1.5e-34      22     175 ..      20     169 ..       7     170 .. 0.94

  Alignments for each domain:
  == domain 1  score: 119.2 bits;  conditional E-value: 8.4e-39
                     EEEEEEEEE-SSSTTSSEEEEEEEEECSSEEEEEECTTTTTT-HGHHHHHHHT-TTSEEEESSHHHHHHHHHHHHTS--SSEEEHHHHHHHTT.H CS
  DNA_pol_A_exo1  22 vvavDtEttsldlisatlvliliqlgekeeayiidplelgddvalealkrlledenitkvghnakfDlevlardfgielenlfdtmlaayvld.y 115
                      va+DtE ++l     +++l+l+ql+ +++a+++++++ +d+  +  lk ll d+ +tk++h  +fD+++l + +g  + n ++t++a+++   y
      AHX11449.1  20 SVAIDTESMGLIN--RRDRLCLVQLSVGDGAAHLVKFNGKDY-SAPRLKDLLLDSCVTKIFHFGRFDIAILRHYIGALTINCYCTKIASRLARtY 111
                     7**********99..**************************8.9*****************************************9999987515 PP

                     STTSSHHHHHHHHHSB---GHCCTTSSTTTSSS-HHHHHHHHHHHHHTHHHHHHHHHHHH CS
  DNA_pol_A_exo1 116 ershsLdsLaekylgdleldkeeqiakwqkarplleeqllYAaeDadvllrlfkkLtkel 175
                     + +hsL++L+ ++lg ++l+k +q ++w  a  l++eq++YAa D+++l+ + ++L  +l
      AHX11449.1 112 TDHHSLKELCSELLG-VKLNKGKQSSDWG-ASSLSREQMSYAASDVLYLHAIKEALDGML 169
                     566************.*************.***********************9998766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (207 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      394  (0.0219756); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1574.42
//
Query:       AHX11450.1  [L=327]
Description: protein RecA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     4e-139  462.5   2.3   4.8e-139  462.2   2.3    1.1  1  RecA      recA bacterial DNA recombination protein
      2e-15   56.8   0.6    4.4e-15   55.6   0.6    1.5  1  Rad51     Rad51
    3.7e-11   42.8   3.1    1.9e-08   34.0   3.1    2.9  1  ATPase    KaiC
      7e-05   22.6   0.0    0.00013   21.8   0.0    1.4  1  AAA_24    AAA domain
    0.00016   21.7   0.1    0.00042   20.3   0.0    1.8  2  ATPase_2  ATPase domain predominantly from Archaea
    0.00081   19.0   0.5      0.024   14.2   0.5    2.2  1  AAA_25    AAA domain
     0.0066   17.0   0.1      0.012   16.1   0.1    1.8  1  ABC_tran  ABC transporter
  ------ inclusion threshold ------
       0.01   15.2   0.0      0.029   13.7   0.0    1.9  2  DnaB_C    DnaB-like helicase C terminal domain
      0.011   16.2   0.0      0.029   14.8   0.0    1.8  1  AAA       ATPase family associated with various cellular acti
      0.019   15.4   0.1      0.029   14.7   0.1    1.2  1  AAA_16    AAA ATPase domain
      0.025   14.2   0.0       0.04   13.5   0.0    1.3  1  CobU      Cobinamide kinase / cobinamide phosphate guanyltran
      0.043   13.8   0.0       0.16   12.0   0.0    2.0  1  AAA_14    AAA domain
      0.043   13.7   0.0       0.12   12.3   0.0    1.7  1  MobB      Molybdopterin guanine dinucleotide synthesis protei
      0.045   14.0   0.0      0.094   13.0   0.0    1.5  1  AAA_22    AAA domain
      0.049   12.5   0.0      0.083   11.7   0.0    1.2  1  AAA_35    AAA-like domain
       0.13   11.4   0.3       0.23   10.5   0.3    1.3  1  PAXNEB    PAXNEB protein


Domain annotation for each model (and alignments):
>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.2   2.3  4.3e-142  4.8e-139       2     263 .]       6     264 ..       5     264 .. 0.99

  Alignments for each domain:
  == domain 1  score: 462.2 bits;  conditional E-value: 4.3e-142
                 HHHHHHHHHHHHH-TTSS--TTS--.-----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEESS----HHHHHH CS
        RecA   2 aleaalkqiekkfGkgsimklgdekeklkvetissGslaldialGiGGlpkGriieiyGpessGkttlalhaiaeaqkkggvaafidaehaldpkyakk 100
                 al+++++qiek+fGkgsim + +e     ve+is+Gs++ld alG GG+pkGriiei+GpessGkttl+lh+iae+qk+gg++afidaehaldp ya++
  AHX11450.1   6 ALRNVIAQIEKAFGKGSIMTFNQEP--AMVECISTGSIGLDHALG-GGIPKGRIIEIFGPESSGKTTLTLHVIAESQKNGGTCAFIDAEHALDPIYARR 101
                 78999****************6665..79****************.***************************************************** PP

                 TT--GGG-EEE--SSHHHHHHHHHHHHTTT--SEEEEE-TTT---STT-----------HHHHHHHHHHHHHHHHHTTT--EEEEEEE----------- CS
        RecA 101 lGvdidellvsqpdtGeqaleiadalvrsgaidlivvdsvaalvpkaeieGemgdskvglqarlmsqalrkltgaisksntvvifinqirekiGvmfgn 199
                 lGv+id+ll+sqpdtGeqalei+d+l++sga+d+iv+dsvaal+pkae+eGemgd +vglqarl+sqalrk+t+++sksn+vvifinqir+kiGvmfg+
  AHX11450.1 102 LGVEIDQLLISQPDTGEQALEIVDSLIKSGAVDVIVIDSVAALTPKAELEGEMGDLHVGLQARLLSQALRKITASVSKSNCVVIFINQIRMKIGVMFGS 200
                 *************************************************************************************************** PP

                 ------HHHHHHH-SEEEEEEEES---------EEEEEEEEEEESSS----EEEEEEETTTEE- CS
        RecA 200 petttGGralkfyasvrldvrrieeikekeevignktkvkvvknkvappfkeaeldilygeGis 263
                 petttGG+alkfy+svrld+rr+++ikeke+vig++t+vkvvknkvappfk++++di+y+eGis
  AHX11450.1 201 PETTTGGNALKFYSSVRLDIRRVGSIKEKEDVIGSQTRVKVVKNKVAPPFKQVDFDIIYNEGIS 264
                 **************************************************************97 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.6     4e-18   4.4e-15       9     252 ..      26     263 ..      17     266 .. 0.75

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 4e-18
                 HHHHHHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEEEESSS---GGGGHHHHHHTT--HHHHGGGEE CS
       Rad51   9 llekrsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavyidtegtfrperlveiaerykldkeevlenva 107
                 ++++   + +++tGs  lD+ LgGGi+ g i eifG   sGkt l+  +        +++G  g +++id+e ++ p      a r +++ +++l+  +
  AHX11450.1  26 FNQEPAMVECISTGSIGLDHALGGGIPKGRIIEIFGPESSGKTTLTLHVIAES----QKNG--GTCAFIDAEHALDPI----YARRLGVEIDQLLISQP 114
                 5556666778*********************************8754443333....3444..68***********96....5999****999998765 PP

                 EEE--STTHHHHHHHHTHHHHHHS-EEEEEEETTTGGG.CH----.---THH..HHHHHHHHHHHHHHHHHHH--EEEEEEE-------.--------- CS
       Rad51 108 yaRaytiehqeellqqaaallaedkfallivDsvtaly.Rtdfsg.rgelak..RqqklgkllrtLrkladefevavvitnqvvaqvdgqaalfsadpk 202
                        +  e+ l+ + +l+++  + ++++Dsv+al  +++ +g  g+l      + l++ lr+++    + +  v+  nq+  +++    +f + p+
  AHX11450.1 115 -------DTGEQALEIVDSLIKSGAVDVIVIDSVAALTpKAELEGeMGDLHVglQARLLSQALRKITASVSKSNCVVIFINQIRMKIGV---MF-GSPE 202
                 .......4455556666677889999**********8647898763577754215667899999999999999***********99988...55.6788 PP

                 ---HHHHHHHH-SEEEEEEE-ST..........TEEEEEEES-SSS-S-EEEEE.EETTEE CS
       Rad51 203 kPigGlvlahasttRlalrkgkg..........eeRivkvvdsPnlpeleavfa.igeeGi 252
                    gG+ l   s++Rl +r+             ++R+  v +    p +++ f  i++eGi
  AHX11450.1 203 TTTGGNALKFYSSVRLDIRRVGSikekedvigsQTRVKVVKNKVAPPFKQVDFDiIYNEGI 263
                 899*************998654444455777754454333333334445555531466666 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   3.1   1.7e-11   1.9e-08       2     188 ..      37     219 ..      36     264 .. 0.68

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 1.7e-11
      ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepaedlrenakslGwdlekleeegklaiidasesaeesaeekd 100
                 +tg  glD+ l gGip+gr++ i G   +GKt++ l+ + ++ ++ g  + f+  e     ++  a++lG+++++l  +         + +        
  AHX11450.1  37 STGSIGLDHALGGGIPKGRIIEIFGPESSGKTTLTLHVIAESQKN-GGTCAFIDAEHALDPIY--ARRLGVEIDQLLIS---------QPD-------- 115
                 79999*************************************666.********999988886..68999999988655.........121........ PP

      ATPase 101 kedleelieelaeaikeikakrvviDsitgl..ayee...........keavaReilrqlvrvlkklgvTailvsekss........seeaaggygvee 178
                     e+ +e + + ik+  +  +viDs+++l  + e            ++ ++ + lr+++  ++k +++ i+++++++         e+++gg++++ 
  AHX11450.1 116 --TGEQALEIVDSLIKSGAVDVIVIDSVAALtpKAELegemgdlhvglQARLLSQALRKITASVSKSNCVVIFINQIRMkigvmfgsPETTTGGNALKF 212
                 ..1233444555556666666666666666632111111111111111344555777888888888888888888888777777754444555555544 PP

      ATPase 179 fivdgvivLd 188
                    +  ++Ld
  AHX11450.1 213 ---YSSVRLD 219
                 ...4445555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   0.0   1.1e-07   0.00013       5      78 ..      57     145 ..      53     153 .. 0.88

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.1e-07
      AAA_24   5 iliyGpsgiGKTtlakel.......gpkplfidtekGlksldadkfpdie..........swedfldevvelaaeladyktlviDtidele 78 
                 i i+Gp+ +GKTtl ++        g + +fid e+ l+ ++a+++  +e          + e+ l+ v++l +  a  +++viD++  l 
  AHX11450.1  57 IEIFGPESSGKTTLTLHViaesqknGGTCAFIDAEHALDPIYARRLG-VEidqllisqpdTGEQALEIVDSLIKSGA-VDVIVIDSVAALT 145
                 679*****************************************986.55579999999888999999999988888.9*******98875 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.3   0.0   3.8e-07   0.00042      21      67 ..      55     101 ..      52     199 .. 0.66
   2 ?   -3.1   0.0       5.2   5.9e+03      62     100 ..     226     264 ..     218     280 .. 0.67

  Alignments for each domain:
  == domain 1  score: 20.3 bits;  conditional E-value: 3.8e-07
    ATPase_2  21 eiyfiYGpegsGKtaLlkeiienledkdkyviyyialreesisklde 67 
                 +i+ i+Gpe+sGKt+L  ++i ++++ +    +++a +  +  ++++
  AHX11450.1  55 RIIEIFGPESSGKTTLTLHVIAESQKNGGTCAFIDAEHALDPIYARR 101
                 6888********************99999999998866655555444 PP

  == domain 2  score: -3.1 bits;  conditional E-value: 5.2
    ATPase_2  62 iskldefieeeeekkklekalgiavpkaeleeilkeksk 100
                 i+++++ i+ +  +k ++++++ +++++ ++ i++e + 
  AHX11450.1 226 IKEKEDVIGSQTRVKVVKNKVAPPFKQVDFDIIYNEGIS 264
                 566666666777777777777777777777766665444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   0.5   2.2e-05     0.024      25     155 ..      46     145 ..      42     187 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.2e-05
      AAA_25  25 lvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelr.rRlravgealrddarllvldlagveslpLfakdrg 122
                  ++g +p+g ++ ++G++ +GKttl+l++ ++  +            g++ +++aE + d +  rRl     ++   ++ll+ + ++           g
  AHX11450.1  46 ALGGGIPKGRIIEIFGPESSGKTTLTLHVIAESQK----------NGGTCAFIDAEHALDPIYaRRLG---VEI---DQLLISQPDT-----------G 117
                 567889*********************98776553..........34677777777776543303333...332...2333333222...........2 PP

      AAA_25 123 gtlltadvdaleaaieevegvrlvviDplsral 155
                     +++++ ++  i++   v+++viD++++++
  AHX11450.1 118 ----EQALEIVDSLIKS-GAVDVIVIDSVAALT 145
                 ....2333344555555.556666666666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.1e-05     0.012       7      45 ..      50      88 ..      45     293 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.1e-05
                EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEET CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  7 klkegekvaivGenGaGKStLlkllagllkpteGeilld 45
                 + +g+++ i+G+  +GK+tL   ++ +++++ G+  + 
  AHX11450.1 50 GIPKGRIIEIFGPESSGKTTLTLHVIAESQKNGGTCAFI 88
                6899*************************9999998543 PP

>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.029       2     113 ..      36     145 ..      35     185 .. 0.78
   2 ?   -2.6   0.0       2.4   2.7e+03     194     218 ..     219     243 ..     216     258 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                 BXSSTHHHHHHC.TSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHHCSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHTTSXHHHHHHHHHHHHHH CS
                 xxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C   2 lstgfkdLDklt.sGlqkgdliiiAarpsmGktalalniaenaavkeklpvavfslemsaeqlvqRllsseaeidskklrtgklkeedweklteaieel 99 
                 +stg   LD+++ +G+ kg +i i +  s Gkt+l+l+++++  + +  ++a++  e + + + +R l    eid+  + + +  e+ +e + + i++ 
  AHX11450.1  36 ISTGSIGLDHALgGGIPKGRIIEIFGPESSGKTTLTLHVIAESQK-NGGTCAFIDAEHALDPIYARRLGV--EIDQLLISQPDTGEQALEIVDSLIKSG 131
                 688899999766267999********************9998775.55589********99999999984..456655555555555555555555555 PP

                 HHSEEEEEEXSSXC CS
                 xxxxxxxxxxxxxx RF
      DnaB_C 100 seaklfiddtpalt 113
                 +   ++id  +alt
  AHX11450.1 132 AVDVIVIDSVAALT 145
                 55556666666655 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 2.4
                 HHCCTTSCCCCXSEEEEEEECCHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C 194 DLreSgsieqdADvvlflyrdeyyk 218
                 D+r  gsi++  Dv+    r ++ k
  AHX11450.1 219 DIRRVGSIKEKEDVIGSQTRVKVVK 243
                 8999999999999997777766655 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   2.6e-05     0.029       3     106 ..      59     185 ..      57     194 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 2.6e-05
                 EESSTTSSHHHHHHHHHHHH...THEEEEEETTTCSSS................STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHH..TTCCCH CS
         AAA   3 lyGppGtGKTllakavakel...gvefleisgsellsk................yvgesekkirelfkeakekakpsilfiDEidalaksr..sgsese 80 
                 ++Gp   GKT+l   v+ e+   g ++  i++   l+                     +e+ ++ + + +k+ a   +++iD + al+++   +g+  +
  AHX11450.1  59 IFGPESSGKTTLTLHVIAESqknGGTCAFIDAEHALDPiyarrlgveidqllisQPDTGEQALEIVDSLIKSGA-VDVIVIDSVAALTPKAelEGEMGD 156
                 68**********99999997333233444444444433455555555555554355555666666666688888.9***************99777777 PP

                 HHHHHHHHHHHHHHHTTTS...SSTEEEE CS
         AAA  81 eeervvnqLlteldgvkkk...eskvivi 106
                  +  +++ Ll++  +  +    +s+++vi
  AHX11450.1 157 LHVGLQARLLSQALRKITAsvsKSNCVVI 185
                 77777777777644433323444556666 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   2.6e-05     0.029      24     141 ..      54     187 ..      43     190 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.6e-05
      AAA_16  24 pelvllsGesGvGKsslvrellralekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleeala...........avpe 110
                 ++++ + G+  +GK++l  ++  + +k+gg ++  ++++      +++ +a+ l   e+ + l +++++   e++ e  ++              +v++
  AHX11450.1  54 GRIIEIFGPESSGKTTLTLHVIAESQKNGGTCAFIDAEHA-----LDPiYARRL-GVEIDQLLISQPDT--GEQALEIVDSL-IksgavdvividSVAA 143
                 3888999***************999999888877777777.....556677777.64666666666444..22333322333.2477789999995555 PP

      AAA_16 111 lagaea..............srllellkrllallsrderplvlvl 141
                 l+++++              + l ++l+++ a  s+ +  +v+++
  AHX11450.1 144 LTPKAElegemgdlhvglqaRLLSQALRKITASVSK-SNCVVIFI 187
                 555555555555888888855555566666677777.44488887 PP

>> CobU  Cobinamide kinase / cobinamide phosphate guanyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.6e-05      0.04       3     125 ..      59     189 ..      57     201 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.6e-05
        CobU   3 vtGgarSGKSefAekla...eeskekvvYiATaealDeemaeRiarHrerR.paeWetveepldlaealkeeekkevvLvDcltlwltnllleeeaek. 96 
                 + G+  SGK ++  +++   +++++++ +i + +alD  +a+R+    ++   ++ +t e+ l++ + l ++ + +v+++D+++ ++ ++ le e  + 
  AHX11450.1  59 IFGPESSGKTTLTLHVIaesQKNGGTCAFIDAEHALDPIYARRLGVEIDQLlISQPDTGEQALEIVDSLIKSGAVDVIVIDSVAALTPKAELEGEMGDl 157
                 78**************96555556889*****************999988868999*********9999998889***********9988777665558 PP

        CobU  97 ....veekleeeveellealkelkatvvlVsnE 125
                     + + l++++++++++++++++ v+++ n 
  AHX11450.1 158 hvglQARLLSQALRKITASVSKSNCVVIFI-NQ 189
                 999666677888888888888888777776.44 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00014      0.16       2      43 ..      54      95 ..      53     161 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00014
      AAA_14  2 rkilvitGaRrvGKTtllkqlikellvkkesilyinldderd 43
                ++i+ i G+  +GKTtl  ++i e+  +   + +i+ ++  d
  AHX11450.1 54 GRIIEIFGPESSGKTTLTLHVIAESQKNGGTCAFIDAEHALD 95
                57899*****************99996777777777777666 PP

>> MobB  Molybdopterin guanine dinucleotide synthesis protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001      0.12       1      37 [.      56      92 ..      56      97 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
        MobB  1 vlgivgksgsGKTtLleklipelkarglrvgtiKhah 37
                ++ i g + sGKTtL  ++i+e +++g + + i  +h
  AHX11450.1 56 IIEIFGPESSGKTTLTLHVIAESQKNGGTCAFIDAEH 92
                68999**********************9999986554 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   8.4e-05     0.094       5     105 ..      54     147 ..      52     189 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8.4e-05
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhl 103
                  +i+ ++G+  +GKTtl   +  + ++       + +++f+++ +  ++   +r+l  ++++ l +++++ e+ le +   +++ av  +++iD +  l
  AHX11450.1  54 GRIIEIFGPESSGKTTLTLHVIAESQKN------GGTCAFIDAEHALDPIY-ARRLGVEIDQLLISQPDTGEQALEIVDSLIKSGAV-DVIVIDSVAAL 144
                 57999******************98754......77777999999885543.577777777777778999*****************.******99999 PP

      AAA_22 104 r.s 105
                 + +
  AHX11450.1 145 TpK 147
                 542 PP

>> AAA_35  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   7.4e-05     0.083      30      70 ..      53      93 ..      51     101 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 7.4e-05
      AAA_35 30 pGalirikapkkmGKtSLlarilakakqqgyktvsldlqla 70
                +G +i i +p+  GKt L  +++a+ +++g   + +d ++a
  AHX11450.1 53 KGRIIEIFGPESSGKTTLTLHVIAESQKNGGTCAFIDAEHA 93
                699***************************99999998876 PP

>> PAXNEB  PAXNEB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.3   0.00021      0.23      19      42 ..      36      59 ..      33      70 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 0.00021
      PAXNEB 19 tStGtpsLDklLgGGLplGsilli 42
                +StG+  LD+ LgGG+p G i+ i
  AHX11450.1 36 ISTGSIGLDHALGGGIPKGRIIEI 59
                8******************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (327 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       584  (0.0325729); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.42
# Mc/sec: 2311.25
//
Query:       AHX11451.1  [L=533]
Description: his Kinase A domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-13   51.4   0.3    3.3e-13   50.1   0.3    1.7  1  HATPase_c    Histidine kinase-, DNA gyrase B-, and HSP90-like
    1.4e-06   28.2   0.0    3.9e-06   26.8   0.0    1.8  1  HisKA        His Kinase A (phospho-acceptor) domain
     0.0011   19.0   0.0     0.0023   17.9   0.0    1.5  1  HATPase_c_2  Histidine kinase-like ATPase domain
  ------ inclusion threshold ------
       0.03   14.5   1.0       0.89    9.6   0.2    2.6  2  TssO         Type VI secretion system, TssO
      0.035   13.9   0.3       0.14   12.0   0.1    2.0  2  HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like


Domain annotation for each model (and alignments):
>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   0.3   9.1e-17   3.3e-13       3     108 ..     408     510 ..     406     514 .. 0.83

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 9.1e-17
                 HHHHHHHHHHHHHHHHHHHSTTTEEEEEEEEEE..TEEEEEEEESSSSSTTHHHTGTCSTTCHHCSTCHTSTSSSHHHHHHHHHHHHTTTEEEEEEETT CS
   HATPase_c   3 ekrLrqiisnlvdNavkfatkageieveikase..ddlvisveDnGiGipkedlkklfekfsqddstkrggggtGlGlsivkklvelmgGeiwvesepg 99 
                   +++++i n+++Navkf++++ ++++e + +   d ++i +eD+GiG++  +      +  + +s +++  g G+Gl +++++++l +G++++ s+ g
  AHX11451.1 408 HNQVKKAITNILSNAVKFSPNGATVSIEASHDPidDSIHIVIEDSGIGMTIVEGM----PTPE-KSLTQKADGLGIGLLLSRNIIRLNNGNLEIYSQVG 501
                 5678999***********889999999999633678**************95544....4444.55667899**************999********** PP

                 TEEEEEEEE CS
   HATPase_c 100 rGttftftl 108
                 +Gt+ ++t+
  AHX11451.1 502 KGTRSVITF 510
                 ****65543 PP

>> HisKA  His Kinase A (phospho-acceptor) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.8   0.0   1.1e-09   3.9e-06       4      31 ..     294     324 ..     291     359 .. 0.70

  Alignments for each domain:
  == domain 1  score: 26.8 bits;  conditional E-value: 1.1e-09
                 HHHHHHHHHHHHHHHHHHHHHHHHHC..... CS
       HisKA   4 rflagvaHELrtPLsailgnaeaLkre...g 31 
                  f++ + HELrtPL++i++++e++k+e    
  AHX11451.1 294 NFISCITHELRTPLNVIIAFSEMIKDEclgS 324
                 688999********************86651 PP

>> HATPase_c_2  Histidine kinase-like ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   0.0   6.4e-07    0.0023      31     108 ..     410     486 ..     390     489 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 6.4e-07
  HATPase_c_2  31 eirlaveEactNavehayleapegpvevrlesdeealtvevaDsGpgfdpetlpdpteeepkeslkegGrGlalikgl 108
                  +++ a++ +++Nav+   ++a+  ++e + +  +++++++++DsG g +  ++ + +e++++++++  G+Gl+l +++
   AHX11451.1 410 QVKKAITNILSNAVKFSPNGAT-VSIEASHDPIDDSIHIVIEDSGIGMTIVEGMPTPEKSLTQKADGLGIGLLLSRNI 486
                  6777888889999999988777.6666667777899***********9999888888999888999999999887765 PP

>> TssO  Type VI secretion system, TssO
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.2   0.00025      0.89       8      75 ..      14      77 ..      11      89 .. 0.83
   2 ?    2.5   0.0     0.039   1.4e+02       4      30 ..     237     260 ..     235     279 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.00025
        TssO  8 sgflyflllFlvtvlllflivffffkssplqekeillkelerkkkfeekqkelkkkvdsiykkIdsLk 75
                +  ++fll Fl+ v +++  + +++    l + +++  e+e +++f+  q+++++    ++++I+  +
  AHX11451.1 14 IRYIKFLLFFLAFVSIFS-SLAYNNG--NLRNYNKI-REIESSSAFKVAQNTIENFYSGVQNEISLVN 77
                667899999999888888.7888888..55555555.89****************9999999999875 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.039
        TssO   4 kErrsgflyflllFlvtvlllflivff 30 
                 kE ++g++ fll ++v++++l+   f+
  AHX11451.1 237 KESIIGVFSFLLPLSVALVILS---FL 260
                 89*****************999...55 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.57     2e+03      37      71 ..     123     158 ..     112     161 .. 0.77
   2 ?   12.0   0.1     4e-05      0.14       4      46 ..     412     457 ..     408     474 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.57
  HATPase_c_3  37 vieDdGkGmsee.elknalrlatsskeakrkstslG 71 
                  +++Dd  G+ ++ +l nal  +  +++ ++++ ++G
   AHX11451.1 123 TVKDDKLGVIKNvTLNNALVHHCVRHQDNHNNYDVG 158
                  799999999988788889988888887777666666 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4e-05
  HATPase_c_3   4 ekAlaelvdNsld..Adaenvkievnknr.gktgeivieDdGkGms 46 
                  +kA++ ++ N++    +  +v+ie+++++  ++  ivieD G Gm+
   AHX11451.1 412 KKAITNILSNAVKfsPNGATVSIEASHDPiDDSIHIVIEDSGIGMT 457
                  89*********986677888****9999977889***********7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (533 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       773  (0.0431145); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.57u 0.23s 00:00:00.80 Elapsed: 00:00:00.40
# Mc/sec: 4033.55
//
Query:       AHX11452.1  [L=256]
Description: succinate dehydrogenase and fumarate reductase iron-sulfur family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-32  111.6   0.0    3.2e-32  110.8   0.0    1.5  1  Fer2_3    2Fe-2S iron-sulfur cluster binding domain
    4.5e-09   36.7   3.6    4.5e-09   36.7   3.6    2.0  2  Fer4_17   4Fe-4S dicluster domain
    9.9e-08   32.0   2.7    9.9e-08   32.0   2.7    2.1  2  Fer4_10   4Fe-4S dicluster domain
    2.3e-07   31.2   6.4    2.3e-07   31.2   6.4    2.3  2  Fer4_8    4Fe-4S dicluster domain
     0.0071   16.3   0.2     0.0071   16.3   0.2    2.0  2  Fer2      2Fe-2S iron-sulfur cluster binding domain
  ------ inclusion threshold ------
      0.021   15.0   7.0      0.021   15.0   7.0    2.6  3  Fer4_9    4Fe-4S dicluster domain
      0.071   13.3   4.1       0.26   11.5   0.1    2.9  3  Fer4_18   4Fe-4S dicluster domain
      0.097   13.3  14.9       0.05   14.2   8.2    3.0  3  Fer4_7    4Fe-4S dicluster domain
       0.22   12.5   7.2        4.1    8.4   0.7    2.9  3  Fer4_16   4Fe-4S double cluster binding domain


Domain annotation for each model (and alignments):
>> Fer2_3  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.8   0.0   1.6e-35   3.2e-32       2     107 ..      28     129 ..      27     131 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.8 bits;  conditional E-value: 1.6e-35
      Fer2_3   2 lkvkRfdprrdrgkqkvqeyeveae.eedtvldaLlkikeevdptlafrasCregiCGscavainGkptlaCtatikdlakqkseieleplpkfpvirD 99 
                 l ++Rf+p   +++++ ++y v+ +    +vldaLlkik+evdptl+fr+sCregiCGsca++i+G++tlaCt+++ d++    ++++ plp++pvi+D
  AHX11452.1  28 LVIYRFSP--GDENPRRDTYYVDSKnCAPMVLDALLKIKNEVDPTLTFRRSCREGICGSCAMNIDGRNTLACTKSMADIKG---PVKIYPLPHMPVIKD 121
                 6799****..4458*********998999*************************************************984...59************* PP

      Fer2_3 100 LvvDidem 107
                 Lv+D   +
  AHX11452.1 122 LVTDLAVF 129
                 ****9776 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.8       2.7   5.4e+03       8      14 ..      82      87 ..      75     103 .. 0.60
   2 !   36.7   3.6   2.3e-12   4.5e-09       2      61 .]     167     239 ..     166     239 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 2.7
     Fer4_17  8 ClpeCps 14
                C   C +
  AHX11452.1 82 CGS-CAM 87
                333.433 PP

  == domain 2  score: 36.7 bits;  conditional E-value: 2.3e-12
     Fer4_17   2 CiqCgyClpeCpsyeaydne...pkkllraakl.glleeaeke.........ekaslCieCgeCerkCPqgld 61 
                 Ci C++C  +Cps+++++++   p+ ll+a+++ +++++++++          k  +C+++ +C++ CP+gl+
  AHX11452.1 167 CILCACCSTSCPSFWWNGTKylgPAALLQAYRWlSDTRDVKRQerlafladaFKLYRCHTIMNCTQTCPKGLN 239
                 ****************999666699999999999445554444455677765699***************996 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.2      0.58   1.2e+03      42      52 ..      74      86 ..      54      99 .. 0.73
   2 !   32.0   2.7     5e-11   9.9e-08       8      56 .]     166     235 ..     162     235 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.58
     Fer4_10 42 vekCtg..cgaCv 52
                  +C +  cg+C+
  AHX11452.1 74 RRSCREgiCGSCA 86
                5566666677774 PP

  == domain 2  score: 32.0 bits;  conditional E-value: 5e-11
     Fer4_10   8 tCirCgkCvkaCPadl.....................tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                  Ci C+ C ++CP+ +                     t++++++e+    a+  k+++C+++ +C++ CP
  AHX11452.1 166 DCILCACCSTSCPSFWwngtkylgpaallqayrwlsdTRDVKRQERLAFLADAFKLYRCHTIMNCTQTCP 235
                 6*************99*****************************************************9 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.6  10.8    0.0013       2.5      35      63 ..     151     179 ..      75     181 .. 0.60
   2 !   31.2   6.4   1.1e-10   2.3e-07       2      64 ..     164     237 ..     163     238 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.0013
      Fer4_8  35 dvqeeqvleeeealwsCttcgaCtevCpv 63 
                   q+ +++e+ ++l+ C  c +C++ Cp 
  AHX11452.1 151 HIQSPDEREQLTGLHDCILCACCSTSCPS 179
                 2344444444589**************96 PP

  == domain 2  score: 31.2 bits;  conditional E-value: 1.1e-10
      Fer4_8   2 lekCieCgaCqsaCp.............vlrrtkkhlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                 l++Ci C +C ++Cp             +l +  ++l d+r+ + +  ++   l ++  l++C+t ++Ct+ Cp+g
  AHX11452.1 164 LHDCILCACCSTSCPsfwwngtkylgpaALLQAYRWLSDTRDVKRQ--ERLAFLADAFKLYRCHTIMNCTQTCPKG 237
                 579***********86666666666664444444777777777555..55555566999***************98 PP

>> Fer2  2Fe-2S iron-sulfur cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   3.6e-06    0.0071      19      61 ..      60      91 ..      40     105 .. 0.73
   2 ?   -2.3   0.8       2.2   4.4e+03      40      43 ..     170     173 ..     143     178 .. 0.50

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3.6e-06
                HHHHHHH.TTTTTSTTSSSSSSSSTTEEEEEESCECTTSSSSTH CS
        Fer2 19 lldaaee.nggidipysCggggCgtClvevlegevqsdeteleg 61
                ll++  e ++ + ++ sC++g Cg+C+  ++            g
  AHX11452.1 60 LLKIKNEvDPTLTFRRSCREGICGSCAMNID------------G 91
                4444445566788999***********9877............3 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.2
                 SSTT CS
        Fer2  40 CgtC 43 
                 C+ C
  AHX11452.1 170 CACC 173
                 3333 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.5      0.47   9.4e+02      35      43 ..      76      86 ..      46     100 .. 0.70
   2 ?    5.6   4.5    0.0089        18      34      48 ..     165     179 ..     145     180 .. 0.66
   3 ?   15.0   7.0     1e-05     0.021       1      49 [.     166     237 ..     166     238 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.47
      Fer4_9 35 aCig..CgaCv 43
                +C +  Cg+C+
  AHX11452.1 76 SCREgiCGSCA 86
                45444567664 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0089
      Fer4_9  34 eaCigCgaCveaCpk 48 
                  +Ci C  C   Cp+
  AHX11452.1 165 HDCILCACCSTSCPS 179
                 678888888888885 PP

  == domain 3  score: 15.0 bits;  conditional E-value: 1e-05
      Fer4_9   1 kCtgCgaCveaCpa.gvvvedaaerkarlraase......................eaCigCgaCveaCpkg 49 
                 +C+ C  C ++Cp+ + +  +  +  a l+a+++                       +C++ + C++ Cpkg
  AHX11452.1 166 DCILCACCSTSCPSfWWNGTKYLGPAALLQAYRWlsdtrdvkrqerlafladafklYRCHTIMNCTQTCPKG 237
                 5***********751555778888888888888899999999999***********99************97 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.2      0.56   1.1e+03      85     102 ..      82     104 ..      61     111 .. 0.66
   2 ?   11.5   0.1   0.00013      0.26      44      73 ..     150     179 ..     118     181 .. 0.75
   3 ?    1.4   0.0      0.18   3.5e+02      60      76 ..     223     239 ..     201     245 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.56
     Fer4_18  85 ciscllcid.....acdkvmekl 102
                 c sc+  id     ac+k m  +
  AHX11452.1  82 CGSCAMNIDgrntlACTKSMADI 104
                 66676666644444566666555 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 0.00013
     Fer4_18  44 kkalkekeerkekgagdcidcescvkvcPt 73 
                 ++ ++  e+++ +g  dci c  c + cP 
  AHX11452.1 150 EHIQSPDEREQLTGLHDCILCACCSTSCPS 179
                 333444556677899**************5 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.18
     Fer4_18  60 dcidcescvkvcPtgid 76 
                  c +   c + cP g++
  AHX11452.1 223 RCHTIMNCTQTCPKGLN 239
                 58888899999999875 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.6      0.29   5.7e+02      23      45 ..      37      86 ..      29      99 .. 0.56
   2 ?    7.0   4.6    0.0045         9      35      50 ..     164     179 ..     139     181 .. 0.74
   3 ?   14.2   8.2   2.5e-05      0.05       2      51 ..     167     237 ..     166     238 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.29
      Fer4_7 23 enekgtekveidpekClg...........................CgaCv 45
                +++++++++++d+ +C                             Cg+C+
  AHX11452.1 37 DENPRRDTYYVDSKNCAPmvldallkiknevdptltfrrscregiCGSCA 86
                45566677888888887322233333333333333334444444456665 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.0045
      Fer4_7  35 pekClgCgaCvavCPt 50 
                   +C+ C  C + CP+
  AHX11452.1 164 LHDCILCACCSTSCPS 179
                 4679999999999996 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 2.5e-05
      Fer4_7   2 CigCgaCvaaCpvkaieldeeenek................gtekv.....eidpekClgCgaCvavCPtg 51 
                 Ci C  C   Cp+ + + +++  ++                ++e++     +++  +C +  +C ++CP+g
  AHX11452.1 167 CILCACCSTSCPSFWWNGTKYLGPAallqayrwlsdtrdvkRQERLafladAFKLYRCHTIMNCTQTCPKG 237
                 ***********9999998875444433333333332222223344466666778889************98 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2       2.7   5.4e+03       5       9 ..      82      86 ..      64      88 .. 0.73
   2 ?    8.4   0.7    0.0021       4.1      44      65 ..     157     178 ..     132     181 .. 0.66
   3 ?    7.0   0.0    0.0058        12       1      15 [.     223     237 ..     193     250 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.7
     Fer4_16  5 CgkCa 9 
                Cg Ca
  AHX11452.1 82 CGSCA 86
                55554 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0021
     Fer4_16  44 deekckkqeaitgCdiCqdvCP 65 
                 ++e+ +   +++ C+ C + CP
  AHX11452.1 157 EREQLTGLHDCILCACCSTSCP 178
                 2333334488999999999999 PP

  == domain 3  score: 7.0 bits;  conditional E-value: 0.0058
     Fer4_16   1 rCgtCgkCaevCPtn 15 
                 rC+t  +C+++CP +
  AHX11452.1 223 RCHTIMNCTQTCPKG 237
                 366666666666654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      379  (0.0211389); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1988.93
//
Query:       AHX11453.1  [L=37]
Description: hypothetical protein NHE_0512 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       219  (0.0122148); expected 358.6 (0.02)
Passed bias filter:                      200  (0.0111551); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 305.02
//
Query:       AHX11454.1  [L=58]
Description: hypothetical protein NHE_0513 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       423  (0.0235931); expected 358.6 (0.02)
Passed bias filter:                      221  (0.0123264); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.19s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 527.21
//
Query:       AHX11455.1  [L=380]
Description: chaperone protein DnaJ [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.7e-39  135.3   0.0    2.2e-39  134.9   0.0    1.2  1  DnaJ_C         DnaJ C terminal domain
    6.6e-28   96.6   8.7    2.5e-27   94.8   6.8    2.4  2  DnaJ           DnaJ domain
    1.9e-09   37.7  22.1    3.5e-09   36.9  22.1    1.5  1  DnaJ_CXXCXGXG  DnaJ central domain
  ------ inclusion threshold ------
       0.54   10.3  20.9       0.88    9.6   0.4    3.3  3  Anti-TRAP      Tryptophan RNA-binding attenuator protein inhi


Domain annotation for each model (and alignments):
>> DnaJ_C  DnaJ C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.9   0.0     5e-43   2.2e-39       2     148 .]     129     342 ..     128     342 .. 0.95

  Alignments for each domain:
  == domain 1  score: 134.9 bits;  conditional E-value: 5e-43
                 EEEEEE-HHHHHH-.EEE.EEEE....................................................................T.EEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx.............................................................xxxxx.xxxxxx RF
      DnaJ_C   2 eveleisleelykGktkkikikrnvi.............................................................kkekk.tlevki 38 
                 +++++i+l+++++Gk+ ki++ +  +                                                             +++k+ t +vki
  AHX11455.1 129 RYDVSINLQDAFRGKEVKISYAKLAEcihcsgtgcegkakpvqcntcngvgavrsqqgfftvertcgtcggsgmivenpckkcggegRSRKEvTTSVKI 227
                 799******************99888************************************************************966666699**** PP

                 -TT--TT-EEEETT-SS..SS..S---EEEEEEE---SS-EEETTEEEEEEEEEHHHHHHTEEEEEE-S.S-EEEEEE...--TT-EEEETT-S-EET. CS
                 xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx...xxxxxxxxxxxxxxxxxx RF
      DnaJ_C  39 paGikdgqkirlegeGd..eeggepGDlivtikvkphpvFkrkgndlyveveislaeallGgklevptl.dgkvklki...tqpgevlrikgkGmpklk 131
                 p+Gi dg k++l+ +G+   +gg++GDl+v+++vk++++F+rk+ndly++++i ++ a+lGg++evp + + k k+k+   tq+g++l+++gkGm  l+
  AHX11455.1 228 PRGISDGAKVVLRSQGEagLRGGKAGDLYVVVHVKEDSFFQRKNNDLYCDAPIRMSLAALGGEIEVPAPeGAKLKIKVpegTQTGDKLKLRGKGMYLLN 326
                 ****************955445***********************************************666788999********************7 PP

                 ..TEE--EEEEEEEE-- CS
                 xxxxxxxxxxxxxxxxx RF
      DnaJ_C 132 kpgkrGdlyvevkvefP 148
                  +++rGd+yv+++ve+P
  AHX11455.1 327 -SEHRGDMYVRITVETP 342
                 .**************99 PP

>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   94.8   6.8   5.6e-31   2.5e-27       1      63 []       7      69 ..       7      69 .. 0.99
   2 ?    0.8   0.0      0.12   5.5e+02       8      29 ..     136     157 ..     130     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 94.8 bits;  conditional E-value: 5.6e-31
                HHHHHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHHHHHHHHHHHTSHHHHHHHH CS
        DnaJ  1 dyYeiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFkeineAyevLsdpekRkqYD 63
                dyY++L+vsk+as++eI+kaY+klalkyHPD+n++d++a+ekFkeineAy+vLsdpek+ +YD
  AHX11455.1  7 DYYDLLEVSKSASQEEIRKAYKKLALKYHPDRNKDDKNAAEKFKEINEAYSVLSDPEKKVSYD 69
                8*************************************************************9 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.12
                 SSTTG-HHHHHHHHHHHHHHHS CS
        DnaJ   8 vskdasedeIkkaYrklalkyH 29 
                 ++     +e+k +Y kla  +H
  AHX11455.1 136 LQDAFRGKEVKISYAKLAECIH 157
                 555567899*********8887 PP

>> DnaJ_CXXCXGXG  DnaJ central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.9  22.1   7.9e-13   3.5e-09       1      67 []     155     215 ..     155     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 36.9 bits;  conditional E-value: 7.9e-13
  DnaJ_CXXCXGXG   1 CkkCkGsgakk.gkkktCktCkGsGvvreeqktlgpfvqqsqstCpeCeGtGkvikekdkCkkCkGkg 67 
                    C +C+G+g++  +k+ +C+tC+G G vr++q   g+f+  +++tC +C+G+G ++  +++CkkC G+g
     AHX11455.1 155 CIHCSGTGCEGkAKPVQCNTCNGVGAVRSQQ---GFFT--VERTCGTCGGSGMIV--ENPCKKCGGEG 215
                    99******975366999********877776...3444..689************..889******86 PP

>> Anti-TRAP  Tryptophan RNA-binding attenuator protein inhibitory protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   6.5    0.0019       8.5      12      47 ..     154     186 ..     151     189 .. 0.89
   2 ?    5.1   7.5     0.005        22       9      40 ..     190     215 ..     189     216 .. 0.94
   3 ?    9.6   0.4    0.0002      0.88      10      48 ..     205     244 ..     203     247 .. 0.85

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0019
                 E-TTTTTTSEETTE......E-TTTTTSSEEE-HHH CS
   Anti-TRAP  12 kCdaCngsGkiepeeprasleCPkCsGkglipTaqG 47 
                 +C +C g+G +  +     ++C  C+G+g +  +qG
  AHX11455.1 154 ECIHCSGTGCEGKA---KPVQCNTCNGVGAVRSQQG 186
                 7********88877...679**********999998 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.005
                 CEEE-TTTTTTSEETTE......E-TTTTTSS CS
   Anti-TRAP   9 LEtkCdaCngsGkiepeeprasleCPkCsGkg 40 
                  E +C +C gsG i  +      +C kC+G+g
  AHX11455.1 190 VERTCGTCGGSGMIVEN------PCKKCGGEG 215
                 599**************......*******87 PP

  == domain 3  score: 9.6 bits;  conditional E-value: 0.0002
                 EEE-TTTTTTSEETTE......E-TT..TTTSSEEE-HHHH CS
   Anti-TRAP  10 EtkCdaCngsGkiepeeprasleCPk..CsGkglipTaqGq 48 
                 E++C++C g G+   e   +s++ P+    G ++++  qG+
  AHX11455.1 205 ENPCKKCGGEGRSRKE-VTTSVKIPRgiSDGAKVVLRSQGE 244
                 99**********9998.889999998335899999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (380 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       981  (0.0547158); expected 358.6 (0.02)
Passed bias filter:                      623  (0.0347482); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2787.36
//
Query:       AHX11456.1  [L=505]
Description: ribosome-associated GTPase EngA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-44  149.9   1.8    5.6e-21   74.8   0.3    2.5  2  MMR_HSR1        50S ribosome-binding GTPase
    3.6e-20   72.0   0.3    1.2e-19   70.4   0.3    1.9  1  KH_dom-like     KH-domain-like of EngA bacterial GTPase enzym
    6.8e-20   71.2   0.6    2.1e-09   37.1   0.1    2.5  2  FeoB_N          Ferrous iron transport protein B
      2e-16   60.3   1.9    7.7e-09   35.8   0.1    3.8  3  Roc             Ras of Complex, Roc, domain of DAPkinase
    1.9e-15   56.9   1.3    1.8e-07   30.9   0.3    2.9  2  Ras             Ras family
    2.8e-09   36.6   3.2    1.9e-05   24.1   0.1    2.7  3  AIG1            AIG1 family
    2.5e-08   34.0   4.8    0.00077   19.4   0.1    3.6  3  RsgA_GTPase     RsgA GTPase
      3e-08   33.9   9.9      0.074   13.1   0.0    4.9  5  Dynamin_N       Dynamin family
    5.6e-08   32.4   2.9      1e-05   25.1   0.2    3.3  3  SRPRB           Signal recognition particle receptor beta sub
    5.8e-08   32.4   6.2    0.00015   21.3   0.8    3.7  2  Arf             ADP-ribosylation factor family
    5.4e-07   29.3   3.5       0.14   11.7   0.1    4.6  3  GTP_EFTU        Elongation factor Tu GTP binding domain
    7.7e-06   25.8   0.0       0.01   15.6   0.0    2.7  2  AAA_24          AAA domain
    1.1e-05   25.2   2.3       0.25   11.1   0.0    4.2  4  PduV-EutP       Ethanolamine utilisation - propanediol utilis
    0.00014   21.8   1.1      0.011   15.7   0.2    2.6  2  MMR_HSR1_Xtn    C-terminal region of MMR_HSR1 domain
    0.00034   20.1   0.1       0.36   10.2   0.0    2.4  2  TniB            Bacterial TniB protein
    0.00035   20.9   0.0        1.3    9.5   0.0    2.6  2  RNA_helicase    RNA helicase
    0.00045   20.7   0.3        1.1    9.8   0.0    2.9  2  ABC_tran        ABC transporter
    0.00082   18.4   0.1      0.045   12.7   0.0    2.6  2  MeaB            Methylmalonyl Co-A mutase-associated GTPase M
     0.0011   18.9   0.0        2.2    8.2   0.0    2.5  2  Ploopntkinase3  P-loop Nucleotide Kinase3
     0.0012   18.2   1.3       0.22   10.8   0.1    2.9  3  Septin          Septin
     0.0034   17.4   0.3        3.3    7.7   0.1    2.9  2  AAA_14          AAA domain
     0.0043   16.3   1.3        1.3    8.2   0.8    2.9  2  NB-ARC          NB-ARC domain
     0.0049   17.2   0.7        5.4    7.3   0.0    3.3  3  AAA_22          AAA domain
     0.0071   16.9   1.9        4.5    7.8   0.0    3.4  3  AAA_18          AAA domain
     0.0099   16.1   0.0        2.5    8.3   0.0    2.7  2  AAA_28          AAA domain
  ------ inclusion threshold ------
       0.02   14.7   0.1        7.7    6.3   0.0    2.4  2  AAA_29          P-loop containing region of AAA domain
       0.17   11.8   7.5          7    6.5   0.1    3.9  4  NTPase_1        NTPase
       0.23   11.2   1.9         51    3.5   0.0    4.0  5  ATP_bind_1      Conserved hypothetical ATP binding protein
       0.25   11.2   4.6        1.7    8.5   0.1    3.5  4  NOG1            Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.8   0.3     9e-24   5.6e-21       1     114 []       6     118 ..       6     118 .. 0.87
   2 !   74.2   0.1   1.4e-23   8.5e-21       1     114 []     178     298 ..     178     298 .. 0.83

  Alignments for each domain:
  == domain 1  score: 74.8 bits;  conditional E-value: 9e-24
                 EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkg.keielvDtpGliegaseekglgkaflaleeadlillvvdaseeklkpldeel 97 
                 +v ivG+ NvGKStL+n+lt++  +i+ d++g+Trd+ e++v+l++ +++ l+Dt+G ++  +++  + ++  a++++++il+v+d   +k++++d  +
  AHX11456.1   6 RVSIVGKANVGKSTLFNKLTKQrLSITMDRKGVTRDVLEKKVSLQNgESFLLLDTAG-FN-PKRSDTIDRTQYAIKKSEIILFVID---DKIDAEDLFF 99 
                 699******************9569******************7766**********.65.3444478899999999*********...56999***** PP

                 HHHHHH..TTSEEEEEEES CS
    MMR_HSR1  98 eellee..akkplilvlnk 114
                  ++l++   + ++ilv nk
  AHX11456.1 100 VSWLRKnaGNSRIILVRNK 118
                 ***9987656668889887 PP

  == domain 2  score: 74.2 bits;  conditional E-value: 1.4e-23
                 EEEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETT.EEEEEEECGGCSS....HHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHH CS
    MMR_HSR1   1 evaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkg.keielvDtpGlie....gaseek.glgkaflaleeadlillvvdaseeklkp 92 
                 ++ i+G+pNvGKStL+n+ +g+ ++ vs ++gtTrd++  ++ ++g + +e++Dt+Gl +    +++ e  + ++a++a  e+d+il++ d+s+ +l++
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMGTdRVLVSPEAGTTRDPVNDEFLWNGhTIFEFIDTAGLRKkrkvSDKLESvSNSRALQASAESDVILFMYDVSNFTLEK 276
                 689******************989*************9999999997889*******6433433333333688899999999*********99557777 PP

                 HHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  93 ldeeleelleeakkplilvlnk 114
                 +d  l +   e++kp+il+ nk
  AHX11456.1 277 QDFILINRVLENGKPVILIGNK 298
                 7777777777899*****9997 PP

>> KH_dom-like  KH-domain-like of EngA bacterial GTPase enzymes, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.4   0.3   1.9e-22   1.2e-19       2      78 ..     357     433 ..     356     434 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.4 bits;  conditional E-value: 1.9e-22
                  --HHHHHHHHHHHHCCS--S.ETTCC-EEEEEEEEETTTTEEEEEECSCCCS-HHHHHHHHHHHHHHCT-TTS--EEE CS
  KH_dom-like   2 istseLnrvleeavekhppp.vkgkrlkiyyatqvgtrpptfvlfvndpelvkesykryLenqlreafgfegtPirlk 78 
                  i++++Lnr+l+e+++khp+p v+ k +k++y+t+v+ + ++f++  n+p+lv +sy +y++n+l ++f++ g+Pi+++
   AHX11456.1 357 IPKHKLNRWLQEVINKHPHPiVNSKSVKLKYITKVKDK-FSFLIRANHPDLVADSYLNYIKNSLAKDFQIYGIPIKFV 433
                  899*****************7779***********976.79***********************************97 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.0   0.1   1.3e-10   7.8e-08       2     125 ..       6     129 ..       5     153 .. 0.75
   2 !   37.1   0.1   3.4e-12   2.1e-09       2     123 ..     178     307 ..     177     330 .. 0.85

  Alignments for each domain:
  == domain 1  score: 32.0 bits;  conditional E-value: 1.3e-10
                 EEEEEESTTSSHHHHHHHHHTTSEEEE.ESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGGHHHHHHHH CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgakqkvg.NwpGvtvekkegklklkg.keveivDlPGiYslsayseeekvardflleeepdvvvnvvdatnlernLyLt 98 
                 +v +vG+ nvGk+tlfn+lt+++ ++     Gvt +  e k++l++ +++ ++D  G     + ++     r+  + ++ ++++ v+d +    +L+++
  AHX11456.1   6 RVSIVGKANVGKSTLFNKLTKQRLSITmDRKGVTRDVLEKKVSLQNgESFLLLDTAGFNPKRSDTI----DRTQYAIKKSEIILFVIDDKIDAEDLFFV 100
                 6899*******************99974789***999999988877699********755444444....444444467899******99999999999 PP

                 HHHHHTT..SSEEEEEETHHHHHHTTEEE CS
      FeoB_N  99 lqllelg..vpvvlalnmideaekkgiei 125
                   l       +++l+ n+id  +k+  ++
  AHX11456.1 101 SWLRKNAgnSRIILVRNKIDCKNKDDCSV 129
                 98876532377888999999988877654 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 3.4e-12
                 EEEEEESTTSSHHHHHHHHHTTS.EEEEESTTSSSEEEEEEEEETT.EEEEEEE----SSSSSSSHH.HHHHHHHHH..CTSSSEEEEEEEGGGH...H CS
      FeoB_N   2 tvalvGnpnvGkttlfnaltgak.qkvgNwpGvtvekkegklklkg.keveivDlPGiYslsaysee.ekvardfll..eeepdvvvnvvdatnl...e 92 
                 +++++G+pnvGk+tl+n+  g++   v+  +G+t +  + ++ ++g + +e++D  G  +  ++s   e+v+++  l  + e dv++ + d +n+   +
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMGTDrVLVSPEAGTTRDPVNDEFLWNGhTIFEFIDTAGLRKKRKVSDKlESVSNSRALqaSAESDVILFMYDVSNFtleK 276
                 7899****************997267999**********99999994567********9999988654777665544237789********99963334 PP

                 HHHHHHHHHHHTTSSEEEEEETHHHHHHTTE CS
      FeoB_N  93 rnLyLtlqllelgvpvvlalnmideaekkgi 123
                 ++++L+ ++le g+pv+l+ n+ d+++++ +
  AHX11456.1 277 QDFILINRVLENGKPVILIGNKKDAVKNADL 307
                 789***********************98865 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.8   0.1   1.3e-11   7.7e-09       2     119 ..       7     120 ..       6     121 .. 0.80
   2 !   20.5   0.1   6.8e-07   0.00042       1     119 [.     178     300 ..     178     301 .. 0.62
   3 ?   -1.4   0.0       4.3   2.7e+03      92     107 ..     359     374 ..     344     380 .. 0.68

  Alignments for each domain:
  == domain 1  score: 35.8 bits;  conditional E-value: 1.3e-11
                 EEEESSTTSSHHHHHHCHCT-CCC-E.EETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTT....T-HHHHCTSCEEEEEEEGHHHHCH CS
         Roc   2 vvlvGdsgvGKtsllkrfvedkfsek.ekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrs....lhplylreaalailvydsrssenl 95 
                 v +vG+++vGK++l++++++++ s +  ++ +  d+l+k+v+    ++n    +  ++ + DtaG +  rs     +++ +++++++++v+d++ +++ 
  AHX11456.1   7 VSIVGKANVGKSTLFNKLTKQRLSITmDRKGVTRDVLEKKVS----LQNG---E--SFLLLDTAGFNPKRSdtidRTQYAIKKSEIILFVIDDKIDAED 96 
                 789*******************98551567788888888873....3333...2..5889*****766554333246777799999999***9998888 PP

                 HHHHHHHHHHCSSS-EEEEEE-TT CS
         Roc  96 keWlkelkkvagkspvilvgnkiD 119
                    ++ l+k+ag+s +ilv nkiD
  AHX11456.1  97 LFFVSWLRKNAGNSRIILVRNKID 120
                 8999999****************9 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 6.8e-07
                 EEEEESSTTSSHHHHHHCHCT-CCC.-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHC...........TSCEEEEEE CS
         Roc   1 KvvlvGdsgvGKtsllkrfvedkfs.ekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylr...........eaalailvy 87 
                 ++ ++G+ +vGK++l+++f+  +    + ++ +  d ++ e+     +   ++  +  +++ DtaG  + r++ +   +           e+++++++y
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMGTDRVlVSPEAGTTRDPVNDEF-----L---WNG-HTIFEFIDTAGLRKKRKVSDKLESvsnsralqasaESDVILFMY 267
                 589*****************8665313333333333334443.....2...222.4679*******887776554332111112222222667889999 PP

                 EGHHHHCHHHHHHHHHHH.CSSS-EEEEEE-TT CS
         Roc  88 dsrssenlkeWlkelkkv.agkspvilvgnkiD 119
                 d ++++  k+ +  +++v  + +pvil+gnk D
  AHX11456.1 268 DVSNFTLEKQDFILINRVlENGKPVILIGNKKD 300
                 988887555555555555155689*******99 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.3
                 HHCHHHHHHHHHHHCS CS
         Roc  92 senlkeWlkelkkvag 107
                 +++l++Wl+e+ ++ +
  AHX11456.1 359 KHKLNRWLQEVINKHP 374
                 368999***9987665 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.9   0.3   2.9e-10   1.8e-07       2     149 ..       7     163 ..       6     176 .. 0.76
   2 !   23.8   0.0   4.6e-08   2.8e-05       2     120 ..     179     305 ..     178     341 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.9 bits;  conditional E-value: 2.9e-10
                 EEEEESTTSSHHHHHHHHHHSSCSSSCT.TTSSEEEEEEEEEETTEEEEEEEEEETTSG..GGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHH CS
         Ras   2 lvlvGdsavGKtslllrfvkdkFkeeye.sTigvdfytkeievdgkevkleiwDTAGqe..efkslrelyyrdaegillvyditsresfenvkkwveei 97 
                 + +vG+ +vGK++l ++ +k++ + +++ + +  d ++k++++++ e  + ++DTAG +  + +++ ++ y   +  ++++ i+++   e++  +v+ +
  AHX11456.1   7 VSIVGKANVGKSTLFNKLTKQRLSITMDrKGVTRDVLEKKVSLQNGES-FLLLDTAGFNpkRSDTIDRTQYAIKKSEIILFVIDDKIDAEDL-FFVSWL 103
                 569*******************997765267889*********98886.5589****75338899*******************99988877.467777 PP

                 HHHSTTTSEEEEEEETTTGGG........G-SS-HHHHHHHHHHHT.SEEEEEBTTTTCTH CS
         Ras  98 krvaeenvpivLvGnKvDlee........kravsteegeelakelg.lkfletSAktnenv 149
                 ++ a  n  i+Lv nK+D ++         ++v + ++e+    ++ l+++e S  ++   
  AHX11456.1 104 RKNAG-NSRIILVRNKIDCKNkddcsvfgFKEVFQISAEHSTGIQElLAYIESSLPQRSSS 163
                 78888.699************7777777733333333333333333377777776655554 PP

  == domain 2  score: 23.8 bits;  conditional E-value: 4.6e-08
                 EEEEESTTSSHHHHHHHHHHSS..CSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGGGHHHHH...........HHHTTESEEEEEEETTBHHHH CS
         Ras   2 lvlvGdsavGKtslllrfvkdk..FkeeyesTigvdfytkeievdgkevkleiwDTAGqeefkslre...........lyyrdaegillvyditsresf 87 
                 + ++G+ +vGK++l+++f+  +    +    T   d  + e+  +g+++ +e  DTAG  + +++ +           +   ++++il +yd+++  ++
  AHX11456.1 179 ITILGQPNVGKSTLMNKFMGTDrvLVSPEAGTT-RDPVNDEFLWNGHTI-FEFIDTAGLRKKRKVSDklesvsnsralQASAESDVILFMYDVSNF-TL 274
                 789***************855411444444555.788877777777766.9*******7665555431111111111123456789*******874.45 PP

                 HTHHHHHHHHHHHSTTTSEEEEEEETTTGGGG- CS
         Ras  88 envkkwveeikrvaeenvpivLvGnKvDleekr 120
                 e+ +  +  i+rv e+  p++L+GnK D  ++ 
  AHX11456.1 275 EKQD--FILINRVLENGKPVILIGNKKDAVKNA 305
                 5544..4457777777789*********88733 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   0.00011     0.067       3      75 ..       7      80 ..       5     113 .. 0.78
   2 ?   -1.5   0.0         2   1.3e+03     164     200 ..     136     173 ..      75     176 .. 0.51
   3 !   24.1   0.1   3.1e-08   1.9e-05       2     146 ..     178     322 ..     177     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00011
                EEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEE.EETTEEEEEEE--SC.CCTTCCHHCHHHHHHH CS
        AIG1  3 ivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksr.twdgkkinViDTPgl.fdlsvsadkiskeivr 75
                + +vGk  +GkS+  N + ++   +  +  ++vt+ + +k+   ++g++    DT g     s++ d+++  i++
  AHX11456.1  7 VSIVGKANVGKSTLFNKLTKQ-RLSITMDRKGVTRDVLEKKVsLQNGESFLLLDTAGFnPKRSDTIDRTQYAIKK 80
                668*************97655.5666679*******98888879***********99733333445555555554 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 2
                 HHHHHHHHHHHHHHHHHHHH.HHHHTTTT--B-HHHHH CS
        AIG1 164 taskeekeeQvkellelvea.ivkenggkpytnelyek 200
                  + ++e+ +  +ell+ +e+ + ++++ + +t+++ ek
  AHX11456.1 136 FQISAEHSTGIQELLAYIESsLPQRSSSEDFTEKIEEK 173
                 34455666667777777764244555566666666655 PP

  == domain 3  score: 24.1 bits;  conditional E-value: 3.1e-08
                 EEEEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEE.EEEE--SCCCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETTB-SHH CS
        AIG1   2 tivlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkki.nViDTPglfdlsvsadkiskeivrclllseegihalllvlslgrftee 99 
                 +i ++G+  +GkS+  N  +g++    +  +++ t+ + + +  w+g++i + iDT gl    +  dk++     + l ++   +++l+  ++++ft  
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMGTDRVLVS-PEAGTTRDPVNDEFLWNGHTIfEFIDTAGLRKKRKVSDKLESVSNSRALQASAESDVILFMYDVSNFT-L 274
                 7999*****************9987777.58999*************88768*******9999888877765444555555669*************.7 PP

                 HHHHHHHHHHHHCGGGGGGEEEEEEEGGGGTTCC...HHHHHHHHH-HHH CS
        AIG1 100 dekalktlkelFGekilkylivvftrkddledds...ledylsksspeaL 146
                 +++ +  ++++ ++   k +i++  +kd +++ +   ++d+++ + ++ L
  AHX11456.1 275 EKQDFILINRVLENG--KPVILIGNKKDAVKNADlknIQDFIKLQGNKLL 322
                 777888899998875..667777777777777666668889888887766 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.2   0.00028      0.18     103     131 ..       8      33 ..       3      66 .. 0.64
   2 !   19.4   0.1   1.3e-06   0.00077      46     125 ..     109     202 ..      65     212 .. 0.67
   3 ?    2.9   0.1      0.14        89      17      77 ..     259     319 ..     238     347 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00028
                  EEECSTTSSHHHHHHHHCTT-----S--- CS
  RsgA_GTPase 103 vlvGqSGvGKStLinallpelelktgevs 131
                   +vG+  vGKStL n+l+ +   + + + 
   AHX11456.1   8 SIVGKANVGKSTLFNKLTKQ---RLSITM 33 
                  589**************987...333333 PP

  == domain 2  score: 19.4 bits;  conditional E-value: 1.3e-06
                  T-EEEEEEE-GGG--HHH...............HHHHHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT--- CS
  RsgA_GTPase  46 giepvivlnKiDlleeee...............eleelkeelealgyevllvsaktkegleelkellkdktsvlvGqSGvGKStLinallpelel 125
                  + ++++v nKiD+ ++++               + + ++e l+ ++ + l  ++++++ +e+++e++++  ++++Gq  vGKStL+n++++++++
   AHX11456.1 109 NSRIILVRNKIDCKNKDDcsvfgfkevfqisaeHSTGIQELLAYIESS-LPQRSSSEDFTEKIEEKFRKIRITILGQPNVGKSTLMNKFMGTDRV 202
                  446777888888888888888888766654432222233333333332.33334456788999999999889999*************9997655 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.14
                  -EEEEEEESTTTT--HHHHHHHHHHHHHTT-EEEEEE.E-GGG--HHHHHHHHHHHHHHTTS CS
  RsgA_GTPase  17 dqllivvslkepelslnlldrfLvlaeekgiepvivl.nKiDlleeeeeleelkeelealgy 77 
                  +  +i++  +  +++l+  d +L+    ++ +pvi++ nK D +++++ l+++++ ++  g 
   AHX11456.1 259 ESDVILFMYDVSNFTLEKQDFILINRVLENGKPVILIgNKKDAVKNAD-LKNIQDFIKLQGN 319
                  555777777777888888888999888888888887769*******99.8877776665554 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.9   0.1   0.00028      0.18       1      37 [.       7      44 ..       7      54 .. 0.83
   2 !    8.9   0.1    0.0023       1.4      84     164 ..      36     115 ..      30     119 .. 0.73
   3 !   13.1   0.0   0.00012     0.074       1      36 [.     179     215 ..     179     216 .. 0.80
   4 ?    4.6   0.0     0.048        30     104     167 ..     228     298 ..     224     299 .. 0.79
   5 ?   -2.8   0.2       9.3   5.8e+03      41      78 ..     437     477 ..     432     496 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00028
                EEEEEBTTTTHHHHHHHHHTS--S-.--SSS---S-EE CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilp.rgpnptTrrple 37
                + +vG+ + GKS++ n+L+++++   ++   +Tr +le
  AHX11456.1  7 VSIVGKANVGKSTLFNKLTKQRLSItMDRKGVTRDVLE 44
                679*******************9884566688888775 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0023
                 SS--SS-EEEEEEETTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTT..EEEE CS
   Dynamin_N  84 kgiskkvillkilsllvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnsealflarevdpkgkr..tivv 164
                 kg++++v+  k+   + +   l+D+ G++       + ++ +ikk+ iil+v + + d+     lf+ ++++++  +  +i v
  AHX11456.1  36 KGVTRDVLEKKVSLQNGESFLLLDTAGFNPKRSDTIDRTQYAIKKSEIILFVIDDKIDAE---DLFFVSWLRKNAGNsrIILV 115
                 5566666666666677778889*******98888879999999**********9887654...77777777776554335555 PP

  == domain 3  score: 13.1 bits;  conditional E-value: 0.00012
                 EEEEEBTTTTHHHHHHHHHTS--S---SS.S---S-E CS
   Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpn.ptTrrpl 36 
                 i+++G+ + GKS+++n+ +g d   ++p+  tTr p+
  AHX11456.1 179 ITILGQPNVGKSTLMNKFMGTDRVLVSPEaGTTRDPV 215
                 7899****************87555555537888775 PP

  == domain 4  score: 4.6 bits;  conditional E-value: 0.048
                 EEEE---B-SSSGTTS.......HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE- CS
   Dynamin_N 104 tlvDlPGldsvnkrdq.......elvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltk 167
                 +++D+ Gl +  k          + + ++  ++d+il++ + ++   +++   l + v ++gk +i + +k
  AHX11456.1 228 EFIDTAGLRKKRKVSDklesvsnSRALQASAESDVILFMYDVSNFTLEKQDFILINRVLENGKPVILIGNK 298
                 689*****995544444999987666777799********9999666667777889999999999998776 PP

  == domain 5  score: -2.8 bits;  conditional E-value: 9.3
                 CCT---CCS...SSEEEE...T-EB--CHHHHHHHHHHHHH CS
   Dynamin_N  41 geeeeaseravkeelkek...ekkledfsevreeieketek 78 
                 +++++a+er+v  e +++    k +++ + v+++++++++ 
  AHX11456.1 437 NKNPYATERSVPRESQQFgtaPKSIRKEKIVDRKVSQSKNA 477
                 55555555555555555533322222222233333333333 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.2   1.7e-08     1e-05       5      92 ..       6      97 ..       2     161 .. 0.85
   2 ?    5.2   0.2      0.02        13       5     135 ..     178     312 ..     174     348 .. 0.62
   3 ?    0.4   0.0      0.61   3.8e+02     107     142 ..     389     424 ..     382     454 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1.7e-08
                EEEEE-STTSSHHHHHHHHHHSS---B---S...S-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGG.EEEEEEEEETTS-HHHH CS
       SRPRB  5 avllvGlsdsGKTslftrLttdsvkktvtSq...essaalkvksekgskltliDfPGheklrqklleklkakss.lkglvfvvDStidpkev 92
                +v +vG  + GK +lf++Lt++    t+         + +kv+ ++g+++ l+D  G +  r++ +++ ++  +    ++fv+D  id  ++
  AHX11456.1  6 RVSIVGKANVGKSTLFNKLTKQRLSITMDRKgvtRDVLEKKVSLQNGESFLLLDTAGFNPKRSDTIDRTQYAIKkSEIILFVIDDKIDAEDL 97
                5779******************665555433223566677778899******************9999887765488899******998776 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.02
                 EEEEE-STTSSHHHHHHHHH.HS..S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETTS..-HHHHHHHHHH CS
       SRPRB   5 avllvGlsdsGKTslftrLt.td..svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDSti..dpkevkevAEl 98 
                 ++ ++G  + GK +l+++ + td   v +        + +++  + ++ +++iD  G  k r k+++kl   s+ ++l    +S +  +  +v +    
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMgTDrvLVSPEAGTTRDPVNDEFLWNGHTIFEFIDTAGLRKKR-KVSDKLESVSNSRALQASAESDVilFMYDVSNFTLE 275
                 68899************986244332223333334555566666778889999999987754.566666555555555544444431133333332222 PP

                 HHHHHHHHHHHTT---EEEEEE-TTSTT---HHHHHH CS
       SRPRB  99 lyeilliteklkdavdiliACnKqelflakspklikd 135
                   + +li+  l+++ ++++  nK++ +     k i+d
  AHX11456.1 276 KQDFILINRVLENGKPVILIGNKKDAVKNADLKNIQD 312
                 2233444444555555555567777776666667766 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.61
                 HHHTT---EEEEEE-TTSTT---HHHHHHHHHHHHH CS
       SRPRB 107 eklkdavdiliACnKqelflakspklikdaLEkEln 142
                 +k kd+ ++li  n  +l+     + ik++L k+ +
  AHX11456.1 389 TKVKDKFSFLIRANHPDLVADSYLNYIKNSLAKDFQ 424
                 45799*************999999*******99865 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.4   0.5   0.00052      0.32      15     128 ..       5     122 ..       1     157 [. 0.68
   2 !   21.3   0.8   2.4e-07   0.00015       5     144 ..     167     318 ..     163     350 .. 0.73

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00052
                 EEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEE.....TTEEEEEEEE-SSGGGGG..GG.GGG.CTTESEEEEEEETT-CTTHHHHHHHH CS
         Arf  15 lrilllGLDnaGKtTilkklkleelvttvPTigfnveelei.....knlkftvwDvGGqeklRp..lW.knY.fektdavifvvDsadreRleeakeeL 104
                 +r+ ++G  n GK+T+ +kl++++l+ t+   g + + le      ++ +f + D  G +  R+  +   +Y  +k + ++fv+D    ++++     +
  AHX11456.1   5 FRVSIVGKANVGKSTLFNKLTKQRLSITMDRKGVTRDVLEKkvslqNGESFLLLDTAGFNPKRSdtIDrTQYaIKKSEIILFVID----DKIDAEDLFF 99 
                 68999**********************9999998876665533333345678888888777775222213342356677778887....3455444445 PP

                 HHHCTSGCCTTSEEEEEEE-TTST CS
         Arf 105 kalleeeelkevallvlaNKqDlp 128
                  + l+++   +  ++++ NK+D +
  AHX11456.1 100 VSWLRKNA-GNSRIILVRNKIDCK 122
                 55554433.344455556666665 PP

  == domain 2  score: 21.3 bits;  conditional E-value: 2.4e-07
                 HHGGTT.TTEEEEEEEESTTSSHHHHHHHHHHSSCEECSSSSSEEEEEEEE.....TTEEEEEEEE-SSGGGGGGGGGG...........CTTESEEEE CS
         Arf   5 laklklkkkelrilllGLDnaGKtTilkklkleelvttvPTigfnveelei.....knlkftvwDvGGqeklRplWknY...........fektdavif 87 
                  +k+++k +++ri +lG  n GK+T+++k++  + v ++P  g + + ++       +  f++ D  G +k R++ ++             ++ d+++f
  AHX11456.1 167 TEKIEEKFRKIRITILGQPNVGKSTLMNKFMGTDRVLVSPEAGTTRDPVNDeflwnGHTIFEFIDTAGLRKKRKVSDKLesvsnsralqaSAESDVILF 265
                 56788899********************************9999888777644554778899***********99876422111111111234556666 PP

                 EEETT-CTTHHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGG CS
         Arf  88 vvDsadreRleeakeeLkalleeeelkevallvlaNKqDlpealseeelrellglee 144
                 + D+++   ++  k+++  l+++   +  ++++++NK+D+ + ++ +++++ ++l+ 
  AHX11456.1 266 MYDVSN---FTLEKQDFI-LINRVLENGKPVILIGNKKDAVKNADLKNIQDFIKLQG 318
                 666554...555566653.45555555678888999999999999999999988875 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.7   0.1   0.00023      0.14       3      69 ..       4      82 ..       2      91 .. 0.68
   2 ?    3.4   0.1     0.076        47     154     192 ..     124     157 ..      34     159 .. 0.57
   3 !    8.3   0.1    0.0025       1.6      91     189 ..     257     347 ..     175     359 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00023
                EEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHST................HCHSHHHHHHTSCSSCEEEEEETTCSS CS
    GTP_EFTU  3 irnigiighvDhGKtTLtdrLlyktgaiskkgekaeeerv................lDtlkeErergiTiksaaisleketkk 69
                +  ++i+g  + GK+TL  +L+++   i+++++    +r                 lDt+    +r  Ti+ ++  ++  +++
  AHX11456.1  4 VFRVSIVGKANVGKSTLFNKLTKQRLSITMDRKGV--TRDvlekkvslqngesfllLDTAGFNPKRSDTIDRTQYAIK--KSE 82
                66899******************999998844333..22223445566667777777777777777777776666666..454 PP

  == domain 2  score: 3.4 bits;  conditional E-value: 0.076
                 HHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHS CS
    GTP_EFTU 154 eeklekygekgekevpvvfgSalkgegvktllealvell 192
                 +++++++g+k     +v+ +Sa +  g+++ll ++ + l
  AHX11456.1 124 KDDCSVFGFK-----EVFQISAEHSTGIQELLAYIESSL 157
                 3344444444.....367777777777777777776665 PP

  == domain 3  score: 8.3 bits;  conditional E-value: 0.0025
                 HHT-SEEEEEEETTTB.STHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHH CS
    GTP_EFTU  91 lrvlDgavlvvdaveG.vepqteevlrlalkegvpiivfiNKmDrl.kaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllea 187
                  +  D+ +++ d+++   e q   +++ +l++g p+i++ NK D + +a+lk+i++ +k +        +k   +    +p +f+S+l+   ++ lle 
  AHX11456.1 257 SAESDVILFMYDVSNFtLEKQDFILINRVLENGKPVILIGNKKDAVkNADLKNIQDFIKLQG-------NKLLLE---RMPTFFISSLRENDFSVLLEE 345
                 44555556666655432566666677778888888999999999997788888888887333.......233333...468888888888888877776 PP

                 HH CS
    GTP_EFTU 188 lv 189
                 + 
  AHX11456.1 346 CS 347
                 65 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0054       3.3       4      34 ..       6      37 ..       4     110 .. 0.82
   2 !   15.6   0.0   1.7e-05      0.01       2      36 ..     176     211 ..     175     231 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0054
      AAA_24  4 kiliyGpsgiGKTtlakelgpkplfidtek.G 34
                ++ i+G++ +GK+tl ++l+++ l i +++ G
  AHX11456.1  6 RVSIVGKANVGKSTLFNKLTKQRLSITMDRkG 37
                6789***************8877777777645 PP

  == domain 2  score: 15.6 bits;  conditional E-value: 1.7e-05
      AAA_24   2 klkiliyGpsgiGKTtlakel.gpkplfidtekGlk 36 
                 k++i i G++ +GK+tl++++ g + +++  e+G+ 
  AHX11456.1 176 KIRITILGQPNVGKSTLMNKFmGTDRVLVSPEAGTT 211
                 799*******************88888888888885 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.9   0.0     0.016       9.7       3      27 ..       6      30 ..       4      36 .. 0.90
   2 !   11.1   0.0   0.00041      0.25     114     142 ..     126     154 ..      85     155 .. 0.89
   3 ?    1.0   0.1      0.52   3.2e+02       3      23 ..     178     198 ..     176     202 .. 0.86
   4 ?    3.6   0.0     0.083        51      57     122 ..     254     321 ..     230     347 .. 0.70

  Alignments for each domain:
  == domain 1  score: 5.9 bits;  conditional E-value: 0.016
   PduV-EutP  3 killiGkvgsGKttLtqalkgeelk 27
                ++ ++Gk ++GK tL ++l++++l+
  AHX11456.1  6 RVSIVGKANVGKSTLFNKLTKQRLS 30
                6789****************99986 PP

  == domain 2  score: 11.1 bits;  conditional E-value: 0.00041
   PduV-EutP 114 lLksaGaekifevsavekegieellkyle 142
                   +  G +++f++sa +++gi+ell+y+e
  AHX11456.1 126 DCSVFGFKEVFQISAEHSTGIQELLAYIE 154
                 56778**********************98 PP

  == domain 3  score: 1.0 bits;  conditional E-value: 0.52
   PduV-EutP   3 killiGkvgsGKttLtqalkg 23 
                 +i ++G+ ++GK tL++++ g
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMG 198
                 7899***********998765 PP

  == domain 4  score: 3.6 bits;  conditional E-value: 0.083
   PduV-EutP  57 livtsaeadvialvqdateeesvfppg..fasvfn..keviGiitkidlaedeenieaveelLksaGaek 122
                 l  +sae+dvi +++d+++ +    +   + +v++  k+vi i  k d + +++++++ ++++k  G + 
  AHX11456.1 254 L-QASAESDVILFMYDVSNFTLEKQDFilINRVLEngKPVILIGNKKDAV-KNADLKNIQDFIKLQGNKL 321
                 4.4689999999999987643332222002233323399**999999999.8999999999999999764 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.2   1.8e-05     0.011      27     100 ..      76     153 ..      70     158 .. 0.80
   2 ?    4.2   0.1      0.07        43      56      97 ..     290     343 ..     263     349 .. 0.70

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.8e-05
  MMR_HSR1_Xtn  27 ykihnaevl...iredvtvDdl..idviegnrvYipclyvlNKiDlisleeldelarepnsvviSaekelnldeLkeki 100
                   y i + e++   i ++++++dl  +  + +n    + ++v NKiD  ++++++ +   ++++ iSae+ ++++eL+  i
    AHX11456.1  76 YAIKKSEIIlfvIDDKIDAEDLffVSWLRKNAGNSRIILVRNKIDCKNKDDCSVFGF-KEVFQISAEHSTGIQELLAYI 153
                   555555553222678899998633677899999******************998877.589**************9877 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.07
  MMR_HSR1_Xtn  56 ipclyvlNKiDlisleeldelare............pnsvviSaekelnldeLk 97 
                   +p++++ NK D++++++l++++                +++iS+ +e ++  L+
    AHX11456.1 290 KPVILIGNKKDAVKNADLKNIQDFiklqgnklllerMPTFFISSLRENDFSVLL 343
                   68999*************999874345555555554355556666666555555 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.4   0.0    0.0043       2.6      38      73 ..       7      43 ..       2      75 .. 0.82
   2 !   10.2   0.0   0.00059      0.36      33      60 ..     174     201 ..     160     215 .. 0.78

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0043
        TniB 38 lllvGdsnnGKtmivekFarlhppe.kdedaekvpvl 73
                + +vG+ n+GK+++++k ++++ +   d +  +++vl
  AHX11456.1  7 VSIVGKANVGKSTLFNKLTKQRLSItMDRKGVTRDVL 43
                679***************9998655145666666666 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00059
        TniB  33 krmpnlllvGdsnnGKtmivekFarlhp 60 
                  r   + ++G++n+GK+++++kF+ +++
  AHX11456.1 174 FRKIRITILGQPNVGKSTLMNKFMGTDR 201
                 4556689****************96654 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.5   0.0    0.0021       1.3       2      23 ..       8      29 ..       7      78 .. 0.75
   2 !    8.9   0.0     0.003       1.9       1      19 [.     179     197 ..     179     250 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0021
  RNA_helicase  2 wlyGpsgeGKStlakeLakall 23
                   ++G++++GKStl ++L+k+ l
    AHX11456.1  8 SIVGKANVGKSTLFNKLTKQRL 29
                  589*************999876 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.003
  RNA_helicase   1 iwlyGpsgeGKStlakeLa 19 
                   i + G++++GKStl+++++
    AHX11456.1 179 ITILGQPNVGKSTLMNKFM 197
                   5689************965 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.0    0.0018       1.1      13      51 ..       6      40 ..       2     113 .. 0.78
   2 !    7.8   0.0    0.0071       4.4      13      36 ..     178     201 ..     172     260 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0018
                EEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 13 kvaivGenGaGKStLlkllagllkpteGeilldgkdlke 51
                +v ivG+   GKStL++ l+++      +i++d k +++
  AHX11456.1  6 RVSIVGKANVGKSTLFNKLTKQRL----SITMDRKGVTR 40
                689**************9998865....45555555554 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0071
                 EEEEEESTTSSHHHHHHHHTTSS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  13 kvaivGenGaGKStLlkllagllk 36 
                 ++ i+G+   GKStL++ ++g  +
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMGTDR 201
                 689**************9999654 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.078        48      31      52 ..       6      27 ..       3      39 .. 0.87
   2 !   12.7   0.0   7.3e-05     0.045       4      50 ..     149     197 ..     137     202 .. 0.83

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.078
                EEEEEE-TTSSHHHHHHHHHHH CS
        MeaB 31 vvGltGvPGaGkstlvealgle 52
                +v + G   +Gkstl ++l+ +
  AHX11456.1  6 RVSIVGKANVGKSTLFNKLTKQ 27
                78999*************9865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 7.3e-05
                 HHHHHH--SH..HHHHHHHHHGGG-S-SEEEEEEE-TTSSHHHHHHHHH CS
        MeaB   4 aitlveserp..eakellerllakaGraqvvGltGvPGaGkstlvealg 50 
                 ++ ++es+ p  ++ e +++ +++  r  ++ + G P +Gkstl+++++
  AHX11456.1 149 LLAYIESSLPqrSSSEDFTEKIEEKFRKIRITILGQPNVGKSTLMNKFM 197
                 68899999998845555555556667999****************9985 PP

>> Ploopntkinase3  P-loop Nucleotide Kinase3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0035       2.2       7      48 ..       8      47 ..       4      53 .. 0.81
   2 !    8.0   0.0     0.004       2.5       6      29 ..     179     201 ..     174     239 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0035
  Ploopntkinase3  7 ylvGqPGaGkstlmaeltkgfdrskveqeeetvphdvlvdrt 48
                     +vG+   Gkstl  +ltk    ++++   + v+ dvl +++
      AHX11456.1  8 SIVGKANVGKSTLFNKLTKQRLSITMD--RKGVTRDVLEKKV 47
                    589***************975555555..5569999998876 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.004
  Ploopntkinase3   6 iylvGqPGaGkstlmaeltkgfdr 29 
                     i ++GqP  Gkstlm ++  g dr
      AHX11456.1 179 ITILGQPNVGKSTLMNKFM-GTDR 201
                     7799***********9874.3444 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.8   0.1   0.00036      0.22       5      52 ..       5      53 ..       2      92 .. 0.77
   2 ?    5.4   0.0     0.015       9.2       5      29 ..     177     201 ..     173     218 .. 0.85
   3 ?   -2.4   0.1       3.6   2.2e+03     181     181 ..     332     332 ..     261     396 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00036
                EEEEEEEBTTSSCCCCCCTTSSSS------------.------S-EEEE CS
      Septin  5 ftlmvvGesglGkttlintlfetdlieeekleease.kkkktveikkkk 52
                f + +vG+  +Gk+tl+n l +++l  +   +  +    +k+v++++ +
  AHX11456.1  5 FRVSIVGKANVGKSTLFNKLTKQRLSITMDRKGVTRdVLEKKVSLQNGE 53
                77889*****************999877544443332455555555444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.015
                 EEEEEEEBTTSSCCCCCCTTSSSS- CS
      Septin   5 ftlmvvGesglGkttlintlfetdl 29 
                 + + + G+  +Gk+tl+n ++ td 
  AHX11456.1 177 IRITILGQPNVGKSTLMNKFMGTDR 201
                 668899*************998875 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.6
                 - CS
      Septin 181 p 181
                  
  AHX11456.1 332 S 332
                 1 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.7   0.1    0.0054       3.3       6      28 ..       8      33 ..       6     101 .. 0.66
   2 ?    6.6   0.0     0.012       7.5       5      25 ..     179     199 ..     175     215 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0054
      AAA_14  6 vitGaRrvGKTtllkqlikell...v 28
                 i+G   vGK+tl ++l k++l   +
  AHX11456.1  8 SIVGKANVGKSTLFNKLTKQRLsitM 33
                6889999***********99995432 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.012
      AAA_14   5 lvitGaRrvGKTtllkqlike 25 
                 ++i G   vGK+tl+++++ +
  AHX11456.1 179 ITILGQPNVGKSTLMNKFMGT 199
                 6899999**********9865 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.8    0.0021       1.3      21      47 ..       5      31 ..       2     143 .. 0.70
   2 ?    5.3   0.0     0.016       9.6      16      40 ..     172     196 ..     159     203 .. 0.81

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0021
                EEEEEEESTTSSHHHHHHHHCCSHCCC CS
      NB-ARC 21 lvvalvGmgGvGKttlakqilnksdev 47
                + v++vG++ vGK+tl+++  ++  ++
  AHX11456.1  5 FRVSIVGKANVGKSTLFNKLTKQRLSI 31
                5699***************99984443 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.016
                 TTSCSEEEEEEESTTSSHHHHHHHH CS
      NB-ARC  16 delqslvvalvGmgGvGKttlakqi 40 
                 +++ ++ +++ G + vGK+tl+++ 
  AHX11456.1 172 EKFRKIRITILGQPNVGKSTLMNKF 196
                 45566889**************986 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.1     0.015         9      10      29 ..       9      28 ..       7     105 .. 0.80
   2 ?   -0.8   0.0       2.8   1.7e+03      44      87 ..     137     175 ..      99     179 .. 0.65
   3 !    7.3   0.0    0.0088       5.4       8      29 ..     179     200 ..     174     296 .. 0.90

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.015
      AAA_22 10 vtGesGtGKTtllrrlleql 29
                ++G + +GK+tl ++l++q 
  AHX11456.1  9 IVGKANVGKSTLFNKLTKQR 28
                89***************997 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 2.8
      AAA_22  44 fvtlpsstsskdllrellralglelkaerlsseellealeqalr 87 
                  + + +st+ ++ll  + + l      +r sse++ e++e+ +r
  AHX11456.1 137 QISAEHSTGIQELLAYIESSLP-----QRSSSEDFTEKIEEKFR 175
                 4555555555555555555555.....24455666666666665 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0088
      AAA_22   8 lvvtGesGtGKTtllrrlleql 29 
                 +++ G++ +GK+tl+++++ ++
  AHX11456.1 179 ITILGQPNVGKSTLMNKFMGTD 200
                 6899*************98765 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0074       4.5       3      25 ..       9      36 ..       7      84 .. 0.78
   2 ?    7.0   0.1     0.013         8       1      18 [.     179     196 ..     179     345 .. 0.70
   3 ?   -2.0   0.0       7.8   4.8e+03      26      59 ..     336     369 ..     318     403 .. 0.64

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0074
      AAA_18  3 ltGtpGvGKttlakeLskrl.gf....g 25
                + G++ vGK+tl + L k    +     
  AHX11456.1  9 IVGKANVGKSTLFNKLTKQRlSItmdrK 36
                89**************776434455553 PP

  == domain 2  score: 7.0 bits;  conditional E-value: 0.013
      AAA_18   1 IlltGtpGvGKttlakeL 18 
                 I + G p vGK+tl +  
  AHX11456.1 179 ITILGQPNVGKSTLMNKF 196
                 899***********9877 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 7.8
      AAA_18  26 vnlrdvakenglllevdpealdeskrldedkldk 59 
                 +n  +v+ e+ + l++ ++++ ++++l+++ +++
  AHX11456.1 336 ENDFSVLLEECSKLYDSAKKHIPKHKLNRWLQEV 369
                 4555555665555555555555555555555433 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0     0.048        30       1      40 [.       6      48 ..       6      83 .. 0.79
   2 !    8.3   0.0    0.0041       2.5       1      33 [.     178     211 ..     178     228 .. 0.91

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.048
      AAA_28  1 kivitGgestGKTtlleaLaargypvv...pEaareileekla 40
                ++ i+G    GK+tl ++L+++  ++    + + r++le+k  
  AHX11456.1  6 RVSIVGKANVGKSTLFNKLTKQRLSITmdrKGVTRDVLEKKVS 48
                5778888899**********88444322357777777777764 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0041
      AAA_28   1 kivitGgestGKTtlleaLaargypvv.pEaare 33 
                 +i i+G +  GK+tl++++  ++ + v pEa+++
  AHX11456.1 178 RITILGQPNVGKSTLMNKFMGTDRVLVsPEAGTT 211
                 699*****************99777666**9975 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.0      0.02        13      26      39 ..       8      21 ..       2      25 .. 0.88
   2 ?    6.3   0.0     0.013       7.7      25      39 ..     179     193 ..     166     205 .. 0.85

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.02
      AAA_29 26 lltGpsGsGKSTll 39
                 ++G+  +GKSTl+
  AHX11456.1  8 SIVGKANVGKSTLF 21
                699*********97 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.013
      AAA_29  25 tlltGpsGsGKSTll 39 
                 + + G+  +GKSTl+
  AHX11456.1 179 ITILGQPNVGKSTLM 193
                 6799**********8 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.1     0.011         7       2      23 ..       7      28 ..       6      50 .. 0.79
   2 ?    6.2   0.0     0.014       8.6       2      20 ..     179     197 ..     178     203 .. 0.88
   3 ?    0.7   0.1      0.71   4.4e+02      91     136 ..     255     300 ..     236     320 .. 0.69
   4 ?   -2.0   0.3       4.7   2.9e+03     136     163 ..     461     490 ..     449     493 .. 0.67

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.011
                EEEE--TTSSHHHHHHHHHHHH CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlell 23
                v i G+  vGK+Tl++k++++ 
  AHX11456.1  7 VSIVGKANVGKSTLFNKLTKQR 28
                7899*************98764 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.014
                 EEEE--TTSSHHHHHHHHH CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvl 20 
                 + i G+p vGK+Tl++k +
  AHX11456.1 179 ITILGQPNVGKSTLMNKFM 197
                 7899***********9975 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.71
                 HHHHHH-.EEEE---STTGGG-HHHHHHHHHHHTTTSEEEEE--SS- CS
    NTPase_1  91 kalsead.viviDEiGkmElkskkfkeaveevLksekpvlavihrrk 136
                 +a  e+d ++ +  + ++ l+ + f+  +++vL+++kpv+ +  +++
  AHX11456.1 255 QASAESDvILFMYDVSNFTLEKQDFI-LINRVLENGKPVILIGNKKD 300
                 34566663445777888888888887.799********999877775 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 4.7
                 -.-SHHHH.HHHT-TT-EEEE--TTTTTTH CS
    NTPase_1 136 k.dlalve.eirerkdvkvfevteenrdal 163
                   ++++v+ +++++k+++  +vt +nr++l
  AHX11456.1 461 IrKEKIVDrKVSQSKNAVRNRVTDKNRKTL 490
                 444556651456666677777999999977 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.082        51       1      19 [.       9      27 ..       9      38 .. 0.85
   2 ?   -0.6   0.0       1.5   9.1e+02     216     238 ..     134     156 ..     127     159 .. 0.86
   3 ?    2.5   0.0      0.17     1e+02       1      21 [.     181     201 ..     181     248 .. 0.68
   4 ?    0.1   0.0       0.9   5.5e+02     149     190 ..     282     323 ..     262     356 .. 0.70
   5 ?   -2.7   0.0       6.6   4.1e+03     164     214 ..     410     429 ..     381     488 .. 0.48

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.082
  ATP_bind_1  1 vvGpaGsGKttfvgalsei 19
                +vG a +GK+t+ ++l++ 
  AHX11456.1  9 IVGKANVGKSTLFNKLTKQ 27
                79************99875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 1.5
  ATP_bind_1 216 rflplssekeesiedllslidea 238
                 +++++s+e  ++i++ll++i+++
  AHX11456.1 134 EVFQISAEHSTGIQELLAYIESS 156
                 78999***************986 PP

  == domain 3  score: 2.5 bits;  conditional E-value: 0.17
  ATP_bind_1   1 vvGpaGsGKttfvgalseile 21 
                 ++G + +GK+t++++++ + +
  AHX11456.1 181 ILGQPNVGKSTLMNKFMGTDR 201
                 6899**********9986655 PP

  == domain 4  score: 0.1 bits;  conditional E-value: 0.9
  ATP_bind_1 149 lsamlrlelPhvvvlnkfDllkeklekeleffedvealslll 190
                 ++ +l+ + P + + nk D +k+ + k+++ f  ++  +lll
  AHX11456.1 282 INRVLENGKPVILIGNKKDAVKNADLKNIQDFIKLQGNKLLL 323
                 466788899***********9955555555555555444444 PP

  == domain 5  score: -2.7 bits;  conditional E-value: 6.6
  ATP_bind_1 164 nkfDllkeklekeleffedvealslllekeeekykklaeaiaelleefalv 214
                 + ++ +k++l k+++ +                               ++ 
  AHX11456.1 410 SYLNYIKNSLAKDFQIY-------------------------------GIP 429
                 33333332222222222...............................222 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       3.5   2.2e+03      15      22 ..      82      89 ..      77      92 .. 0.87
   2 ?    2.5   0.0       0.2   1.3e+02      41      58 .]     103     120 ..      99     120 .. 0.89
   3 ?    8.5   0.1    0.0028       1.7      15      58 .]     261     300 ..     253     300 .. 0.82
   4 ?   -2.9   0.0        10   6.2e+03      36      56 ..     348     372 ..     343     374 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 3.5
        NOG1 15 davlFllD 22
                +++lF++D
  AHX11456.1 82 EIILFVID 89
                68*****9 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.2
        NOG1  41 ikelfankpvivvlnKiD 58 
                 ++++ +n ++i v nKiD
  AHX11456.1 103 LRKNAGNSRIILVRNKID 120
                 67888899*********9 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.0028
        NOG1  15 davlFllDpseecgysleeQ.lsLleeikelfankpvivvlnKiD 58 
                 d++lF+ D+s+   ++le+Q + L++ + e+   kpvi + nK D
  AHX11456.1 261 DVILFMYDVSN---FTLEKQdFILINRVLEN--GKPVILIGNKKD 300
                 89*******96...68999955666777766..38*******987 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 10
        NOG1  36 sLleeikelfankp....vivvlnK 56 
                 +L+++ k+ +++ +    +  v+nK
  AHX11456.1 348 KLYDSAKKHIPKHKlnrwLQEVINK 372
                 6888888888864445544567777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       987  (0.0550505); expected 358.6 (0.02)
Passed bias filter:                      538  (0.0300073); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              29  [number of targets reported over threshold]
# CPU time: 0.68u 0.24s 00:00:00.92 Elapsed: 00:00:00.40
# Mc/sec: 3816.72
//
Query:       AHX11457.1  [L=1039]
Description: isoleucine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.5e-184  613.1   2.6   6.5e-184  612.5   2.6    1.2  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    1.2e-25   90.3   0.1    2.8e-25   89.1   0.1    1.7  1  Anticodon_1    Anticodon-binding domain of tRNA
    4.7e-14   51.9   3.5    9.6e-06   24.6   0.1    4.0  3  tRNA-synt_1g   tRNA synthetases class I (M)
     0.0065   15.9   0.0      0.016   14.6   0.0    1.6  1  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.023   14.2   0.0      0.047   13.2   0.0    1.4  1  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  612.5   2.6  1.8e-187  6.5e-184       1     596 [.      21     633 ..      21     638 .. 0.94

  Alignments for each domain:
  == domain 1  score: 612.5 bits;  conditional E-value: 1.8e-187
  tRNA-synt_1   1 klyekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgre 98 
                  k++++W+e+d+f k+ ++++ ++ef+++dgPP+++G +H+Gh l+   kd++ ry++m Gk+v++++GwD++Gl+ e+  ek+l +++k+e  k+g e
   AHX11457.1  21 KILQFWKENDTFSKSISTRDGRNEFVFYDGPPFANGLPHYGHLLTGFAKDTIARYHTMLGKKVERRFGWDCHGLPAEMYTEKQLRISGKDEIRKFGIE 118
                  589*********************************************************************************************** PP

  tRNA-synt_1  99 efrekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEv....eykdkkdalihvaf 192
                  +f++++r+ ++ +++e+++ v+r  ++vDf ++y+T+d++++e+v+++f++++ kgliy++ k+v++s++++t+ls++E+     y++kk+ +++vaf
   AHX11457.1 119 DFNAECRKSVMLFSSEWEEYVSRQARWVDFHNDYKTMDTSFMESVIWAFKEMYRKGLIYESVKVVPYSWACQTPLSNFETridnSYREKKSKAVTVAF 216
                  *******************************************************************************999988************* PP

  tRNA-synt_1 193 pl.....adkeevklviaTTtPeTllgdtavavnpeldyv...itkeklilaeallkslvkke.sekkiledergkeLegkevelpl.....vnrkip 276
                  +l     +d+++ +l ++TTtP+Tl++++ + v  + +y    ++++++i       s++k++ +  +i        L+g+++++++     +++++ 
   AHX11457.1 217 KLeedlfEDGKKSYLLAWTTTPWTLPSNMMLGVSRNTKYKrfeKDGRYYIAS----ASFYKEDpEGVEIST----DLLIGRKYKPLFdffsdEKNAFF 306
                  **99988788889**************************9996677777754....466777745556655....5699*******999997777888 PP

  tRNA-synt_1 277 iiaddyvdkeaGtGvVkiaPahdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiy 374
                  + + d+v+ e GtG+V+iaP+++e+D+e++++yn+++i+++d++g++t+e++ f+g +vf++++ +++ lkek +l+k+e+  hs+p+c+r+++p+iy
   AHX11457.1 307 VQHADFVTDEDGTGIVHIAPGFGEEDFELAREYNVKPICPVDDSGKFTDEVPLFSGKHVFETNNEIISILKEKRQLIKVEEYLHSYPHCWRTDTPLIY 404
                  8889********************************************************************************************** PP

  tRNA-synt_1 375 rateqWfvrvkeladaalkavekvqfvpks.kekryaswleniqdWciSRqrwWGhriplfvsketeevvvreelkelvagreee.eaekkalekeak 470
                  +++++W+v+v++++  +l+ ++ ++++p   k+  + +wlen++dW+iSR+r+WG ++p++ s + +  + r ++    a++e++  +++++l++ ++
   AHX11457.1 405 KVVPSWYVNVTKIKTRMLELNKTINWIPSHlKDGLMGKWLENAKDWAISRNRFWGAPVPVWKSTDPK--YPRVDVYGSIAEIEKDfGTKISDLHRPFI 500
                  *****************************989999***************************99987..66666666666555542678899****** PP

  tRNA-synt_1 471 dkl.......kkekgelekdedvlDvWFsSgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeG 561
                  d+l        ++k  + ++e vlD+WF+Sgs+pf++++yp+e+++ ++k    d+++e + ++rgW+++li+ls+al++++Pfk+ l hg+++d++G
   AHX11457.1 501 DQLtrqnpddPSGKSMMVRVEAVLDCWFESGSMPFAQIHYPFENKKWFEKHSSSDFVTEYVAQTRGWFYTLIVLSTALFDKVPFKNCLAHGVILDKDG 598
                  ****999988789999********************************************************************************** PP

  tRNA-synt_1 562 rKmSKslgNvidpldvikkygadalRltlilsdvg 596
                  +K+SK+l N+ dp ++ ++ygadalR+ +++s+v+
   AHX11457.1 599 KKLSKRLNNYKDPREIFDEYGADALRFLMLSSSVM 633
                  ******************************88875 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.1   0.1   7.8e-29   2.8e-25       1     149 [.     688     828 ..     688     832 .. 0.91

  Alignments for each domain:
  == domain 1  score: 89.1 bits;  conditional E-value: 7.8e-29
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkra.aqevllevletllrllaPfmPfitEelwqreeeel. 96 
                  d++i+s++++ v+e++ a++ y+++ a++ + +f  ++l +wy++ +++r+ + +     + a +vl+ v++ +l++laP +P ++E +w      l 
   AHX11457.1 688 DKYIISKYAQSVQEIKIAMDAYNLHSACKGILDF-FDTLNNWYIRRSRDRFINGE-----KiAFRVLYFVFSGVLKVLAPLLPMMSERIW----LALs 775
                  89*******************************7.799*************6654.....5588**************************....6675 PP

  Anticodon_1  97 gkkesimlaewpe.kaeelekeleeeevellkeivkairklrselkikpsselk 149
                  ++ +si+l+e+p+ ++   ++++  +++++l+ei++ + ++r++++i  +++l+
   AHX11457.1 776 KNGTSIHLEEYPQvDSITVDEQI-IASMDILREICNSALSIRNKNNIRIRQPLR 828
                  777*********97776667777.99*********************9999865 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.1   2.7e-09   9.6e-06       8     128 ..      52     191 ..      49     202 .. 0.63
   2 !   12.3   0.2   1.4e-05     0.051     167     239 ..     393     466 ..     381     475 .. 0.83
   3 !   12.3   0.0   1.5e-05     0.053     273     359 ..     545     632 ..     506     643 .. 0.66

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 2.7e-09
                   B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT.TS-HHHH.....HHHHHHHHHHHHHHTT---SEE.......... CS
  tRNA-synt_1g   8 pYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke.gvtpeel.....vekvheeikelfkklnisfdky.......... 88 
                   p+ang +H Ghll+  + D +aRy+ + g++v    g D hG p e+  ek+  ++ ++      +e++++e ++    ++ ++++y          
    AHX11457.1  52 PFANGLPHYGHLLTGFAKDTIARYHTMLGKKVERRFGWDCHGLPAEMYTEKQlRISGKDEirkfgIEDFNAECRKSVMLFSSEWEEYvsrqarwvdf 148
                   89*******************************************9988775345554430111223344444444444444444441111111111 PP

                   ...EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTE CS
  tRNA-synt_1g  89 ...grttseehkelvqeifkklkekgliyekeieqlycpkder 128
                      ++t +++  e v   fk++++kgliye+   + y+ ++++
    AHX11457.1 149 hndYKTMDTSFMESVIWAFKEMYRKGLIYESVKVVPYSWACQT 191
                   1112344444444455556666777777777666666666665 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 1.4e-05
                   ..........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET..T CS
  tRNA-synt_1g 167 pksaisgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP..g 239
                   p++  +++  ++k   +++ ++ k+++++ e  ++ +   ++     + +wl++  kd+aisr+  wG pvP  +
    AHX11457.1 393 PHCWRTDTPLIYKVVPSWYVNVTKIKTRMLELNKTINWIPSHLKDGLMGKWLEN-AKDWAISRNRFWGAPVPvwK 466
                   77888888888999999***********999996666556677778899***99.9****************552 PP

  == domain 3  score: 12.3 bits;  conditional E-value: 1.5e-05
                   G.G--S.......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE-.-EEE--------------HHHHHHHH-HHHHHHHHHHHS- CS
  tRNA-synt_1g 273 keyWakdkeve.lvhfigkdiikFHtifwPaillgaelklpkkvvahe.yltvegkKlSkSrgvvvkakealerldadllRYylaaeap 359
                   k++++k++ ++ +++ +++    F t++  ++ l  ++ +  +  ah+  l  +gkKlSk  ++  +++e+ +++ ad+lR+ +++++ 
    AHX11457.1 545 KKWFEKHSSSDfVTEYVAQTRGWFYTLIVLSTALFDKVPFK-NCLAHGvILDKDGKKLSKRLNNYKDPREIFDEYGADALRFLMLSSSV 632
                   55553322222133444444444555554444444555554.4555551577899***************************9998765 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.4e-06     0.016     228     283 ..     574     630 ..     571     634 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.4e-06
                   HHHHHSS.S--EEEEEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHSS CS
  tRNA-synt_1e 228 qseaafd.kqlvkyflhnghlkiegekmsksLknfitikdvlkkfdprqlRllllsa 283
                    s+a+fd  ++ +   h  +l  +g+k+sk L+n+   ++++ ++ + +lR+l+ls 
    AHX11457.1 574 LSTALFDkVPFKNCLAHGVILDKDGKKLSKRLNNYKDPREIFDEYGADALRFLMLSS 630
                   68999**777888888999999*******************************9986 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   1.3e-05     0.047     100     137 ..     307     344 ..     299     374 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
  tRNA-synt_1_2 100 iwvanyvlmeygtgavmavPahdqrDfeFakkynlpik 137
                    +  a++v  e gtg v   P+  ++Dfe a++yn++ +
     AHX11457.1 307 VQHADFVTDEDGTGIVHIAPGFGEEDFELAREYNVKPI 344
                    5569******************************8654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1039 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      477  (0.0266049); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.22s 00:00:00.98 Elapsed: 00:00:00.41
# Mc/sec: 7657.97
//
Query:       AHX11458.1  [L=206]
Description: orotate phosphoribosyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.8e-11   42.8   0.2    6.5e-11   42.0   0.2    1.3  1  Pribosyltran  Phosphoribosyl transferase domain
  ------ inclusion threshold ------
        0.1   12.0   0.1        0.2   11.1   0.1    1.6  1  UPRTase       Uracil phosphoribosyltransferase


Domain annotation for each model (and alignments):
>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   0.2   7.2e-15   6.5e-11       7     140 ..      44     167 ..      40     183 .. 0.88

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 7.2e-15
                   T---EEEEEEETTEEEEEE.--GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHH CS
  Pribosyltran   7 enpaildavarlaaeilee.yngkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgT 102
                   +np+++ + a+++ e++ e  ++k d++v +a gG+++++++a+ L+ ++++ ++v  + +   +++           + ++++Vl+V+D+++t+g+
    AHX11458.1  44 KNPKLATKFASALIEKIPEkVKNKLDLIVSPALGGLIIGYEVARLLNKEFMFFERVAGEFQLRRGFV-----------IEKNQRVLLVEDVVTTAGS 129
                   56777777776666666666999*******************************************8...........78***************** PP

                   HHHHHHHHHCC-BSEEEEEEEEE-HHHHHHHHHH-TTS CS
  Pribosyltran 103 llaalelLkekgpeevriavlvdkpateeevdknakrv 140
                      +l+ + e g  ++ +a ++d++++  +++++ + +
    AHX11458.1 130 SVDVLRKILELGGLVISAASIIDRSSGCAKKKFEEFGC 167
                   ******99999999************999998877766 PP

>> UPRTase  Uracil phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1   2.2e-05       0.2     120     168 ..     113     159 ..      35     181 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2.2e-05
     UPRTase 120 aertvlllDpviaTGgsaaaaiqlLkergvgeekIlvlsvlaseegvkr 168
                 ++++vll++ v+ T gs ++++++++e g     I  +s++  ++g+++
  AHX11458.1 113 KNQRVLLVEDVVTTAGSSVDVLRKILELGG--LVISAASIIDRSSGCAK 159
                 5677***********************765..57999999988887744 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (206 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       505  (0.0281667); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1680.90
//
Query:       AHX11459.1  [L=301]
Description: hypothetical protein NHE_0518 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (301 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       472  (0.0263261); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.36
# Mc/sec: 2486.22
//
Query:       AHX11460.1  [L=448]
Description: signal recognition particle protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      6e-63  212.0   0.4      1e-62  211.3   0.4    1.4  1  SRP54        SRP54-type protein, GTPase domain
    1.2e-24   86.8   1.1    5.8e-24   84.6   0.2    2.4  2  SRP_SPB      Signal peptide binding domain
    7.5e-17   61.3   1.0    3.9e-16   59.0   1.0    2.3  1  SRP54_N      SRP54-type protein, helical bundle domain
    5.2e-05   23.3   0.8    0.00014   21.9   0.1    2.1  2  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    0.00035   20.9   0.2    0.00094   19.5   0.0    1.7  1  AAA_22       AAA domain
    0.00054   19.9   5.7        0.1   12.5   0.5    2.8  2  AAA_31       AAA domain
     0.0032   17.8   0.0      0.014   15.7   0.0    2.1  1  FlgM         Anti-sigma-28 factor, FlgM
     0.0039   17.6   0.0      0.011   16.2   0.0    1.8  1  AAA_17       AAA domain
     0.0044   16.3   0.0     0.0088   15.3   0.0    1.4  1  Zeta_toxin   Zeta toxin
     0.0079   15.7   0.1      0.019   14.4   0.1    1.6  1  ParA         NUBPL iron-transfer P-loop NTPase
     0.0083   15.3   4.0       0.35   10.0   0.2    2.7  2  ArsA_ATPase  Anion-transporting ATPase
     0.0087   16.1   0.4      0.026   14.5   0.1    1.9  2  ResIII       Type III restriction enzyme, res subunit
  ------ inclusion threshold ------
      0.017   14.8   0.0      0.033   13.9   0.0    1.8  1  AAA_15       AAA ATPase domain
      0.021   14.9   0.0      0.047   13.7   0.0    1.6  1  AAA_14       AAA domain
      0.031   14.7   0.2       0.13   12.7   0.1    2.1  1  AAA          ATPase family associated with various cellular a
      0.034   14.3   0.0      0.084   13.0   0.0    1.7  1  AAA_33       AAA domain
      0.041   13.0   0.3       0.26   10.4   0.0    1.9  2  G-alpha      G-protein alpha subunit
      0.047   14.1   0.0      0.091   13.1   0.0    1.6  1  AAA_16       AAA ATPase domain
      0.052   14.1   0.1       0.15   12.7   0.1    1.9  1  AAA_18       AAA domain
      0.087   13.1   0.0       0.24   11.6   0.0    1.8  1  Roc          Ras of Complex, Roc, domain of DAPkinase
        0.1   12.1   0.2       0.47   10.0   0.0    2.1  2  AAA_7        P-loop containing dynein motor region
       0.19   11.3   1.9       0.73    9.4   1.8    2.0  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.3   0.4   1.3e-65     1e-62       2     196 .]     101     296 ..     100     296 .. 0.97

  Alignments for each domain:
  == domain 1  score: 211.3 bits;  conditional E-value: 1.3e-65
                 EEEEEEESTTSSHHHHHHHHHHHHHHT..TS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTH CS
       SRP54   2 nvillvGlqGaGKTttlaKLaallkke..gkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqnd 98 
                 ++++lvGlqG+GKTtt+aKLa  ++k+  +k++ll + D++R+aA +QL++la++++v  +   e++d   ++ ++++++++ ++dv+++DTaGr+q+d
  AHX11460.1 101 SILMLVGLQGVGKTTTAAKLALFMRKKfkKKNILLSSIDVYRPAARKQLEILARQIDVASVPIVEDDDVRMILDRTMNMFDD-SYDVLILDTAGRSQID 198
                 689***********************998999*****************************999999888888888888887.89************** PP

                 HHHHHHHHHHHHHHSSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHHTS-EEEEE-SSSTTGEEE--HHHHHHHHHT CS
       SRP54  99 kelmeelkkikkvvkpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaaelklPikfigvGekiedleefdperlvsrllg 196
                  elm+elk +k+ ++p e+l v+d+++gq+ ++ ak+Fk+++g tgvi++++D+d++gGa+lsi++ ++lPikf g Gek++dleef+p+r++ r+lg
  AHX11460.1 199 LELMNELKLVKQDLQPCEILQVVDSMMGQDSLNVAKTFKDEIGTTGVIVSRVDSDTRGGAMLSIKHCTGLPIKFCGAGEKVNDLEEFHPDRIAGRILG 296
                 ***********************************************************************************************985 PP

>> SRP_SPB  Signal peptide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1       2.4   1.9e+03      14      33 ..     294     313 ..     289     325 .. 0.65
   2 !   84.6   0.2   7.1e-27   5.8e-24       1      96 [.     327     421 ..     327     423 .. 0.92

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.4
                 HHCCCCCCHHHHCCC..... CS
     SRP_SPB  14 ikkmGplskllsmiPgmsae 33 
                 i  mG++++l++     + e
  AHX11460.1 294 ILGMGDVESLMEYASSEMGE 313
                 7789******9998863333 PP

  == domain 2  score: 84.6 bits;  conditional E-value: 7.1e-27
                 SSCTHHHHHHHHHHHCCCCCCHHHHCCC......H...CCCCCHHHHHHHHHTTSBHHHHHSGCG-..HHHHHHHHHHTTS-HHHHHHHHHHHHHHH CS
     SRP_SPB   1 eftlrdlleqlqqikkmGplskllsmiPgmsae.akaeeeaekklkrieaiidSMTkeErdspekllkesRkrRiArGsGtsvqevnellkqfeqmk 96 
                 +f+++dl  q+++i+k+G++ kll+ iPg+++  + ++ ++++ lkr  aii+SMTk+Er+  + ++++sRk RiA+G+G+++ +vn+l+++feq +
  AHX11460.1 327 KFDYDDLVMQFKTIDKLGGIAKLLKFIPGINKIpM-EQLTNDTVLKRNLAIIKSMTKRERKCVD-VINQSRKLRIAAGAGVKTVDVNKLMRNFEQAR 421
                 69***************************776664.34456789********************.889**************************986 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.0   1.0   4.8e-19   3.9e-16       1      75 []       5      82 ..       5      82 .. 0.96

  Alignments for each domain:
  == domain 1  score: 59.0 bits;  conditional E-value: 4.8e-19
                HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS...S-HHHHHHHHHHHHH CS
     SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk...lkpkqqvkkivkdeL 75
                L++k+++al ++++k+ ++e+d+++++++l+ +LleaDV v+v+k++i+nvk++ vg++    ++++ ++ +++kdeL
  AHX11460.1  5 LSRKISGALDGIKSKGIVTEKDFDNFVRKLRLSLLEADVPVSVTKEFISNVKEEVVGKSLrrgVSQSVTISNVIKDEL 82
                799**************************************************99**55599999************8 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.9   0.1   1.7e-07   0.00014       9      89 ..     110     255 ..     102     274 .. 0.81
   2 ?   -2.2   0.0       5.1   4.1e+03      93     118 ..     370     397 ..     309     408 .. 0.68

  Alignments for each domain:
  == domain 1  score: 21.9 bits;  conditional E-value: 1.7e-07
                 TSSHHHHHHHHHHHHHH..TT--EEEEEEEESSCCCCHHTTEB-HHHH................................................... CS
                 xxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxx................................................... RF
        CbiA   9 GvGKTtlaanLaralar..rglrVllvDaDpqannlaileglendiep................................................... 54 
                 GvGKTt+aa+La  + +  +++++ll   D+ +++++  ++le+  ++                                                   
  AHX11460.1 110 GVGKTTTAAKLALFMRKkfKKKNILLSSIDVYRPAAR--KQLEILARQidvasvpivedddvrmildrtmnmfddsydvlildtagrsqidlelmnelk 206
                 9****************666999************99..44444444466688**********************************999999999999 PP

                 .....................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS... CS
                 .....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA  55 .....................dlkrllellealgkkkalllkiagvvlnrvdgene 89 
                                      d   + +++       ++++   gv++ rvd++ +
  AHX11460.1 207 lvkqdlqpceilqvvdsmmgqDSLNVAKTF-------KDEIGTTGVIVSRVDSDTR 255
                 999999888888887555433333333333.......3336668999999999854 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 5.1
                 CHHHHHHHHHHC..TS-EEEEEE--CCH CS
                 xxxxxxxxxxxx..xxxxxxxxxxxxxx RF
        CbiA  93 lkealeelkqry..gvpvlgviprdeav 118
                 lk +l+ +k ++  ++++++vi ++ ++
  AHX11460.1 370 LKRNLAIIKSMTkrERKCVDVINQSRKL 397
                 3444444443334466666666666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   1.1e-06   0.00094       4     114 ..      99     207 ..      97     223 .. 0.68

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.1e-06
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelka..erlsseellealeqalraravielliiDEa 100
                 +++il+++G  G+GKTt++++l+      +k ++++  + ++++  +  +k+l + l+r++++      e ++ + +l++  + +++ ++  +li+D a
  AHX11460.1  99 GKSILMLVGLQGVGKTTTAAKLALFMR--KKFKKKNILLSSIDVYRPAARKQL-EILARQIDVASVPivEDDDVRMILDRTMNMFDDSYD--VLILDTA 192
                 799*********************984..333333333336666666633333.555555555444454446666666888888888888..9999999 PP

      AAA_22 101 qhlr.seealeeLrs 114
                  +     e+++eL+ 
  AHX11460.1 193 GRSQiDLELMNELKL 207
                 886335888888854 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.5   0.00012       0.1      12      35 ..     110     135 ..     100     145 .. 0.77
   2 !    8.9   0.5    0.0016       1.3      78     126 ..     146     192 ..     137     217 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 0.00012
      AAA_31  12 GvGKTTtsvnlaaalaklgkk..vLl 35 
                 GvGKTTt+ +la ++ k+ kk  +Ll
  AHX11460.1 110 GVGKTTTAAKLALFMRKKFKKknILL 135
                 9**************96543312565 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.0016
      AAA_31  78 venldlipssidLaeaeielvelekkeeilkellekvkdeYDyiiiDcp 126
                  ++l+++  +id+a++   +ve ++ + il+++++ ++d+YD+ i+D+ 
  AHX11460.1 146 RKQLEILARQIDVASVP--IVEDDDVRMILDRTMNMFDDSYDVLILDTA 192
                 56677888888877765..5789999*********************96 PP

>> FlgM  Anti-sigma-28 factor, FlgM
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.7e-05     0.014      21      45 ..     307     331 ..     298     332 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.7e-05
        FlgM  21 aapevreekVaelKeaIasGtYqvd 45 
                 a++e+ eekV++lK++I+sG ++ d
  AHX11460.1 307 ASSEMGEEKVDSLKKKIESGKFDYD 331
                 456899**************99876 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.3e-05     0.011       1     108 [.     106     220 ..     106     224 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.3e-05
                 EE-TTSSHHHHHHHHH....HHH..TEEEEEHHHHHHHHHHTT.TSHSSHHHHCTSHHHHHHHHHHHHHHHHHHHHHS.SEEEEEE-SEEEETTEEEES CS
      AAA_17   1 lGgPGsGKgtqceklv....eky..gfthlsaGdllreeakrg.glakardemrklpleekkelqkeaaekiaeeakk.kgvlvdghprikeqagfldg 91 
                 +G+ G+GK+t ++kl+    +k+  +   ls  d+ r  a+++ +    + +++ +p++e+++++ ++ ++++  +++ + +++d+  r + + +++ +
  AHX11460.1 106 VGLQGVGKTTTAAKLAlfmrKKFkkKNILLSSIDVYRPAARKQlEILARQIDVASVPIVEDDDVRMILDRTMNMFDDSyDVLILDTAGRSQIDLELMNE 204
                 79*************8666556644555678889999666555455455566779**************999887755266799999998777777777 PP

                 SHHHHHHHH..SEEEEE CS
      AAA_17  92 lpkevleelkpdaiill 108
                 l+  v+++l+p  i+ +
  AHX11460.1 205 LKL-VKQDLQPCEILQV 220
                 775.8999999888765 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.0   1.1e-05    0.0088      15     103 ..      99     192 ..      89     207 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 1.1e-05
  Zeta_toxin  15 rPklillgGqpGAGKselaellkdele...rqgnvvrldpDdlRelhPeyeeilka..dpkkaseltqkdaselvekllqeaiengyni.ivegt 103
                  + +++l+G +G GK+++a++l+  ++   +++n++  + D +R+  ++  eil+   d++++ ++ ++d++ + +++++  ++  y++ i++++
  AHX11460.1  99 GKSILMLVGLQGVGKTTTAAKLALFMRkkfKKKNILLSSIDVYRPAARKQLEILARqiDVASVPIVEDDDVRMILDRTMNM-FDDSYDVlILDTA 192
                 5667899***************999988889*********************99954688888899999999999988764.5555554255665 PP

>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   2.4e-05     0.019       6      68 ..     102     163 ..      99     188 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.4e-05
        ParA   6 iavlSgKGGVGKStvavnlAlaLakkglkvgll..DaDiyGpsiprllgveeekpeqsekkliPv 68 
                 i++l g  GVGK+t+a++lAl ++kk +k  +l   +D+y p   + l++  +++ + +   +P+
  AHX11460.1 102 ILMLVGLQGVGKTTTAAKLALFMRKKFKKKNILlsSIDVYRPAARKQLEILARQIDVAS---VPI 163
                 67778888***************98766655553389***9999999998887665554...454 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.2   0.00043      0.35       3      37 ..     102     138 ..     100     146 .. 0.76
   2 !    6.0   0.4    0.0071       5.8     101     153 ..     158     213 ..     142     243 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00043
                  EEEEEESTTSSHHHHHHHHHHHHHHT..TS-EEEEE- CS
  ArsA_ATPase   3 vilvgGKGGVGKttvsaatavklsek..gkkvllist 37 
                  ++++ G  GVGKtt +a +a+ + +k  +k++ll s 
   AHX11460.1 102 ILMLVGLQGVGKTTTAAKLALFMRKKfkKKNILLSSI 138
                  67889999*************9987621334455555 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.0071
                  HTSSTTHHHHHHHHHHHHHHH..CSSSSEEEEESBSCCH.TCGGGGHHHHHHHHHH CS
  ArsA_ATPase 101 laslPGideilsfeellkyvk..eeeydvvvlDtaPTGh.tlrllslpevleklle 153
                  +as+P +++    + l + ++  ++ ydv++lDta   +  l l++  + +++ l+
   AHX11460.1 158 VASVPIVEDDDVRMILDRTMNmfDDSYDVLILDTAGRSQiDLELMNELKLVKQDLQ 213
                  46778777654444445554444789********9654424666665555555555 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.1   3.2e-05     0.026      21      59 ..      85     135 ..      47     147 .. 0.77
   2 ?   -3.0   0.0       7.7   6.2e+03     127     147 ..     178     198 ..     165     219 .. 0.67

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 3.2e-05
                 ..............TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEE CS
      ResIII  21 s............krdkrglikmaTGtGKTlvaaklierllkkgkeekflf 59 
                 +            +++  ++++   G+GKT +aakl+  ++kk+k++++l+
  AHX11460.1  85 IlggtvskfelpkDGKSILMLVGLQGVGKTTTAAKLALFMRKKFKKKNILL 135
                 25566666666635555666999**********************999986 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 7.7
                 HHHTTT-SEEEEETGGGTTS. CS
      ResIII 127 ellrdrfdviiiDEaHrlgak 147
                  + +d++dv+i D a r++ +
  AHX11460.1 178 NMFDDSYDVLILDTAGRSQID 198
                 556778889999988887765 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     4e-05     0.033      25      80 ..     102     153 ..      89     439 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 4e-05
      AAA_15  25 ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikId 80 
                 +  l+G +++GK++ +  l lF  +k    +k+++i  +++++++  ++++   ++
  AHX11460.1 102 ILMLVGLQGVGKTTTAAKLALFMRKK----FKKKNILLSSIDVYRPAARKQLEILA 153
                 889*********************99....44555666666665555554444444 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   5.8e-05     0.047       3      50 ..     101     150 ..      99     195 .. 0.73

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 5.8e-05
      AAA_14   3 kilvitGaRrvGKTtllkqlikell....vkkesilyinldderdkkladpe 50 
                  il+++G+  vGKTt + +l+   +     kk++il  ++d  r +++++ e
  AHX11460.1 101 SILMLVGLQGVGKTTTAAKLAL--FmrkkFKKKNILLSSIDVYRPAARKQLE 150
                 6899************998852..22355699****9999998887666554 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00016      0.13       1      56 [.     103     159 ..     103     190 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00016
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEE..TTTCSSSSTTHHHHHHHHHHHHHHHT CS
         AAA   1 vllyGppGtGKTllakavakelgvefleis..gsellskyvgesekkirelfkeakek 56 
                 ++l+G  G+GKT++a  +a  +  +f + +  +s++   y  ++ k+++ l +++   
  AHX11460.1 103 LMLVGLQGVGKTTTAAKLALFMRKKFKKKNilLSSID-VYRPAARKQLEILARQIDVA 159
                 589****************999766654440044443.67777777777666666554 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0    0.0001     0.084       2      20 ..     103     121 ..     102     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.0001
      AAA_33   2 vllvGlpGsGKstlaerll 20 
                 ++lvGl+G+GK+t a +l+
  AHX11460.1 103 LMLVGLQGVGKTTTAAKLA 121
                 79**************994 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00032      0.26      25     109 ..     102     184 ..      74     238 .. 0.78
   2 ?    0.1   0.2      0.43   3.5e+02     278     292 ..     315     329 ..     313     394 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00032
                 EEEEEESTTSSHHHHHHHHHHHCS----HHHH.HCCHHHHHHHHHHHHHHHHHHHHHTT.......HHHC-SS-SCCCS-HCHHHH CS
     G-alpha  25 kllllGqseSGKsTilkqlkllykkgfseeel.atwraviqlnivrsiktilealesleselsesfelqelkerldplkkveasli 109
                  l+l+G ++ GK+T+  +l l+ +k+f+++++  +  +v +    ++++ + ++++  + ++    e+++++  ld+ +++ ++ +
  AHX11460.1 102 ILMLVGLQGVGKTTTAAKLALFMRKKFKKKNIlLSSIDVYRPAARKQLEILARQIDVASVPIV---EDDDVRMILDRTMNMFDDSY 184
                 5899**************************996668899999999999999999999888874...55555555555555544444 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.43
                 -HHHHHHHCCCS-GG CS
     G-alpha 278 KlDileeKlkkgkls 292
                 K+D l++K+++gk+ 
  AHX11460.1 315 KVDSLKKKIESGKFD 329
                 99*******999654 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   0.00011     0.091      22      60 ..      98     132 ..      77     220 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 0.00011
      AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkc 60 
                 ++ ++++l+G +GvGK++ + +l+  ++k+    ++ k+
  AHX11460.1  98 DGKSILMLVGLQGVGKTTTAAKLALFMRKK----FKKKN 132
                 4449****************9998666665....44444 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.1   0.00018      0.15       2      57 ..     104     156 ..     103     230 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.00018
      AAA_18   2 lltGtpGvGKttlakeLskrlgfgvnlrdvakenglllevdpe..aldeskrldedkl 57 
                 +l G +GvGKtt a  L+      +  ++  k+n ll + d +  a ++++++   + 
  AHX11460.1 104 MLVGLQGVGKTTTAAKLAL-----FMRKKFKKKNILLSSIDVYrpAARKQLEILARQI 156
                 689**************32.....2344444444444444444443333333333333 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0    0.0003      0.24       2      40 ..     103     144 ..     102     160 .. 0.81

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 0.0003
                 EEEESSTTSSHHHHHHC...HCT-CCC-EEETTTTEEEEEEE CS
         Roc   2 vvlvGdsgvGKtsllkr...fvedkfsekekstigvdfltke 40 
                 ++lvG +gvGKt+ + +   f+++kf++k+    ++d+++  
  AHX11460.1 103 LMLVGLQGVGKTTTAAKlalFMRKKFKKKNILLSSIDVYRPA 144
                 69***********9876444799******9999999998754 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0   0.00057      0.47      35      71 ..     102     137 ..      93     149 .. 0.83
   2 ?   -1.0   0.1       1.3   1.1e+03      45      73 ..     405     431 ..     376     439 .. 0.69

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00057
       AAA_7  35 pvllvGptGtGKtviikdllkkldkekylsltinfsa 71 
                  ++lvG +G+GKt+++ +l   +  +k++ ++i +s+
  AHX11460.1 102 ILMLVGLQGVGKTTTAAKLALFMR-KKFKKKNILLSS 137
                 5799*************9887777.888888877775 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.3
       AAA_7  45 GKtviikdllkkldkekylsltinfsaqt 73 
                  Ktv +++l++++++ +   l ++f ++ 
  AHX11460.1 405 VKTVDVNKLMRNFEQAR--ALAVKFGKSS 431
                 39999999999999544..4444444444 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.4   1.8    0.0009      0.73      34      58 ..     101     125 ..      97     199 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.0009
      AAA_25  34 elallaGapgtGKttlaldlalava 58 
                 ++ +l+G +g+GKtt a  lal + 
  AHX11460.1 101 SILMLVGLQGVGKTTTAAKLALFMR 125
                 6789******************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (448 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       682  (0.0380389); expected 358.6 (0.02)
Passed bias filter:                      466  (0.0259914); expected 358.6 (0.02)
Passed Vit filter:                        74  (0.00412739); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.55u 0.30s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3346.30
//
Query:       AHX11461.1  [L=436]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (436 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       754  (0.0420548); expected 358.6 (0.02)
Passed bias filter:                      195  (0.0108762); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 3554.16
//
Query:       AHX11462.1  [L=202]
Description: RDD family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-16   60.8   2.6    2.4e-16   60.2   2.6    1.3  1  RDD       RDD family


Domain annotation for each model (and alignments):
>> RDD  RDD family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.2   2.6   1.3e-20   2.4e-16       1     141 []      38     188 ..      38     188 .. 0.80

  Alignments for each domain:
  == domain 1  score: 60.2 bits;  conditional E-value: 1.3e-20
         RDD   1 laslgrRllAfliDlvllliislllallivall.................nakasaneavagslllllllvlllvllvyqllllsk.kgqTlGklllgl 81 
                 +as ++R ++ l+Dl+++++++    +++ + +                  +   + +  + ++ +l++ v  l+llv  ++ ++  +g+T+Gk++l+l
  AHX11462.1  38 YASQFKRSISILTDLLFCILFLKCSGYVLSSFVdisfpmevieryrfalpVSPLDNELMANFYKKMLFIQVIQLLLLVSLVITSWHrFGCTPGKWILRL 136
                 78999*********99999887655555555446667*******9998764444444444555555555555555555555555557************ PP

         RDD  82 kvvd.edgrklglaqaliRalllllllvlglslvlllllligflfvlfsrkrqalhDklag 141
                 +v+d  +  +++l ++++Ra+         ++ +++ +l++g+++++f++k +a+hD +ag
  AHX11462.1 137 RVLDdVTLGRPSLSACVKRAV---------MFPISVGCLFLGIFWIIFDKKGRAWHDVVAG 188
                 ****9999************9.........899*************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      352  (0.019633); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1576.51
//
Query:       AHX11463.1  [L=370]
Description: methyltransferase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.1e-14   52.4   0.2    1.8e-13   51.1   0.2    1.7  1  Methyltransf_12  Methyltransferase domain
    8.5e-14   51.6   2.1    4.2e-13   49.4   0.7    2.3  3  Methyltransf_31  Methyltransferase domain
    3.5e-13   49.7   0.0    5.2e-13   49.2   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    8.4e-12   45.7   0.1      2e-11   44.4   0.1    1.7  1  Methyltransf_25  Methyltransferase domain
    2.9e-11   43.9   0.1    7.3e-11   42.6   0.1    1.7  1  Methyltransf_11  Methyltransferase domain
    4.7e-07   29.5   0.0    7.7e-07   28.8   0.0    1.3  1  MTS              Methyltransferase small domain
    2.7e-06   26.9   0.1    3.9e-06   26.4   0.1    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.1e-05   25.0   0.0    4.1e-05   24.0   0.0    1.4  1  TPR_19           Tetratricopeptide repeat
    0.00026   20.8   0.1    0.00046   20.0   0.1    1.4  1  Methyltransf_16  Lysine methyltransferase
      0.002   18.1   0.0       0.19   11.9   0.0    2.8  2  TPR_2            Tetratricopeptide repeat
     0.0022   17.6   0.0     0.0033   17.0   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
     0.0055   16.3   0.1      0.015   14.9   0.1    1.7  2  MetW             Methionine biosynthesis protein MetW
     0.0079   15.6   0.1      0.016   14.7   0.1    1.4  1  TehB             Tellurite resistance protein TehB
     0.0091   16.6   0.0      0.032   14.9   0.0    2.0  1  TPR_6            Tetratricopeptide repeat
  ------ inclusion threshold ------
       0.01   15.5   0.0      0.015   14.9   0.0    1.2  1  NodS             Nodulation protein S (NodS)
      0.041   13.3   0.3      0.062   12.7   0.3    1.2  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
      0.045   13.5   0.1      0.095   12.4   0.1    1.4  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
      0.091   13.0   0.2        1.2    9.5   0.0    2.8  2  TPR_8            Tetratricopeptide repeat
      0.099   13.1   0.7       0.58   10.7   0.1    2.6  1  TPR_17           Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.1   0.2   1.9e-16   1.8e-13       1      99 []     205     302 ..     205     302 .. 0.89

  Alignments for each domain:
  == domain 1  score: 51.1 bits;  conditional E-value: 1.9e-16
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      L++GcGtG +++ l  +    + +gvDis++++e ak+ la+ ++  ++ +  e++ ++ ++ ++++Dl++a++ + +l d+++v+ ++ ++L+
       AHX11463.1 205 LDLGCGTGVCAHFLKLSGVVGNTCGVDISENMLEIAKRCLADGKA-VFDSISQENIGSFLSSNKDKYDLIIAADSFTYLGDLQDVIPQCVDALN 297
                      8****************999*************777777777665.6677777777766666679***************************** PP

  Methyltransf_12  95 pgGrl 99 
                      ++G+l
       AHX11463.1 298 DDGVL 302
                      ***87 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       3.6   3.4e+03      56      81 ..      78     101 ..      68     135 .. 0.61
   2 !   49.4   0.7   4.4e-16   4.2e-13       6     110 ..     203     305 ..     201     322 .. 0.92
   3 ?   -0.1   0.0      0.77   7.2e+02      33      55 ..     338     360 ..     322     370 .] 0.79

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 3.6
  Methyltransf_31  56 veFeqgdieeleklledekfDlilsn 81 
                      ++F++g+i++++  +  +  + i  +
       AHX11463.1  78 YHFHKGNITDAK--FRFRILNAIYKD 101
                      688889888877..544444445444 PP

  == domain 2  score: 49.4 bits;  conditional E-value: 4.4e-16
  Methyltransf_31   6 rvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsnevlnaladpdkileeie 98 
                      ++lDlGCGtG  ++ l  + g  ++  G+Dise+++e A+  +++ +    + +q++i + l++  +++k+Dli++ + + +l d+++++ +  
       AHX11463.1 203 SILDLGCGTGVCAHFLK-LSGVVGNTCGVDISENMLEIAKRCLADGKAVFDSISQENIGSfLSS--NKDKYDLIIAADSFTYLGDLQDVIPQCV 293
                      69***************.8899999****************9999999999*********8884..579************************* PP

  Methyltransf_31  99 rvlkpggillie 110
                      ++l+++g+l++ 
       AHX11463.1 294 DALNDDGVLVVL 305
                      ********9975 PP

  == domain 3  score: -0.1 bits;  conditional E-value: 0.77
  Methyltransf_31  33 GiDiseeaielArenaqklgldn 55 
                      G+Di+ +++++++ ++++ g+  
       AHX11463.1 338 GLDIKSHVVRKCTFKSACEGIIA 360
                      99***********9999999864 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.2   0.0   5.5e-16   5.2e-13      22     121 ..     200     308 ..     174     348 .. 0.81

  Alignments for each domain:
  == domain 1  score: 49.2 bits;  conditional E-value: 5.5e-16
  Methyltransf_23  22 aggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae...........kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppell 102
                       ++++Ld+GcGtG  +  l+  g+  + +gvD+s+++ eia+           ++++ +  +f     + +++k+dlI++ +++  + d+  ++
       AHX11463.1 200 MSSSILDLGCGTGVCAHFLKLSGVvgNTCGVDISENMLEIAKrcladgkavfdSISQENIGSF----LSSNKDKYDLIIAADSFTYLGDLQDVI 289
                      5679*********999999***9999***************9666444433333333333333....556999********************* PP

  Methyltransf_23 103 rqiatllkpgGylllsepl 121
                       q  + l+++G+l++++  
       AHX11463.1 290 PQCVDALNDDGVLVVLVRS 308
                      ***************9973 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.4   0.1   2.1e-14     2e-11       1      97 []     204     300 ..     204     300 .. 0.85

  Alignments for each domain:
  == domain 1  score: 44.4 bits;  conditional E-value: 2.1e-14
                      EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCG.BSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgdaed.lpfedgsfDlvvssgalhhlsdedlekalkeiar 91 
                      +LdlGcGtG  +  l    g  ++  gvDise+mle+a++ +++ ++   ++ q ++ + l+ +++++Dl++++ ++ +l   dl++++ ++ +
       AHX11463.1 204 ILDLGCGTGVCAHFLKLS-GvVGNTCGVDISENMLEIAKRCLADGKAvFDSISQENIGSfLSSNKDKYDLIIAADSFTYLG--DLQDVIPQCVD 294
                      8********999988877.4489*******************885553444577777554889999*******988***98..899******** PP

                      HEEEEE CS
  Methyltransf_25  92 vLkpgG 97 
                      +L+++G
       AHX11463.1 295 ALNDDG 300
                      999988 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.1   7.8e-14   7.3e-11       1      96 []     205     304 ..     205     304 .. 0.94

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 7.8e-14
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCC.TSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaek.lpfednsfDlvvssevlhhvedpekalkeiaRvLkp 90 
                      Ld+GcGtG  a  l+  g  +++ gvD+s++ml++ak++  + +    ++ ++++ + l  +++++Dl+++  +++++ d+++++ +++  L  
       AHX11463.1 205 LDLGCGTGVCAHFLKLSGvvGNTCGVDISENMLEIAKRCLADGKAvFDSISQENIGSfLSSNKDKYDLIIAADSFTYLGDLQDVIPQCVDALND 298
                      8**************88899*******************9999987667899999995599999****************************** PP

                      EEEEEE CS
  Methyltransf_11  91 gGllvi 96 
                      +G+lv+
       AHX11463.1 299 DGVLVV 304
                      ***986 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.8   0.0   8.1e-10   7.7e-07      30     143 ..     198     310 ..     178     325 .. 0.82

  Alignments for each domain:
  == domain 1  score: 28.8 bits;  conditional E-value: 8.1e-10
                 C.TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTTTST..TS-EEEEEE---STTTCHCHHHHHHHHHHH CS
         MTS  30 e.lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvleeve..ekkfdlivsNPPfhagkatelavaeeliae 124
                 + +s ++lDlGcG+Gv +  l+      +   vd++ + le+ak+ l++ k+   ++ ++++ + ++  ++k+dli+    f    +      +++i +
  AHX11463.1 198 AlMSSSILDLGCGTGVCAHFLKLSGVVGNTCGVDISENMLEIAKRCLADGKAVfDSISQENIGSFLSsnKDKYDLIIAADSFTYLGD-----LQDVIPQ 291
                 256778************999999999999*******************9998655666665443332259******9999988888.....999**** PP

                 HHHHEEEEEEEEEEEETTS CS
         MTS 125 AkeaLkegGeLliVanrkl 143
                   +aL+++G L++ ++++ 
  AHX11463.1 292 CVDALNDDGVLVVLVRSHK 310
                 ***********99998876 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   4.2e-09   3.9e-06      46     158 ..     199     311 ..     160     341 .. 0.79

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 4.2e-09
                      --TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEE..E--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHH CS
  Ubie_methyltran  46 krgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkiniefl..qanaeeLpfeddsfDvvtvsfGlrnvtDklkaLk 137
                      + ++++lD+ +Gtg   +++++  g  g+  ++Di+enmL+++++ l +  k   + +     +  L  ++d +D++  +  +  + D + ++ 
       AHX11463.1 199 LMSSSILDLGCGTGV-CAHFLKLSGVVGNTCGVDISENMLEIAKRCLADG-KAVFDSIsqENIGSFLSSNKDKYDLIIAADSFTYLGDLQDVIP 290
                      56789********95.5678899999****************99877664.4444444104457889999*********9999*********** PP

                      HHHHHEEEEEEEEEEEE---- CS
  Ubie_methyltran 138 eayrvlkpGGrlvvlefskve 158
                      +    l   G lvvl  s+ +
       AHX11463.1 291 QCVDALNDDGVLVVLVRSHKQ 311
                      ***************999865 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   4.4e-08   4.1e-05       5      61 ..      83     140 ..      80     141 .. 0.90

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 4.4e-08
      TPR_19   5 gdyaeAlalleqalqedpknaearllLAeallalgqldeAealLdalpeedpdd.ary 61 
                 g+ ++A  +++ + + + + +  +++LA++ll +g+ d+A+ + ++++ ++ +d +++
  AHX11463.1  83 GNITDAKFRFRILNAIYKDKPLPAYNLARCLLLSGDKDKAKVTFEDILSKNSKDyEEV 140
                 8899999999888899********************************9999976665 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   4.9e-07   0.00046      43     164 ..     197     312 ..     165     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 4.9e-07
  Methyltransf_16  43 nelsklsvlELGsGtGlvGlavael..l.peakviltDleellellkknielnknalkskvkvevLdWgeeleedllekeevDlilaaD.cvYl 132
                      ++l   s+l+LG GtG++   ++++  + + + v ++  e++le+ k+ ++  k a+ ++++ e +  g  l     +k ++Dli+aaD  +Yl
       AHX11463.1 197 EALMSSSILDLGCGTGVCAHFLKLSgvVgNTCGVDIS--ENMLEIAKRCLADGK-AVFDSISQENI--GSFL---SSNKDKYDLIIAADsFTYL 282
                      5677889************999999643456666554..679******999955.88888888766..4455...4467789*******44787 PP

  Methyltransf_16 133 edslelLvkvLkellkkeskvlvaykkrreae 164
                       d  + + ++++ l +    vlv++ +++++e
       AHX11463.1 283 GDLQDVIPQCVDALNDDG--VLVVLVRSHKQE 312
                      777666666666665544..666666666655 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.0      0.14   1.3e+02       7      23 ..      75      91 ..      70      99 .. 0.87
   2 !   11.9   0.0    0.0002      0.19       5      32 ..     107     134 ..     103     136 .. 0.89

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.14
       TPR_2  7 lGlayyklgdyeeAlea 23
                lGl ++++g+  +A+  
  AHX11463.1 75 LGLYHFHKGNITDAKFR 91
                9************9865 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.0002
       TPR_2   5 ynlGlayyklgdyeeAleafekAleldP 32 
                 ynl+++++ +gd ++A+  fe  l+ + 
  AHX11463.1 107 YNLARCLLLSGDKDKAKVTFEDILSKNS 134
                 9*******************99998876 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.0   0.0   3.5e-06    0.0033      54     163 ..     199     308 ..     182     348 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.0 bits;  conditional E-value: 3.5e-06
  Methyltransf_PK  54 revkvaldcGaGiGrvtknl.LlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPe.egrYdliWiqWcvghLtDedlvaflk 145
                         + +ld G+G G  ++ l L  ++++   v+  e++le ak+ la++k    ++ +  +  f    +++Ydli      + L D  l + + 
       AHX11463.1 199 LMSSSILDLGCGTGVCAHFLkLSGVVGNTCGVDISENMLEIAKRCLADGKAVFDSISQENIGSFLSSnKDKYDLIIAADSFTYLGD--LQDVIP 290
                      556789********888877445677888889999*************9999999999*****9764399**************97..668899 PP

  Methyltransf_PK 146 rckkalkpnGlivvkenv 163
                      +c+ al+++G++vv    
       AHX11463.1 291 QCVDALNDDGVLVVLVRS 308
                      ***********9985433 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       6.5   6.1e+03     159     188 ..     121     150 ..     117     154 .. 0.75
   2 !   14.9   0.1   1.6e-05     0.015      13      82 ..     200     276 ..     189     293 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 6.5
        MetW 159 nlkvedrvaldekgrkvpavklvanllgel 188
                 ++kv  + +l++++++  +vk++ n+++ +
  AHX11463.1 121 KAKVTFEDILSKNSKDYEEVKFFLNFISGQ 150
                 566666777888888888999999998866 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.6e-05
        MetW  13 pgsrvldlGcGdGellellkeekqvdgr..Gleldeegv...aecvakGlsviqgdldkdlenf...edksfdyvvls 82 
                   s +ldlGcG G   ++lk   +v g+  G++++e+ +   ++c+a G +v +   ++++  f   + +++d+++ +
  AHX11463.1 200 MSSSILDLGCGTGVCAHFLKL-SGVVGNtcGVDISENMLeiaKRCLADGKAVFDSISQENIGSFlssNKDKYDLIIAA 276
                 5799***************87.5555432399999876522268*****99998888888877722234567777765 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.1   1.6e-05     0.016      30     119 ..     200     295 ..     184     304 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.6e-05
                 -S-EEEEES-TTSHHHHHHHHTT-..EEEEEES-HHHHHHHHHH..HHHTT-TTEEEEE--GGG----S-EEEEEEESSGGGS-..GGGHHHHHHH CS
        TehB  30 kpgkvldlgcgqgrnslylsllgy..dvtawdknensiafleei..kekenlknistalydineaklderydfilstvvlmfle..aeripsiien 119
                   + +ldlgcg g  + +l+l g   +   +d  en ++  ++     k  +++is + +     + +++yd+i+++  + +l   ++ ip+ ++ 
  AHX11463.1 200 MSSSILDLGCGTGVCAHFLKLSGVvgNTCGVDISENMLEIAKRClaDGKAVFDSISQENIGSFLSSNKDKYDLIIAADSFTYLGdlQDVIPQCVDA 295
                 56789*****************984466778998888887777511446677888887777777888999******99999996224667777665 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   3.4e-05     0.032       4      29 ..     107     132 ..     106     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 3.4e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6   4 yklalsyrklgdtdkAlealerlike 29 
                 y+la++++  gd+dkA+ ++e+++++
  AHX11463.1 107 YNLARCLLLSGDKDKAKVTFEDILSK 132
                 9********77***********9987 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.0   1.6e-05     0.015      45     143 ..     202     303 ..     186     311 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.6e-05
        NodS  45 adalevGcaaG..alterlapyckrltvvdvveeaiararervkesshi..swivsdvqqf..stdekfdlivvaevlyyiedvaelraavrnlvslla 137
                 +++l++Gc +G  a   +l+ +  +   vd+ e+ ++ a++ + +   +  s  + ++  f  s ++k+dli+ a+ + y++d++++   +   v+ l 
  AHX11463.1 202 SSILDLGCGTGvcAHFLKLSGVVGNTCGVDISENMLEIAKRCLADGKAVfdSISQENIGSFlsSNKDKYDLIIAADSFTYLGDLQDV---IPQCVDALN 297
                 6789*****993344568999999999************99998876662233445677764467789**************98764...666777777 PP

        NodS 138 pdgqlv 143
                  dg lv
  AHX11463.1 298 DDGVLV 303
                 777766 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.5e-05     0.062     162     233 ..     201     276 ..     189     308 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
        PrmA 162 geevlDvGtGSGiLaiaaakLga.kkvvavDiDevAvkvakeNaelNk.veaklevalseellk..eekadvivaN 233
                  +++lD+G+G+G+ a   ++ g   + ++vDi e  +++ak+ ++  k v ++++  + ++ l+  + k+d+i+a 
  AHX11463.1 201 SSSILDLGCGTGVCAHFLKLSGVvGNTCGVDISENMLEIAKRCLADGKaVFDSISQENIGSFLSsnKDKYDLIIAA 276
                 5689*********998877777526899*************98776641444554444444442346889999985 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1    0.0001     0.095      75     124 ..     202     250 ..     191     325 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
                 -EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTC CS
        PCMT  75 arvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldle 124
                 +++L++G+G+G  +  + +l g +g+  +++ ++++ e akr l   ++ 
  AHX11463.1 202 SSILDLGCGTGVCAH-FLKLSGVVGNTCGVDISENMLEIAKRCLADGKAV 250
                 689********8765.556667777777*************999765544 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       2.1     2e+03       5      21 ..      73      89 ..      69      91 .. 0.84
   2 ?    9.5   0.0    0.0013       1.2       5      28 ..     107     130 ..     106     136 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 2.1
                HHHHHHHHHTT-HHHHH CS
       TPR_8  5 ynlgsiylklgdyeeAk 21
                + lg+ ++ +g++  Ak
  AHX11463.1 73 LSLGLYHFHKGNITDAK 89
                6799999*****99987 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.0013
                 HHHHHHHHHTT-HHHHHHHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkeyyekal 28 
                 ynl++++l  gd+++Ak ++e  l
  AHX11463.1 107 YNLARCLLLSGDKDKAKVTFEDIL 130
                 9*******************9876 PP

>> TPR_17  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.1   0.00062      0.58       9      33 ..      99     123 ..      95     123 .. 0.86

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00062
      TPR_17   9 dPnnadaynnLAelllknGdlmtAr 33 
                 +++ + + +nLA++ll  Gd+++A+
  AHX11463.1  99 YKDKPLPAYNLARCLLLSGDKDKAK 123
                 56678899**************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.55u 0.27s 00:00:00.82 Elapsed: 00:00:00.44
# Mc/sec: 2548.06
//
Query:       AHX11464.1  [L=309]
Description: nitronate monooxygenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-39  136.4   0.0    2.1e-37  129.3   0.0    2.0  1  NMO           Nitronate monooxygenase
    2.3e-05   23.8   0.3    3.4e-05   23.3   0.3    1.2  1  ThiG          Thiazole biosynthesis protein ThiG
    4.8e-05   22.5   0.7      0.037   13.0   0.3    2.4  2  IMPDH         IMP dehydrogenase / GMP reductase domain
     0.0009   18.8   0.0      0.003   17.0   0.0    1.8  2  His_biosynth  Histidine biosynthesis protein
     0.0021   18.0   0.0     0.0048   16.8   0.0    1.6  1  LpxI_N        LpxI N-terminal domain
     0.0035   16.6   0.1     0.0049   16.1   0.1    1.2  1  DHO_dh        Dihydroorotate dehydrogenase
  ------ inclusion threshold ------
       0.15   11.0   0.4       0.32   10.0   0.4    1.5  1  FMN_dh        FMN-dependent dehydrogenase


Domain annotation for each model (and alignments):
>> NMO  Nitronate monooxygenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.3   0.0   8.3e-41   2.1e-37      17     329 ..       3     302 ..       1     304 [. 0.88

  Alignments for each domain:
  == domain 1  score: 129.3 bits;  conditional E-value: 8.3e-41
         NMO  17 pgmggiskarLaaavsnaGgLGvlasgyltaDrlakeirkvkaltdk.Pfgvnlflpkkdaadraekykkeleeaalelnieegvrfyrkvevvldekv 114
                 + m++is+ rL++a+sn+G+ Gv+a   + + +l+ ei+  + l+   Pfgvnl l +++  d               +  + gv+             
  AHX11464.1   3 GAMSWISEHRLVSAISNEGAFGVIACSAMEPEQLETEIHLTQGLVGGnPFGVNLILMHPQIRDL------------ISVCKQSGVT------------- 76 
                 68*******************************************999***************9............5677788888............. PP

         NMO 115 evvsfgfglpteevvarlkeagvvliptissvkearkvearGaDalivqGpeaGGhqGtpevgdkglfaLvpq.vldavdiPviAaGGiidrrgvaaaL 212
                   + ++ g p++e ++   +a++ +++ + s   a+k++++G  ali++G eaGGh+    v   ++  L ++  ++  d+P+  aGGi     v+   
  AHX11464.1  77 -HIVLAGGIPPKEILNLILDADIKVMVFAPSLSVAKKMCRLGVSALIIEGREAGGHIS--RV---STSVLAQEiLPECQDVPIFVAGGIGSSSIVKSYV 169
                 .5567779999***********************************************..44...344454441578889******************* PP

         NMO 213 alGAsgvqigtrfLltkesdakdahkkklleaklddteltsavsGr....paRalatelleeleeakiatlalpeah.............elakkiraa 294
                  +GAsg q+gt f  +kes a++  k+k + a   dt++  + + r    p R l++  + e  e++ + l     +               a+ +r a
  AHX11464.1 170 DMGASGCQVGTLFACAKESIAHPKFKEKCIGASSHDTVVSVQLDPRltviPVRSLKNSATMEFMEFQKEVLHKFDSGliskdeaqlgiekFWAGSLRRA 268
                 *************************************9998888654444899999999888888776666666666566666666665445555**** PP

         NMO 295 lveagnteegllwagqgidrldkiisvkeLiesLv 329
                 + ++ + ++g++++g++ + ++ + +vke++ +Lv
  AHX11464.1 269 VIDG-DVDKGSVMVGEVVGLVKYERTVKEILGDLV 302
                 ****.**************************9998 PP

>> ThiG  Thiazole biosynthesis protein ThiG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.3   1.3e-08   3.4e-05     125     216 ..      99     191 ..      88     208 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.3e-08
                 EEEEEE-S-HHHHHHHHHTT-SEBEEBSSSTTS----S-HHHH.HHHHHH-.SS-BEEES---SHHHHHHHHHTT-SEEEESHHHHTSSSHHHH CS
        ThiG 125 evlpYvsdDlvlarrleevGcaavmPlaapiGsglGllnkeal.kiiieea.kvPvivDAGigspsdaaqamelGadavllntavaeakdpvam 216
                 +v+++  + l +a+++  +G++a++  +   G     +++ +l + i+ e+ +vP+ v  Gigs+s +   +++Ga+++ + t  a ak+ +a 
  AHX11464.1  99 KVMVF-APSLSVAKKMCRLGVSALIIEGREAGGHISRVSTSVLaQEILPECqDVPIFVAGGIGSSSIVKSYVDMGASGCQVGTLFACAKESIAH 191
                 56655.456889****************999988776666555345555555************************************999875 PP

>> IMPDH  IMP dehydrogenase / GMP reductase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.2   0.0   0.00085       2.2      40      74 ..       3      38 ..       1      45 [. 0.80
   2 !   13.0   0.3   1.4e-05     0.037     203     248 ..     146     191 ..     114     199 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00085
                -SSTTT-SHHHHHHHHHTTSEEEE-SS.S-HHHHHH CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxx RF
       IMPDH 40 aamdtvtesemAialareGgigvihkn.lsieeqae 74
                 am +++e+++  a+++eG+ gvi  + +++e+  +
  AHX11464.1  3 GAMSWISEHRLVSAISNEGAFGVIACSaMEPEQLET 38
                68**********************976255555444 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 1.4e-05
                 HCTCT-EEEEES---SHHHHHHHHHTT-SEEEESCCCTTBTTSSSE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       IMPDH 203 akkagvpviaDGGikysgdivkAlaaGadavmlGsllagteEspge 248
                  + ++vp+   GGi +s  +   + +Ga+ + +G l+a  +Es ++
  AHX11464.1 146 PECQDVPIFVAGGIGSSSIVKSYVDMGASGCQVGTLFACAKESIAH 191
                 45569*********99987777789*****************9875 PP

>> His_biosynth  Histidine biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0       0.7   1.8e+03      64      99 ..      66     101 ..      60     123 .. 0.66
   2 !   17.0   0.0   1.2e-06     0.003      65     165 ..     141     248 ..     127     259 .. 0.76

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.7
                   HHHHHHHH-SSEEEEESSSSSHHHHHHHHHCT-SEE CS
  His_biosynth  64 lveeiaeevfipvqvGGGIrsledveelleagadkv 99 
                   l++   ++   ++ + GGI   e ++ +l+a ++ +
    AHX11464.1  66 LISVCKQSGVTHIVLAGGIPPKEILNLILDADIKVM 101
                   455555555566777777777777777777666544 PP

  == domain 2  score: 17.0 bits;  conditional E-value: 1.2e-06
                   HHHHHHH-S.SEEEEESSSSSHHHHHHHHHCT-SEEEESHH......HHH-THHHHHHHHHHCGGGEEEEE..EEEECEEEEETTTTEEEEEEHHHH CS
  His_biosynth  65 veeiaeevf.ipvqvGGGIrsledveelleagadkviigta......avknpelikelaekfgsqkivvai..Darrgykvaikgwreetgldavel 152
                    +ei+ e++ +p+ v GGI s + v++++++ga+ + +gt        + +p++ ++++ +      vv++  D r    + ++  +++ +++++e+
    AHX11464.1 141 AQEILPECQdVPIFVAGGIGSSSIVKSYVDMGASGCQVGTLfacakeSIAHPKFKEKCIGASSH-DTVVSVqlDPRLT-VIPVRSLKNSATMEFMEF 235
                   5677777766******************************977766678888888888876555.5555550055555.788899999999999999 PP

                   HHHHHHTT-SEEE CS
  His_biosynth 153 akkleelgageil 165
                    k++ ++  + ++
    AHX11464.1 236 QKEVLHKFDSGLI 248
                   9988876665555 PP

>> LpxI_N  LpxI N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   1.9e-06    0.0048      53      93 ..      62     102 ..      57     126 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 1.9e-06
      LpxI_N  53 qlgklikaLkregvtevvmaGkvekpklldlrpDlralkll 93 
                 q+  li+  k++gvt++v+aG+++ +++l+l  D+ ++ ++
  AHX11464.1  62 QIRDLISVCKQSGVTHIVLAGGIPPKEILNLILDADIKVMV 102
                 788999*********************99888765544333 PP

>> DHO_dh  Dihydroorotate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   1.9e-06    0.0049     221     283 ..     127     189 ..      84     197 .. 0.74

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 1.9e-06
                 EEEGGGHHHHHHHHHH.HHHHTTT.S-EEEESS--SHHHHHHHHHHTECEEEESHHHHHHGTCH CS
      DHO_dh 221 lsGkalkdialkvire.lykrlkkeipiIgvGGiesgeDalekieaGAslvqvytalvfegpki 283
                  +G ++ ++++ v+ + +  + + ++pi   GGi s+  +  ++  GAs +qv+t +  +   i
  AHX11464.1 127 EAGGHISRVSTSVLAQeILPECQ-DVPIFVAGGIGSSSIVKSYVDMGASGCQVGTLFACAKESI 189
                 46788999999999761555555.9******************************987665555 PP

>> FMN_dh  FMN-dependent dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.4   0.00012      0.32     230     306 ..     110     185 ..     106     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.00012
                 HHHHHHTTESEEEE-..-GGGTSSTT---HHHCH.HHHHHHH..SS-EEEESS--SHHHHHHHHHTT-SEEEESHHHHHH CS
      FMN_dh 230 akraveaGvdgivvS..NHGGRqldgapatidvL.peiveavggrievlvDgGirrGsDvlkAlalGAdavllGRpflyg 306
                 ak+++++Gv+++++     GG+  + +  t  vL +ei  +++ +++++v gGi + s v   + +GA+++ +G  f+ +
  AHX11464.1 110 AKKMCRLGVSALIIEgrEAGGHISRVS--TS-VLaQEILPECQ-DVPIFVAGGIGSSSIVKSYVDMGASGCQVGTLFACA 185
                 778888888888885113455443322..22.33378899997.9**********9998888899*********988665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.44
# Mc/sec: 2131.45
//
Query:       AHX11465.1  [L=46]
Description: hypothetical protein NHE_0524 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       265  (0.0147805); expected 358.6 (0.02)
Passed bias filter:                      158  (0.00881254); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.25s 00:00:00.57 Elapsed: 00:00:00.39
# Mc/sec: 355.92
//
Query:       AHX11466.1  [L=309]
Description: signal recognition particle-docking protein FtsY [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-69  232.0   0.3    7.2e-69  231.4   0.3    1.3  1  SRP54            SRP54-type protein, GTPase domain
    1.9e-08   34.4   2.6    1.9e-08   34.4   2.6    2.8  3  SRP54_N          SRP54-type protein, helical bundle domain
    1.5e-06   27.7   0.0    2.5e-06   26.9   0.0    1.3  1  Zeta_toxin       Zeta toxin
    8.3e-06   25.6   0.0    1.7e-05   24.6   0.0    1.5  1  AAA_30           AAA domain
    2.7e-05   24.5   0.0    6.1e-05   23.3   0.0    1.5  1  AAA_22           AAA domain
      6e-05   22.2   0.2    0.00015   20.9   0.1    1.7  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      8e-05   22.7   0.0    0.00041   20.4   0.0    2.1  2  CbiA             CobQ/CobB/MinD/ParA nucleotide binding domai
    0.00031   20.3   0.3      0.002   17.7   0.2    2.2  2  Fer4_NifH        4Fe-4S iron sulfur cluster binding proteins,
     0.0013   18.7   3.0     0.0061   16.5   0.1    2.6  3  AAA_31           AAA domain
     0.0027   17.4   0.1       0.12   12.0   0.0    2.3  2  GT-D             Glycosyltransferase GT-D fold
     0.0033   17.3   0.4       0.67    9.8   0.1    2.5  2  NTPase_1         NTPase
     0.0066   16.0   0.2      0.035   13.7   0.2    2.1  1  AAA_25           AAA domain
     0.0093   15.9   0.1      0.017   15.0   0.1    1.4  1  NACHT            NACHT domain
  ------ inclusion threshold ------
      0.014   15.1   0.7      0.074   12.7   0.1    2.3  3  Thymidylate_kin  Thymidylate kinase
      0.016   15.1   0.0      0.043   13.7   0.0    1.7  1  APS_kinase       Adenylylsulphate kinase
      0.016   15.6   0.3      0.056   13.9   0.0    2.0  2  AAA              ATPase family associated with various cellul
      0.018   15.0   0.0      0.034   14.1   0.0    1.5  1  DUF2481          Protein of unknown function (DUF2481)
      0.018   15.2   0.0      0.033   14.3   0.0    1.5  1  AAA_33           AAA domain
      0.022   14.3   0.1      0.062   12.8   0.0    1.8  2  GTP_EFTU         Elongation factor Tu GTP binding domain
      0.023   15.1   0.1      0.067   13.6   0.0    1.8  1  AAA_17           AAA domain
      0.023   13.9   0.2      0.032   13.4   0.2    1.3  1  DUF815           Protein of unknown function (DUF815)
      0.023   14.3   1.1       0.12   12.0   1.1    2.0  1  cobW             CobW/HypB/UreG, nucleotide-binding domain
       0.03   14.8   0.0      0.062   13.8   0.0    1.6  1  ABC_tran         ABC transporter
      0.041   13.3   0.4      0.094   12.2   0.0    1.7  2  KTI12            Chromatin associated protein KTI12
       0.06   12.5   1.9       0.21   10.8   0.1    2.3  3  ArsA_ATPase      Anion-transporting ATPase
      0.062   13.1   0.0       0.13   12.2   0.0    1.5  1  Helicase_RecD    Helicase
      0.063   12.9   0.1       0.18   11.4   0.0    1.7  2  SWI2_SNF2        SWI2/SNF2 ATPase
      0.071   13.1   0.0       0.14   12.1   0.0    1.6  1  AAA_14           AAA domain
      0.073   12.8   0.1       0.35   10.6   0.1    2.1  1  ATP_bind_1       Conserved hypothetical ATP binding protein
      0.081   12.4   0.3       0.63    9.5   0.3    2.1  1  adh_short        short chain dehydrogenase
       0.73    9.3   4.1        1.3    8.5   4.1    1.4  1  DUF5394          Family of unknown function (DUF5394)


Domain annotation for each model (and alignments):
>> SRP54  SRP54-type protein, GTPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.4   0.3   1.2e-71   7.2e-69       1     195 [.     102     303 ..     102     304 .. 0.98

  Alignments for each domain:
  == domain 1  score: 231.4 bits;  conditional E-value: 1.2e-71
                 SEEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEEESTSSTTHHHHHHHHHHHTTEEEEESSTTSCHHHHHHHHHHHHHHTTSSEEEEEE--SSTTHH CS
       SRP54   1 pnvillvGlqGaGKTttlaKLaallkkegkkvllvaaDtfRaaAveQLktlaeklgvpvikkkeeadpaavakeavekakeekidvvlvDTaGrlqndk 99 
                 p+vi+++G++G GKTtt++KL+ +l++egkkv+++a+D fRaaAveQL+++ae+  + +++ ++ +++ ++a++a+eka +e++d++++DT+Grl++++
  AHX11466.1 102 PQVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACDLFRAAAVEQLRVWAERSSALFFSDETSKSASSTAYRALEKAIDERVDILIIDTSGRLHTHN 200
                 689************************************************************************************************ PP

                 HHHHHHHHHHHHH......SSSEEEEEEETTBHTHHHHHHHHHHHHSSCSEEEEESTTSSSSTTHHHHHHHHH.TS-EEEEE-SSSTTGEEE--HHHHH CS
       SRP54 100 elmeelkkikkvv......kpdevllvldattgqeavkqakaFkeavgitgviltklDgdakgGaalsiaael.klPikfigvGekiedleefdperlv 191
                 elmeelkki +v+      +p+ev+l lda+tgq+a++q+k Fke+v++tg+++tklDg++kgG ++++a+++ +l i+fig+Geki+dl+ef++ +++
  AHX11466.1 201 ELMEELKKICRVLsklipnAPHEVILALDASTGQNALSQVKIFKETVNLTGLVVTKLDGTSKGGVIVALAEKHpELGIYFIGTGEKITDLQEFSAADFA 299
                 ********************************************************************99876489*********************** PP

                 HHHH CS
       SRP54 192 srll 195
                 ++ll
  AHX11466.1 300 TSLL 303
                 *998 PP

>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   2.6   3.3e-11   1.9e-08       1      71 [.      20      88 ..      20      89 .. 0.82
   2 ?   -0.7   0.0       2.9   1.7e+03      19      34 ..     199     213 ..     188     215 .. 0.76
   3 ?   -1.9   0.0       7.2   4.2e+03      29      39 ..     297     307 ..     283     308 .. 0.74

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 3.3e-11
                HHHHHHHHHHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHCTTS.......S-HHHHHHHHH CS
     SRP54_N  1 LgkklnsalkklsgkskideedleealkeleeaLleaDVgvkvvkklienvkkkavgekk.......lkpkqqvkkiv 71
                L++++++++     k+ki++ ++ee    lee Ll+aD+g  v++k+i +v+k +v   +       + +++q+++i+
  AHX11466.1 20 LSSGIDRIFV----KEKINDSTIEE----LEELLLSADIGSTVTDKIIMEVRKIKVSDGEslrqvksV-TSKQIIRIL 88
                6788888887....599********....**********************99888854488875432.667776665 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 2.9
                 HHHHHHHHHHHHHHHH CS
     SRP54_N  19 deedleealkeleeaL 34 
                 ++e++ee lk++++ L
  AHX11466.1 199 HNELMEE-LKKICRVL 213
                 5677888.99999887 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 7.2
                 HHHHHHHHTT- CS
     SRP54_N  29 eleeaLleaDV 39 
                 +  ++Lle DV
  AHX11466.1 297 DFATSLLEVDV 307
                 67889999999 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   4.4e-09   2.5e-06      11     119 ..      97     208 ..      90     214 .. 0.84

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.4e-09
  Zeta_toxin  11 psqerPklillgGqpGAGKselaellkdelerqgnvvrldp.DdlRelhPeyeeilkadpkk..aseltqkdaselvekllqeaiengyniivegtlrs 106
                 +++ +P +i+  G  G GK++++ +l  +l+++g+ v + + D +R+   e   + +++++   +s+ t+k as  + ++l++ai+++++i++  t   
  AHX11466.1  97 VTGVTPQVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAAcDLFRAAAVEQLRVWAERSSAlfFSDETSKSASSTAYRALEKAIDERVDILIIDTSGR 195
                 55679**************************7777777765499**9997777766665544238**************************99999999 PP

  Zeta_toxin 107 pdvvkklaealkk 119
                  ++ ++l+e+lkk
  AHX11466.1 196 LHTHNELMEELKK 208
                 9999999988886 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.6   0.0     3e-08   1.7e-05      19     104 ..     103     200 ..      93     217 .. 0.69

  Alignments for each domain:
  == domain 1  score: 24.6 bits;  conditional E-value: 3e-08
      AAA_30  19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLa................eelgieastiakllkrlkgrarlepg.tllivDEagmv 100
                 +v v  G  G GKtt++++l   ++++g++v+++A     A++++                e +  ++st  + l     +++++++ ++li+D +g +
  AHX11466.1 103 QVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACDLFRAAAVEqlrvwaerssalffsdETSKSASSTAYRAL-----EKAIDERvDILIIDTSGRL 196
                 588999*****************************9866666665222555544333333323333444444444.....46788888******99998 PP

      AAA_30 101 dtkq 104
                  t++
  AHX11466.1 197 HTHN 200
                 6653 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   1.1e-07   6.1e-05       5     118 ..     102     212 ..      99     229 .. 0.71

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 1.1e-07
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevv..fvtlpsstsskdllrellralglelka..erlsseellealeqalraravielliiDE 99 
                  +++v +G  G GKTt++ +l ++l++e      +++v+   ++l      ++l+ +  r   l  ++  +   s+  ++ale+a+++r +  +liiD 
  AHX11466.1 102 PQVIVFCGINGNGKTTTIGKLSYKLQQE------GKKVMiaACDLFRAAAVEQLRVWAERSSALFFSDetSKSASSTAYRALEKAIDERVD--ILIIDT 192
                 5799*********************876......444443466666666666666665555443222222334566666777777777777..****** PP

      AAA_22 100 aqhlr.seealeeLrsllnl 118
                   +l  ++e++eeL+++  +
  AHX11466.1 193 SGRLHtHNELMEELKKICRV 212
                 ****6559999999888764 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   2.6e-07   0.00015      23      66 ..      95     139 ..      72     143 .. 0.85
   2 ?   -2.5   0.0       3.3   1.9e+03     194     194 ..     211     211 ..     174     262 .. 0.46

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-07
                 GGG-S-S.EEEEEEE-TTSSHHHHHHHHHHHHHCTT--EEEEEE- CS
        MeaB  23 lakaGra.qvvGltGvPGaGkstlvealglelrrrGkrvavlavD 66 
                 +a +G + qv+ + G+ G Gk t++ +l  +l+++Gk+v + a D
  AHX11466.1  95 FAVTGVTpQVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACD 139
                 5566654378999****************************9988 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 3.3
                 H CS
        MeaB 194 e 194
                 +
  AHX11466.1 211 R 211
                 3 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0       3.1   1.8e+03      54      72 ..      52      97 ..       7     110 .. 0.56
   2 !   20.4   0.0   7.1e-07   0.00041       9     119 ..     112     294 ..     104     300 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 3.1
                H...........................CCHCCCHHHHHHCHCHHH CS
                x...........................xxxxxxxxxxxxxxxxxx RF
        CbiA 54 p...........................dlkrllellealgkkkal 72
                                            + k+++++le + k++a+
  AHX11466.1 52 StvtdkiimevrkikvsdgeslrqvksvTSKQIIRILEPVEKSFAV 97
                0333333344444444555555555555666777777766666655 PP

  == domain 2  score: 20.4 bits;  conditional E-value: 7.1e-07
                 TSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH..................................................... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..................................................... RF
        CbiA   9 GvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep..................................................... 54 
                 G GKTt+  +L   l+++g++V    +D  + ++   e+l+   e+                                                     
  AHX11466.1 112 GNGKTTTIGKLSYKLQQEGKKVMIAACDLFRAAAV--EQLRVWAERssalffsdetsksasstayralekaidervdiliidtsgrlhthnelmeelkk 208
                 88***************************977754..3333333336888999999999************************************9999 PP

                 ....................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHCTS-EEE...EEE--CCHC CS
                 ....................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxx RF
        CbiA  55 ....................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqrygvpvlg...viprdeava 119
                                     d++ + + l+++++  +  +++ g+v+++ dg  ++   + al+e   ++g+ ++g   +i   ++++
  AHX11466.1 209 icrvlsklipnaphevilalDASTGQNALSQVKIF-KETVNLTGLVVTKLDGT-SKGGVIVALAEKHPELGIYFIGtgeKITDLQEFS 294
                 99999999999999999999888877888777764.44499**********98.6777888888877788888888777777666665 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.2   3.4e-06     0.002       3      37 ..     105     139 ..     103     149 .. 0.92
   2 ?   -0.4   0.0       1.1   6.5e+02     171     214 ..     244     287 ..     232     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 3.4e-06
   Fer4_NifH   3 iaiyGkGGiGksttsqnlsaalaemgkkvlivGCD 37 
                 i + G  G Gk+tt+  ls  l++ gkkv+i  CD
  AHX11466.1 105 IVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACD 139
                 6778999***************************9 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 1.1
   Fer4_NifH 171 sggvrlgGliinsrkvddereliekfaeelgtkvlevvPrdeiv 214
                 +++v+l+Gl++ + + +++ ++i ++ae+ +   + ++ + e++
  AHX11466.1 244 KETVNLTGLVVTKLDGTSKGGVIVALAEKHPELGIYFIGTGEKI 287
                 45799******999999999999999999877777777666665 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       8.1   4.7e+03      69      86 ..      29      48 ..       7      87 .. 0.52
   2 !   16.5   0.1   1.1e-05    0.0061      12      40 ..     112     140 ..     103     165 .. 0.85
   3 ?    1.9   0.0      0.33   1.9e+02     105     130 ..     172     197 ..     157     207 .. 0.74

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 8.1
      AAA_31 69 ikeaiiktkvenl..dlips 86
                +ke i+ +++e+l   l+ +
  AHX11466.1 29 VKEKINDSTIEELeeLLLSA 48
                33334333333333223333 PP

  == domain 2  score: 16.5 bits;  conditional E-value: 1.1e-05
      AAA_31  12 GvGKTTtsvnlaaalaklgkkvLlvDlDp 40 
                 G GKTTt  +l++ l ++gkkv++  +D 
  AHX11466.1 112 GNGKTTTIGKLSYKLQQEGKKVMIAACDL 140
                 78*********************988886 PP

  == domain 3  score: 1.9 bits;  conditional E-value: 0.33
      AAA_31 105 eilkellekvkdeYDyiiiDcpPsLg 130
                 ++++ l ++++++ D+ iiD++  L 
  AHX11466.1 172 TAYRALEKAIDERVDILIIDTSGRLH 197
                 4445555778999********98776 PP

>> GT-D  Glycosyltransferase GT-D fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.1     0.096        55      71     152 ..       6      95 ..       1     104 [. 0.64
   2 !   12.0   0.0   0.00021      0.12      79     146 ..     147     214 ..     114     228 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.096
        GT-D  71 rkllkkllkkeklygntfitrpYidykdksksekifeklkkiwkdkdi.......liveGeksrlgvgndLfd....naksierilapsknAf 152
                  + lk++++k+k+y ++ i r++++ k +    +++e+l+++  + di       +i+e +k ++  g +L +    + k+i ril p +++f
  AHX11466.1   6 VSSLKNSIEKSKEYLSSGIDRIFVKEKIN---DSTIEELEELLLSADIgstvtdkIIMEVRKIKVSDGESLRQvksvTSKQIIRILEPVEKSF 95 
                 5678899999***********99976654...4445555555554444333344467777777777777764322224456667777776666 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00021
        GT-D  79 kkeklygntfitrpYidykdksksekifeklkkiwkdk.diliveGeksrlgvgndLfdnaksierila 146
                 ++ +++ + +   ++ d + ks+s++ ++ l+k  +++ dili+   + rl   n+L+++ k+i r+l 
  AHX11466.1 147 EQLRVWAERSSALFFSDETSKSASSTAYRALEKAIDERvDILIID-TSGRLHTHNELMEELKKICRVLS 214
                 55566677777778999*************988888774677776.678*****************985 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.8   0.1    0.0012      0.67       2      30 ..     105     133 ..     104     144 .. 0.88
   2 ?    5.3   0.0     0.029        17      80     117 ..     168     205 ..     163     256 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.0012
                 EEEE--TTSSHHHHHHHHHHHH...GGGE CS
    NTPase_1   2 vfiTGppGvGKtTlvkkvlellkssgvkv 30 
                 ++  G  G GKtT + k++ +l+++g kv
  AHX11466.1 105 IVFCGINGNGKTTTIGKLSYKLQQEGKKV 133
                 5667999*******************998 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.029
                 HHHHHHHHHHHHHH.HHH-EEEE---STTGGG-HHHHHH CS
    NTPase_1  80 sfeelalealrkal.seadviviDEiGkmElkskkfkea 117
                 s+++ a +al+ka+ ++ d+++iD  G++    + + e+
  AHX11466.1 168 SASSTAYRALEKAIdERVDILIIDTSGRLHTHNELM-EE 205
                 67788999*****98999*********997654433.33 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.2     6e-05     0.035      36     159 ..     105     201 ..      74     216 .. 0.66

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 6e-05
      AAA_25  36 allaGapgtGKttlaldlalava.tGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgealrddarllvldlagveslpLfakdrggtlltadvdal 133
                 ++++G  g GKtt    l++++  +Gk           kV++ +++  ++   + lr + e     + l++ d            ++  ++   +++al
  AHX11466.1 105 IVFCGINGNGKTTTIGKLSYKLQqEGK-----------KVMIAACDLFRAAAVEQLRVWAERS---SALFFSD------------ETSKSASSTAYRAL 177
                 555555555555555555555552222...........5555555555544445555444443...5555554............23334467789*** PP

      AAA_25 134 eaaieevegvrlvviDplsralggde 159
                 e+ai+e  +v+ ++iD+  r++ ++e
  AHX11466.1 178 EKAIDE--RVDILIIDTSGRLHTHNE 201
                 ******..4************99987 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1     3e-05     0.017       2     129 ..     104     232 ..     103     257 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3e-05
                 CEEEEC-TTTCHHHHHHHHHHHHCTS-SCCCC-SEEEEEETTTTTTS-....-HCHHHCCCCTS--SSS-CCHHHHCCSCCCE.EEEEE-STT-SS-TC CS
       NACHT   2 lvilqGeaGsGKTtLlqklalawaegklpqgafklvFflslrelsrsgna.rsladllfsqlpepaapvsevwavllelperl.LlilDglDelvtdlg 98 
                 +++  G +G GKTt + kl  +++++  +  +     +++ +++++      +   l fs+   ++a ++ ++a+  ++ er+  li+D   +l+t+++
  AHX11466.1 104 VIVFCGINGNGKTTTIGKLSYKLQQEGKKV-MIAACDLFRAAAVEQLRVWaERSSALFFSDETSKSASSTAYRALEKAIDERVdILIIDTSGRLHTHNE 201
                 68889********************99555.444444444444444433356788899999999999999999999999999956***********999 PP

                 H..........HHHHHCTTTTT--EEEEEEEC CS
       NACHT  99 q.kekqpvrtlLselirkkllpeasllltvrp 129
                   +e +++ ++Ls+li+   + e+ l l +++
  AHX11466.1 202 LmEELKKICRVLSKLIPN-APHEVILALDAST 232
                 9888899999******98.5666655555444 PP

>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       6.7   3.9e+03      49      76 ..      30      61 ..      14      67 .. 0.63
   2 ?   12.7   0.1   0.00013     0.074       3      29 ..     109     135 ..     107     139 .. 0.92
   3 ?   -0.7   0.0       1.6   9.5e+02      90     107 ..     169     186 ..     146     208 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 6.7
                     CS---HHH....HHHHHHHHHHHTTHHHHHHH CS
  Thymidylate_kin 49 eeeleeqt....eallfaadriehleekikpa 76
                     +e+++++t    e ll++ad   ++++ki+ +
       AHX11466.1 30 KEKINDSTieelEELLLSADIGSTVTDKIIME 61
                     45555555555566777777767777777655 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 0.00013
                      ESTTSSHHHHHHHHHHHHHHTTE.EEE CS
  Thymidylate_kin   3 GlDGaGKttqaellkerlkeegikvvl 29 
                      G++G GKtt + +l  +l++eg+kv++
       AHX11466.1 109 GINGNGKTTTIGKLSYKLQQEGKKVMI 135
                      9*********************99765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 1.6
                      HHHHHHHHTTTTTTCHHH CS
  Thymidylate_kin  90 fSslaYqgakegvdldlv 107
                      +Ss aY ++++++d ++ 
       AHX11466.1 169 ASSTAYRALEKAIDERVD 186
                      577888888877777665 PP

>> APS_kinase  Adenylylsulphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   7.4e-05     0.043       2      49 ..     102     149 ..     101     158 .. 0.88

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 7.4e-05
                 -EEEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHTTTTTTT- CS
  APS_kinase   2 gvvvwltGlsgsGKstianalekkLvekgisvylLdGdnvRhgLnkdL 49 
                 + v+ + G+ g GK+t   +l+ kL+++g++v++   d  R    ++L
  AHX11466.1 102 PQVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACDLFRAAAVEQL 149
                 5799*****************************999998887666555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.1       4.3   2.5e+03      66     105 ..      61      97 ..      28     104 .. 0.66
   2 ?   13.9   0.0   9.7e-05     0.056       2      80 ..     106     204 ..     105     239 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 4.3
                 TGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEE CS
         AAA  66 EidalaksrsgseseeeervvnqLlteldgvkkkeskviv 105
                 E+ ++  s+ +s +++++ + +q+++ l+ v+k+   + v
  AHX11466.1  61 EVRKIKVSDGESLRQVKSVTSKQIIRILEPVEKS---FAV 97 
                 4444444444455566666667777777777663...444 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 9.7e-05
                 EEESSTTSSHHHHHHHHHHHHT..HEEEEEETTTCSSS.................STTHHHHHHHHHHHHHHHTS...TSEEEEEETGGGHHHHHTTCC CS
         AAA   2 llyGppGtGKTllakavakelg..vefleisgsellsk.................yvgesekkirelfkeakeka...kpsilfiDEidalaksrsgse 78 
                 +++G  G GKT+++  +  +l+   + + i + +l+                   +  e++k+ + +  +a eka   +  il+iD   +l++++  + 
  AHX11466.1 106 VFCGINGNGKTTTIGKLSYKLQqeGKKVMIAACDLFRAaaveqlrvwaerssalfFSDETSKSASSTAYRALEKAideRVDILIIDTSGRLHTHN--EL 202
                 799*****************973344566777777744577888889999999999999999999999999999999555******999999888..32 PP

                 CH CS
         AAA  79 se 80 
                  e
  AHX11466.1 203 ME 204
                 33 PP

>> DUF2481  Protein of unknown function (DUF2481)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0     6e-05     0.034      42      77 ..      10      45 ..       4      77 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6e-05
     DUF2481 42 entiekqktywtktfdrivkkkkwaeitirefadlr 77
                +n+iek k y +  +dri  k k  + ti e+ +l 
  AHX11466.1 10 KNSIEKSKEYLSSGIDRIFVKEKINDSTIEELEELL 45
                699****************************98874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.8e-05     0.033       1      69 [.     104     183 ..     104     225 .. 0.65

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.8e-05
      AAA_33   1 lvllvGlpGsGKstlaerl...lkklg.avllssdtlrrrlfg......tdqqskt.....dytrvldrlyqilnelarkalsa 69 
                 +++++G +G GK+t + +l   l+++g  v ++  +l+r+ ++       ++ s        ++ +++ +y+ l++ ++    +
  AHX11466.1 104 VIVFCGINGNGKTTTIGKLsykLQQEGkKVMIAACDLFRAAAVeqlrvwAERSSALffsdeTSKSASSTAYRALEKAID----E 183
                 89*****************555555559777877777776665344444333322232222333344445555544443....3 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       6.9     4e+03      17      32 ..      52      67 ..      49      82 .. 0.77
   2 ?   12.8   0.0   0.00011     0.062       6      80 ..     105     195 ..     102     212 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 6.9
                HHHHHHHHHHTTSSCH CS
    GTP_EFTU 17 tTLtdrLlyktgaisk 32
                +T+td+++++  +i+ 
  AHX11466.1 52 STVTDKIIMEVRKIKV 67
                8999999998888775 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 0.00011
                 EEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE.................TTCSSEEEEEEEESSS CS
    GTP_EFTU   6 igiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle.................ketkkylinliDtPGH 80 
                 i+++g    GKtT++++L yk+++  kk + a        ++ E+ r     s+a  ++                 +  ++  i +iDt G 
  AHX11466.1 105 IVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAA-CDLFRAAAVEQLRVWAERSSALFFSdetsksasstayralekAIDERVDILIIDTSGR 195
                 567777889***************999888875.4466777888888888888888887777777888887877633677888999999985 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.0   0.00012     0.067       2     100 ..     109     213 ..     108     235 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 0.00012
                 E-TTSSHHHHHHHHHHHH....TEEEEEHHHHHHHHHHTTTS..HSSHHHHCTSHHHHHHHHHHHHHHHHHHHH..HSSEEEEEE-SEEEETTEEEESS CS
      AAA_17   2 GgPGsGKgtqceklveky....gfthlsaGdllreeakrggl..akardemrklpleekkelqkeaaekiaeea..kkkgvlvdghprikeqagfldgl 92 
                 G+ G GK+t + kl  k+    +  ++ a dl+r+ a ++    a +r+     + e  k    +a ++++++   + + +++d+  r+ + ++++++l
  AHX11466.1 109 GINGNGKTTTIGKLSYKLqqegKKVMIAACDLFRAAAVEQLRvwA-ERSSALFFSDETSKSASSTAYRALEKAIdeRVDILIIDTSGRLHTHNELMEEL 206
                 999***********9777666577889*******99998843223.33333333333333333333333333221135679*******99999999988 PP

                 HHHHHHHH CS
      AAA_17  93 pkevleel 100
                 +k +++ l
  AHX11466.1 207 KK-ICRVL 213
                 86.55544 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.2   5.5e-05     0.032      46     164 ..      94     208 ..      54     247 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 5.5e-05
      DUF815  46 qf.leglpannvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklve.llrerperfilfvDDLsFeeeeeeyksLksvLeGsleakpen 142
                  f ++g + + +++ G  G GK +++  l  ++++eg ++  ++  dl    ++ +  + +++   + f D  s  ++ ++y++L  +++  +     +
  AHX11466.1  94 SFaVTGVTPQVIVFCGINGNGKTTTIGKLSYKLQQEGKKV-MIAACDLFRAAAVEQlRVWAERSSALFFSDETSKSASSTAYRALEKAIDERV-----D 186
                 34257888888999**********************9775.577778877766644135577788999****************999888555.....6 PP

      DUF815 143 vliyaTsNrRhLlpeklsdnee 164
                 +li  Ts r h  +e +++ ++
  AHX11466.1 187 ILIIDTSGRLHTHNELMEELKK 208
                 8999999999999998888665 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   1.1    0.0002      0.12       2     151 ..     104     258 ..     103     273 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0002
                 EEEEEESTTCCHHHHHHHHH..CT--SS-EEEEESS-SS.CHCCCCCCHCCCT.EEEETTTTECCHCTT-HHHHHHHHHHHHTT-SEEEEEECT.TTTH CS
        cobW   2 vtvltGflGsGKTtLlnhll..enraglklavivNefge.vsiDaellretgveivelenGciCctlredllkelealeereerldviliEttG.laeP 96 
                 v+v++G  G GKTt + +l    +++g+k+ +   ++    ++++ ++ ++ ++++ +++     + ++ + ++le+  +++  +d+++i t+G l + 
  AHX11466.1 104 VIVFCGINGNGKTTTIGKLSykLQQEGKKVMIAACDLFRaAAVEQLRVWAERSSALFFSDET-SKSASSTAYRALEKAIDER--VDILIIDTSGrLHTH 199
                 7899***************9988889999999999976648899999988877766666532.3333556666666666665..9*********65555 PP

                 HHHHTT....SHHHHH..CCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HH CS
        cobW  97 apvaft....eeelks..dltldavvavvDaknleaeeekieekaedqlaaadllvlnKtD 151
                 ++++ +     + l++  +     v+  +Da+   ++  ++ + +++ ++ + l v++K D
  AHX11466.1 200 NELMEElkkiCRVLSKliPNAPHEVILALDASTG-QNALSQVKIFKETVNLTGL-VVTKLD 258
                 5553333233222222222334556666676544.5556666666666666654.445666 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   0.00011     0.062      12      80 ..     103     180 ..      94     251 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.00011
                 SEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.....B-HHHCCHCEEEE-SS--S-TTSBHHHH....H CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxx....x RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.....qeleslrkeigvlpqepqlfpeltvren....e 80 
                 +++++ G nG GK+t +  l+ +l+++  ++ +   dl +     q + +++++++ ++ +++ ++ ++ + +    +
  AHX11466.1 103 QVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACDLFRaaaveQLRVWAERSSALFFSDETSKSASSTAYRalekA 180
                 68999********************99999988888888778884445555555555566655554444333235551 PP

>> KTI12  Chromatin associated protein KTI12
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.1       5.6   3.2e+03      41      64 ..      61      84 ..      36      98 .. 0.48
   2 ?   12.2   0.0   0.00016     0.094       4      41 ..     105     142 ..     103     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 5.6
                H.TTSSS--GGGHHHHHHHHHHHH CS
       KTI12 41 giekdsykdsakekalRsslrsav 64
                +++k ++ d ++ ++++s + +++
  AHX11466.1 61 EVRKIKVSDGESLRQVKSVTSKQI 84
                333333333333333333333333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 0.00016
                 EEEE--TTSSHHHHHHHHHHHHHHTT--EEEE-THHHH CS
       KTI12   4 vvltGlPssGKstrakeLakaleeekrsvvviddeslg 41 
                 +v++G+   GK+t   +L+ +l++e+++v++   + ++
  AHX11466.1 105 IVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACDLFR 142
                 9*****************************99887776 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.1       4.8   2.8e+03     172     205 ..      16      49 ..       3      84 .. 0.51
   2 ?   10.8   0.1   0.00036      0.21       2      38 ..     103     139 ..     102     141 .. 0.94
   3 ?    0.6   0.0      0.43   2.5e+02     114     195 ..     175     248 ..     167     274 .. 0.52

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 4.8
                  CSHCHHHHHHHHHHHHHHHHHHHHHHHHHHTSTT CS
  ArsA_ATPase 172 llglggvsieealeeleetkeeikkveeiltdpe 205
                    +  ++ i++ + + + +  +i+++ee l   +
   AHX11466.1  16 SKEYLSSGIDRIFVKEKINDSTIEELEELLLSAD 49 
                  4444444444444444444444555544444433 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00036
                  EEEEEEESTTSSHHHHHHHHHHHHHHTTS-EEEEE-S CS
  ArsA_ATPase   2 kvilvgGKGGVGKttvsaatavklsekgkkvllistD 38 
                  +vi++ G  G GKtt    +++kl ++gkkv++ + D
   AHX11466.1 103 QVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACD 139
                  589*****************************98776 PP

  == domain 3  score: 0.6 bits;  conditional E-value: 0.43
                  HHHHHHHHCSSSSEEEEESBSCCHTCGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSHCHHHHHHHHHHHHHHHHHHHH CS
  ArsA_ATPase 114 eellkyvkeeeydvvvlDtaPTGhtlrllslpevleklleklvklkeklsplakqlvkllglggvsieealeeleetkeeik 195
                   +l k ++e   d++++Dt+   h      + + l + l+k++++  kl p a +   +l l +++ ++al++++ +ke+++
   AHX11466.1 175 RALEKAIDE-RVDILIIDTSGRLH------THNELMEELKKICRVLSKLIPNAPHE-VILALDASTGQNALSQVKIFKETVN 248
                  555555554.45777777754333......33333344444444444444433222.2334444444467777777776666 PP

>> Helicase_RecD  Helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00022      0.13       6     102 ..     111     196 ..     106     214 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00022
  Helicase_RecD   6 RGRGKSaalGlalaaliaegksnilvtapskenvktlfeflakglealglkeeekkkkaekaelrvrkqrieyiapdellklkeqadllvvDEAAa 101
                     G GK++++G++  +l +egk +++++a +   ++         +e+l++  e++++   + e++++ ++  y a +++++++   d+l++D +  
     AHX11466.1 111 NGNGKTTTIGKLSYKLQQEGK-KVMIAACDLFRAAA--------VEQLRVWAERSSALFFSDETSKSASSTAYRALEKAIDER--VDILIIDTSGR 195
                    599**************9998.99999976433222........222222223333333344456667888999999999865..69999986655 PP

  Helicase_RecD 102 i 102
                    +
     AHX11466.1 196 L 196
                    5 PP

>> SWI2_SNF2  SWI2/SNF2 ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       3.6   2.1e+03      82     190 ..      37      62 ..      17     103 .. 0.53
   2 ?   11.4   0.0   0.00031      0.18      79     147 ..     115     183 ..     100     192 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 3.6
   SWI2_SNF2  82 srkeLkellekesekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpnaafigFTGTPilkkdkktkevFgeyidkYtike 180
                 + +eL+ell                                                                                    + +i  
  AHX11466.1  37 TIEELEELL-----------------------------------------------------------------------------------LSADIGS 52 
                 334444444...................................................................................2222223 PP

   SWI2_SNF2 181 aveDgavvpi 190
                  v+D+ ++++
  AHX11466.1  53 TVTDKIIMEV 62 
                 3333322222 PP

  == domain 2  score: 11.4 bits;  conditional E-value: 0.00031
   SWI2_SNF2  79 qaesrkeLkellekesekiifttiqKfeeeekeklevlsereniivlvDEaHRsqygelakklrkalpn 147
                 ++++  +L  +l++e +k++++  + f++++ e+l+v  er+  +++ DE  +s +++  + l+ka+ +
  AHX11466.1 115 KTTTIGKLSYKLQQEGKKVMIAACDLFRAAAVEQLRVWAERSSALFFSDETSKSASSTAYRALEKAIDE 183
                 67788899****999************9887788************************99999999876 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00025      0.14       3     109 ..     103     202 ..     101     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00025
      AAA_14   3 kilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqev..pewekalkslvdegknldvivt. 98 
                 +++v  G+   GKTt + +l ++l  + ++++  ++d  r ++ ++     +++ e+       ++f DE +++  +++++al + +de+  +d+++  
  AHX11466.1 103 QVIVFCGINGNGKTTTIGKLSYKLQQEGKKVMIAACDLFRAAAVEQL----RVWAER----SSALFFSDETSKSasSTAYRALEKAIDER--VDILIId 191
                 688999**************999997788888888998777665544....788886....4568999**99875578999999999988..5555440 PP

      AAA_14  99 GSnskllskei 109
                  S  ++  +e+
  AHX11466.1 192 TSGRLHTHNEL 202
                 34444444455 PP

>> ATP_bind_1  Conserved hypothetical ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.1   0.00061      0.35       2     131 ..     108     229 ..     107     257 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00061
  ATP_bind_1   2 vGpaGsGKttfvgalseilelrgrsvavvNLDPAaeelpYeaavdirelitledvmedlglgpngalvvaleflresldwldeelekeeddyllfDtPG 100
                 +G  G GKtt +g+ls  l+++g++v +     A++ +  +a    r + +  ++    +  ++ a  +a+  l++ +   de++     d l++Dt G
  AHX11466.1 108 CGINGNGKTTTIGKLSYKLQQEGKKVMI----AACDLFRAAAVEQLRVWAERSSALFFSDETSKSASSTAYRALEKAI---DERV-----DILIIDTSG 194
                 7999********************9988....5777777666666666666666666677777778888888777777...7777.....888888888 PP

  ATP_bind_1 101 Qielft.hseslakiveeLes...efalvvvyLvD 131
                  + + + ++e+l+ki++ L++   + +  v+  +D
  AHX11466.1 195 RLHTHNeLMEELKKICRVLSKlipNAPHEVILALD 229
                 77665325677777777777765455555555555 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.3    0.0011      0.63      10      88 ..     117     198 ..     110     273 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.0011
                 SHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHH.SSESEEEE---S...S CS
   adh_short  10 sGIGraiakelakeGakvvvvdrseekleevakelkee.gakalaiqvDvtdreevealvekavkkl.gkldvLvnNAGi...t 88 
                   IG+ ++++l +eG kv++++    ++ +++++l+   +++   +  D t++++ ++++++ +k + +++d+L+  ++    t
  AHX11466.1 117 TTIGK-LSYKLQQEGKKVMIAACDLFRA-AAVEQLRVWaERSSALFFSDETSKSASSTAYRALEKAIdERVDILIIDTSGrlhT 198
                 56664.6888999999999988888877.6666666655666666777888888888888988888888999997665552332 PP

>> DUF5394  Family of unknown function (DUF5394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.5   4.1    0.0023       1.3      18      88 ..       8      75 ..       3      95 .. 0.77

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0023
     DUF5394 18 ltkeslitssdnLsyevkeiyeklkkNeefeaElealistlelnlDvsklqtklillikklLkskksskkk 88
                  k+s++ s + Ls  +++i+ k k N+   +Ele+l+ + ++    s +  k+i  ++k+  s+ +s ++
  AHX11466.1  8 SLKNSIEKSKEYLSSGIDRIFVKEKINDSTIEELEELLLSADI--G-STVTDKIIMEVRKIKVSDGESLRQ 75
                679***********************************44333..3.567889999999987666555444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       922  (0.0514251); expected 358.6 (0.02)
Passed bias filter:                      664  (0.037035); expected 358.6 (0.02)
Passed Vit filter:                        98  (0.005466); expected 17.9 (0.001)
Passed Fwd filter:                        31  (0.00172904); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              31  [number of targets reported over threshold]
# CPU time: 0.60u 0.28s 00:00:00.88 Elapsed: 00:00:00.43
# Mc/sec: 2179.02
//
Query:       AHX11467.1  [L=216]
Description: ftsJ-like methyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-50  171.1   0.0      3e-50  170.8   0.0    1.1  1  FtsJ             FtsJ-like methyltransferase
    7.7e-05   20.9   0.0    0.00065   17.9   0.0    1.9  2  Methyltrans_Mon  Virus-capping methyltransferase
    0.00033   20.4   0.0    0.00078   19.1   0.0    1.6  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
     0.0016   17.6   0.0      0.074   12.2   0.0    2.1  2  Fibrillarin      Fibrillarin
      0.002   17.9   0.1      0.013   15.3   0.1    2.0  1  Methyltransf_31  Methyltransferase domain
     0.0038   17.1   0.0      0.011   15.6   0.0    1.8  1  Methyltransf_23  Methyltransferase domain
  ------ inclusion threshold ------
      0.053   13.3   0.0      0.077   12.7   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
       0.12   13.0   0.1        1.2    9.8   0.1    2.6  2  Methyltransf_25  Methyltransferase domain


Domain annotation for each model (and alignments):
>> FtsJ  FtsJ-like methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  170.8   0.0   1.3e-53     3e-50       1     177 []      36     211 ..      36     211 .. 0.96

  Alignments for each domain:
  == domain 1  score: 170.8 bits;  conditional E-value: 1.3e-53
                 CCCCHHHHHHHHHHHHT-S-TT-EEEECT-TTSHHHHHHCCT.T.-SEEEEEESSSSHHHTTEEEECS-CCCSSHHHHHCHCHHHSSEEEEEE--S-SS CS
        FtsJ   1 yrsRsayKLleidekfklfkpgktvvDlgaaPGgwsqvllqrlgakgkvvavDlqpmaplpgvttiqgditdpetiekikealserkvdlvvsDgapdv 99 
                 yrsR++yKLlei+ekf ++++g  v++lg+aPGgw+qv++q l  +g++va Dl +m+p++gv++++ di  ++    + e+l+ +k+dlv+sD+ap+ 
  AHX11467.1  36 YRSRASYKLLEINEKFTVIQKGSSVLELGSAPGGWTQVISQILDGTGRIVAADLTEMDPISGVEFLKLDIEAQASV--LDEYLNSSKFDLVLSDLAPNA 132
                 9******************************************778************************777554..5788899************** PP

                 -CHHHHHHHHHCCCCHHHHCCHCCCCECCCEEEECCCHCCCHH.HHHHHHHCCEEEEEEEE-SS--CCG-EEEEEEEEC CS
        FtsJ 100 sgvhdldeylqsqLllaalelalkllkpggtfvlkifrgeete.allkqlkkfFekvsvvkPkssrsesseeflvcrgf 177
                 sg +++d++ +++L +  l  a k lk +g++v+ki++g+e+e +l++ lkk+F+kv+++kP+ssr++s+e++lv rg+
  AHX11467.1 133 SGSSATDSIASIRLSRVVLDYARKYLKGDGSVVMKILKGSEDEyELIRLLKKKFKKVEYFKPNSSRKASREIYLVMRGR 211
                 *******************************************9*******************************9985 PP

>> Methyltrans_Mon  Virus-capping methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.037        83     291     350 ..      15      76 ..       4      96 .. 0.77
   2 !   17.9   0.0   2.9e-07   0.00065     433     508 ..     137     210 ..     114     214 .. 0.79

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.037
                      -----------HHHHHH--S-SS-THHHHHHHHHHHT----S..EEEEES-SSSHHHHHHHH CS
  Methyltrans_Mon 291 klkelskrfqnPlisGlRvvqlatGahYklrsilndldityr..dflvvGDGsGGitralLr 350
                        + l +++++P +   R   +   a Ykl  i ++  ++ +   +l  G   GG t+++ +
       AHX11467.1  15 SNRWLYRHINDPFVRKARSDNYRSRASYKLLEINEKFTVIQKgsSVLELGSAPGGWTQVISQ 76 
                      4566778999999999999999***************99986225677888889*9999865 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 2.9e-07
                      ---HHHHHHHHHHHHHHGGGTS-SS-EEEEEE-HHHHHHSS-HHHH---SEEEEEEEETTS-TT---EEEEEE--- CS
  Methyltrans_Mon 433 vtdiesiekielnvkdfvlsildeqgvLifktYgtylveenkkaidiLgrlfksvtlvqtelsssktseiYllfkk 508
                       td+ ++ ++   v d++ + l+++g +++k       e++++ i++L + fk+v+ ++ + s   + eiYl++++
       AHX11467.1 137 ATDSIASIRLSRVVLDYARKYLKGDGSVVMKILKG--SEDEYELIRLLKKKFKKVEYFKPNSSRKASREIYLVMRG 210
                      45666666778899*****************9876..59*********************************9986 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   3.5e-07   0.00078       7     105 ..      55     148 ..      52     166 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 3.5e-07
                      -TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CTCCHHHHCC..EEEEEEE.E-.-CCGGGTTT- CS
  Methyltr_RsmB-F   7 qeeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDarkidkvlggelfDriLlD.aP.Csgtgvirrd 98 
                      q++  +l+l +aPGg T  i+++++ +g++vA d  +      ++ ++ L +     +ea a+  d++l  ++fD +L D aP  sg  + +  
       AHX11467.1  55 QKGSSVLELGSAPGGWTQVISQILDGTGRIVAADLTEMD--P-ISGVEFLKLD----IEAQASVLDEYLNSSKFDLVLSDlAPnASGSSATDSI 141
                      567789****************************98753..3.2344555555....6788888899999999999998855534666666666 PP

                      TCHHHH- CS
  Methyltr_RsmB-F  99 pdvklrr 105
                       +++l+r
       AHX11467.1 142 ASIRLSR 148
                      6666666 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   3.3e-05     0.074      51     104 ..      36      90 ..      31     111 .. 0.78
   2 ?    3.5   0.0     0.015        33     148     179 ..     141     172 ..     136     192 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.3e-05
                  TTSHHHHHHHTT-S-.-S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESS CS
  Fibrillarin  51 frsKlaaailkglke.lpikkgskvLYlGaasGttvsHvsDivgeegvvyavefs 104
                  +rs+ +  +l+  ++ + i+kgs+vL lG+a G     +s i++ +g++ a + +
   AHX11467.1  36 YRSRASYKLLEINEKfTVIQKGSSVLELGSAPGGWTQVISQILDGTGRIVAADLT 90 
                  5666555555544441579*****************************9997654 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.015
                  SSSTTHHHHHHHHHHHHEEEEEEEEEEEEHHH CS
  Fibrillarin 148 vaqpdqarilaknaklflkeggyllisikars 179
                  +a  +  r++ + a+ +lk +g +++ i   s
   AHX11467.1 141 IASIRLSRVVLDYARKYLKGDGSVVMKILKGS 172
                  566677899*****************996555 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.1   5.8e-06     0.013      49     127 ..      91     187 ..      54     209 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 5.8e-06
  Methyltransf_31  49 qklgldnveFeqgdiee.leklled.....ekfDlilsn...........evlnaladpdkileeiervlkpggilliedpr...llaelpakv 122
                      +   ++ veF + die+ ++  + d     +kfDl+ls+           + ++ +  +  +l  + ++lk +g +++   +    ++el++ +
       AHX11467.1  91 EMDPISGVEFLKLDIEAqAS--VLDeylnsSKFDLVLSDlapnasgssatDSIASIRLSRVVLDYARKYLKGDGSVVMKILKgseDEYELIRLL 182
                      45567899*******99555..33447788*********5555555544444499999999999*************99888655444555555 PP

  Methyltransf_31 123 eeesk 127
                      +++ k
       AHX11467.1 183 KKKFK 187
                      55555 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   4.9e-06     0.011      17      87 ..      51     125 ..      32     204 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 4.9e-06
  Methyltransf_23  17 lpklraggrvLdiGcGtGillevlren..gf.svtgvDlspea.veiaekakkaqkdqfdeqeaaepqgkfdlIv 87 
                      ++  ++g++vL++G + G +++v+++   g+  +++ Dl +++ ++ +e  k  +  q+   ++  ++ kfdl+ 
       AHX11467.1  51 FTVIQKGSSVLELGSAPGGWTQVISQIldGTgRIVAADLTEMDpISGVEFLKLDIEAQASVLDEYLNSSKFDLVL 125
                      33489999****************996556677777777543212333333333333333333334555666654 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   3.4e-05     0.077      69     105 ..      52      88 ..      25     112 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 3.4e-05
                 TT--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEE CS
        PCMT  69 lelkkgarvLevGsGsGyltavlarlvgekgrvvsie 105
                   ++kg++vLe+Gs  G  t v+++++  +gr+v+ +
  AHX11467.1  52 TVIQKGSSVLELGSAPGGWTQVISQILDGTGRIVAAD 88 
                 3499*****************************9876 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   0.00055       1.2       1      70 [.      60     126 ..      60     162 .. 0.77
   2 ?   -0.1   0.0      0.72   1.6e+03      54      54 ..     172     172 ..     127     210 .. 0.52

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00055
                      EEEET-TTSHHHHHHHCTS.TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl.gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvs 70 
                      vL+lG  +G +t+ +++ l g +++++ D++e       e +   +l++e +   ++++ +++++fDlv+s
       AHX11467.1  60 VLELGSAPGGWTQVISQILdGTGRIVAADLTEMDPISGVEFL---KLDIEAQASVLDEY-LNSSKFDLVLS 126
                      8***************999889********987666555555...34555444433333.45567777776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.72
                      B CS
  Methyltransf_25  54 d 54 
                      +
       AHX11467.1 172 S 172
                      1 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       392  (0.021864); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.43
# Mc/sec: 1519.21
//
Query:       AHX11468.1  [L=194]
Description: thymidylate kinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.8e-41  140.2   0.0    7.3e-41  139.9   0.0    1.1  1  Thymidylate_kin  Thymidylate kinase
    4.2e-07   30.3   0.0    5.1e-07   30.1   0.0    1.2  1  AAA_28           AAA domain
    0.00095   19.4   0.0     0.0019   18.5   0.0    1.5  2  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.011   15.6   0.1        5.1    6.9   0.1    2.8  2  dNK              Deoxynucleoside kinase
      0.052   14.1   0.0       0.82   10.2   0.0    2.2  2  AAA_18           AAA domain
       0.06   12.8   0.0       0.13   11.8   0.0    1.5  1  PPK2             Polyphosphate kinase 2 (PPK2)
      0.073   12.0   0.0       0.51    9.3   0.0    1.9  2  MeaB             Methylmalonyl Co-A mutase-associated GTPase 
      0.084   13.0   0.0       0.27   11.4   0.0    1.9  2  AAA_33           AAA domain


Domain annotation for each model (and alignments):
>> Thymidylate_kin  Thymidylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   3.2e-44   7.3e-41       1     185 []       5     183 ..       5     183 .. 0.90

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 3.2e-44
                      EEESTTSSHHHHHHHHHHHHHHTTE.EEEESSSTTSHHHHHHHHHHHTCS---HHHHHHHHHHHHHHTTHHHHHHHHHTT-EEEEES-HHHHHH CS
  Thymidylate_kin   1 iEGlDGaGKttqaellkerlkeegikvvltrepggteiGekirelllkeeeleeqteallfaadriehleekikpalkqgktvivdRylfSsla 94 
                      +EG+DGaGK+tq++ l + l+++g   + trepggt+ +ek+r+++l+  +l++++ +ll+ a+rieh  ++i pal++gk+vi+dR+++S+la
       AHX11468.1   5 FEGVDGAGKSTQMRRLEDFLRNRGFPCICTREPGGTPSAEKFRSVILHDSTLDPLSRLLLIIAARIEHCNKVIFPALERGKVVICDRFIYSTLA 98 
                      8***********************99******************************************************************** PP

                      HHHTTTTTTCHHHHHHGGGTTSE-SEEEEEESSHHHHHTSCCTTSS.TTTSHHHHHHHHHHHHHHHHHHHHTTSTEEEEETTS-HHHHHHHH CS
  Thymidylate_kin  95 YqgakegvdldlvlslnedvllkPdltflldvdpevalkRlakrde.ldeeeeeqldflrkvrerylelakederiliidasksieevheeI 185
                      Yqg++eg+d +++l l++ ++       ++dvd  + l+  +kr+  +d++e +++d++++v  +y e+a++ ++i+ i     i+++h+eI
       AHX11468.1  99 YQGYGEGIDPQMILDLHKMLG------CIIDVDLTILLAPPRKRRVgRDNFERMSEDYFNRVLNGYEEIARQYDNIHLI-NRMGINQTHSEI 183
                      *******************87......555555555555555555556779********************88888888.455577777776 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.1   0.0   2.3e-10   5.1e-07       2     117 ..       3     133 ..       2     174 .. 0.71

  Alignments for each domain:
  == domain 1  score: 30.1 bits;  conditional E-value: 2.3e-10
      AAA_28   2 ivitGgestGKTtlleaLa....argypvv..pEaareileeklakgedalpwv.edllafaervleeqleeeaaa.....aankvlfcDrglldtlaY 88 
                 iv+ G  ++GK+t +++L+    +rg+p++  +E++ +   ek ++    l+++  d+l    +++++++e + +      + +kv++cDr +  tlaY
  AHX11468.1   3 IVFEGVDGAGKSTQMRRLEdflrNRGFPCIctREPGGTPSAEKFRSVI--LHDStLDPLSRLLLIIAARIEHCNKVifpalERGKVVICDRFIYSTLAY 99 
                 99*****************888777***9999********99987765..55544677777788888888888666677779***************** PP

      AAA_28  89 arayggeaeaelea....aarekrydl.vfllpp 117
                   + +g  ++ + +      +    dl ++l pp
  AHX11468.1 100 QGYGEGIDPQMILDlhkmLGCIIDVDLtILLAPP 133
                 9998886344333322222223345664444444 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.0   8.6e-07    0.0019       7      70 ..       2      60 ..       1      91 [. 0.80
   2 ?   -2.7   0.0         3   6.7e+03     107     112 ..     156     161 ..     141     185 .. 0.50

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 8.6e-07
      AAA_22  7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka 70
                ++v  G  G+GK+t +rrl + l ++      + +++    p++t s +++++ +l++ +l+  +
  AHX11468.1  2 FIVFEGVDGAGKSTQMRRLEDFLRNR------GFPCICTREPGGTpSAEKFRSVILHDSTLDPLS 60
                688899*****************776......99999999999999**********999876665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3
      AAA_22 107 ealeeL 112
                 + +ee+
  AHX11468.1 156 NGYEEI 161
                 222333 PP

>> dNK  Deoxynucleoside kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0099        22       1      22 [.       3      24 ..       3      36 .. 0.87
   2 ?    6.9   0.1    0.0023       5.1     123     174 ..     124     169 ..      62     193 .. 0.60

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0099
                EEEEESTTSSHHHHHHHHHCCS CS
         dNK  1 ivveGnIgaGKstlvklLskkl 22
                iv eG  gaGKst + +L++ l
  AHX11468.1  3 IVFEGVDGAGKSTQMRRLEDFL 24
                789************9999755 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0023
                 -SEEEEEE--HHHHHHHHHHCTTCCCTTS-HHHHHHHHHHHHHHHTSGGCS- CS
         dNK 123 pdlliYLkasletclerikkRgreeekkieldYlekLhekyeewlkklnevp 174
                 +dl i L  +      r ++ gr + + +++dY++++ + yee  ++++++ 
  AHX11468.1 124 VDLTILLAPP------RKRRVGRDNFERMSEDYFNRVLNGYEEIARQYDNIH 169
                 4444444332......222334444448999999999999999999999874 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   0.00037      0.82       1      30 [.       3      33 ..       3     101 .. 0.69
   2 ?    2.0   0.0      0.12   2.8e+02      45      76 ..     139     167 ..     109     189 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00037
      AAA_18  1 IlltGtpGvGKttlakeLskrl.gfgvnlrd 30
                I+  G+ G+GK+t  ++L++ l + g+ +++
  AHX11468.1  3 IVFEGVDGAGKSTQMRRLEDFLrNRGFPCIC 33
                8899**************7766333544444 PP

  == domain 2  score: 2.0 bits;  conditional E-value: 0.12
      AAA_18  45 aldeskrldedkldklldaleenssaleegkn 76 
                   d+++r+ ed+ +++l++ ee+++   + +n
  AHX11468.1 139 GRDNFERMSEDYFNRVLNGYEEIAR---QYDN 167
                 4578899999999999999999986...3333 PP

>> PPK2  Polyphosphate kinase 2 (PPK2)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   5.6e-05      0.13      33      69 ..       2      38 ..       1      50 [. 0.84

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 5.6e-05
                EEEEEESTTS-HHHHHHHHHTTS-GGG-EEEE--S-- CS
        PPK2 33 vvifegrDaAGKgGaikrvtealnprvarvvalkaPt 69
                 ++feg D+AGK   ++r+ + l  r+      ++P 
  AHX11468.1  2 FIVFEGVDGAGKSTQMRRLEDFLRNRGFPCICTREPG 38
                68*********************99998877777775 PP

>> MeaB  Methylmalonyl Co-A mutase-associated GTPase MeaB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00023      0.51      34      57 ..       5      28 ..       1      37 [. 0.91
   2 ?    0.4   0.0      0.12   2.6e+02     121     147 ..     164     191 ..     160     193 .. 0.84

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00023
                EEE-TTSSHHHHHHHHHHHHHCTT CS
        MeaB 34 ltGvPGaGkstlvealglelrrrG 57
                + Gv GaGkst + +l   lr+rG
  AHX11468.1  5 FEGVDGAGKSTQMRRLEDFLRNRG 28
                679********************9 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.12
                 T-SEE.EEEEESSTTHHHHHHTT-SEEE CS
        MeaB 121 GfDvv.lietvGvGqsevdvaevvdtfv 147
                  +D + li+ +G+ q   ++++vv+  +
  AHX11468.1 164 QYDNIhLINRMGINQTHSEIVKVVQQKI 191
                 5787768999************998766 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.27       2      20 ..       3      24 ..       2      90 .. 0.88
   2 ?   -0.7   0.0      0.65   1.5e+03      24      54 ..     142     173 ..     133     192 .. 0.54

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
      AAA_33  2 vllvGlpGsGKstlaerl...l 20
                +++ G+ G+GKst  +rl   l
  AHX11468.1  3 IVFEGVDGAGKSTQMRRLedfL 24
                799**************94444 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.65
      AAA_33  24 gavllssdtlrrrlfg.tdqqsktdytrvldr 54 
                  +++ s+d++ r l g ++  ++ d +++ +r
  AHX11468.1 142 NFERMSEDYFNRVLNGyEEIARQYDNIHLINR 173
                 46666777666666654444445555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (194 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1503.97
//
Query:       AHX11469.1  [L=418]
Description: dihydrolipoyllysine-residue succinyltransferase, E2 component [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.6e-81  272.0   0.0    4.8e-81  271.6   0.0    1.2  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    1.5e-20   72.8   1.2    4.1e-20   71.4   1.2    1.8  1  Biotin_lipoyl    Biotin-requiring enzyme
    7.4e-08   32.6   0.1    1.4e-07   31.7   0.1    1.5  1  E3_binding       e3 binding domain
    9.5e-06   25.4   1.0     0.0042   16.9   0.0    3.4  3  Biotin_lipoyl_2  Biotin-lipoyl like
     0.0029   16.8   0.0      0.035   13.3   0.0    2.2  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
  ------ inclusion threshold ------
      0.059   13.0   0.3         32    4.3   0.0    3.3  3  PYNP_C           Pyrimidine nucleoside phosphorylase C-termin


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  271.6   0.0   1.6e-84   4.8e-81       4     233 .]     189     416 ..     186     416 .. 0.98

  Alignments for each domain:
  == domain 1  score: 271.6 bits;  conditional E-value: 1.6e-84
                   XXXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG-EE.EESEEEE--SS--EE CS
  2-oxoacid_dh   4 eervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelnasvdeeekeivvkkhvniG 100
                   e+ vp+s++r+ ia rl+es+++++++t+++evd+ +++++rk++k+ ++k + +kl +++f++kav+l l+efPe+na++ +++  iv+k+++niG
    AHX11469.1 189 ERIVPMSKLRQKIAYRLKESQNTAAMLTTFNEVDMGNVMQIRKQYKDTFEKIHGVKLGFMSFFVKAVILGLEEFPEINAEIRDTD--IVYKDYYNIG 283
                   6789*********************************************97777***************************9999..********** PP

                   EE--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---------------TT-SEEEEE---.B--TTSTT-HT---E CS
  2-oxoacid_dh 101 vAvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGmlGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkv 197
                   vAv +++GL+vPvi+na+++s++ i+k++ e+ +kar+gk++p+d++ g+ftisN G +G+ ++tPiinppq+ Ilg+++iker+vv +g++ vr++
    AHX11469.1 284 VAVGSKNGLVVPVIRNAQDLSFAGIEKAILEYGKKARDGKIQPDDMQRGSFTISNGGIYGSLMSTPIINPPQSGILGMHAIKERAVVINGQILVRPM 380
                   ************************************************************************************************* PP

                   EEEEEEEETTT--HHHHHHHHHHHHHTT-HHXXXXX CS
  2-oxoacid_dh 198 mtlslsaDHRvidGaeaarFlntlkkllenpeelll 233
                   m+l ls+DHR++dG+ea++Fl ++k+++enpe+lll
    AHX11469.1 381 MYLALSYDHRIVDGKEAVSFLVRVKEYVENPERLLL 416
                   *********************************985 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.4   1.2   1.4e-23   4.1e-20       1      73 []       2      75 ..       2      75 .. 0.98

  Alignments for each domain:
  == domain 1  score: 71.4 bits;  conditional E-value: 1.4e-23
                   TEEEESSSEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEEE CS
  Biotin_lipoyl  1 keiksPmiGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllaki 73
                   ke+ +P +Ges++e+ v+++ ++ Gd V+a++ l e+e++K++mei++p++G++ ei+v +Gd+v+ +d+la+i
     AHX11469.1  2 KEVVVPRMGESIAEAsVAKIVKNIGDPVQADELLFELETDKASMEIPSPATGILREIKVMVGDNVSPDDILATI 75
                   5899********************************************************************97 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.7   0.1   4.7e-11   1.4e-07       5      36 .]     128     159 ..     127     159 .. 0.98

  Alignments for each domain:
  == domain 1  score: 31.7 bits;  conditional E-value: 4.7e-11
                 HHHHHHHHHCT--TTTS---CTTTBE-HHHHC CS
  E3_binding   5 PaaRklAkelGidLsdvkGtGpgGRItkeDVl 36 
                 Paa+ l + + ++ sd+ +tG+gGRItkeDVl
  AHX11469.1 128 PAAKVLMANNALSASDIIATGKGGRITKEDVL 159
                 9******************************7 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.019        58      21      36 ..      26      41 ..      15      44 .. 0.86
   2 !   16.9   0.0   1.4e-06    0.0042       4      37 ..      46      79 ..      43      85 .. 0.90
   3 ?    1.3   0.1       0.1     3e+02       5      31 ..     351     377 ..     350     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.019
  Biotin_lipoyl_2 21 GqrVkaGdvLaelDsr 36
                     G+ V+a  +L+el+++
       AHX11469.1 26 GDPVQADELLFELETD 41
                     9************986 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 1.4e-06
  Biotin_lipoyl_2  4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsra 37
                     +I +p  G + ++ V  G+ V   d+La++D+  
       AHX11469.1 46 EIPSPATGILREIKVMVGDNVSPDDILATIDDNV 79
                     6779999************************865 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.1
  Biotin_lipoyl_2   5 IaapvsGrVaqlnVkdGqrVkaGdvLa 31 
                      I +p+sG +   ++k+  +V  G++L+
       AHX11469.1 351 INPPQSGILGMHAIKERAVVINGQILV 377
                      899*****9999999999*******97 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0     0.068     2e+02      27      53 ..      15      40 ..      11      43 .. 0.82
   2 !   13.3   0.0   1.2e-05     0.035     107     141 ..      43      77 ..      39      81 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.068
                XXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 27 eGwveklyvnatgdkVkkGqpLaelys 53
                e+ v k+  n +gd+V++++ L+el+ 
  AHX11469.1 15 EASVAKIVKN-IGDPVQADELLFELET 40
                5667777777.************9975 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.2e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23 107 ktvtvkapisGvVteknvreGqyvqpgdtlftiad 141
                  ++++ +p++G+  e +v+ G+ v+p+d l+ti d
  AHX11469.1  43 ASMEIPSPATGILREIKVMVGDNVSPDDILATIDD 77 
                 67999****************************98 PP

>> PYNP_C  Pyrimidine nucleoside phosphorylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.017        52      36      53 ..      21      38 ..      19      46 .. 0.85
   2 ?    4.3   0.0     0.011        32      35      53 ..      57      75 ..      41      86 .. 0.82
   3 ?    0.7   0.0      0.14   4.3e+02      18      29 ..     149     160 ..     136     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.017
                ES--TT-EEBTTSEEEEE CS
      PYNP_C 36 lhkklGdkVkkGeplati 53
                + k +Gd V+++e l+ +
  AHX11469.1 21 IVKNIGDPVQADELLFEL 38
                5799***********987 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
                EES--TT-EEBTTSEEEEE CS
      PYNP_C 35 elhkklGdkVkkGeplati 53
                e+++ +Gd+V+ +++lati
  AHX11469.1 57 EIKVMVGDNVSPDDILATI 75
                345568************9 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.14
                 TTSBSSTTS--- CS
      PYNP_C  18 GAGRakkeDpid 29 
                 ++GR +keD ++
  AHX11469.1 149 KGGRITKEDVLN 160
                 699******875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       586  (0.0326845); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2941.90
//
Query:       AHX11470.1  [L=439]
Description: modulator of DNA gyrase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-38  132.0   0.2    5.1e-38  131.5   0.2    1.2  1  PmbA_TldD  Putative modulator of DNA gyrase


Domain annotation for each model (and alignments):
>> PmbA_TldD  Putative modulator of DNA gyrase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.5   0.2   2.8e-42   5.1e-38       1     278 [.      20     306 ..      20     307 .. 0.84

  Alignments for each domain:
  == domain 1  score: 131.5 bits;  conditional E-value: 2.8e-42
                 EEEEEEEEEEEEEEEEETTEEEEEEEEEEEEEEEEEEETTEEEEEE...ESSHHHHHHHHHHHHHHCCS---TT-................GGS-HHHH CS
   PmbA_TldD   1 eaevrleesestsvrfengevetnsssedsglgvrvikggrlgfastldtsdealeeaveraveiaklapedpea................eevsaeek 83 
                 +a+v +++ e+  v+ +n  ve +++s+ sgl++r+ik++r+ ++++++++  +l+++  ra+e+ ++ ped++                 +    +  
  AHX11470.1  20 QADVLVSKIENIIVNTRNLVVEKLEESSFSGLTFRLIKDKRSTSVQCNTSA--NLKQMFSRALESLEHVPEDQYIslpehshhvsntgnisD----NIG 112
                 69******************************************9999888..9********************99*999988886633332....222 PP

                 H.....HHHHHHHHH.CHCSTTEEEEEEEEEE......EEE.EEEEEEETTSEEEEEEEEEEEEEEEEEE..STCSETEEEEEEEE...SSHHHS..SS CS
   PmbA_TldD  84 i.....elleelekalrsadpkienskgarisgvsaslsaskeeklianSeGldveqtrtrvslslsviad.dggsgdgmgggsgy...edleeedlee 173
                 i     el+ ++e+ ++s  +          +   ++ +a++ ek++an++G++++  ++ +s  ++v+a+ +g   + + +g++y     l + ++ e
  AHX11470.1 113 IadilkELAIKTEQSAYSEGK--------LKTTEKIEFEAKTIEKILANTNGFFGTFDTQIFSGAVTVVAEaEG---N-LNSGFSYlssNILTDLNPNE 199
                 232223456666666566655........233345678899999**************************5352...2.23355555665556688899 PP

                 HHHHHHHHHHCTTT-B---SEEEEEEE-HHHHHHHHHGHHHHHTBHHHHHTT--TTTT-TTSB-S-TT--EEEETT...-.....-SB-TTSBB--.-E CS
   PmbA_TldD 174 iaeeaaekalasleakplppgkypVvlspeavgsllheavghaleadavlegrSflkdklGekvaselltivddpt...sgglgsypfDdEGvptq.rt 268
                 +++eaa++a + l+++++ + k +V+++ +++ ++l+  +g  l++ +v++  +flkd++ + +++  ++i+ +p+     ++ ++ fDdEG  t  + 
  AHX11470.1 200 LGKEAAKRAFEGLKPRKIQTCKREVIFDFRCASNFLS-NFGDFLSGASVARSATFLKDQMEQSILPRSISIFNNPLgeqC-RIKTSDFDDEGNTTInKL 296
                 ************************************9.8*****************999*****************8651.6677**********9455 PP

                 EEEETTEE-- CS
   PmbA_TldD 269 vlIenGvLkn 278
                 +l+enGvLk 
  AHX11470.1 297 PLVENGVLKR 306
                 6*******96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      363  (0.0202465); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 3318.11
//
Query:       AHX11471.1  [L=185]
Description: ahpC/TSA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    8.2e-40  135.8   0.0      1e-39  135.5   0.0    1.1  1  SCO1-SenC  SCO1/SenC
    0.00051   19.9   0.0    0.00074   19.4   0.0    1.2  1  AhpC-TSA   AhpC/TSA family
  ------ inclusion threshold ------
      0.012   15.7   1.2      0.034   14.2   0.1    2.3  3  RinB       Transcriptional activator RinB


Domain annotation for each model (and alignments):
>> SCO1-SenC  SCO1/SenC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.5   0.0   1.7e-43     1e-39       1     133 [.      38     163 ..      38     164 .. 0.96

  Alignments for each domain:
  == domain 1  score: 135.5 bits;  conditional E-value: 1.7e-43
   SCO1-SenC   1 ggpFelvdqdgeavteedlegkpslvffgFthCpdvCpttlanmaevldalgeeaekvqplfiTvDPerDtpevlkeyleafdpriigltGskeeiaka 99 
                 gg F+l+dq+g++vte+ l+gk+s+v fgF++Cp vCp++l+ +a+ lda      k+q++fiT+DP+rDt+e+l e+ ++f++ri  ltG++e i+k+
  AHX11471.1  38 GGTFDLTDQEGHQVTEQILKGKYSIVLFGFSRCPHVCPVQLSILAKSLDAS----PKLQAIFITLDPKRDTVERLDEFSKSFHERILMLTGTEEMIKKV 132
                 589***************************************999988764....668***************************************** PP

   SCO1-SenC 100 akefrvyvekvedeesdytvdHsssvyLvdpdgr 133
                 ++ ++vyve +ed+e    ++Hs+++yL++pdg+
  AHX11471.1 133 VNDYKVYVEANEDPER---FNHSTIMYLIGPDGN 163
                 ****************...*************97 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.4   0.0   1.2e-07   0.00074       7     105 ..      40     143 ..      36     166 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.4 bits;  conditional E-value: 1.2e-07
                 --EEESTTCEEEECHHHTTSEEEEEEESTST-C.CHHHHHHHHHHCHHHCCCTTEEEEEEES..SSCHHHHHHHHH-H....SSEEEE-TTSHHHHHTT CS
    AhpC-TSA   7 dfelknadgetvslsdykgkpvvlffypkdwcp.vCttelpalaklyeefkergvevigvsv..dspeshkkfiekes...lnfpllsDeegkvakayg 99 
                  f l++++g +v+ + +kgk+ +++f  +  cp vC+ +l+ lak +++  ++ +  i + +  d++e++ +f +      l ++      +kv+++y+
  AHX11471.1  40 TFDLTDQEGHQVTEQILKGKYSIVLFGFS-RCPhVCPVQLSILAKSLDASPKLQAIFITLDPkrDTVERLDEFSKSFHeriLMLTGTEEMIKKVVNDYK 137
                 599**********9999****99999877.67748****************888877777766677778888877766455666666667889999999 PP

                 -EETTT CS
    AhpC-TSA 100 vlkeek 105
                 v+ e++
  AHX11471.1 138 VYVEAN 143
                 998873 PP

>> RinB  Transcriptional activator RinB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.1       0.6   3.6e+03       4      15 ..       8      19 ..       7      23 .. 0.86
   2 ?   -3.3   0.0       1.7     1e+04      17      24 ..      49      56 ..      48      56 .. 0.79
   3 ?   14.2   0.1   5.7e-06     0.034       5      34 ..     118     147 ..     117     148 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.6
        RinB  4 lkLlfllaaleL 15
                lkL++ +++ eL
  AHX11471.1  8 LKLMIVVSIIEL 19
                799999999988 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 1.7
        RinB 17 KkvvEsll 24
                 +v+E++l
  AHX11471.1 49 HQVTEQIL 56
                679**986 PP

  == domain 3  score: 14.2 bits;  conditional E-value: 5.7e-06
        RinB   5 kLlfllaaleLvKkvvEsllvyleANDdVE 34 
                 ++l+l    e+ Kkvv    vy+eAN d E
  AHX11471.1 118 RILMLTGTEEMIKKVVNDYKVYVEANEDPE 147
                 78999999******************9966 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       634  (0.0353617); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1553.61
//
Query:       AHX11472.1  [L=474]
Description: replicative DNA helicase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.8e-98  327.1   0.6    6.8e-98  327.1   0.6    1.9  2  DnaB_C      DnaB-like helicase C terminal domain
    2.3e-27   95.1   1.0      6e-27   93.7   1.0    1.8  1  DnaB        DnaB-like helicase N terminal domain
    1.7e-11   44.1   0.0      3e-11   43.3   0.0    1.3  1  AAA_25      AAA domain
    4.8e-07   29.3   0.9      1e-06   28.3   0.1    2.0  2  ATPase      KaiC
    0.00015   21.1   0.1     0.0016   17.8   0.0    2.1  2  Rad51       Rad51
     0.0018   17.8   0.0     0.0035   16.8   0.0    1.4  1  RecA        recA bacterial DNA recombination protein
  ------ inclusion threshold ------
      0.031   14.7   2.4        2.5    8.5   0.1    2.9  3  AAA         ATPase family associated with various cellular ac
      0.053   12.6   0.0        2.5    7.1   0.0    2.2  2  FemAB_like  Peptidogalycan biosysnthesis/recognition
      0.084   12.6   0.1       0.47   10.2   0.0    2.1  2  IstB_IS21   IstB-like ATP binding protein
       0.22   11.6   0.9        7.8    6.6   0.9    3.0  1  MMR_HSR1    50S ribosome-binding GTPase
        3.6    7.9   5.3         30    5.0   0.9    3.1  3  DUF2175     Uncharacterized protein conserved in archaea (DUF


Domain annotation for each model (and alignments):
>> DnaB_C  DnaB-like helicase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.3      0.29   4.8e+02      63     111 ..     119     168 ..      78     182 .. 0.61
   2 !  327.1   0.6  4.2e-101   6.8e-98       2     255 .]     187     462 ..     186     462 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.29
                 HHHHHHHHHHTXXHHHHHHTTSXHHHHHHHHHH.HHHHHHSEEEEEEXSS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx RF
      DnaB_C  63 lvqRllsseaeidskklrtgklkeedwekltea.ieelseaklfiddtpa 111
                 l+qR++s+ ++ +sk+  + +++e + +  + a  +e+  + l+i ++ +
  AHX11472.1 119 LAQRMISTASDEESKSSTSEQIEEVEHSLYQLAsSGEFDPTCLHISKSIE 168
                 56777777777666666666666544333332213445555555555555 PP

  == domain 2  score: 327.1 bits;  conditional E-value: 4.2e-101
                 BXSSTHHHHHHCTSBXTTXEEEEEEXTTSSHHHHHHHHHHHHHH...CSTSEEEEEESSSXHHHHHHHHHHHHHTXXHHHHHHT.TSXHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
      DnaB_C   2 lstgfkdLDkltsGlqkgdliiiAarpsmGktalalniaenaav...keklpvavfslemsaeqlvqRllsseaeidskklrtg.klkeedweklteai 96 
                 +stgf+d+D++++Glq++dl+iiA+rpsmGkt+la+++  +++    k+ ++ ++fs+emsa+q+++R+ls ++++d+ ++rtg k++ee ++k+ e+ 
  AHX11472.1 187 ISTGFRDIDNFLGGLQNSDLVIIAGRPSMGKTSLAISMSLRVTCaleKQGMSACFFSMEMSADQIASRMLSVHSGVDAFSIRTGkKFSEEGLQKVIESS 285
                 79************************************96654322266678********************************668899********* PP

                 HHHHHSEEEEEEXSSXCHHHHHHHHHHHHHHTTEEEEEEEEGGGTBTSCSSS.CCCHHHHHHHHHHHHHHHHCTSXEEEEEEXSGGGCCSCCHSXXHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C  97 eelseaklfiddtpaltvseirskarrlkkekglgliviDyLqlmegseeke.nreqevseisrsLkalakelnvpvialsqLsravesredkrPvlsD 194
                 +els+++lfiddtpa+++s +r+k+rrl+++++lg i++DyLql++gs+ +e nr+qevsei+++Lk++akelnvpv+alsqLsr ve+r+dkrP+lsD
  AHX11472.1 286 KELSRLPLFIDDTPAISISALRTKLRRLHRKTKLGAIFVDYLQLIKGSKGSEfNRVQEVSEITKGLKSIAKELNVPVVALSQLSRLVEQRDDKRPQLSD 384
                 **********************************************9855556********************************************** PP

                 HCCTTSCCCCXSEEEEEEECCHH.......HHHHC.............HHCEEEEEEEEETTSXXEEEEEEEETTTTEEEX CS
                 xxxxxxxxxxxxxxxxxxxxxxx.......xxxxx.............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      DnaB_C 195 LreSgsieqdADvvlflyrdeyy.......kedse.............ekgkaeiiiaKhRnGptgtvklafekeytrFen 255
                 LreSgsieqdADvv+f++r+ yy       +   e              k+kaeiiiaK+RnGp+gt  l f++++t F++
  AHX11472.1 385 LRESGSIEQDADVVMFVFREAYYmmrkqpsN---EdenyenwqfkmdeVKNKAEIIIAKQRNGPVGTALLFFDQSTTVFDD 462
                 ***********************55443321...1445667777777677789************************9985 PP

>> DnaB  DnaB-like helicase N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   1.0   3.7e-30     6e-27       2     103 .]       8     109 ..       7     109 .. 0.98

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 3.7e-30
                 HHHHHHHHHHHHHHHHHSTTHHHHHHCC--GGGSSSHHHHHHHHHHHHHHHTTTS-SHHHHHHHSCSSS-GGHGT.HHHHHHHHHC-S-CCCHHHHHHH CS
        DnaB   2 ppqsieaEqavLgalLldpeaidevadilkpedFyepahrliFeailelyekgepiDlvtvkeelekkgkledvggaaylaelvaavpsaanieeyaei 100
                 +p+++eaEq +LgalL++++a++++ + ++p +Fy pahr+iFe+il+l +k+  +++vt+k++l++++++++vgg++y+ +++++++   +i + a++
  AHX11472.1   8 LPNNVEAEQLILGALLTNNDAYEDIEELISPSSFYVPAHRRIFEIILHLRSKELVANAVTLKNYLNSSNEIKNVGGQEYILSIIEKASIIIDIMSLARV 106
                 79************************************************************************************************9 PP

                 HHH CS
        DnaB 101 vke 103
                 +++
  AHX11472.1 107 IQD 109
                 986 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.3   0.0   1.8e-14     3e-11      20     190 ..     192     369 ..     175     372 .. 0.84

  Alignments for each domain:
  == domain 1  score: 43.3 bits;  conditional E-value: 1.8e-14
      AAA_25  20 pprrwlvkgllpagelallaGapgtGKttlaldlalavatGkpwlgpvapeqgkVlyvsaEdsedelrrRlravgeal...........rddarllvld 107
                 +  +  ++gl    +l+++aG+p  GKt la++++l v+         + + +   + s E+s+d+++ R+  v+  +           ++ +   v+ 
  AHX11472.1 192 RDIDNFLGGL-QNSDLVIIAGRPSMGKTSLAISMSLRVTCAL------EKQGMSACFFSMEMSADQIASRMLSVHSGVdafsirtgkkfSEEGLQKVIE 283
                 5555566666.6899************************544......34889**********************999999****99976666668888 PP

      AAA_25 108 lagv.eslpLfakdrggtlltadvdaleaaieevegvrlvviDplsralgg...densnsdvgalvealeriarrtgaavllvhHvg 190
                   ++  +lpLf +d+    + a   +l++  ++  +++ + +D l+ + g    + n+  +v+++ + l++ia+++++ v+++ +++
  AHX11472.1 284 SSKElSRLPLFIDDTPAISISALRTKLRRLHRK-TKLGAIFVDYLQLIKGSkgsEFNRVQEVSEITKGLKSIAKELNVPVVALSQLS 369
                 89999*******888887799988888888888.56***********999998444555667*******************998765 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       0.8   1.3e+03      80     110 ..     113     146 ..      83     175 .. 0.55
   2 !   28.3   0.1   6.4e-10     1e-06       1     165 [.     187     369 ..     187     410 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.8
      ATPase  80 egklaiidasesaeesaee...kdkedleeliee 110
                 + +++++   + ++ s ee   +++e++ee+ ++
  AHX11472.1 113 KRQIILLAQRMISTASDEEsksSTSEQIEEVEHS 146
                 3333333332222222222222444444444444 PP

  == domain 2  score: 28.3 bits;  conditional E-value: 6.4e-10
      ATPase   1 vktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlik...gaekygepgvfvtveepaedlrenak..slGwdlekleeegklaiidasesaee 94 
                 ++tg   +D++l gG+ +   v i+G p  GKt +a    ++    +ek g    f ++e +a ++  ++   + G+d   ++   k+    + +  e 
  AHX11472.1 187 ISTGFRDIDNFL-GGLQNSDLVIIAGRPSMGKTSLAISMSLRvtcALEKQGMSACFFSMEMSADQIASRMLsvHSGVDAFSIRTGKKFSEEGLQKVIES 284
                 57999******9.********************998776544222457889999***************984456888766655555554444444443 PP

      ATPase  95 saee..........kdkedleelieelaeaikeikakrvviDsitglayeekeavaR.....eilrqlvrvlkklgvTailvseks 165
                  ++e          +   ++++l ++l++  +++k  ++ +D ++ ++ ++ ++  R     ei + l+++ k+l+v  +  s+ s
  AHX11472.1 285 -SKElsrlplfiddTPAISISALRTKLRRLHRKTKLGAIFVDYLQLIKGSKGSEFNRvqevsEITKGLKSIAKELNVPVVALSQLS 369
                 .33346667779889999*************************9999665555554521110333444444466666666666655 PP

>> Rad51  Rad51
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   9.8e-07    0.0016      13      76 ..     181     241 ..     146     273 .. 0.83
   2 ?    0.8   0.0      0.14   2.3e+02     157     189 ..     339     371 ..     329     384 .. 0.85

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 9.8e-07
                 HHSS-EE--S-HHHHHHHTSSEESSSEEEEEESTTSSHHHHHHHHHHHTTS-TTTS--SSEEEE CS
       Rad51  13 rsellqlttGskklDelLgGGietgsiteifGefrsGktqlchtlcvtvqlplelgGgegkavy 76 
                 +    +++tG +++D+ L GG++   +  i G    Gkt l+ ++++ v   le++G+    ++
  AHX11472.1 181 KAPFQNISTGFRDIDNFL-GGLQNSDLVIIAGRPSMGKTSLAISMSLRVTCALEKQGMSA--CF 241
                 444556**********99.89********************9999999999999999964..33 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                 HHHHHHHHHHHHHHHHHHHH--EEEEEEE---- CS
       Rad51 157 kRqqklgkllrtLrkladefevavvitnqvvaq 189
                 +R q+++++ + L+ +a+e +v vv   q +  
  AHX11472.1 339 NRVQEVSEITKGLKSIAKELNVPVVALSQLSRL 371
                 688999999***************998887655 PP

>> RecA  recA bacterial DNA recombination protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.2e-06    0.0035      28     104 ..     181     259 ..     165     279 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.2e-06
                 -----EE--S-HHHHHHTSSSSEETTSEEEEEESTTSSHHHHH....HHHHHHHHHTT--EEEEESS----HHHHHHTT-- CS
        RecA  28 klkvetissGslaldialGiGGlpkGriieiyGpessGkttla....lhaiaeaqkkggvaafidaehaldpkyakklGvd 104
                 k   + is+G   +d+ lG  Gl +  ++ i G  s Gkt+la    l++ +  +k+g  a+f   e + d   ++ l v+
  AHX11472.1 181 KAPFQNISTGFRDIDNFLG--GLQNSDLVIIAGRPSMGKTSLAismsLRVTCALEKQGMSACFFSMEMSADQIASRMLSVH 259
                 5667899*****9999987..*******************87622226789999******************999999875 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       3.6   5.9e+03      41      81 ..      92     139 ..      61     163 .. 0.55
   2 ?    8.5   0.1    0.0015       2.5       1      71 [.     207     302 ..     207     321 .. 0.72
   3 ?    5.1   0.0     0.018        29      15      99 ..     351     433 ..     348     457 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 3.6
                 HHHHHHHHHHHHHHHTS....TS.EEEEEETGGGHHHHH..TTCCCHH CS
         AAA  41 esekkirelfkeakeka....kp.silfiDEidalaksr..sgsesee 81 
                 e+++ i ++++ a+  +    k   il+   + + a+++  ++s+se+
  AHX11472.1  92 EKASIIIDIMSLARVIQdlylKRqIILLAQRMISTASDEesKSSTSEQ 139
                 455555555555555555555331333334444444444432333333 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0015
                 EEEESSTTSSHHHHHHHHHHHH.........THE..EEEEETTTCSSS...............STTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHH CS
         AAA   1 vllyGppGtGKTllakavakel.........gve..fleisgsellsk...............yvgesekkirelfkeakekakpsilfiDEidala 71 
                 v++ G p +GKT+la ++   +         ++    +e+s+ ++ s                  + se+ +++++++ ke +    lfiD+  a+ 
  AHX11472.1 207 VIIAGRPSMGKTSLAISMSLRVtcalekqgmSACffSMEMSADQIASRmlsvhsgvdafsirtGKKFSEEGLQKVIESSKELS-RLPLFIDDTPAIS 302
                 6789***********99988853333332222222236777777775578888888888887766668888888888888887.7889999877765 PP

  == domain 3  score: 5.1 bits;  conditional E-value: 0.018
                 HHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTS..TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA  15 akavakelgvefleisgsellskyvgesekkirelfkeakeka..kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                  k++akel+v+++ +s  + l +   ++  ++++l ++ + ++  + + +++ E++ +++++     ++e++  +    ++d+vk+k
  AHX11472.1 351 LKSIAKELNVPVVALSQLSRLVEQRDDKRPQLSDLRESGSIEQdaDVVMFVFREAYYMMRKQ----PSNEDENYENWQFKMDEVKNK 433
                 589***********998777768888888888888888554445244666689999999999....344444445555566666664 PP

>> FemAB_like  Peptidogalycan biosysnthesis/recognition
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.1   0.0    0.0015       2.5     118     182 ..     136     203 ..     119     249 .. 0.76
   2 ?    3.3   0.0     0.022        36     212     274 ..     392     457 ..     372     460 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0015
  FemAB_like 118 aeallealkelaeeeklss...lhvlfveeeeaelleeagllerldvqfhwknegyasfddfLaalss 182
                 +++ +e++++ + +   s+     +l+++++  +++e+a+++ r++  f+   +g+++ d+fL  l++
  AHX11472.1 136 TSEQIEEVEHSLYQLASSGefdPTCLHISKSIETAIERAKITFRTKAPFQNISTGFRDIDNFLGGLQN 203
                 333344444433333222211146899999999******************************99976 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.022
  FemAB_like 212 eeewdafyefYqetyskkwgspyLtreffella...erlaekvllvlaeregeliagalnligedt 274
                 e++ d ++ +++e y  +  +p    e +e+++   +++++k  +++a++ + ++++al + +++t
  AHX11472.1 392 EQDADVVMFVFREAYYMMRKQPSNEDENYENWQfkmDEVKNKAEIIIAKQRNGPVGTALLFFDQST 457
                 5666777777777777777777777777766651115567899*****************999765 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.74   1.2e+03     130     152 ..     103     125 ..      99     130 .. 0.85
   2 ?   10.2   0.0   0.00029      0.47      45      85 ..     202     246 ..     166     259 .. 0.81

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.74
   IstB_IS21 130 lfeviekryerrsiiitsnlpfa 152
                 l +vi++ y +r ii+ ++  ++
  AHX11472.1 103 LARVIQDLYLKRQIILLAQRMIS 125
                 779************99997665 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00029
   IstB_IS21  45 ekkenivllGpsGvGKshlaialgve...avr.aglsvlfvrved 85 
                 ++++ +++ G + +GK+ lai+++ +   a + +g+s  f+++e 
  AHX11472.1 202 QNSDLVIIAGRPSMGKTSLAISMSLRvtcALEkQGMSACFFSMEM 246
                 677889****************99762223334888988888865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   0.9    0.0048       7.8       2      20 ..     207     225 ..     206     441 .. 0.87

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0048
                 EEEEESTTSSHHHHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinalt 20 
                 v+i+Grp  GK++L  +++
  AHX11472.1 207 VIIAGRPSMGKTSLAISMS 225
                 7899*********976665 PP

>> DUF2175  Uncharacterized protein conserved in archaea (DUF2175)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.7   2.7e+03      61      83 ..      64      87 ..      49     104 .. 0.58
   2 ?    5.0   0.9     0.019        30      56      90 ..     114     148 ..      90     153 .. 0.77
   3 ?    3.3   0.1     0.063     1e+02      43      76 ..     346     379 ..     334     398 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.7
     DUF2175 61 klkelerv.aedeevkkvleqkrk 83
                ++  l++  ++++e+k+v  q ++
  AHX11472.1 64 NAVTLKNYlNSSNEIKNVGGQEYI 87
                333333333677788877666554 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.019
     DUF2175  56 neeivklkelervaedeevkkvleqkrkelEkaaa 90 
                 +++i  ++++ + a+dee+k  ++++  e+E+   
  AHX11472.1 114 RQIILLAQRMISTASDEESKSSTSEQIEEVEHSLY 148
                 3556678899999*****************98765 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.063
     DUF2175  43 edaaaLleleevlneeivklkelervaedeevkk 76 
                 e ++ L++++++ln  +v l +l+r++e+++ k+
  AHX11472.1 346 EITKGLKSIAKELNVPVVALSQLSRLVEQRDDKR 379
                 56677999*****************977665554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       838  (0.0467399); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        62  (0.00345808); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.57u 0.22s 00:00:00.78 Elapsed: 00:00:00.37
# Mc/sec: 3833.96
//
Query:       AHX11473.1  [L=37]
Description: hypothetical protein NHE_0533 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       150  (0.00836633); expected 358.6 (0.02)
Passed bias filter:                      137  (0.00764125); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 297.40
//
Query:       AHX11474.1  [L=81]
Description: caudovirus prohead protease family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    5.3e-14   52.7   0.0    5.7e-14   52.6   0.0    1.0  1  Peptidase_S78  Caudovirus prohead serine protease


Domain annotation for each model (and alignments):
>> Peptidase_S78  Caudovirus prohead serine protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.6   0.0   3.2e-18   5.7e-14      74     146 ..       3      73 ..       1      80 [. 0.94

  Alignments for each domain:
  == domain 1  score: 52.6 bits;  conditional E-value: 3.2e-18
  Peptidase_S78  74 eDekGlrfelkl.pdttvardlyellkrgdldglSfgFrvvedeweereekvvvrtikkveLlEvSvVtvPAyd 146
                    e e+Gl+ + ++ ++ +++ ++y+ll+ g l+glS+g+ +++  +++++     r+i++v+L+EvS Vt+PA++
     AHX11474.1   3 ETERGLYLKGQIiTEVKQGYEAYKLLQSGVLNGLSIGYILKDYRLDKATG---TRIITAVKLIEVSLVTFPANE 73 
                    6799*************************************999999988...9******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (81 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       314  (0.0175135); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 659.99
//
Query:       AHX11475.1  [L=442]
Description: hypothetical protein NHE_0535 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.023   14.3   5.6        5.4    6.5   0.0    2.1  2  SseC             Secretion system effector C (SseC) like fami
      0.084   13.8   0.0       0.17   12.8   0.0    1.5  1  EphA2_TM         Ephrin type-A receptor 2 transmembrane domai
       0.21   11.9   1.7       0.56   10.5   0.6    2.1  2  PSII_Pbs27       Photosystem II Pbs27
       0.26   11.7   2.4         23    5.5   0.7    3.0  3  GlutR_dimer      Glutamyl-tRNAGlu reductase, dimerisation dom
       0.28   11.3   1.6         20    5.3   0.0    3.2  3  GMP_synt_C       GMP synthase C terminal domain
       0.53    9.9   5.8          2    8.1   1.8    2.2  2  Laminin_I        Laminin Domain I
        1.2    9.6   3.9        2.6    8.6   1.8    2.4  2  SAA              Serum amyloid A protein
        2.2    8.2   9.9        5.6    7.0   0.1    2.5  2  Chlorosome_CsmC  Chlorosome envelope protein C
        3.9    7.6   9.7       0.69   10.0   3.9    2.4  2  GLYCAM-1         Glycosylation-dependent cell adhesion molecu


Domain annotation for each model (and alignments):
>> SseC  Secretion system effector C (SseC) like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0027       5.4     168     250 ..      49     153 ..      42     155 .. 0.69
   2 ?    5.9   5.3    0.0041       8.2     132     216 ..     158     238 ..     155     294 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0027
        SseC 168 aklaeavaeaigkaikkaaekagkevaeqvskq..........vlnelakkatkva.......kavkegv...vasavakalikavvv..........a 236
                 +k++ +++++i  a++++  +a++ ++   + +           +++                ++++eg+    ++   + ++++vv+          a
  AHX11475.1  49 TKFTHNITDKIVNAVTNVTRNAAEILSNTEG-TsatlfkttstQADSS-------TrlttvysQELQEGIeryFKNYGHTPALRCVVAsyptanryfnA 139
                 5777888888888888888888888774222.2355444333333333.......2444555577778779865555666777888779999999999* PP

        SseC 237 eggngiaqGainiq 250
                 +g+n ++q+a n+ 
  AHX11475.1 140 DGTNHATQAALNKV 153
                 **********9975 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0041
        SseC 132 ageivgavv.aavavvaavvavgsaakgaaaavksgaaklaeavaeaigkaikkaaekagkevaeqvskqvlnelakkatkvakav 216
                 ag++v++v  a  +++ a++a+++  +         a+  ++a+ +++ +  ++++++  ke++  + k+++n++a  ++ v +++
  AHX11475.1 158 AGKVVNTVAsATRSAAEAFFATKGTNTTPFE-----ATSTQAALNKVTHSITEEIMNTTNKEIMNTTNKEIMNTVANATKGVTEFI 238
                 6777777774444555566666665555543.....44555555555555556666666666666666777777777776665433 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   8.7e-05      0.17       1      36 [.     291     326 ..     291     378 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.7e-05
    EphA2_TM   1 iiaaavaglvllvilvilvlvlvrrrsknrkqksdl 36 
                 i+a ++++l+ll i+  +++++++rr++ rk ++ +
  AHX11475.1 291 IAACSIVALLLLGITCRCCMLCLNRRRRTRKTMNVD 326
                 67899*************************999765 PP

>> PSII_Pbs27  Photosystem II Pbs27
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.62   1.2e+03      53      91 ..      82     121 ..      49     130 .. 0.69
   2 ?   10.5   0.6   0.00028      0.56       2      86 ..     154     240 ..     153     260 .. 0.93

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.62
  PSII_Pbs27  53 ktlresleldkkddakreraa..kaakesireyvskYrsak 91 
                  tl +++ +++ d+++r  ++  ++++e i+ y ++Y+  +
  AHX11475.1  82 ATLFKTTSTQA-DSSTRLTTVysQELQEGIERYFKNYGHTP 121
                 45555555555.55555555433678888888888888766 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 0.00028
  PSII_Pbs27   2 RrflllsaaaalvallasavgaiaslfdpnektkadkalpkaYlkdarevvktlresleldk..kddakreraakaakesireyvsk 86 
                 Rr ++ +++  +++++ sa++a+ +++  n+++ +      a  k +  + +++ ++++ ++    ++++ +++++a + + e++s+
  AHX11475.1 154 RRGIAGKVVNTVASATRSAAEAFFATKGTNTTPFEATSTQAALNKVTHSITEEIMNTTNKEImnTTNKEIMNTVANATKGVTEFISD 240
                 77888888999999999***********9****999999**********************98889999***************995 PP

>> GlutR_dimer  Glutamyl-tRNAGlu reductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.032        65      58      81 ..      48      74 ..      44      88 .. 0.76
   2 ?   -0.7   0.0      0.97   1.9e+03      52      80 ..     144     172 ..     133     185 .. 0.74
   3 ?    5.5   0.7     0.012        23      53      90 ..     191     226 ..     150     234 .. 0.74

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.032
                 -TTHHHHHHHHHHHHHHHHHHSS...- CS
  GlutR_dimer 58 lekltrslvnkllheptarLkea...e 81
                 l k+t+++++k++++ t+  ++a    
   AHX11475.1 48 LTKFTHNITDKIVNAVTNVTRNAaeiL 74
                 6899**************999994441 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.97
                  -------TTHHHHHHHHHHHHHHHHHHSS CS
  GlutR_dimer  52 gedreelekltrslvnkllheptarLkea 80 
                    ++++l+k+ r++  k++++  ++ ++a
   AHX11475.1 144 HATQAALNKVRRGIAGKVVNTVASATRSA 172
                  44555588889999999998888888877 PP

  == domain 3  score: 5.5 bits;  conditional E-value: 0.012
                  ------TTHHHHHHHHHHHHHHHHHHSS-TTTTHHHHH CS
  GlutR_dimer  53 edreelekltrslvnkllheptarLkeaedeeeellea 90 
                   ++++l+k+t+s++  +++++ +++ +   ++ e++++
   AHX11475.1 191 STQAALNKVTHSITEEIMNTTNKEIMNT-TNK-EIMNT 226
                  3455599999999999999998888887.222.44444 PP

>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.3   0.0      0.01        20      59      88 ..      50      79 ..      37      82 .. 0.84
   2 ?   -0.1   0.0       0.5     1e+03      26      50 ..     109     133 ..      90     173 .. 0.58
   3 ?    2.9   0.1     0.058   1.2e+02      45      79 ..     204     238 ..     182     248 .. 0.63

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.01
                HHHHHHHHHHHHHSTT---EEEE---TTTS CS
  GMP_synt_C 59 evLekissrivnevkgvnrvvyditskPpa 88
                ++ ++i+++ivn v++v+r   +i s   +
  AHX11475.1 50 KFTHNITDKIVNAVTNVTRNAAEILSNTEG 79
                56789**************98888776655 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.5
                 ---------EEEEEEEEE------- CS
  GMP_synt_C  26 GvmgdkRtyeyvvalRaveseDamt 50 
                 G+    ++y+++ alR+v ++   +
  AHX11475.1 109 GIERYFKNYGHTPALRCVVASYPTA 133
                 5666667888888999887653332 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.058
                 --------B----HHHHHHHHHHHHHHSTT---EE CS
  GMP_synt_C  45 seDamtadvaelpyevLekissrivnevkgvnrvv 79 
                 +e+ m ++  e+  ++ ++i++ + n  kgv+  +
  AHX11475.1 204 TEEIMNTTNKEIMNTTNKEIMNTVANATKGVTEFI 238
                 45556666666666666666666666666666555 PP

>> Laminin_I  Laminin Domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.025        49      84     122 ..      56      94 ..      49     119 .. 0.64
   2 ?    8.1   1.8     0.001         2      52     129 ..     157     232 ..     135     240 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.025
   Laminin_I  84 akeLaekikkladnikeilekvatlneneealpssklse 122
                 + + + ++ ++ +n+ eil+ ++ ++   +++ s++ ++
  AHX11475.1  56 TDKIVNAVTNVTRNAAEILSNTEGTSATLFKTTSTQADS 94 
                 555666666777777777777777666666666655444 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.001
   Laminin_I  52 LaqeteeLqkkatqvlakaqkvnaesertlnnakeLaekikkladnikeilekvatlneneealpssklseelaeaqr 129
                 +a  + + +  at+  a+a+   + +++t  +a++ +++ +k+  +i+e +    t+n++ +++ ++++ ++ a+a++
  AHX11475.1 157 IAGKVVNTVASATRSAAEAFFATKGTNTTPFEATSTQAALNKVTHSITEEIM--NTTNKEIMNTTNKEIMNTVANATK 232
                 555566667789999********************************87443..346******************986 PP

>> SAA  Serum amyloid A protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.68   1.4e+03      49      75 ..      68      94 ..      64     113 .. 0.76
   2 ?    8.6   1.8    0.0013       2.6      23      71 ..     127     182 ..     100     202 .. 0.73

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.68
         SAA 49 awaAkvisdarellqellsgrgaedse 75
                + aA+++s++  +  +l++ +++++ +
  AHX11475.1 68 RNAAEILSNTEGTSATLFKTTSTQADS 94
                689******999988888655554443 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.0013
         SAA  23 eanvknsdkYfhargnydAaq.......RGpGgawaAkvisdarellqellsgrga 71 
                  a++  +++Yf a g  +A+q       RG  g++  +v s +r + + ++  +g+
  AHX11475.1 127 VASYPTANRYFNADGTNHATQaalnkvrRGIAGKVVNTVASATRSAAEAFFATKGT 182
                 578999*******9998887555555559****************99998843333 PP

>> Chlorosome_CsmC  Chlorosome envelope protein C
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.1    0.0028       5.6     101     131 ..      50      80 ..      45      91 .. 0.81
   2 ?    3.1   5.4     0.044        87      23     116 ..     137     236 ..     130     261 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0028
  Chlorosome_CsmC 101 knvenvtdnaakavGdvgvsasevvknvags 131
                      k  +n+td++ +av +v+ +a+e++ n +g+
       AHX11475.1  50 KFTHNITDKIVNAVTNVTRNAAEILSNTEGT 80 
                      5568999****************99998876 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.044
  Chlorosome_CsmC  23 flaeavlltGqsavvgg.lelaGsvvetvagtvgslidatGiskllgst...sgvvgetidrva..itvkdvsraaGelysdavknvenvtdna 110
                      f a+++  + q+a+     ++aG vv+tva++  s  +a   +k  ++t   +     ++++v+  it   +  +  e+ + + k++ n+  na
       AHX11475.1 137 FNADGTNHATQAALNKVrRGIAGKVVNTVASATRSAAEAFFATKGTNTTpfeATSTQAALNKVThsITEEIMNTTNKEIMNTTNKEIMNTVANA 230
                      667788888888887752589**************99998877776666221233444577775225555566677777766666666666666 PP

  Chlorosome_CsmC 111 akavGd 116
                      +k+v +
       AHX11475.1 231 TKGVTE 236
                      665543 PP

>> GLYCAM-1  Glycosylation-dependent cell adhesion molecule 1 (GlyCAM-1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.1      0.61   1.2e+03     100     128 ..      48      76 ..      46      82 .. 0.87
   2 ?   10.0   3.9   0.00035      0.69      84     131 ..     180     229 ..     162     233 .. 0.74

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.61
    GLYCAM-1 100 LaklgheieknLektikeivkylksllpg 128
                 L+k +h+i++++ + + ++ + + ++l++
  AHX11475.1  48 LTKFTHNITDKIVNAVTNVTRNAAEILSN 76 
                 89999999999999999999999999986 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00035
    GLYCAM-1  84 etteltpsaattsegkLaklgheieknLekt.ikeivkyl.ksllpgase 131
                   t+ tp +at +   L k++h i++++ +t  kei++   k+++    +
  AHX11475.1 180 KGTNTTPFEATSTQAALNKVTHSITEEIMNTtNKEIMNTTnKEIMNTVAN 229
                 45899999******************987651689998652667666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.54u 0.27s 00:00:00.81 Elapsed: 00:00:00.38
# Mc/sec: 3457.89
//
Query:       AHX11476.1  [L=307]
Description: RNA pseudouridylate synthase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.8e-31  108.3   0.0    6.5e-31  107.6   0.0    1.4  1  PseudoU_synth_2  RNA pseudouridylate synthase
    0.00017   21.2   0.0    0.00037   20.1   0.0    1.6  1  S4               S4 domain


Domain annotation for each model (and alignments):
>> PseudoU_synth_2  RNA pseudouridylate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.6   0.0   7.3e-35   6.5e-31       1     159 [.      98     244 ..      98     245 .. 0.94

  Alignments for each domain:
  == domain 1  score: 107.6 bits;  conditional E-value: 7.3e-35
  PseudoU_synth_2   1 dlvvvnKPagvpvqpeakdgsekekettatssraeeekkelklvhRLDkatsGllllAksseaanklakafeerkvrKkYlalvfgapeeeega 94 
                      +++++nKP g+ vq+++       k     +   +  + e+++vhRLDk t+G+ll+Ak+ ea ++  ++f++r ++KkYl++v+g+ ee+eg+
       AHX11476.1  98 NILAINKPFGISVQSGN-------KVSNSIDCIMKAINPEYRVVHRLDKHTTGVLLFAKTLEATREIWQLFANRLISKKYLGIVVGKVEEKEGE 184
                      5789*************.......44444445556778899***************************************************** PP

  PseudoU_synth_2  95 ikkkiskdtekqegarrkaeeldgkkavtylkvlksgsseksakvslveleletGrkhQiRvhla 159
                      i+  i+k+ +k+e  +r  +  dg++a+t+++ ++ +      + slvel ++tGrkhQiR+++a
       AHX11476.1 185 IDCFIKKTLYKGEEIMRCNNIGDGERAITRFRAVSCF-----DDLSLVELYPVTGRKHQIRAQMA 244
                      *************************************.....*********************98 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.1e-08   0.00037       1      47 [.      11      56 ..      11      57 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.1e-08
                EEHHHHH.HHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCE CS
          S4  1 rRLdkvl.arlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDv 47
                +RLdk+l  r g  +  +  +++ +++ +++NGk+++ ++++V+ g+ 
  AHX11476.1 11 QRLDKYLrLRFGSFP-QSALEKALRKKLIKLNGKRAD-AATPVTKGES 56
                6******66666666.*********************.******9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.21s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2385.30
//
Query:       AHX11477.1  [L=311]
Description: thioredoxin-disulfide reductase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.7e-51  173.1   0.0    8.8e-51  172.9   0.0    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    3.2e-21   75.9   0.0      1e-16   61.1   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    5.6e-19   68.5   0.8    1.1e-14   54.7   0.0    2.5  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    5.4e-12   45.5   0.5    1.3e-05   24.5   0.4    4.0  4  GIDA            Glucose inhibited division protein A
    3.3e-10   39.6   6.0    4.5e-07   29.3   2.6    3.6  4  FAD_binding_2   FAD binding domain
    1.6e-09   37.8   3.2     0.0044   16.6   2.0    3.4  4  DAO             FAD dependent oxidoreductase
    1.7e-08   34.2   7.7    1.1e-07   31.5   1.2    2.6  3  FAD_oxidored    FAD dependent oxidoreductase
    1.6e-07   30.4   0.5     0.0012   17.7   0.5    3.4  3  HI0933_like     HI0933-like protein
    2.4e-06   27.0   0.2     0.0045   16.3   0.6    2.4  2  Thi4            Thi4 family
    1.3e-05   25.3   0.4    0.00044   20.4   0.0    2.5  2  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    1.9e-05   23.9   1.1     0.0054   15.8   1.0    2.9  3  Lycopene_cycl   Lycopene cyclase protein
    0.00018   21.9   0.0       0.23   11.9   0.0    2.3  2  NAD_binding_7   Putative NAD(P)-binding
    0.00093   18.5   0.7      0.034   13.4   0.5    2.1  2  FAD_binding_3   FAD binding domain
     0.0073   14.8   0.0       0.21   10.0   0.0    2.1  2  FMO-like        Flavin-binding monooxygenase-like
  ------ inclusion threshold ------
      0.016   15.3   0.1       0.26   11.3   0.0    2.3  2  Shikimate_DH    Shikimate / quinate 5-dehydrogenase
      0.027   14.5   0.1        5.9    6.9   0.0    3.2  4  NAD_binding_9   FAD-NAD(P)-binding
      0.035   13.3   0.3       0.11   11.6   0.0    1.9  2  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
       0.14   11.4   0.9        1.2    8.4   0.8    2.1  2  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.18   10.6   0.9        1.6    7.5   0.5    2.0  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  172.9   0.0   9.3e-54   8.8e-51       2     294 .]       4     297 ..       3     297 .. 0.93

  Alignments for each domain:
  == domain 1  score: 172.9 bits;  conditional E-value: 9.3e-54
                  SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH.......HHHHCHHHHCCCCHCCTCEEEEESC.EEEEETEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias.......evvkklnqgielllgeevvkidpgk.kkvklekkk 91 
                  dv+viG+GpAG+aaa+++a+a ++v+lv   g+  +g+  +++++++++++a+ ++        + + +n g  ++++ ++ +i+      ++l+   
   AHX11477.1   4 DVLVIGSGPAGCAAAIYAARAALDVVLV--SGNQSGGQLTITTEVENYPGFASPVHgpwlmeqMQQQAINVGCSFIND-HISSIESPYvPPFTLR--- 95 
                  8***************************..88899******************999*****98445789999999999.9****98887999995... PP

                  CTCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  92 egdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkelsaal 189
                  ++++++++++++++AtG+++r l+i+ ++++ g++v+ +++++++  k+++  ++v+GgG+++vE A +l+k +k+v+l+++rd l       ++++l
   AHX11477.1  96 GESGNEYKAKSIIVATGAQARWLDIESEKKYRGYGVSGCATCDGFFFKNQD--VIVIGGGNTAVEEALYLTKHAKKVYLLHRRDVLR------AEKIL 185
                  566789*******************************************99..*****************************99996......9**** PP

                  HHHHHHT.TEEEEESCEEEEEEETTE.......EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTSBE..SSTTEEE-GG CS
                  xxxxxxx.xxxxxxxxxxxxxxxxxx.......xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx RF
  Pyr_redox_2 190 eealeke.Gvevklgtsvkeidgnge.......kle.vvledgeeidadlvvvavGvrpstelleeklglelderggivvdeflrt..nvpgiyaiGD 276
                  +++l ++ ++e  ++++ ke+ g ++       +l+ v++++ + + ++ v+va+G +p+tel+  +  l ld++g+i v + +rt  n+pgi+a+GD
   AHX11477.1 186 QQRLFDNpKIEPIWNSVLKEVLGTENplsvtgvRLRsVIDNSLRDLSVSGVFVAIGHSPNTELF--RGVLDLDPGGYIIVPDPGRTttNIPGIFACGD 281
                  ****************************888665669**************************6..8999********99999975447********* PP

                  GCTECCSS--HHHHHHHH CS
                  xxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 277 vaggkggpelaqaAvqqG 294
                  v   + ++++a++A  +G
   AHX11477.1 282 VR--DAVYRQAVTAAGSG 297
                  **..99*******99876 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.4   6.1e-05     0.057       1      28 [.       6      32 ..       6      48 .. 0.83
   2 !   61.1   0.0   1.1e-19     1e-16     114     305 .]      92     280 ..      66     280 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.1e-05
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilE 28
                 ++iG GPaG aaai + +a l d++ + 
   AHX11477.1  6 LVIGSGPAGCAAAIYAARAAL-DVVLVS 32
                 69*******************.565554 PP

  == domain 2  score: 61.1 bits;  conditional E-value: 1.1e-19
  Pyr_redox_3 114 fevetske.tyeAkkviiAtGefdkPnklnipGeek...lvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdps 207
                  f+++ +++ +y+Ak++i+AtG   + ++l+i+ e+k   + +      +   +++q+v+ViGg+n+av+ Al l ++ ++V +++r++ +++e+   +
   AHX11477.1  92 FTLRGESGnEYKAKSIIVATGA--QARWLDIESEKKyrgYGVSGCATCDGFFFKNQDVIVIGGGNTAVEEALYLTKHAKKVYLLHRRDVLRAEK-ILQ 186
                  6666655449***********9..9*********97432233333333333678**********************************998876.455 PP

  Pyr_redox_3 208 ysl..kpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvlatGykpdlsflkkslfeldedgrpvl.teeteetnvpglf 302
                  ++l  +p ie+  ++++k e +  +   +v+ ++ ++    v  ++ + ++v + v++a+G +p++++++  +++ld  g++ + ++    tn+pg+f
   AHX11477.1 187 QRLfdNPKIEPIWNSVLK-EVLGTENPLSVTGVRLRS----VIDNSLRDLSV-SGVFVAIGHSPNTELFR-GVLDLDPGGYIIVpDPGRTTTNIPGIF 277
                  555447888888888776.446777777777777653....23333355555.778999**********9.9999999998665277999******** PP

  Pyr_redox_3 303 laG 305
                   +G
   AHX11477.1 278 ACG 280
                  999 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.2   0.00029      0.27       2      29 ..       5      32 ..       4      41 .. 0.92
   2 !   54.7   0.0   1.2e-17   1.1e-14       2      79 ..     147     221 ..     146     227 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00029
                EEEECSSHHHHHHHHHHHHTTSEEEEEE CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvve 29
                v+v+G+G  g+ +A ++a+ + +V +v 
  AHX11477.1  5 VLVIGSGPAGCAAAIYAARAALDVVLVS 32
                89**********************9996 PP

  == domain 2  score: 54.7 bits;  conditional E-value: 1.2e-17
                 EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTS..EEEEEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedg..vesvklk 79 
                 v+v+GgG++++E+A +l++++kkV++++r+d l+      a+kilq++l +n +ie ++n++++e+ g+e+   v++v+l+
  AHX11477.1 147 VIVIGGGNTAVEEALYLTKHAKKVYLLHRRDVLR------AEKILQQRLFDNpKIEPIWNSVLKEVLGTENPlsVTGVRLR 221
                 89********************************......***************************99985468888886 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.5   0.4   1.4e-08   1.3e-05       1      29 [.       4      34 ..       4      59 .. 0.85
   2 !    5.6   0.0    0.0076       7.2     132     162 ..      95     124 ..      60     137 .. 0.81
   3 !    7.9   0.0    0.0015       1.4       1      30 [.     146     174 ..     146     193 .. 0.85
   4 ?    2.7   0.0     0.057        54     352     388 ..     270     308 ..     266     311 .] 0.77

  Alignments for each domain:
  == domain 1  score: 24.5 bits;  conditional E-value: 1.4e-08
                CEEEE-SSHHHHHHHHHHHHTT--EEEE..E CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi..t 29
                dv ViG G AGc+AA+ aar+ ++v+L+   
  AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAALDVVLVsgN 34
                79*************************9552 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0076
                 EETTS-EEEECEEEE--TT-BT-EEEETTEE CS
        GIDA 132 vtedgetikakavviatGtflkgkihigeke 162
                 + e+g+++kak++++atG+  + +  i +++
  AHX11477.1  95 RGESGNEYKAKSIIVATGA-QARWLDIESEK 124
                 56899*************9.55555555554 PP

  == domain 3  score: 7.9 bits;  conditional E-value: 0.0015
                 CEEEE-SSHHHHHHHHHHHHTT--EEEEES CS
        GIDA   1 dviViGgGhAGceAAlaaarlGakvlLith 30 
                 dviViGgG   +e Al + +   kv L+ h
  AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAKKVYLL-H 174
                 8*************************99.2 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.057
                 BSSSBTEEE-CGGGTB-SH...HHHHHHHHHHHHHHHHHH CS
        GIDA 352 tkkvkgLflAGqinGteGY...eEaaaqGllAGinaarka 388
                 t +++g+f++G++     Y   + aa++G++A++ aar +
  AHX11477.1 270 TTNIPGIFACGDVRDAV-YrqaVTAAGSGCMAALDAARFL 308
                 66799999999999887.612245677*********9976 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.3   2.6   4.8e-10   4.5e-07       1      38 [.       4      40 ..       4      44 .. 0.92
   2 ?   -1.9   0.0       1.4   1.3e+03     187     206 ..      99     117 ..      84     135 .. 0.79
   3 !    5.6   0.0    0.0077       7.2       1      33 [.     146     178 ..     146     183 .. 0.90
   4 ?    3.4   0.0     0.034        32     388     414 ..     269     295 ..     262     298 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.3 bits;  conditional E-value: 4.8e-10
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                   Dv+ViGsG AG+aAA+ aa+a l+v++v+  q+ gg++
     AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAALDVVLVSGNQS-GGQL 40
                   9****************************9998.7765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.4
                    EEEEEESEEEE-----GG.. CS
  FAD_binding_2 187 evrirakavvlatgGfgral 206
                      +++ak +++atg+  r +
     AHX11477.1  99 GNEYKAKSIIVATGAQAR-W 117
                    4579999******98876.4 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0077
                    SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSG CS
  FAD_binding_2   1 DviViGsGlAGLaAAleaaeaGlkvavvekeqe 33 
                    DviViG+G      Al ++++ +kv ++   ++
     AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAKKVYLLHRRDV 178
                    9************************99987665 PP

  == domain 4  score: 3.4 bits;  conditional E-value: 0.034
                    EEESSBTEEE-STCEESSSSTTS--TT CS
  FAD_binding_2 388 dgqpipGLYAaGevaaggvhganrlgG 414
                    + ++ipG +A+G v  + +  a   +G
     AHX11477.1 269 TTTNIPGIFACGDVRDAVYRQAVTAAG 295
                    5789**********9777776665555 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.6   2.0   4.7e-06    0.0044       1      31 [.       4      35 ..       4      42 .. 0.86
   2 !   10.0   0.0    0.0005      0.47     147     207 ..      60     118 ..      50     136 .. 0.72
   3 !    8.2   0.0    0.0017       1.6       1      31 [.     146     178 ..     146     183 .. 0.90
   4 ?   -3.4   0.0       5.7   5.4e+03     325     335 ..     233     243 ..     211     269 .. 0.69

  Alignments for each domain:
  == domain 1  score: 16.6 bits;  conditional E-value: 4.7e-06
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31
                dv++iG+G +G+++A ++ar+   V+l+  + +
  AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAAldVVLVSGN-Q 35
                8*****************9997789999877.4 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.0005
                 HHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECTEEEEEEEEEEE--GGGHHHH CS
         DAO 147 kltaalaraaealGveilegtevtgleeedgkvwgverttpgendaadavVnaaGawsdll 207
                  l+  ++++a + G+ +++   + ++e +     ++ r ++g++ +a+ +++a+Ga+++ l
  AHX11477.1  60 WLMEQMQQQAINVGCSFIND-HISSIESPYVPPFTL-RGESGNEYKAKSIIVATGAQARWL 118
                 578899999**********9.*****8865334555.444465545688********9844 PP

  == domain 3  score: 8.2 bits;  conditional E-value: 0.0017
                 EEEEECTSHHHHHHHHHHHHTT..EEEEESSSS CS
         DAO   1 dvviiGGGiiGlstAyeLarrg..Vtllekgdi 31 
                 dv++iGGG + +  A++L+++   V ll ++d 
  AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAkkVYLLHRRDV 178
                 9******************99558****99965 PP

  == domain 4  score: -3.4 bits;  conditional E-value: 5.7
                 EEEEEEEEECT CS
         DAO 325 vkglylatGhs 335
                 v+g+++a Ghs
  AHX11477.1 233 VSGVFVAIGHS 243
                 55677777765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.5   1.2   1.2e-10   1.1e-07       1      39 [.       4      41 ..       4      54 .. 0.91
   2 !    6.6   0.0    0.0046       4.3       1      34 [.     146     179 ..     146     179 .. 0.97
   3 ?   -3.8   0.4       6.2   5.9e+03      10      20 ..     296     306 ..     295     306 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.5 bits;  conditional E-value: 1.2e-10
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGllt 39
                  Dv+V+G+gpaG+aAAi Aara   v+Lv+ ++  GG+lt
    AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAALDVVLVSGNQ-SGGQLT 41
                  9***************************8665.699998 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0046
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvl 34 
                   Dv+V+GGg   v  A+   ++ +kv L+++r+vl
    AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAKKVYLLHRRDVL 179
                   9*****************************9986 PP

  == domain 3  score: -3.8 bits;  conditional E-value: 6.2
  FAD_oxidored  10 aGvaAAiaAar 20 
                   +G++AA+ Aar
    AHX11477.1 296 SGCMAALDAAR 306
                   79*******98 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.7   0.5   1.2e-06    0.0012       2      36 ..       4      38 ..       3      44 .. 0.89
   2 ?    3.5   0.0     0.024        23     129     165 ..      78     114 ..      59     121 .. 0.77
   3 !    4.9   0.0    0.0091       8.5       2      33 ..     146     177 ..     145     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 17.7 bits;  conditional E-value: 1.2e-06
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 dv+viG G+AG  aAi aa++  +V+l+  +++ g
   AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAALDVVLVSGNQSGG 38
                 89*************************99887655 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.024
                  S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
  HI0933_like 129 etevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                  + +++s+e+     f+++ +s++e++a+++++AtG +
   AHX11477.1  78 NDHISSIESPYVPPFTLRGESGNEYKAKSIIVATGAQ 114
                  566777777777788999999**************87 PP

  == domain 3  score: 4.9 bits;  conditional E-value: 0.0091
                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSS CS
  HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekak 33 
                  dviviGgG   +  A+ + k+ k+V ll + +
   AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAKKVYLLHRRD 177
                  8**************************98765 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.6   4.8e-06    0.0045      16      50 ..       1      34 [.       1      42 [. 0.87
   2 !    8.0   0.0    0.0016       1.5      15      50 ..     142     176 ..     136     205 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.8e-06
                TEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
        Thi4 16 aesDvvivGaGssGLtaayylakkpdlkvailers 50
                +esDv+++G+G++G +aa y a++  l v+++  +
  AHX11477.1  1 MESDVLVIGSGPAGCAAAIYAARA-ALDVVLVSGN 34
                69*********************9.9999988655 PP

  == domain 2  score: 8.0 bits;  conditional E-value: 0.0016
                 HTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESS CS
        Thi4  15 yaesDvvivGaGssGLtaayylakkpdlkvailers 50 
                 + ++Dv+++G+G + +  a yl+k+   kv +l r+
  AHX11477.1 142 FKNQDVIVIGGGNTAVEEALYLTKH-AKKVYLLHRR 176
                 5689********************9.8889888765 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.0   4.7e-07   0.00044       1      38 [.       7      43 ..       7      71 .. 0.81
   2 ?    2.5   0.0      0.18   1.7e+02       1      29 [.     149     177 ..     149     181 .. 0.90

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 4.7e-07
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-EE CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraasy 38
                   ++G+G +G++aA ++a+a +dv+l+ ++++ GG+++  
     AHX11477.1  7 VIGSGPAGCAAAIYAARAALDVVLV-SGNQSGGQLTIT 43
                   8************************.9999**999844 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.18
                    EE--SHHHHHHHHHHHCCTEEEEEE-SSS CS
  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrd 29 
                    ++G+G ++   A +L+k+ ++v ll +rd
     AHX11477.1 149 VIGGGNTAVEEALYLTKHAKKVYLLHRRD 177
                    89****************99999998887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   1.0   5.7e-06    0.0054       1      33 [.       4      34 ..       4      60 .. 0.87
   2 ?    2.4   0.0     0.067        64      89     143 ..      61     115 ..      54     131 .. 0.87
   3 ?    2.1   0.0     0.084        80       1      30 [.     146     173 ..     146     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.7e-06
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieas 33
                   Dv+viG+GpAg++ A     a+++l vvl+ + 
     AHX11477.1  4 DVLVIGSGPAGCAAAIYA--ARAALDVVLVSGN 34
                   9***********999888..**********544 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.067
  Lycopene_cycl  89 lkeellerlvengvklleakvesveeeeageslvvleggrkirarlvvdarglas 143
                    l e+++++ ++ g ++ +  + s+e   +   +   e g++ +a+ +++a+g+ +
     AHX11477.1  61 LMEQMQQQAINVGCSFINDHISSIESPYVPPFTLRGESGNEYKAKSIIVATGAQA 115
                    7899**********************99999999999***************544 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.084
  Lycopene_cycl   1 DvvviGaGpAglslAarlteakpglkvvli 30 
                    Dv+viG+G   +  A  l   k + kv l+
     AHX11477.1 146 DVIVIGGGNTAVEEALYL--TKHAKKVYLL 173
                    9********999999999..5555556555 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.2   0.0    0.0034       3.2       9      45 ..       4      37 ..       1     124 [. 0.81
   2 !   11.9   0.0   0.00025      0.23       5      40 ..     142     177 ..     140     254 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.0034
  NAD_binding_7  9 kvlvvGgGevAarkvrklleagakvtvvapevkeele 45
                    vlv+G G+ +   +   ++a  +v++v+ +   ++ 
     AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAALDVVLVSGN---QSG 37
                   79***************************99...443 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00025
  NAD_binding_7   5 lkgkkvlvvGgGevAarkvrklleagakvtvvapev 40 
                    +k++ v+v+GgG+ A + +  l +  +kv ++  + 
     AHX11477.1 142 FKNQDVIVIGGGNTAVEEALYLTKHAKKVYLLHRRD 177
                    6899*************************9987764 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.5   3.6e-05     0.034       2      31 ..       3      32 ..       2      39 .. 0.90
   2 ?    3.3   0.0     0.041        39       3      34 ..     146     177 ..     144     189 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.6e-05
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlve 31
                    dVl++G+GpaG  +a   ++a  +vvlv 
     AHX11477.1  3 SDVLVIGSGPAGCAAAIYAARAALDVVLVS 32
                   79***************9999999999986 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.041
                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrs 34 
                    dV+++G+G + +  al L+++  +v l+ +r+
     AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAKKVYLLHRRD 177
                    8********************99999999986 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.0     0.034        32     185     215 ..       4      34 ..       1      51 [. 0.79
   2 !   10.0   0.0   0.00022      0.21     180     217 ..     141     178 ..     125     218 .. 0.84

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.034
    FMO-like 185 rvlviGlGnsggdiavelsrtaeqvllstrs 215
                  vlviG G +g+  a+ ++r+a +v+l + +
  AHX11477.1   4 DVLVIGSGPAGCAAAIYAARAALDVVLVSGN 34 
                 59********************988775433 PP

  == domain 2  score: 10.0 bits;  conditional E-value: 0.00022
    FMO-like 180 vfkgkrvlviGlGnsggdiavelsrtaeqvllstrsGs 217
                  fk++ v+viG Gn++ + a  l++ a++v+l  r+  
  AHX11477.1 141 FFKNQDVIVIGGGNTAVEEALYLTKHAKKVYLLHRRDV 178
                 58999**************************9888765 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.1      0.36   3.4e+02      13      41 ..       3      31 ..       1      48 [. 0.81
   2 ?   11.3   0.0   0.00028      0.26      10      55 ..     142     187 ..     138     207 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.36
                  -EEEEES-SHHHHHHHHHHHCCT-CEEEE CS
  Shikimate_DH 13 kkvlliGaGemaelvakhLlakgvkkvvv 41
                  + vl+iG G  +  +a + +++ ++ v+v
    AHX11477.1  3 SDVLVIGSGPAGCAAAIYAARAALDVVLV 31
                  679*******9999988877777776665 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00028
                   .TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHH CS
  Shikimate_DH  10 lkekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaee 55 
                   +k++ v++iG G++a + a +L ++  k  +   R++ ra+++ ++
    AHX11477.1 142 FKNQDVIVIGGGNTAVEEALYLTKHAKKVYLLHRRDVLRAEKILQQ 187
                   57899*****************977777666777899999998776 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.1     0.066        63       2      37 ..       7      37 ..       6      49 .. 0.76
   2 ?    6.9   0.0    0.0062       5.9     102     155 ..      60     113 ..      57     114 .. 0.86
   3 ?   -1.3   0.0         2   1.9e+03       2      20 ..     149     167 ..     148     177 .. 0.82
   4 ?   -2.3   0.0         4   3.8e+03     136     155 ..     223     242 ..     215     243 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.066
  NAD_binding_9  2 ivGaGprGlavlerLlarakkkspleitlfdpsepg 37
                   ++G Gp+G a++   ++ a     l++ l+  +++g
     AHX11477.1  7 VIGSGPAGCAAAIYAARAA-----LDVVLVSGNQSG 37
                   8*********999888775.....777777666665 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0062
  NAD_binding_9 102 dlfeellarlpegvtvevhraevvdleeradg.qavlladgaslaadaVvLAlGh 155
                    +l+e++++++  +v  +++++++ ++e      ++++ ++g++++a+++++A+G 
     AHX11477.1  60 WLMEQMQQQAI-NVGCSFINDHISSIESPYVPpFTLRGESGNEYKAKSIIVATGA 113
                    77788888885.589999********998866379999****************6 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 2
  NAD_binding_9   2 ivGaGprGlavlerLlara 20 
                    ++G+G +++  +  L ++a
     AHX11477.1 149 VIGGGNTAVEEALYLTKHA 167
                    89***99999999999887 PP

  == domain 4  score: -2.3 bits;  conditional E-value: 4
  NAD_binding_9 136 vlladgaslaadaVvLAlGh 155
                    v+ ++ + l +  V++A+Gh
     AHX11477.1 223 VIDNSLRDLSVSGVFVAIGH 242
                    5566778899999******9 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.2       1.1   1.1e+03       4      21 ..       4      21 ..       2      39 .. 0.59
   2 ?   11.6   0.0   0.00012      0.11     142     226 ..      97     177 ..      59     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.1
  K_oxygenase  4 DligiGiGpsnLsLaill 21
                 D+  iG Gp+  + ai +
   AHX11477.1  4 DVLVIGSGPAGCAAAIYA 21
                 445555555544444443 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00012
  K_oxygenase 142 geeeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeifedllrrqkkvelklvtrse 226
                  ++ +e++a+++++++G ++   ++  + +   r +  s  ++      ++++++V+G+G +a e +  l++++k  ++ l+ r++
   AHX11477.1  97 ESGNEYKAKSIIVATGAQARWLDIESEKK--YRGYGVSGCATCDGFFFKNQDVIVIGGGNTAVEEALYLTKHAK--KVYLLHRRD 177
                  4567999*********9999877766544..677777777777777999**************98888877766..666666665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.4   0.8    0.0012       1.2      29      57 ..       3      31 ..       1      40 [. 0.86
   2 ?    0.5   0.0      0.33   3.1e+02      28      58 ..     144     174 ..     124     191 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.4 bits;  conditional E-value: 0.0012
                 -EEEEESTSHHHHHHHHHHHHTT-EEEEE CS
  AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvl 57
                 + vlviG G aG +A+  a++   +V+++
   AHX11477.1  3 SDVLVIGSGPAGCAAAIYAARAALDVVLV 31
                 679****************9998888765 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.33
                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEE CS
  AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlD 58 
                  +  v+viGgG   ++ +   ++   kV++l 
   AHX11477.1 144 NQDVIVIGGGNTAVEEALYLTKHAKKVYLLH 174
                  5679999999777766666666566666555 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.5    0.0017       1.6       1      33 [.       4      33 ..       4      39 .. 0.89
   2 ?    1.2   0.0      0.14   1.3e+02       1      30 [.     146     172 ..     146     184 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0017
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE- CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlves 33
                    +++++G G+aG  aA++ a+a    l+v lv  
      AHX11477.1  4 DVLVIGSGPAGCAAAIYAARAA---LDVVLVSG 33
                    699*****************99...99999975 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.14
                     EEEEE--SHHHHHHHHHHHHHTTTSSEEEE CS
  Trp_halogenase   1 kivivGGGtaGwlaAaalakalkgklevtl 30 
                     +++++GGG  +   A +l k+ k+   v l
      AHX11477.1 146 DVIVIGGGNTAVEEALYLTKHAKK---VYL 172
                     699****************99954...554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      480  (0.0267723); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2261.83
//
Query:       AHX11478.1  [L=200]
Description: ahpC/TSA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    4.5e-32  110.6   0.0    5.6e-32  110.3   0.0    1.1  1  AhpC-TSA    AhpC/TSA family
    5.6e-10   38.9   0.0    9.7e-10   38.1   0.0    1.4  1  1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
    1.2e-09   38.0   0.0    1.4e-09   37.8   0.0    1.1  1  Redoxin     Redoxin


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.3   0.0   9.3e-36   5.6e-32       1     123 [.       5     139 ..       5     140 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.3 bits;  conditional E-value: 9.3e-36
                 TTSB----EEE....STTC.EEEECHHH.TTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H........SSEE CS
    AhpC-TSA   1 vgdkapdfelk....nadg.etvslsdy.kgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekes.......lnfpl 86 
                 vg+ka df++k     + + ++++l++   gk+ vlffyp d+++vC+te+ a+++++ +f+er++ vigvsvds++sh+++ +          +++pl
  AHX11478.1   5 VGKKAIDFTAKavmkGGSFcDDFNLQEQlLGKYGVLFFYPLDFTFVCPTEIIAFNNRISAFTERDAVVIGVSVDSHFSHAAWRNSSVkdggigeIEYPL 103
                 79*********77653333478***8877********************************************************999*********** PP

                 EE-TTSHHHHHTT-EETTTTECSCEEEEE-TTSBEEE CS
    AhpC-TSA  87 lsDeegkvakaygvlkeekglalratfvidkegkiry 123
                 +sD ++ ++++y+vl ++  +alratf+id++ ++r 
  AHX11478.1 104 VSDLKKSISRDYQVLIDD-SVALRATFIIDPDFNVRS 139
                 ***************998.*************99985 PP

>> 1-cysPrx_C  C-terminal domain of 1-Cys peroxiredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.0   1.6e-13   9.7e-10       1      38 [.     160     193 ..     160     195 .. 0.96

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 1.6e-13
                 HHHHHHHHT-BB-TTT.TBT-EEE---SSHHHHHHHHH CS
  1-cysPrx_C   1 ALQladkhgvatPAnWkpGdkvivpPpateedavkryl 38 
                 AL++++++g+++PA+W++G++++    at e +v +yl
  AHX11478.1 160 ALRHSAEYGEVCPAGWNKGKEAM---RATHE-GVSDYL 193
                 9**********************...*****.9*9997 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   2.3e-13   1.4e-09       3     136 ..       6     146 ..       4     158 .. 0.81

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 2.3e-13
                 TSBB---ECCEETTCEE...EEEHHH.HTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHH........TT-TSEE CS
     Redoxin   3 gdkaPdftlplaatdgn...svslse.fkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgk........eglkfpv 89 
                 g+ka dft + + ++g+   +++l+e + gk  v++f+p  f+ +C +e++++++    + e++  v++v++d+  f  ++w +         ++ +p+
  AHX11478.1   6 GKKAIDFTAKAVMKGGSfcdDFNLQEqLLGKYGVLFFYPLDFTFVCPTEIIAFNNRISAFTERDAVVIGVSVDS-HFSHAAWRNssvkdggiGEIEYPL 103
                 666666665555555543337899*99************************999886666*****999998765.68888888888889***888**** PP

                 EE-TTSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSC CS
     Redoxin  90 lsDgsaaftkalGlrleedaseglrtpryavidedgkvvylevepep 136
                 +sD ++++++++ + ++      ++++++++id d +v+   v + +
  AHX11478.1 104 VSDLKKSISRDYQVLIDDS----VALRATFIIDPDFNVRSAAVNDLN 146
                 *************887644....8***********999988877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1575.69
//
Query:       AHX11479.1  [L=377]
Description: cell cycle family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      3e-80  269.9  27.9    3.6e-80  269.7  27.9    1.0  1  FTSW_RODA_SPOVE  Cell cycle protein


Domain annotation for each model (and alignments):
>> FTSW_RODA_SPOVE  Cell cycle protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  269.7  27.9     2e-84   3.6e-80       6     358 ..      12     358 ..       7     359 .. 0.93

  Alignments for each domain:
  == domain 1  score: 269.7 bits;  conditional E-value: 2e-84
  FTSW_RODA_SPOVE   6 lvllllvilGlvmiysaslveslvlfgdsfvlfirqlvylllglivfvlllriplkfleklakllliislllLvlvkvplgssanGAkrWirlg 99 
                      l+++l ++ Gl + ysas        g    +  + +v +++gl  f+  l +  +f    a+ + i  + lLvl +  +g+++ GA rWi++ 
       AHX11479.1  12 LCFFLQIAAGLYVQYSASN----GEIG--PLFLHQLVVLIAVGLPFFLGALFLGTSFFYDKAFGIHILAISLLVLAAT-IGKTSMGATRWIQIM 98 
                      5555555567777776666....2222..4555566677889**************99999*************9999.*************** PP

  FTSW_RODA_SPOVE 100 gisiqPsEfvkialilflAavlskkkkevksrlrellillvivllilvlillqpdlgtavllliillvvlflsglslklilaivlalilviaiv 193
                      g+++qP E++k++ +l+l++++s +++    r + l+++++ ++ +l li+ qp lgt++ lli+++++ + ++++ + +l +vl+ +l+++++
       AHX11479.1  99 GVTFQPTELLKLSTVLMLSRYFSIARPSDLRRSTFLFLPFLHLMPVLYLIIRQPSLGTVIFLLILIFAIYYSAAVRYSFFLRLVLLGLLISPFL 192
                      ************************999999999999999999999999*************************************9999***** PP

  FTSW_RODA_SPOVE 194 llilledyqvkrvtslldpfkdplgsgYqviqsliAigsGGllGkGlgnsqq.kleyLPeahtDfIfavigEelGlvGvllllllffllivrgl 286
                      + + ++dyq++r++++  p+kd ++sgY ++qs iAigsGG+ G G+  + q +l++LPe+htDf+++vi+EelG++ +l+l + +++++v+gl
       AHX11479.1 193 WKYGVKDYQKERIMTFFHPSKDRRSSGYNIFQSEIAIGSGGFCGLGIVSGPQtQLKFLPERHTDFVLSVIAEELGFFAILILTISYLVIFVKGL 286
                      **************************************************999***************************************** PP

  FTSW_RODA_SPOVE 287 riarkakdrfgsllavgivllivvqsfinigmvlGllPvtGltlPflSyGGsSllalliligillnisreek 358
                       ia++++  f +ll  gi+++i+++ +in+ m++G++Pv+G++lP++SyGGs+ l+ +i++g+ll+i+  +k
       AHX11479.1 287 IIASRSEAVFTRLLSTGITTMIFLHFLINASMITGIIPVVGMPLPLISYGGSAALISMIALGVLLRIDVDQK 358
                      *******************************************************************98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       762  (0.042501); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.53
# Mc/sec: 2125.63
//
Query:       AHX11480.1  [L=139]
Description: nucleoside diphosphate kinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-52  176.7   0.0    2.4e-52  176.5   0.0    1.0  1  NDK       Nucleoside diphosphate kinase


Domain annotation for each model (and alignments):
>> NDK  Nucleoside diphosphate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.5   0.0   1.3e-56   2.4e-52       1     135 []       2     136 ..       2     136 .. 0.99

  Alignments for each domain:
  == domain 1  score: 176.5 bits;  conditional E-value: 1.3e-56
                 EEEEEEE-HHHHHTT-HHHHHHHHHHHT-EEEEEEEECE-HHHHHHHTGGGTTSTTHHHHHHHHTSSEEEEEEEESTTHHHHHHHHH--SSTTTSSTTS CS
         NDK   1 ertlvliKPdavkrgligeiisrleekglkivalkmlrlteeqaeehYaehkgkpffeelvefmtsgpvvalvlegedaiekvreliGatnpaeaapgt 99 
                 +rtl+++KPdav++++ig+i s +e++gl+i+a+k ++lt +qae++Ya hk++pff +lvefmtsgpvv++vl g+da++++r+l+G t+p++a+ gt
  AHX11480.1   2 QRTLSILKPDAVSKNIIGKINSYIESAGLRIIAIKQMTLTIDQAENFYAIHKDRPFFGDLVEFMTSGPVVVQVLCGDDAVSRYRQLMGDTDPRKADRGT 100
                 79************************************************************************************************* PP

                 HHHHH-SSSTT-SEEE-SSHHHHHHHHHHHSTGGGS CS
         NDK 100 iRadfgvslgeNlvHgSdseesaereiklfFkeeei 135
                 iR+df+ s++ N+vHgSds e+ae ei++fF++ ei
  AHX11480.1 101 IRGDFAESIDANCVHGSDSLENAETEIAFFFSKCEI 136
                 ********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (139 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      287  (0.0160076); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1032.54
//
Query:       AHX11481.1  [L=38]
Description: hypothetical protein NHE_0541 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.36
# Mc/sec: 319.14
//
Query:       AHX11482.1  [L=506]
Description: integral membrane protein MviN [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.8e-92  308.9  46.8    5.7e-92  308.7  46.8    1.1  1  MurJ             Lipid II flippase MurJ
    9.4e-14   51.7  18.4    9.4e-14   51.7  18.4    3.9  4  Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domai
    6.5e-07   29.1  11.1    6.5e-07   29.1  11.1    3.9  4  MatE             MatE


Domain annotation for each model (and alignments):
>> MurJ  Lipid II flippase MurJ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.7  46.8   9.5e-96   5.7e-92       1     438 [.      26     463 ..      26     478 .. 0.94

  Alignments for each domain:
  == domain 1  score: 308.7 bits;  conditional E-value: 9.5e-96
        MurJ   1 iaallGaglladaFnvAfklPnllrrlfaegalssaFvPvlaeakkkdeekaaefvrkvltllilvlllvtligilaapllirllatgf.deetlelav 98 
                 ia+++G++  +d+F+ Af++Pnllr +faega+s +F+P+++++++ ++ +a ef  k+  +l++vl +  + + ++++ +  ++a+g+  +  +    
  AHX11482.1  26 IANAFGTSISSDIFFAAFRIPNLLRSIFAEGAFSGVFLPIFSRLYDRNRVAALEFSYKIQLMLMGVLFITFITAEIFMEKILLFFAPGImGATSRDTFL 124
                 79*******************************************99*********************99999****************6344444446 PP

        MurJ  99 sllrillpylllvslsavfgavLnarkkFfapafsPvllNvsvIltllllanklgeeailaLaiGvliGgvlqllvqlpalkkaglllkprfafrdegl 197
                 +++ri++py++++ l+++  a+L++rkkF++ af P+++N++ I+t+ll   + +    + +++++++ g++q+l+ l  l + g+l  p     d + 
  AHX11482.1 125 TIARIIFPYIIFIALTSLYCAMLQSRKKFAPTAFCPIIMNICLIATVLLTTGTGT-VLLFHMSYAIVLSGIIQMLFLLLLLERNGMLPLPSPLKFDTNS 222
                 799********************************************99988777.89999**************************99999999999* PP

        MurJ 198 kkflklllptllgvsvsqlnllvdtalAsflaegsvsilayadrilqlPlglfgvsistvlLPrlSrsakekdedevrdllsqairltllllipvsfgl 296
                 + f++++lp+ l+  ++q+n +vdt++As  ++ ++s l+y+dri+qlPl+l+g+++ tv+L+  S ++++ d+d + + ++ a+ + ++l ip+++g+
  AHX11482.1 223 TIFFRKFLPAALSAEMYQINIFVDTFFAS-TIPCAISFLYYSDRIIQLPLALIGIALNTVILSLASDAVARTDTDRLIKIQNRALGIAIILGIPATVGV 320
                 *****************************.889****************************************************************** PP

        MurJ 297 lvlskpivsllfe.rGnFseedveataevLaayalgLipyalvklllrvfYAredtktPvkislislvlnillsllllpplgvvglalatslsaliglv 394
                 ++ ++ i++ lf   G+F+  +v +t ++L+++a++L++ +l+k++l+vf+A ++t+ P++ slis+ lni++++++++++++vg+ +++ ++a+++++
  AHX11482.1 321 IFTAQHIIESLFLlGGKFDSDSVINTTKALKVFAFALPAHILNKIFLAVFFAIGNTRIPTIFSLISVLLNIVMNYIFVQYYSYVGIIISSCIAAWFNAI 419
                 ********99996378*********************************************************************************** PP

        MurJ 395 llyvllrkrlklteargiktflaklvvllalaavvilllssltq 438
                 l++v+l+k+  ++ +++i t l+ +   ++l+   + l +++t+
  AHX11482.1 420 LMIVYLKKEQIFKLSKKIPTLLRDVFFSTSLMIFFLQLCNAFTE 463
                 ************************88888888888888877775 PP

>> Polysacc_synt_C  Polysaccharide biosynthesis C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.4       1.2   7.2e+03     102     114 ..      90     100 ..      74     118 .. 0.47
   2 ?    0.8  13.9      0.08   4.8e+02       3      86 ..     128     220 ..     126     262 .. 0.70
   3 ?    2.4   0.9     0.025   1.5e+02      54     106 ..     272     322 ..     265     336 .. 0.61
   4 !   51.7  18.4   1.6e-17   9.4e-14       1     138 [.     349     494 ..     349     499 .. 0.82

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 1.2
  Polysacc_synt_C 102 givvylllllllg 114
                      g++  +++ ++ +
       AHX11482.1  90 GVL--FITFITAE 100
                      222..22222222 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.08
  Polysacc_synt_C   3 ailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgi...vGaaiatvlallvvavlnlyalrrllgikl.......e 86 
                      +i+ ++iif++l++++ ++Lq+ ++   ++ + +i   + li ++ll+   g+     +++a+vl+ ++ ++++l +l r   ++l       +
       AHX11482.1 128 RIIFPYIIFIALTSLYCAMLQSRKKFAPTAFCPIIM-NICLIATVLLTTGTGTvllFHMSYAIVLSGIIQMLFLLLLLERNGMLPLpsplkfdT 220
                      7899******************98876666554443.34566666666555546668899***************9999988887766655541 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.025
  Polysacc_synt_C  54 givGaaiatvlallvvavlnlyalrrllgiklellrrll.kpllaalvmgivvy 106
                       ++G+a+ tv+  l++ ++      rl++i+    r l   ++l   + ++v++
       AHX11482.1 272 ALIGIALNTVILSLASDAVARTDTDRLIKIQN---RALGiAIILGIPATVGVIF 322
                      47899999999999999999999999999998...2222022222222222222 PP

  == domain 4  score: 51.7 bits;  conditional E-value: 1.6e-17
  Polysacc_synt_C   1 vLailalsiiflslstvlssiLqglgrqkialkalvigalvklilnllliplfgivGaaiatvlallvvavlnlyalrrllgikl.ellrrll. 92 
                      +L ++a++++ + l+ ++ +++ ++g ++i++++++i++l+++++n++++ ++++vG++i++++a  + a+l++++l+++  +kl + + +ll 
       AHX11482.1 349 ALKVFAFALPAHILNKIFLAVFFAIGNTRIPTIFSLISVLLNIVMNYIFVQYYSYVGIIISSCIAAWFNAILMIVYLKKEQIFKLsKKIPTLLr 442
                      5899*********************************************************************************944666664 PP

  Polysacc_synt_C  93 kpllaalvmgivvylllllllglllla........alalllavlvgalvYllll 138
                       +++++ +m   +  l++ + +  ++         a  +++++   + +Y+l l
       AHX11482.1 443 DVFFSTSLMIFFLQ-LCNAFTESHQGIlevyvlriASLMVICA-TSVGIYFLTL 494
                      77777777777766.5555555555557888774332444444.7888888776 PP

>> MatE  MatE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   8.7   9.1e-05      0.54      54     155 ..      64     167 ..      40     174 .. 0.80
   2 ?   -1.9   0.2      0.38   2.3e+03      74     101 ..     177     204 ..     171     209 .. 0.65
   3 !   29.1  11.1   1.1e-10   6.5e-07      35     161 .]     264     396 ..     231     396 .. 0.81
   4 ?    1.1   4.6     0.047   2.8e+02      79     154 ..     405     480 ..     398     487 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 9.1e-05
        MatE  54 tlvgqalGaknfkrakealrqglilllllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyisl 149
                 ++ ++ +  +++ ++++++ + l+l+ +l + ++ +  +f e+il +f              ++ ri++++i+++al+ +++++l++ +k+ +++++ +
  AHX11482.1  64 PIFSRLYDRNRVAALEFSYKIQLMLMGVLFITFITA-EIFMEKILLFFAPGIMgatSRDTFLTIARIIFPYIIFIALTSLYCAMLQSRKKFAPTAFCPI 161
                 566777777888888888888777777776666666.***********76654444777778899*****************************99988 PP

        MatE 150 isllln 155
                 i +++ 
  AHX11482.1 162 IMNICL 167
                 877654 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.38
        MatE  74 qglilllllsliiallvllfseqilslf 101
                 +g++ll+ +s +i+l +++   ++l l+
  AHX11482.1 177 TGTVLLFHMSYAIVLSGIIQMLFLLLLL 204
                 5666666667666666666666666665 PP

  == domain 3  score: 29.1 bits;  conditional E-value: 1.1e-10
        MatE  35 lsilsllfv.fllglstalttlvgqalGaknfkrakealrqglilllllsliiallvllfseqils.lftqdee....vlelakrylrililgipalal 127
                  +i++l  + ++++l+t + +l++ a+   +++r+ ++ +++l ++++l++++++ v++ +++i+  lf    +     +  + + l++ ++ +pa +l
  AHX11482.1 264 DRIIQLPLAlIGIALNTVILSLASDAVARTDTDRLIKIQNRALGIAIILGIPATVGVIFTAQHIIEsLFLLGGKfdsdSVINTTKALKVFAFALPAHIL 362
                 55555555558888888888999********************************99999998875244443334467666677889************ PP

        MatE 128 qlvlsgilrgagktkvplyislislllniplnyl 161
                 + ++ +++ ++g+t++p+++slis+llni++ny+
  AHX11482.1 363 NKIFLAVFFAIGNTRIPTIFSLISVLLNIVMNYI 396
                 *********************************7 PP

  == domain 4  score: 1.1 bits;  conditional E-value: 0.047
        MatE  79 llllsliiallvllfseqilslftqdee...vlelakrylrililgipalalqlvlsgilrgagktkvplyislislll 154
                 ++++s  ia+   +f  +++ ++ ++e+   +++++ ++lr +++++ +++++l l++++       + +y++ i++l 
  AHX11482.1 405 GIIISSCIAA---WFNAILMIVYLKKEQifkLSKKIPTLLRDVFFSTSLMIFFLQLCNAFTESHQGILEVYVLRIASLM 480
                 3333333333...345555555555555355566666789999999999999999999999999999999998888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (506 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       938  (0.0523175); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.40
# Mc/sec: 3811.05
//
Query:       AHX11483.1  [L=474]
Description: NADH-Ubiquinone/plastoquinone (complex I), various chains family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.5e-54  183.1  28.6    6.5e-54  183.1  28.6    1.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.2e-06   28.4   0.8    8.7e-06   25.7   0.2    2.9  1  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   2.5       0.5   4.5e+03     216     221 ..      42      47 ..       2     123 .. 0.56
   2 !  183.1  28.6   7.3e-58   6.5e-54       1     291 [.     127     417 ..     127     419 .. 0.90

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 0.5
  Proton_antipo_M 216 Fllags 221
                      Fl+ + 
       AHX11483.1  42 FLATLL 47 
                      222222 PP

  == domain 2  score: 183.1 bits;  conditional E-value: 7.3e-58
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLl.gilllynltgtlefeelskalelglnslelllllllllvgll 93 
                      +++L++l++++El  l++y L++   ++ ks++ +  ++ +  l s++L+l +il+ y+ltgt  f+e + +    ++s +  ++lll+++  +
       AHX11483.1 127 SGNLITLFIFYELLTLATYALVKHEDTE-KSNKCAKTYLSYLILPSVALFLpAILITYTLTGTFTFNETLHV----VSSGTPRVMLLLMFIYGI 215
                      789********************99666.8888999999999999988877478899************999....777777777777777789 PP

  Proton_antipo_M  94 vKsaqvplhlWlpdayveaPtpvsall.Aatlvkagvlllirllllla....vssneisqlllilaiismllgslvalaqtdiKrllAySsish 182
                       K+a +p+h Wlp+a + aPtpvsall A  +vkagv+ +++++  ++    +++ ++ ++l  +   +++++s++al++ ++K++lAyS+is+
       AHX11483.1 216 SKAAIFPMHGWLPKA-MVAPTPVSALLhAVAVVKAGVFCITKVVIYVFtmsdQANTQLGSILSYICGFTIIFASIMALRKESLKEILAYSTISQ 308
                      9**************.***********9999*********9988766643455666677888999999************************** PP

  Proton_antipo_M 183 lGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaav 276
                      l y++i l++ t+ +v+ a+ ++l+ha+ k++lF  +g++ +++    +  ++ g+  +mPi+ + +++++l++ GlPpta +l k+ i++ a+
       AHX11483.1 309 LSYITITLGIFTANSVQHALSYMLMHAFAKITLFFTVGAIFSAT-GKMNKSQIDGIGRHMPITMISFTIGALAMIGLPPTATLLCKAHIFSEAL 401
                      *************************************8886665.7778899****************************************** PP

  Proton_antipo_M 277 avslillvla.vvasv 291
                      +v+ ++++++ +v+++
       AHX11483.1 402 SVKNYFIIFTlIVSTG 417
                      ********99666665 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.2   9.7e-10   8.7e-06      11      55 ..      66     112 ..      57     117 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 9.7e-10
  Proton_antipo_N  11 sieigfllDklsalmllvvtfvsllvhlYSigYMa.dd.egyqRFfa 55 
                      +i i+f +D+  ++++l+ +f+s    +Y+i+YM+ ++ ++++ Ff+
       AHX11483.1  66 QIGIAFHIDQAVIVFALLCSFLSIPASIYAISYMHlNEaNKKASFFS 112
                      7899*******************************544146888987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       913  (0.0509231); expected 358.6 (0.02)
Passed bias filter:                      261  (0.0145574); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 3444.56
//
Query:       AHX11484.1  [L=42]
Description: hypothetical protein NHE_0544 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       178  (0.00992805); expected 358.6 (0.02)
Passed bias filter:                      126  (0.00702772); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.40
# Mc/sec: 315.78
//
Query:       AHX11485.1  [L=45]
Description: hypothetical protein NHE_0545 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       202  (0.0112667); expected 358.6 (0.02)
Passed bias filter:                      159  (0.00886831); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.39
# Mc/sec: 348.92
//
Query:       AHX11486.1  [L=187]
Description: hypothetical protein NHE_0546 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0054   16.5   0.1      0.055   13.2   0.0    1.9  2  TPR_21    Tetratricopeptide repeat-like domain
  ------ inclusion threshold ------
       0.03   14.6   0.2        2.5    8.6   0.0    3.2  3  HEAT      HEAT repeat


Domain annotation for each model (and alignments):
>> TPR_21  Tetratricopeptide repeat-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.1e-06     0.055      14     117 ..      21     120 ..      15     130 .. 0.68
   2 ?    2.4   0.0     0.012   1.1e+02      60     115 ..     119     178 ..      95     185 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.1e-06
      TPR_21  14 gvvlalvglaGwqgwqdyqeeq.aeeAsalYqqlqeaveakdaakakeaaeeladeyggtaYaalaaLllAkaaveagdlaaAkaqLewvlekakdeel 111
                  +vl + glaG  ++++  +++   e  alY++l+ + ++k+++++++ +++ ++      Y ++aa++l    v+a+d  + ++ +e+v  ++++  +
  AHX11486.1  21 FLVLLVSGLAGLAIYRYVDKTHyLMESVALYDALNISDTSKSKEALHRIVGRKIEP-----YSSIAAMQLSWLLVSADDEVQRSEIYERVSLESPSVYV 114
                 5788899**********976551688999*****9766666666555555555544.....66666666666666666666666666666666666666 PP

      TPR_21 112 kalarl 117
                 ++la+l
  AHX11486.1 115 RELAQL 120
                 666665 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.012
      TPR_21  60 eaaeeladey..ggtaYaalaaLllAkaaveag.dlaaAkaqLewvlek.akdeelkala 115
                 ++  ++ d +  +++ Ya  a +l A   +++g ++++ +a+L++v++   ++  +++la
  AHX11486.1 119 QLNVQITDGNvdPQSVYAFTARFLDAFMRFSSGhEVDEVRASLSNVVAAiDANPYVRDLA 178
                 5555555544225789**********99998874799******99987624455666666 PP

>> HEAT  HEAT repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0     0.059   5.3e+02       9      22 ..     107     120 ..     104     123 .. 0.82
   2 ?    1.0   0.0     0.078     7e+02       3      26 ..     143     167 ..     141     168 .. 0.69
   3 ?    8.6   0.0   0.00028       2.5      10      29 ..     168     187 .]     161     187 .] 0.87

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.059
                 HT-SSHHHHHHHHH CS
        HEAT   9 lsDpspeVReaAak 22 
                 l++ps  VRe A +
  AHX11486.1 107 LESPSVYVRELAQL 120
                 789*******9865 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.078
                 HHHHHHH.T-SSHHHHHHHHHHHHH CS
        HEAT   3 Plllkll.sDpspeVReaAakaLga 26 
                 +++++    ++  eVR++  + ++a
  AHX11486.1 143 DAFMRFSsGHEVDEVRASLSNVVAA 167
                 5666664488999***987766665 PP

  == domain 3  score: 8.6 bits;  conditional E-value: 0.00028
                 T-SSHHHHHHHHHHHHHHHH CS
        HEAT  10 sDpspeVReaAakaLgalae 29 
                  D +p VR+ A k L a++e
  AHX11486.1 168 IDANPYVRDLASKLLKAISE 187
                 599**************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       564  (0.0314574); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1401.73
//
Query:       AHX11487.1  [L=388]
Description: NADH dehydrogenase (quinone), D subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   2.1e-122  407.5   0.0   2.6e-122  407.2   0.0    1.1  1  Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd s
  ------ inclusion threshold ------
      0.034   13.0   0.0      0.056   12.3   0.0    1.3  1  NiFeSe_Hases    Nickel-dependent hydrogenase


Domain annotation for each model (and alignments):
>> Complex1_49kDa  Respiratory-chain NADH dehydrogenase, 49 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.2   0.0  2.9e-126  2.6e-122       1     271 []     118     388 .]     118     388 .] 1.00

  Alignments for each domain:
  == domain 1  score: 407.2 bits;  conditional E-value: 2.9e-126
                     HTT-HHHHHHHHHHHHHHHHHHHHHHSSSSS-TTBESSBBSS---TTHHHHHHHHHHHHHHHHHHHHHHHHSSSSHHHHHSSSS-BSHHHHHHHT CS
  Complex1_49kDa   1 DlGaltvflyafreRekildlleevtGaRltasyiriGGvarDlpegllekikeflkelekkldeleklltknrifkkRtkgvgvlskeealelg 95 
                     D+Ga+ +++++f+eRek+l+++e+++GaR++a+yir+GG+++D+pegl e+i +fl+++++kld++ ++lt+n+ifk+R++++g ++keea+ lg
      AHX11487.1 118 DVGAMNPLFWMFEEREKMLSFYEKASGARFHAAYIRPGGLSADIPEGLDEEIMSFLENFPQKLDDVADVLTNNPIFKQRLVDIGRVTKEEAVMLG 212
                     9********************************************************************************************** PP

                     T-SSSSGGGT-TTTHHHHSS-SSGGGS-------SSBSHHHHHHHHHHHHHHHHHHHHHHHHT--.S-SB---TTTS---GGGGGT-HHHHHHHH CS
  Complex1_49kDa  96 ltGpvlRasGvkyDlRkaepYeaYdeldfdvpvgeegDvydRylvrveEmrqSlkIieqaleklpegpvlaedkkvalpkkeevkksmealihhf 190
                     ++Gp++RasG+++DlR+++pYe+Yd+l+f++pvg++gD+ydRylvr++Em +S+kI +q+le lpegpv+++d+k+++p+++++k+smealihhf
      AHX11487.1 213 FSGPLIRASGIPWDLRRSQPYEVYDSLEFKIPVGKNGDCYDRYLVRMAEMYESVKIAKQCLEALPEGPVVVDDPKIVPPSRDKMKTSMEALIHHF 307
                     *********************************************************************************************** PP

                     HHHHS-----SEEEEEEEEETTEEEEEEEEEESSSS-SEEEEE-HHHHTTTTHHHHTTTS-SGGGTHHHHTT---HHHHH- CS
  Complex1_49kDa 191 klvtegfkvpkgevyaavEapkGelgvylvsdgsskpyrlkirapsfvnlqaleellkgellaDvvailgsldivlgevDR 271
                     kl++eg++vp+ge+y  vE+pkGe+gvy+vsdg++kpyr++irap+fv+lqal+ l++g++laD++ai+gsldiv+gevDR
      AHX11487.1 308 KLYSEGYHVPEGELYLPVESPKGEFGVYIVSDGTNKPYRCRIRAPGFVHLQALDFLSRGHMLADIPAIIGSLDIVFGEVDR 388
                     ********************************************************************************9 PP

>> NiFeSe_Hases  Nickel-dependent hydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   6.3e-06     0.056       1      77 [.      43     118 ..      43     122 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 6.3e-06
                   --HHHHTTTS-GGGHHHHHHTT-SSSTTHHHHHHHHHHHHHHT----HHHHHHHHHHHHHHHHHHHHHHHHHTTGGG CS
  NiFeSe_Hases   1 RGlElilkgrdprdawalvqRiCGVCttvHalasvravedAlgikipknarlirnliaaalllhdhivhFYhLhalD 77 
                   RG E++++ ++  +a  + +R   V +++  +a   +ve+ lgi+ p  a++ir +    + l +h++   + halD
    AHX11487.1  43 RGTEKLIEYKTYLQALPYFDRLDYVSPMAQEHAYSLCVEKLLGITAPIRAQYIRVIFLELTRLLNHLLNV-TTHALD 118
                   9*********************************************************999999999864.445555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (388 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       360  (0.0200792); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.37
# Mc/sec: 3108.39
//
Query:       AHX11488.1  [L=418]
Description: serine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.6e-31  109.6   0.0    2.9e-31  108.8   0.0    1.4  1  tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, 
    1.1e-11   44.9   2.9    1.8e-11   44.2   2.9    1.4  1  Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain


Domain annotation for each model (and alignments):
>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  108.8   0.0   3.3e-35   2.9e-31      12     179 .]     221     392 ..     215     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 108.8 bits;  conditional E-value: 3.3e-35
                   EE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTS....TBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.SCEEEEEE CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b  12 iLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEks....dsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlglefraiiel 104
                    L+Pt+e t+ + ++d+  + ++LP+++++++ ++R E+     d++G++R+++F + + + + +++++ ++l+ +++ +++++++lg+++r+++++
    AHX11488.1 221 RLIPTSEVTLLNFVSDNFFQAEELPIRMTAYSECFRSEAGssgkDTKGMIRQHQFGKVELVGVTTPEESGEELERMVQIVEDLLQKLGIPYRVVLLC 317
                   599**************9999******************558999**************************************************** PP

                   GTTSCBTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEE.EEHHHHHHHHHHHH CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxx RF
  tRNA-synt_2b 105 msaksadykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaa.igveRllsaileqn 179
                    +++ + + +++++e++ +s++ ++ei++++++g+ +++rl++++ +  +r+ + ++++ + +++ R+l aile++
    AHX11488.1 318 AGDIGFCARKTYDIEVWIPSQGCYREISSCSNCGDFQARRLSIKY-KFGKRKGFLHTLNGSsLALGRTLVAILENY 392
                   *********************************************.6667888999999999************96 PP

>> Seryl_tRNA_N  Seryl-tRNA synthetase N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   2.9   2.1e-15   1.8e-11       1     107 [.       1     103 [.       1     104 [. 0.96

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 2.1e-15
                   ---HHHHHH-HHHHHHHHCCCTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCTTS-TCCCCCCCHHHHHHHHHHHHHHHHHHHHH CS
  Seryl_tRNA_N   1 MLDiklirenpeavkeklkkRgedkadvdelleldekrrelqveleelqaerNelskeIgkakkkkedaeeliaevkelkeelkaleaelkeleael 97 
                   M D+ +i +n++ ++e ++kRg    d  ++++l++++re +++l+ lqa +N l+k+++        ++++i+++k +  e+++++++ + ++++l
    AHX11488.1   1 MNDLEYIASNTKRFAEMMEKRG-LRFDPTSVIDLYKQKREQITTLNTLQAAKNDLAKSFSDPD---VVRSKIIEKSKFIDSEIAKIKEAIQIVSERL 93 
                   77*******************5.999********************************98776...568**************************** PP

                   HHHHCTS--- CS
  Seryl_tRNA_N  98 eklllaiPNi 107
                   +++ll++PNi
    AHX11488.1  94 DTILLNLPNI 103
                   *********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (418 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       811  (0.045234); expected 358.6 (0.02)
Passed bias filter:                      716  (0.0399353); expected 358.6 (0.02)
Passed Vit filter:                        59  (0.00329076); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 3119.37
//
Query:       AHX11489.1  [L=309]
Description: IPP transferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    1.9e-40  139.1   0.0    2.5e-40  138.7   0.0    1.1  1  IPPT       IPP transferase
    1.3e-05   24.8   0.2     0.0022   17.4   0.0    2.2  2  IPT        Isopentenyl transferase
  ------ inclusion threshold ------
      0.012   15.3   0.0      0.022   14.5   0.0    1.5  1  IstB_IS21  IstB-like ATP binding protein
      0.024   14.9   0.0       0.21   11.9   0.0    2.3  2  AAA_22     AAA domain
      0.035   14.4   0.1      0.067   13.5   0.1    1.4  1  Vhr1       Transcription factor Vhr1
      0.056   13.6   0.0       0.14   12.3   0.0    1.6  2  LEH        Limonene-1,2-epoxide hydrolase catalytic domain
       0.07   12.2   0.0       0.12   11.4   0.0    1.3  1  T2SSE      Type II/IV secretion system protein
      0.099   13.3   0.0       0.17   12.5   0.0    1.4  1  SnoaL_2    SnoaL-like domain
       0.14   12.3   0.0       0.33   11.1   0.0    1.6  2  AAA_33     AAA domain
       0.15   11.5   0.0       0.32   10.4   0.0    1.6  1  TniB       Bacterial TniB protein


Domain annotation for each model (and alignments):
>> IPPT  IPP transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.7   0.0   1.4e-43   2.5e-40       1     224 [.      44     286 ..      44     290 .. 0.85

  Alignments for each domain:
  == domain 1  score: 138.7 bits;  conditional E-value: 1.4e-43
                 TTBTT-HTTTT---HHHHTTS-EESSS-B-TTS---HHHHHHHHHHHHHHHHHTT-EEEEEES-HHHHHHHHCTG-S--B--HHHHHHHHHHHHHSHHH CS
        IPPT   1 qvYrgmdIgTakptaeeragvphhlidildpdeeysvadFqkdalkaieeilargkipilvGGTglYikallegldelpeadeelraeleeeaeeegle 99 
                 qvY+++++ T ++ a+   g+ +  +++ +   + sv ++ +d+ + +e ++ +gkip++vGGT +Yi +l++g++ lp+  ++l ++l+ e+++ g +
  AHX11489.1  44 QVYKEVPVLTSQAPADS--GLLYGYLSVFSS-CRASVFEWMRDCADSLETVWMEGKIPLVVGGTPMYIYSLIHGVNLLPSLPPSLLRDLSLEYDRLGSS 139
                 9***********98654..455544555554.589***************************************9778988899999998877777877 PP

                 H.HHHHHHHC-HHHHTTS-TT-HHHHHHHHHHHHHHSS-HH................ECEEEEEECSHHHHHHHHHHHHHHHHHTTHHHHHHHHHH... CS
        IPPT 100 a.lheelkevdpeaaakihpndrqRiiRalevyeetgkpls................ellviglesdreelyeridkRvdemleaGlleEveklla... 178
                 + l + ++  + +   ++ p+d+++++R + ++ +tgk+++                e +v ++ ++re+ly+ri++R+ e l++G+++Ev++l++   
  AHX11489.1 140 SfLSSFVAGFNLDI--SLFPSDKYKLVRDVAYLVHTGKTIQqlydgstifrvpyssiE-VVSVIPESREVLYSRINERFVEALDSGAMDEVKALIQdee 235
                 74777777777655..789**********************88888888877776332.4444437*****************************8887 PP

                 ....C.CCCSTTSHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHTT CS
        IPPT 179 ....k.alqaigykelleylegelsleeaieklkaatrqyaKrQltWfrkk 224
                     + +++  g++e+ +yl++e+s+e++++k ++++r+yaKrQltWfr+k
  AHX11489.1 236 iyknPaVTTICGFREIASYLRSEISFEQMVSKSQQSIRHYAKRQLTWFRNK 286
                 77764358999**************************************98 PP

>> IPT  Isopentenyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   1.2e-06    0.0022       3      51 ..      10      60 ..       8      65 .. 0.84
   2 !    5.3   0.0    0.0061        11     149     197 ..     220     269 ..     199     279 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 1.2e-06
         IPT  3 vylifGatttGKtaeaiklaketg.apvivlDRvqcyselav.gsGrplee 51
                v ++ G+t+ GKta a +l +++  + vi +D  q y+e+ v +s +p ++
  AHX11489.1 10 VLVLTGPTSAGKTAIACSLHQSNEiFTVINADSKQVYKEVPVlTSQAPADS 60
                67899***************9875379************976467777665 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0061
         IPT 149 gaslldElaelwkepk..arailedidGyryildyarkkkvtidklanlda 197
                  ++ +dE+++l ++++  +++++  i+G+r i +y r  +++++++ +  +
  AHX11489.1 220 DSGAMDEVKALIQDEEiyKNPAVTTICGFREIASYLRS-EISFEQMVSKSQ 269
                 4567999999998776336789*************975.789988876554 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.2e-05     0.022      42      70 ..       3      31 ..       1      59 [. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.2e-05
   IstB_IS21 42 sfiekkenivllGpsGvGKshlaialgve 70
                 f++++  +vl+Gp+ +GK+ +a++l ++
  AHX11489.1  3 GFVNSRRVLVLTGPTSAGKTAIACSLHQS 31
                6999*********************9875 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00012      0.21       4      53 ..       7      55 ..       5      67 .. 0.80
   2 ?   -0.3   0.0      0.69   1.2e+03     106     135 ..      75     110 ..      65     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00012
      AAA_22  4 tagilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstss 53
                ++++lv+tG++ +GKT  +  l++++++     ++++++v+ ++p++ts+
  AHX11489.1  7 SRRVLVLTGPTSAGKTAIACSLHQSNEI-FTVINADSKQVYKEVPVLTSQ 55
                6899*******************99843.344448888888888888765 PP

  == domain 2  score: -0.3 bits;  conditional E-value: 0.69
      AAA_22 106 eealeeLrsllnl.....srkgvqliLvGtp.elrk 135
                 + ++e+ r++++       + +++l++ Gtp  ++ 
  AHX11489.1  75 ASVFEWMRDCADSletvwMEGKIPLVVGGTPmYIYS 110
                 668999999999999999999999999999977765 PP

>> Vhr1  Transcription factor Vhr1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.1   3.8e-05     0.067      18      88 ..     205     279 ..     199     281 .. 0.76

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.8e-05
        Vhr1  18 ekkWkrfssrrLeLidkleLsekkaseqdeeikkiaei.Lrtefe...ypeetlkefekLvraavqsvrrnrkrs 88 
                 e ++ r  +r +e +d+  + e ka  qdeei k  ++     f+      ++  +fe++v  + qs+r   kr 
  AHX11489.1 205 EVLYSRINERFVEALDSGAMDEVKALIQDEEIYKNPAVtTICGFReiaSYLRSEISFEQMVSKSQQSIRHYAKRQ 279
                 6678899999**********************764433133344310033344568**************99995 PP

>> LEH  Limonene-1,2-epoxide hydrolase catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       4.5   8.1e+03      29      71 ..      42      86 ..      37      93 .. 0.59
   2 ?   12.3   0.0   7.7e-05      0.14       5      54 ..     210     258 ..     208     279 .. 0.80

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 4.5
                EE.EEEETTTEEEE-HHHHHHHHHTT...TTT-EEEEEEEEEEEE CS
         LEH 29 dlevyeneglstihGraeaiallerl..sadilavevkilriaad 71
                 ++vy+++++ t + +a+   l+  l  + ++ a  ++ +r  ad
  AHX11489.1 42 SKQVYKEVPVLTSQAPADSGLLYGYLsvFSSCRASVFEWMRDCAD 86
                556677777666666666555555554455555555555555555 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 7.7e-05
                 HHHHHHHHHHHHT-HHHHHHHEEEEE.EEEETTTEEEE-HHHHHHHHHTT CS
         LEH   5 rvVeaFlaalqeddydaavrrlatdlevyeneglstihGraeaiallerl 54 
                 r+ e F++al+   +d  v++l +d+e+y+n+ ++ti G +e +  l+  
  AHX11489.1 210 RINERFVEALDSGAMD-EVKALIQDEEIYKNPAVTTICGFREIASYLRSE 258
                 5678999**9776665.5788999999***************99998865 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   6.6e-05      0.12     126     148 ..       5      27 ..       3      46 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.6e-05
       T2SSE 126 vrerglilvsGgTgsGKttllya 148
                 v++r +++++G+T+ GKt ++ +
  AHX11489.1   5 VNSRRVLVLTGPTSAGKTAIACS 27 
                 67899*************88744 PP

>> SnoaL_2  SnoaL-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   9.8e-05      0.17       2      47 ..     213     259 ..     212     288 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 9.8e-05
                 HHHHHHHHTTCHHHHHHTEEEEEEEEET.TSEEESHHHHHHHHHHHH CS
     SnoaL_2   2 raflaalnagdldalaalfapdvvwedp.ggelrGreairaffralf 47 
                 ++f++al++g +d++ al  ++  + +p + ++ G  +i+ ++r+  
  AHX11489.1 213 ERFVEALDSGAMDEVKALIQDEEIYKNPaVTTICGFREIASYLRSEI 259
                 79**************************877799****999998765 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00018      0.33       1      38 [.      10      46 ..      10      90 .. 0.75
   2 ?   -3.2   0.0       4.9   8.7e+03      28      50 ..     255     277 ..     251     285 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00018
      AAA_33  1 lvllvGlpGsGKstlaerllkklg.avllssdtlrrrlf 38
                +++l G+  +GK+  a +l++ +  +++++ d+  ++++
  AHX11489.1 10 VLVLTGPTSAGKTAIACSLHQSNEiFTVINADS--KQVY 46
                68999*******************999999997..3333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 4.9
      AAA_33  28 lssdtlrrrlfgtdqqsktdytr 50 
                 l+s + +++++ + qqs++ y++
  AHX11489.1 255 LRSEISFEQMVSKSQQSIRHYAK 277
                 56666677787777777776665 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   0.00018      0.32      36      82 ..       9      61 ..       5      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00018
        TniB 36 pnlllvGdsnnGKtmivekFarlhppek......dedaekvpvlvvqappkpd 82
                + l+l G++  GKt+i+ + +++++  +      ++  ++vpvl+ qap  + 
  AHX11489.1  9 RVLVLTGPTSAGKTAIACSLHQSNEIFTvinadsKQVYKEVPVLTSQAPADSG 61
                56899************999988865321211112334589*******98764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      542  (0.0302304); expected 358.6 (0.02)
Passed Vit filter:                        70  (0.00390429); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 2272.12
//
Query:       AHX11490.1  [L=102]
Description: hypothetical protein NHE_0551 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (102 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 768.48
//
Query:       AHX11491.1  [L=45]
Description: hypothetical protein NHE_0552 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       455  (0.0253779); expected 358.6 (0.02)
Passed bias filter:                      226  (0.0126053); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.27s 00:00:00.62 Elapsed: 00:00:00.43
# Mc/sec: 311.50
//
Query:       AHX11492.1  [L=605]
Description: cytochrome C assembly family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-38  130.2  20.0    8.9e-38  130.2  20.0    4.1  3  Cytochrom_C_asm  Cytochrome C assembly protein
    1.5e-26   93.4   6.0    2.1e-26   93.0   4.6    1.9  2  CcmF_C           Cytochrome c-type biogenesis protein CcmF C-
  ------ inclusion threshold ------
       0.21   11.7   5.2         13    5.9   0.8    4.1  3  DUF962           Protein of unknown function (DUF962)


Domain annotation for each model (and alignments):
>> Cytochrom_C_asm  Cytochrome C assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.6      0.23   1.4e+03      19      53 ..      16      50 ..       8      69 .. 0.59
   2 !  130.2  20.0   1.5e-41   8.9e-38       1     208 [.      72     276 ..      72     283 .. 0.88
   3 ?   -7.6  10.6         3   1.8e+04     165     197 ..     406     435 ..     291     523 .. 0.66

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.23
  Cytochrom_C_asm 19 gllleylarklnlsllaavaliaalillgfalfll 53
                       ll++l r +n+sl+ +++++++l+  +++   l
       AHX11492.1 16 LSLLSSLFRRVNISLFLNSIIFLTLFHAYISDNFL 50
                     33344455666777666666666665555554433 PP

  == domain 2  score: 130.2 bits;  conditional E-value: 1.5e-41
  Cytochrom_C_asm   1 lsnleesllllawilsllgllleylarklnlsllaavaliaalillgfalf.........lllaelqesadlnpalqspilmiHvplallsYat 85 
                      +  +e+s++l+ w+lsl+ +l+++++r+   ++ + v+ +++ +l +f++f          ++    ++  lnp+lq+  lmiH+p+++l+Y++
       AHX11492.1  72 WTTHEGSMILWIWSLSLYLFLFSKFYRT--SQIRQLVITTQSYVLSIFLVFiiysgnpfkKVILSSTNGLGLNPILQDLALMIHPPILYLGYVG 163
                      789*********************9999..5555566666666666666667789**99955555667889*********************** PP

  Cytochrom_C_asm  86 liigallsialliierqlkkkkklklsanlkllkqldrlsyriiliGfvlltigiilGsvWa..eeaWGsywsWDpketaslitWlvfaallhs 177
                       +i+++++ia l+ +r              ++ +   +++ ++ l++f +lt+gi lG +W   e++WG++wsWDp+e++sl++Wl+ +++lhs
       AHX11492.1 164 TSICFSIAIAILLSSR-------------SREEE--FKILNHFLLVAFTFLTLGIGLGGWWSyrELGWGGFWSWDPVENVSLMPWLLLLGALHS 242
                      ************4333.............33333..478999**************************************************** PP

  Cytochrom_C_asm 178 ri..ek.gwrgkkaailailgflllllayfgvrl 208
                       +   k g+ +  ++il+ilgf+ ++ ++f+ r 
       AHX11492.1 243 SFlsAKrGLFKGLSIILSILGFIASICGTFITRT 276
                      9999667***********************9986 PP

  == domain 3  score: -7.6 bits;  conditional E-value: 3
  Cytochrom_C_asm 165 litWlvfaallhsriekgwrgkkaailailgfl 197
                      +i +++ a ll +    ++++  +a+l++ g+l
       AHX11492.1 406 FIILILLASLLSLG---NFNNTLTAFLSFSGML 435
                      22222222222222...3444444444444443 PP

>> CcmF_C  Cytochrome c-type biogenesis protein CcmF C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.1     0.062   3.7e+02      94     184 ..     242     335 ..     227     336 .. 0.61
   2 !   93.0   4.6   3.5e-30   2.1e-26      34     322 ..     333     604 ..     296     605 .] 0.78

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.062
      CcmF_C  94 GpllrWkraklaellkrllvalvlalvlall.lal.ll...gelkvlaalglalavwvvlaalaelaerlrakakellarlrklprsawGmvlAHl 184
                 +++l+ kr+ ++ l   l +  ++a +++++ + + ++   +++++ a  g+ l ++ ++  +++++  +  +++++l  ++     + G ++AH+
  AHX11492.1 242 SSFLSAKRGLFKGLSIILSILGFIASICGTFiTRTgMTeslHTFNTNAESGVYLLIITLVLFVTSMWILI--TRHRSLYAAEPKDIRFSGNMVAHF 335
                 5566677777777776676665555555554322323344466777777777777777777777777776..456677777777888888888886 PP

  == domain 2  score: 93.0 bits;  conditional E-value: 3.5e-30
      CcmF_C  34 EsaLllnNllLvvaaavVllGTLyPlvldalglgkiSVGaPyFnavfvplmvplllllgvGpllrWkraklaellkrllvalvlalvlalllal.llge 131
                   ++l+ N+l +   +v++  T++P + + lg + + + + ++n++f  + ++l + l +   l  k  + ++l  ++++     ++la ll l  ++ 
  AHX11492.1 333 AHFILIQNILCILLFVVIFTATILPAASKLLGYDAMYIDQSFYNSIFGQIGAILGICLSLFIGL--K--SYKKLYLEFIIL----ILLASLLSLgNFN- 422
                 4689**********************************************99988877654433..2..223333333333....3333333321222. PP

      CcmF_C 132 lkvlaalglalavwvvlaalaelaerlrakakellarlrklprsawGmvlAHlGvavtvlGvalvsayeverdvrlkpgesvevagyefefegveeveG 230
                  ++l+a+  + ++  +l++ ++ ++ l    k+ ++ ++  ++++ +  l HlG+++++  +a   ++++e +   kpg++++++ y++ +++ ++++ 
  AHX11492.1 423 -NTLTAFLSFSGMLTILSVSVSYIRNL----KKEVRITAIATNKMNSSFLTHLGFGLLLYSIAGFASHSAEVKKYFKPGDQITIKTYNIGLKEYSKIDN 516
                 .23333333333333333333443443....334455556678888999************************************************** PP

      CcmF_C 231 pNYtaeraelevsrdgkevatlepekRlYtvqempmteaaidagllrdlYvalGeeledeawavrlyvkpfvrwiWlGallmalGGllalld 322
                   +t+ r+ ++v++ g    +lepe R+Y+++++  te+a  + ll d+ v++    e+  +av +y+k  +++iWl  +++ +G l  ++d
  AHX11492.1 517 LLFTGIRGVFTVNQTG----RLEPEFRFYKQEKTLNTESATIHYLLDDVQVVISGVDEKFGLAVEIYYKEKIQLIWLSLIIILFGVLYKICD 604
                 ************9877....8********************************9955555*************************9988887 PP

>> DUF962  Protein of unknown function (DUF962)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.2   0.0    0.0038        23      21      44 ..       4      43 ..       1     274 [. 0.83
   2 ?   -2.1   0.1      0.68   4.1e+03      32      50 ..     295     313 ..     278     321 .. 0.59
   3 ?    5.9   0.8    0.0022        13      20      63 ..     330     373 ..     311     378 .. 0.83

  Alignments for each domain:
  == domain 1  score: 5.2 bits;  conditional E-value: 0.0038
      DUF962 21 rllHfigvplilltvlllllrak................l 44
                +  H+ig++l++l++l  l+r                  +
  AHX11492.1  4 IPHHYIGTTLLYLSLLSSLFRRVnislflnsiifltlfhA 43
                567********99999988776534433333333333330 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 0.68
      DUF962  32 lltvlllllraklklllal 50 
                 ll+++l+l+ +++++l++ 
  AHX11492.1 295 LLIITLVLFVTSMWILITR 313
                 3444444445555555554 PP

  == domain 3  score: 5.9 bits;  conditional E-value: 0.0022
      DUF962  20 nrllHfigvplilltvlllllraklklllalfvvgyifafvGHf 63 
                 n   Hfi +  il+++l++++++   l +a+ ++gy + ++   
  AHX11492.1 330 NMVAHFILIQNILCILLFVVIFTATILPAASKLLGYDAMYIDQS 373
                 7899********************************99888655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (605 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1012  (0.0564449); expected 358.6 (0.02)
Passed bias filter:                      347  (0.0193541); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.27s 00:00:00.88 Elapsed: 00:00:00.42
# Mc/sec: 4344.02
//
Query:       AHX11493.1  [L=334]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.035   14.4   0.3       0.12   12.6   0.3    2.0  1  DUF5379   Family of unknown function (DUF5379)
       0.35    9.6   0.6        3.7    6.2   0.1    2.1  2  DUF2207   Predicted membrane protein (DUF2207)
        1.1    9.0  10.1       0.99    9.2   1.7    2.5  3  Amastin   Amastin surface glycoprotein


Domain annotation for each model (and alignments):
>> DUF5379  Family of unknown function (DUF5379)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.3   2.1e-05      0.12      25      48 ..      33      56 ..      30      89 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 2.1e-05
     DUF5379 25 vytlglgllsglatllflfiglvi 48
                vy   l ++sg+at++f+++++ +
  AHX11493.1 33 VYLGVLSVFSGIATFVFIYVAACL 56
                7777899************99765 PP

>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2   0.1   0.00062       3.7     377     448 ..      29     110 ..      19     115 .. 0.67
   2 ?    1.7   0.0     0.014        85     191     403 ..     219     251 ..     185     301 .. 0.56

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.00062
     DUF2207 377 kkklkklsalglgliilglilillallllvll..............lvfllilllillliaiivlllfsrllgrrteeGaellakw 448
                 kk   +l++l+++ +i+ +++i +a++    l              ++f+ i++l+l++ ++++ l+++ ++ r +++ + +l+++
  AHX11493.1  29 KKLEVYLGVLSVFSGIATFVFIYVAAC----LaqaglfrrdlkeqvWTFIEIVSLVLAVTCVAMHLVSRCYVVRGKANLRSELDEI 110
                 334444444444444444444444444....3455599***********************9998887666666566666666655 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.014
     DUF2207 191 keeqkntreraarlslallillilllilllllllllliklllwkkygrepkvkevdpeYerdvPedlsPavvgylvkgdkvdengltAtlldLavkgyi 289
                 + e +   ++++ ++ ++++l++l+++l+                                                                      
  AHX11493.1 219 EKESD--PSKKQGRFSSYFALPLLACLLV---------------------------------------------------------------------- 245
                 33333..3444444444444444444444...................................................................... PP

     DUF2207 290 tieeekkkkkkgkdtltilkkndeeldpyEkalldlLfdkseegkslkeikkyakkskkkakkfkkalkkwksavkkkergyfdkkgkkklkklsalgl 388
                                                                                                                    
  AHX11493.1   - ---------------------------------------------------------------------------------------------------   -
                 ................................................................................................... PP

     DUF2207 389 gliilglilillall 403
                          i+ +++
  AHX11493.1 246 ---------ICSTIG 251
                 .........333333 PP

>> Amastin  Amastin surface glycoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.2   1.7   0.00016      0.99      51     114 ..      21      95 ..      13     107 .. 0.60
   2 ?    5.4   0.0    0.0024        15      55     153 ..     139     250 ..     118     251 .. 0.54
   3 ?   -3.2   0.4       1.1   6.9e+03      69      89 ..     277     297 ..     273     305 .. 0.69

  Alignments for each domain:
  == domain 1  score: 9.2 bits;  conditional E-value: 0.00016
     Amastin  51 lwkeCprrrsrfraaqafsiisilvlaaalllsvllllcc..............sslkwvclllnivsvvtllivwal 114
                 l+++C+r+++       + ++s++  +a++++  ++++                  + +v l+l++  v++ l++   
  AHX11493.1  21 LLAKCERIKKLE---VYLGVLSVFSGIATFVFIYVAACLAqaglfrrdlkeqvwTFIEIVSLVLAVTCVAMHLVSRCY 95 
                 556665555432...234567777777777777776666567777776655555555555555555555555555444 PP

  == domain 2  score: 5.4 bits;  conditional E-value: 0.0024
     Amastin  55 Cprrrsrfraaqafsiisilvlaaalllsvllllcc.sslkwvclllnivsvvtlli.vwalmvavyykrfCdalk............sttakygaGFg 139
                 C   r  f+   a s+i ++  + a++  ++  +++ +++k + + +n+ s+v   + + +++++v +  + d+ +            +++ ++++ F+
  AHX11493.1 139 CFLQRAAFNFEFAASLIFLASELIAVIEIFVP-YGLrNCHKSLGIPVNLQSAVDFSAlTLVIVASVLKIMVADEQRrrehdekesdpsKKQGRFSSYFA 236
                 44444444444454444444444443333332.222256666667777766663333033333333333333333334444555555555559999*** PP

     Amastin 140 Llvvawlldliniv 153
                 L ++a+ll ++ ++
  AHX11493.1 237 LPLLACLLVICSTI 250
                 ********999765 PP

  == domain 3  score: -3.2 bits;  conditional E-value: 1.1
     Amastin  69 siisilvlaaalllsvllllc 89 
                 +ii  + l a ++l+v+ +++
  AHX11493.1 277 YIIRAISLSALIVLGVIKVFS 297
                 566666667777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (334 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1013  (0.0565006); expected 358.6 (0.02)
Passed bias filter:                      628  (0.0350271); expected 358.6 (0.02)
Passed Vit filter:                        56  (0.00312343); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.21s 00:00:00.72 Elapsed: 00:00:00.37
# Mc/sec: 2680.06
//
Query:       AHX11494.1  [L=402]
Description: D-alanyl-D-alanine carboxypeptidase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-60  203.7   2.2      4e-60  203.2   2.2    1.1  1  Peptidase_S11    D-alanyl-D-alanine carboxypeptidase
    3.8e-11   43.0   0.0    5.4e-11   42.5   0.0    1.2  1  Beta-lactamase2  Beta-lactamase enzyme family
      4e-08   33.4   0.2    1.6e-07   31.4   0.0    2.0  2  PBP5_C           Penicillin-binding protein 5, C-terminal dom


Domain annotation for each model (and alignments):
>> Peptidase_S11  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.2   2.2   6.8e-64     4e-60       5     232 ..      50     273 ..      47     281 .. 0.94

  Alignments for each domain:
  == domain 1  score: 203.2 bits;  conditional E-value: 6.8e-64
                    S---.--SSSEEEEEETTTTEEEEEESTTS-BE-GGGHHHHHHHHHHHHHHTTSS-TTSEEE--GGGHGCCSGTTSSTTS-TTT-EEEHHHHHHHH CS
  Peptidase_S11   5 asepleiaaksailvdantGkvLyeknadevveiASltKlmTaylvlealkkgklkeddkvtisedayalgnnkevsniflkkgskvsvkdLlegl 100
                    ++++++ +ak+a+++d++ + vL e+nade +++ S++KlmT yl+   lk+g +k+dd +++s++a+++      s +flk+g+kv+v+dLl+g+
     AHX11494.1  50 SAADFTTSAKQALILDYTNNIVLFEHNADEIMHPSSMSKLMTLYLMFSKLKAGIVKMDDVYRVSKNAWEKR----GSTMFLKEGQKVKVEDLLKGI 141
                    5678899***************************************************************9....8******************** PP

                    HCC--HHHHHHHHHHHHSSHHHHHHHHHHHHHHTT-TT-B-SSSSSTSHTTCBB-HHHHHHHHHHHHHHHHHHHHGGGESEEEETTECTEEEESST CS
  Peptidase_S11 101 lvssgNdAavalAekiaGsekaFvkmMnkkakelGlkntkfvnptGLdnenqvssArdlailakallkdlpeelkitkeksltfngikklnyknkn 196
                    ++ sgNdA+v +Ae   Gse+aFv+ Mn+ ak++Gl+n +fvn+tGL+++n+++sArd+  la+++ +d+pe + + +ek l+fn   +++++n+n
     AHX11494.1 142 AILSGNDASVVVAEGSMGSEEAFVEEMNQTAKSMGLSNSSFVNTTGLTAQNHYMSARDVVKLAVKIYEDFPEYYYLFSEKGLMFN---NIKQNNTN 234
                    ************************************************************************************9...99999999 PP

                    G...GGGTTTSEEEEEEEEEETTTEEEEEEEEEETTEEE CS
  Peptidase_S11 197 k...llyrktlnvdglktGytkkAgeclvatavenqmrl 232
                    +   l+ ++ l++dg+ktG t++ g   v +   ++ r 
     AHX11494.1 235 EmlsLYHQRDLKFDGIKTGSTDAGGFGVVVSFLADGRRF 273
                    72225678889***************9999987777765 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5   0.0     9e-15   5.4e-11       6     181 ..      72     255 ..      67     277 .. 0.80

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 9e-15
                      EEEESTTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEGGHHHHTSSSTSGGGST.TSEEEHHHHHHHHHHTT-HHHHHHHHHHH.....T. CS
  Beta-lactamase2   6 elgvnadeefpaaStiKvpillalleavlegklslderltltaedivggsgilqklp.gktlslrdlltlmiavSDNtAtnlLidrl.....g. 92 
                      ++++nade ++  S+ K++ l+ ++ ++++g ++ d+ +++++++ ++   ++ +l+ g+++ ++dll+   ++S N A+ ++ +         
       AHX11494.1  72 LFEHNADEIMHPSSMSKLMTLYLMFSKLKAGIVKMDDVYRVSKNAWEKRGSTM-FLKeGQKVKVEDLLKGIAILSGNDASVVVAEGSmgseeAf 164
                      4799**************************************99877644444.466377***********************99888777656 PP

                      HHHHHHHHHHCTHTTSB--SHTTCCHHHTTSSTTEE-HHHHHHHHHHHHHT.....TSSHHH.HHHHHHHT-STTTTTTTTTTTTSEE.EEEEE CS
  Beta-lactamase2  93 leavnawlkelglretrlrrklpdleaadkdkrntttardlarllealarg.....ellspe.elleilsnqqfrdrlaaglpegvrv.ahKtG 179
                      +e++n+++k++gl++  + ++   +      ++ + +ard+++l  +++++      l s++  + + ++++  +++l+ + + ++++   KtG
       AHX11494.1 165 VEEMNQTAKSMGLSNSSFVNTTGLTA-----QNHYMSARDVVKLAVKIYEDfpeyyYLFSEKgLMFNNIKQNNTNEMLSLYHQRDLKFdGIKTG 253
                      899****************9876653.....799****************86666456666688888888888888888776666666224666 PP

                      EE CS
  Beta-lactamase2 180 el 181
                      + 
       AHX11494.1 254 ST 255
                      64 PP

>> PBP5_C  Penicillin-binding protein 5, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.59   3.5e+03       8      42 ..     127     157 ..     121     166 .. 0.57
   2 !   31.4   0.0   2.7e-11   1.6e-07       1      70 [.     301     369 ..     301     385 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.59
                 XTTCESEEEEEESSSSSEEEEEESSXEEEEEETTH CS
      PBP5_C   8 kkgkvvktvsvlkgkekeVplvakediyvtvkkge 42 
                 k+g++vk  + lk     + ++  +d +v+v +g+
  AHX11494.1 127 KEGQKVKVEDLLK----GIAILSGNDASVVVAEGS 157
                 5555442222222....255566667777776665 PP

  == domain 2  score: 31.4 bits;  conditional E-value: 2.7e-11
                 EEEEEEEXTTCESEEEEEESSSSSEEEEEESSXEEEEEETTHCCTEEEEEEESSSEESGBGTTSEEEEEE CS
      PBP5_C   1 FetkklykkgkvvktvsvlkgkekeVplvakediyvtvkkgekkklkakvelkksleapikkGqkvGklk 70 
                 F++k +++kg+ +  ++vl+++++ +p+ +++d+y +    +++ +++ +++++ + ap+ kG+ vG l 
  AHX11494.1 301 FKSKRIFSKGEHIAILNVLYSSKRVLPITVPKDVYAV-YGKSEEGITVTLKYRDCVPAPVRKGEIVGELI 369
                 99********************************885.6778899**********************984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 3169.85
//
Query:       AHX11495.1  [L=192]
Description: ruvA domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-18   66.2   4.0    7.2e-17   61.2   0.8    2.6  3  RuvA_N    RuvA N terminal domain
    3.4e-11   43.4   0.5    1.3e-10   41.6   0.1    2.1  2  RuvA_C    RuvA, C-terminal domain
    1.5e-06   28.7   3.0    2.9e-06   27.8   1.9    2.1  2  HHH_5     Helix-hairpin-helix domain
  ------ inclusion threshold ------
      0.035   13.9   0.0       0.48   10.3   0.0    2.3  2  TusA      Sulfurtransferase TusA
       0.08   12.9   0.1        2.7    8.0   0.0    2.7  2  UBA_6     UBA-like domain
      0.091   13.0   0.1       0.32   11.3   0.0    1.9  2  HHH_6     Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> RuvA_N  RuvA N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.2   0.8   2.4e-20   7.2e-17       1      60 []       1      61 [.       1      61 [. 0.99
   2 !    5.3   0.0    0.0068        20      15      31 ..      71      87 ..      65     112 .. 0.74
   3 ?   -1.3   0.0       0.8   2.4e+03      15      26 ..     105     116 ..      97     148 .. 0.68

  Alignments for each domain:
  == domain 1  score: 61.2 bits;  conditional E-value: 2.4e-20
                -EEEEEEEEEEESSCEEEEEETTEEEEEEE-HHHHCC.-TTSEEEEEEEEEEETTEEEEEE CS
      RuvA_N  1 MIaylkGkvvekepdsivvevggvGYevfvplstlss.kegeevklythlivrEdalsLYG 60
                MI++l+G+v e++ dsi+++vggvGY vf++ + +++ ++g++  +y+++++ E+ ++LYG
  AHX11495.1  1 MIGRLTGTVNEINSDSIILDVGGVGYNVFTTRRAMENlRTGQKLSIYIEHYIAENTIKLYG 61
                *******************************999999*99********************9 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0068
                CEEEEEETTEEEEEEE- CS
      RuvA_N 15 dsivvevggvGYevfvp 31
                ++i+v v g+ Y++ ++
  AHX11495.1 71 AKILVKVKGINYKIALT 87
                579***********998 PP

  == domain 3  score: -1.3 bits;  conditional E-value: 0.8
                 CEEEEEETTEEE CS
      RuvA_N  15 dsivvevggvGY 26 
                 +++ + v g+G 
  AHX11495.1 105 NEVKLKVKGIGD 116
                 456677777774 PP

>> RuvA_C  RuvA, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0       0.7   2.1e+03      18      29 ..      68      79 ..      66      99 .. 0.75
   2 !   41.6   0.1   4.3e-14   1.3e-10       3      44 ..     148     190 ..     146     192 .] 0.95

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.7
                HHHHHHHHHHHC CS
      RuvA_C 18 keaekAvakvla 29
                +e++k++ kv+ 
  AHX11495.1 68 QEIAKILVKVKG 79
                899999999975 PP

  == domain 2  score: 41.6 bits;  conditional E-value: 4.3e-14
                 HHHHHHHHHHCTS-HHHHHHHHHHHHC.-TTS-HHHHHHHHHC CS
      RuvA_C   3 ledaveALlaLGYkekeaekAvakvla.npgasveelIraALk 44 
                  ++av+AL+ LG+ +k  +kAv+++ a np+  + +lI++ALk
  AHX11495.1 148 SNEAVSALVKLGFQQKSSQKAVSEIIAnNPDIEINDLIKLALK 190
                 68****************************************9 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   1.9   9.8e-10   2.9e-06       3      54 ..      73     125 ..      71     126 .. 0.79
   2 ?   -2.2   0.0       2.3   6.9e+03      32      50 ..     150     167 ..     146     179 .. 0.57

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 9.8e-10
                 HHHTSTT--HHHHHHHHTT.T--SH.HHHHHS-HHHHHTSTTS-HHHHHHHHHH CS
       HHH_5   3 eLlsvsGiGpktAlallsa.Giesv.edlaaadveeLakipGiGkktAeriile 54 
                  L +v+Gi+ k+Al+ll++ G++ + + + ++++ +  k++GiG k+ +rii e
  AHX11495.1  73 ILVKVKGINYKIALTLLDHlGVNELiASIRDKNEVK-LKVKGIGDKLIKRIITE 125
                 6899***************66666424555554444.58*************87 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.3
                 S-HHHHHTSTTS-HHHHHH CS
       HHH_5  32 adveeLakipGiGkktAer 50 
                 ++v +L k+ G+ +k  ++
  AHX11495.1 150 EAVSALVKL-GFQQKSSQK 167
                 555566665.555555444 PP

>> TusA  Sulfurtransferase TusA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00016      0.48      14      44 ..      28      58 ..      26      60 .. 0.90
   2 ?    0.8   0.0      0.14   4.3e+02      28      48 ..     168     189 ..     160     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00016
                HHHHHHHHCCCGCT-EEEEEESSCHHHHHHH CS
        TusA 14 llklkkalekleegevlevladdpaatedip 44
                +  +++a+e+l+ g++l +   +  a+++i+
  AHX11495.1 28 VFTTRRAMENLRTGQKLSIYIEHYIAENTIK 58
                7789*******************99999997 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.14
                 -EEEEEESSCHHH.HHHHHHHH CS
        TusA  28 evlevladdpaat.ediprfak 48 
                 +v e++a++p+ + +d+ ++a 
  AHX11495.1 168 AVSEIIANNPDIEiNDLIKLAL 189
                 6679*******99788887775 PP

>> UBA_6  UBA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.0   0.0    0.0009       2.7       6      29 ..     128     151 ..     125     159 .. 0.84
   2 ?    2.2   0.1     0.058   1.7e+02       9      22 ..     156     169 ..     152     186 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.0 bits;  conditional E-value: 0.0009
       UBA_6   6 dfflKLGYseeqvqavLekLGpea 29 
                 + flKL Yse+ v  v   L  ea
  AHX11495.1 128 EEFLKLDYSEDHVNNVHTSLSNEA 151
                 679************988887766 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.058
       UBA_6   9 lKLGYseeqvqavL 22 
                  KLG+ ++  q++ 
  AHX11495.1 156 VKLGFQQKSSQKAV 169
                 69***998776665 PP

>> HHH_6  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.5   4.4e+03      25      44 ..      70      89 ..      53     104 .. 0.69
   2 ?   11.3   0.0   0.00011      0.32      31      79 ..     110     160 ..     109     170 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.5
       HHH_6 25 irlGLaaikglgeaaaeriv 44
                i   L ++kg++ + a +++
  AHX11495.1 70 IAKILVKVKGINYKIALTLL 89
                55556677777777666655 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00011
       HHH_6  31 aikglgeaaaerivaeRekegpfksl...edlarrvds.lnkrqleaLakaGa 79 
                 ++kg+g++ ++ri++e    ++f +l   ed ++ v++ l+++++ aL+k G 
  AHX11495.1 110 KVKGIGDKLIKRIITET--YEEFLKLdysEDHVNNVHTsLSNEAVSALVKLGF 160
                 59*************66..5677776333688888888************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (192 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       901  (0.0502538); expected 358.6 (0.02)
Passed bias filter:                      517  (0.028836); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1443.67
//
Query:       AHX11496.1  [L=325]
Description: holliday junction DNA helicase RuvB [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-77  257.2   0.1    6.5e-77  256.7   0.1    1.2  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    3.2e-26   91.0   0.4    1.2e-25   89.1   0.0    2.2  2  RuvB_C           RuvB C-terminal winged helix domain
      1e-24   86.1   0.2    1.8e-24   85.3   0.2    1.4  1  AAA_lid_4        RuvB AAA lid domain
    6.8e-20   71.8   0.0    1.6e-19   70.6   0.0    1.7  1  AAA              ATPase family associated with various cellul
      3e-08   33.8   0.1    5.7e-06   26.4   0.1    2.5  1  AAA_5            AAA domain (dynein-related subfamily)
    4.3e-06   27.2   0.1    0.00039   20.9   0.0    2.6  3  AAA_16           AAA ATPase domain
    9.5e-06   25.1   0.6      0.048   13.0   0.0    3.3  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    4.7e-05   22.8   0.0    0.00035   19.9   0.0    2.0  2  TIP49            TIP49 P-loop domain
    7.3e-05   22.5   0.0       0.13   12.0   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
     0.0002   21.4   0.1     0.0021   18.1   0.0    2.5  3  AAA_14           AAA domain
    0.00021   21.6   0.0    0.00039   20.8   0.0    1.4  1  RNA_helicase     RNA helicase
    0.00024   20.4   0.0      0.038   13.2   0.0    2.6  3  NB-ARC           NB-ARC domain
     0.0003   20.7   0.1     0.0087   16.0   0.0    2.4  2  NTPase_1         NTPase
    0.00034   19.8   0.0      0.072   12.2   0.0    2.2  2  DUF815           Protein of unknown function (DUF815)
    0.00074   19.8   0.2      0.096   13.0   0.0    2.6  2  AAA_22           AAA domain
      0.001   19.1   0.0       0.62   10.0   0.0    2.4  2  ResIII           Type III restriction enzyme, res subunit
     0.0028   16.8   0.0      0.092   11.8   0.0    2.3  1  MCM              MCM P-loop domain
     0.0033   17.4   0.0     0.0054   16.7   0.0    1.3  1  Rad17            Rad17 P-loop domain
     0.0035   17.1   0.1       0.13   12.0   0.1    2.8  2  IstB_IS21        IstB-like ATP binding protein
     0.0046   16.8   0.0       0.63    9.9   0.0    2.3  2  AAA_3            ATPase family associated with various cellul
     0.0051   16.7   0.2      0.059   13.2   0.2    2.4  1  Bac_DnaA         Bacterial dnaA  protein
     0.0075   16.8   0.0      0.035   14.6   0.0    2.1  2  AAA_18           AAA domain
  ------ inclusion threshold ------
      0.049   14.1   0.0      0.094   13.2   0.0    1.6  1  ABC_tran         ABC transporter
      0.068   12.9   0.1       0.18   11.5   0.0    1.7  1  AAA_24           AAA domain
       0.07   12.6   0.0        0.2   11.2   0.0    1.8  2  AAA_7            P-loop containing dynein motor region
      0.071   13.0   0.0       0.15   12.0   0.0    1.5  1  NACHT            NACHT domain
      0.087   13.2   0.0       0.25   11.8   0.0    1.8  1  AAA_17           AAA domain
       0.17   12.1   0.0       0.33   11.1   0.0    1.5  1  AAA_33           AAA domain
       0.18   11.8   0.0       0.34   10.9   0.0    1.4  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
       0.19   12.1   0.2        8.2    6.8   0.0    2.6  2  AAA_19           AAA domain


Domain annotation for each model (and alignments):
>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  256.7   0.1   1.1e-79   6.5e-77       1     159 []      17     175 ..      17     175 .. 0.99

  Alignments for each domain:
  == domain 1  score: 256.7 bits;  conditional E-value: 1.1e-79
      RuvB_N   1 lrPksleeyigqekvkeklkifieaakkreealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekagdlaalltnleekdvlfideihrlsra 99 
                 +rP+s+e+++gq++v e+l+ifi++a++r++aldh+l+yGpPGlGkttla+ii++el +k+ +tsgP l+kagd+aa+ltnl+++d+lfideihrl ++
  AHX11496.1  17 VRPQSMEKFVGQKHVIENLQIFIDSAQRRNDALDHILFYGPPGLGKTTLAHIISNELRSKIYTTSGPLLSKAGDIAAILTNLQRNDILFIDEIHRLPST 115
                 6************************************************************************************************** PP

      RuvB_N 100 veevlysamedfrldivigkGpsarsikldlpkftlvgattragllssPlrdrfgivarl 159
                 veevly+amed++ldi++g+Gp+a+si+++l+kftlv+attr g+ls+Plrdrfgi++rl
  AHX11496.1 116 VEEVLYPAMEDYCLDIIVGDGPAAKSIRINLAKFTLVAATTRIGMLSNPLRDRFGITMRL 175
                 *********************************************************997 PP

>> RuvB_C  RuvB C-terminal winged helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       8.3   4.9e+03      25      45 ..     179     199 ..     176     200 .. 0.84
   2 !   89.1   0.0     2e-28   1.2e-25       2      71 ..     253     322 ..     252     323 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 8.3
                 -HHHHHHHTT--HHHHHHTTH CS
      RuvB_C  25 glktlaailgeeketiedviE 45 
                  ++ l+++l+e +++++  iE
  AHX11496.1 179 TIDELVELLREASDKLSVRIE 199
                 588999999999999988887 PP

  == domain 2  score: 89.1 bits;  conditional E-value: 2e-28
                 T---HHHHHHHHHHHHT.TT--B-HHHHHHHTT--HHHHHHTTHHHHHHTTSEEEETTEEEE-HHHHHHH CS
      RuvB_C   2 lGLdeldikyLkllkekfkggpvglktlaailgeeketiedviEPyLlkeglIertsrGRilTkkglkyl 71 
                  GLd+ld +y++++ ++++++pvg+kt+a++++e+++ ie++iEPyL+k+g++ rt+rGR+l+kk+l+yl
  AHX11496.1 253 FGLDKLDYTYMNFISKHYSDSPVGIKTIASAISEKEDSIEEMIEPYLIKIGFLHRTPRGRKLSKKALDYL 322
                 7********************************************************************9 PP

>> AAA_lid_4  RuvB AAA lid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.3   0.2   2.9e-27   1.8e-24       1      74 []     178     251 ..     178     251 .. 0.99

  Alignments for each domain:
  == domain 1  score: 85.3 bits;  conditional E-value: 2.9e-27
   AAA_lid_4   1 YeeeeLeeivkrsakilgveieeegaaeiarRsRGTPRianrLLrRvrDfaqvkgdgkitkevakkaLellevd 74 
                 Y+ +eL e+++ +++ l+v+iee+g  e+a+RsRGTPRia rLL+R+rDf +v++++ it+ +a+ aL+++e+d
  AHX11496.1 178 YTIDELVELLREASDKLSVRIEEDGIVELAKRSRGTPRIALRLLKRIRDFLEVSENDLITTGFADYALNKMEID 251
                 999*********************************************************************98 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.6   0.0   2.7e-22   1.6e-19       1     130 [.      52     175 ..      52     177 .. 0.95

  Alignments for each domain:
  == domain 1  score: 70.6 bits;  conditional E-value: 2.7e-22
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCSSSSTTHHHHHHHHHHHHHHHTSTSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTS CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsellskyvgesekkirelfkeakekakpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkk 99 
                 +l+yGppG GKT+la+ + +el ++++++sg+ l       ++ +i++++++++++    ilfiDEi++l ++             ++L+++++++  +
  AHX11496.1  52 ILFYGPPGLGKTTLAHIISNELRSKIYTTSGPLLS------KAGDIAAILTNLQRN---DILFIDEIHRLPSTV-----------EEVLYPAMEDYCLD 130
                 69*******************************99......9**********9877...5**********6666...........************** PP

                 ...............SSTEEEEEEESSGGGSTHHHHSTTSSEEEET CS
         AAA 100 ...............eskvivigatnrpdkldpallrgRfdrkiei 130
                                 +k+++++at+r+ +l+++l+ +Rf + +++
  AHX11496.1 131 iivgdgpaaksirinLAKFTLVAATTRIGMLSNPLR-DRFGITMRL 175
                 ***************999******************.***998876 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   9.6e-09   5.7e-06       1     138 []      51     169 ..      51     169 .. 0.88

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 9.6e-09
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--HHHHHHHHHHHHSSEEE..-S CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraesevlnsLlslleerrllleeg 99 
                 ++l  GppG gK++la  ++  l++++ +  ++   ++ d+                ++ ++ ++ +il++DE++r++s v ++L + +e+  l++  g
  AHX11496.1  51 HILFYGPPGLGKTTLAHIISNELRSKIYTTSGPLLSKAGDI---------------AAILTNLQRNDILFIDEIHRLPSTVEEVLYPAMEDYCLDIIVG 134
                 6899************************9999986665555...............4455599************************************ PP

                 SSEEE---......-EEEEEESS--.-TT-TTHHHHTT- CS
       AAA_5 100 gelvkaknddllerfrviatanpldrslnelspalrsRf 138
                 ++   ++    l +f+++a++ +       ls +lr+Rf
  AHX11496.1 135 DGPAAKSIRINLAKFTLVAATTRIG----MLSNPLRDRF 169
                 ***98777555555*******9999....8899999998 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   6.5e-07   0.00039       1      56 [.      24      80 ..      24      87 .. 0.83
   2 ?    3.0   0.0      0.21   1.2e+02     128     156 ..      93     121 ..      84     133 .. 0.78
   3 ?   -1.4   0.1       4.6   2.7e+03      85     130 ..     186     231 ..     173     235 .. 0.63

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 6.5e-07
      AAA_16  1 rlvGReeeleqLlsale.rvrsgrp.elvllsGesGvGKsslvrellralekdggifl 56
                ++vG ++ +e L+  ++ + r+++    +l++G++G GK++l+  + ++l+ + ++++
  AHX11496.1 24 KFVGQKHVIENLQIFIDsAQRRNDAlDHILFYGPPGLGKTTLAHIISNELRSK-IYTT 80
                699**************544444449*****************9999998887.5555 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.21
      AAA_16 128 allsrderplvlvlDdlqwadeaslqlla 156
                 a l++ +r  +l++D+++++ ++  ++l+
  AHX11496.1  93 AILTNLQRNDILFIDEIHRLPSTVEEVLY 121
                 44555566669*********999998887 PP

  == domain 3  score: -1.4 bits;  conditional E-value: 4.6
      AAA_16  85 lldeaesaeleawrekleealaavpelagaeasrllellkrllall 130
                 ll+ea++++  +  e    +la  +  ++ +a rll  ++++l+ +
  AHX11496.1 186 LLREASDKLSVRIEEDGIVELAKRSRGTPRIALRLLKRIRDFLEVS 231
                 4444445455555555555555666667777788888888877655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0     8e-05     0.048      23      43 ..      50      70 ..      21      80 .. 0.76
   2 !    6.9   0.0    0.0059       3.5     104     155 ..      98     154 ..      81     159 .. 0.73
   3 ?    1.7   0.0      0.24   1.5e+02     184     200 ..     160     176 ..     154     183 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 8e-05
  Mg_chelatase 23 HnlllvGppGsGKtmlakrlp 43
                   ++l++GppG GKt la+ ++
    AHX11496.1 50 DHILFYGPPGLGKTTLAHIIS 70
                  589**************9876 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.0059
  Mg_chelatase 104 lahnGvLfLDElpefkrkvlevLRePledgevtisr....akakve.fparfqlvaa 155
                   l +n +Lf+DE+  + ++v evL   +ed  + i      a+++++   a+f+lvaa
    AHX11496.1  98 LQRNDILFIDEIHRLPSTVEEVLYPAMEDYCLDIIVgdgpAAKSIRiNLAKFTLVAA 154
                   56789***********************98877753111133333313466666666 PP

  == domain 3  score: 1.7 bits;  conditional E-value: 0.24
  Mg_chelatase 184 klsgplldRidlqvevk 200
                    ls+pl dR+ ++++++
    AHX11496.1 160 MLSNPLRDRFGITMRLE 176
                   69**********99876 PP

>> TIP49  TIP49 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   5.8e-07   0.00035      22      79 ..      21      78 ..       8      84 .. 0.91
   2 ?    0.0   0.1      0.64   3.8e+02     281     308 ..     103     130 ..      96     135 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 5.8e-07
                XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49 22 eeeglvGqkkareaagvivelikekklaGravLlaGpsgtGktalaiaiskelgedvp 79
                + e +vGqk+  e   ++++  + ++ a   +L+ Gp+g Gkt la  is+el +++ 
  AHX11496.1 21 SMEKFVGQKHVIENLQIFIDSAQRRNDALDHILFYGPPGLGKTTLAHIISNELRSKIY 78
                55789************************************************98875 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.64
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
       TIP49 281 vlfiDevhmlDiecfsylnraleselaP 308
                 +lfiDe+h l   +   l  a+e+    
  AHX11496.1 103 ILFIDEIHRLPSTVEEVLYPAMEDYCLD 130
                 89******99877777777777766555 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0029       1.7       8      46 ..      35      73 ..      25      83 .. 0.76
   2 !   12.0   0.0   0.00021      0.13      94     138 ..     101     145 ..      87     180 .. 0.76

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0029
                     HHHHHHHHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHS CS
  Sigma54_activat  8 lkelleqikkvaktdlsvlitGesGtGKellaraiheas 46
                     l+  ++++++  +   ++l  G  G GK++la+ i ++ 
       AHX11496.1 35 LQIFIDSAQRRNDALDHILFYGPPGLGKTTLAHIISNEL 73
                     44455566666666689****************998754 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00021
                      TSEEEEETGGGS-HHHHHHHHHHHHHSEEESBTSSSEEE--EEEE CS
  Sigma54_activat  94 gGtlfLDeigelplelQekLlrvlqegevervGsskeikvdvrii 138
                      + +lf+Dei++lp ++ e L  ++++  +  + ++ +   ++ri 
       AHX11496.1 101 NDILFIDEIHRLPSTVEEVLYPAMEDYCLDIIVGDGPAAKSIRIN 145
                      679**********************99988765444444444443 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0       1.7     1e+03      55      83 ..      25      52 ..       7      55 .. 0.66
   2 !   18.1   0.0   3.5e-06    0.0021       6      85 ..      53     121 ..      50     135 .. 0.64
   3 ?   -1.7   0.0       4.5   2.7e+03      28      43 ..     255     270 ..     220     296 .. 0.62

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 1.7
      AAA_14 55 lilek.lkeekktylflDEiqevpewekal 83
                ++ +k +   ++  +f+D +q+ +++ +++
  AHX11496.1 25 FVGQKhV-I-ENLQIFIDSAQRRNDALDHI 52
                3333322.2.45679****99999887766 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 3.5e-06
      AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinldderdkkladpekllelileklkeekktylflDEiqevpewekalks 85 
                 +  G+   GKTtl+ ++i+++l   +s +y +     ++k+ d      +il +l  +++ +lf+DEi+++p+  + + +
  AHX11496.1  53 LFYGPPGLGKTTLA-HIISNEL---RSKIYTTSGP-LLSKAGDI----AAILTNL--QRNDILFIDEIHRLPSTVEEVLY 121
                 5679999******6.7777888...5666655444.33333433....4455544..36799*********986655544 PP

  == domain 3  score: -1.7 bits;  conditional E-value: 4.5
      AAA_14  28 vkkesilyinldderd 43 
                  +k ++ y+n+ ++++
  AHX11496.1 255 LDKLDYTYMNFISKHY 270
                 3444555666655554 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.8   0.0   6.6e-07   0.00039       1      64 [.      52     115 ..      52     129 .. 0.84

  Alignments for each domain:
  == domain 1  score: 20.8 bits;  conditional E-value: 6.6e-07
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkklklkkkdsvys.rnpeddfwdgYtgqevvvidDfgqvkde 64 
                   i++yGp+g GK+tla+ ++++l +k+ +++++ + s  +    ++ + ++++++ id++ + +++
    AHX11496.1  52 ILFYGPPGLGKTTLAHIISNELRSKI-YTTSGPLLSkAGDIAAILTNLQRNDILFIDEIHRLPST 115
                   789***********************.55556666747777888899999999999999998866 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.0   6.4e-05     0.038      17      45 ..      48      74 ..      30      80 .. 0.82
   2 ?    4.0   0.0     0.039        23     134     199 ..     152     215 ..     143     233 .. 0.84
   3 ?   -1.9   0.0       2.5   1.5e+03     195     218 ..     271     295 ..     261     304 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 6.4e-05
                TSCSEEEEEEESTTSSHHHHHHHHCCSHC CS
      NB-ARC 17 elqslvvalvGmgGvGKttlakqilnksd 45
                 l+   + ++G +G+GKttla+ i n++ 
  AHX11496.1 48 ALD--HILFYGPPGLGKTTLAHIISNELR 74
                344..8899*************9999865 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.039
                 EEEEESBCCCCCCS-S-.EEEEEESS--HHHHHHHHHHCCTS-GGCHH..CHHHHHHHHHHCTT-HH CS
      NB-ARC 134 vllTTRdeevanavsat.sekievelLekdeawellenkvfekkleekesleevakeivekckGlPl 199
                 v+ TTR   ++n   ++   ++++e+ ++de  ell +   + ++     +e+   e++++++G P 
  AHX11496.1 152 VAATTRIGMLSNPLRDRfGITMRLEFYTIDELVELLREASDKLSVR---IEEDGIVELAKRSRGTPR 215
                 778*************9999****************9987776666...468889999999999993 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 2.5
                 TT-HHHHHHHHHHHC-T.CSCCHHH CS
      NB-ARC 195 kGlPlalkvlggllstk.ktveewk 218
                 + +P+ +k++++++s k + +ee+ 
  AHX11496.1 271 SDSPVGIKTIASAISEKeDSIEEMI 295
                 5567888888888887777777764 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   1.5e-05    0.0087       1      32 [.      51      82 ..      51      88 .. 0.89
   2 ?    2.2   0.0      0.24   1.5e+02      88     107 ..      93     112 ..      85     121 .. 0.77

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 1.5e-05
                EEEEE--TTSSHHHHHHHHHHHH...GGGEEE CS
    NTPase_1  1 kvfiTGppGvGKtTlvkkvlellkssgvkvgG 32
                +++  GppG GKtTl + ++++l+s+ ++ +G
  AHX11496.1 51 HILFYGPPGLGKTTLAHIISNELRSKIYTTSG 82
                56777********************9998887 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.24
                 HHHHHHHHH-EEEE---STT CS
    NTPase_1  88 alrkalseadviviDEiGkm 107
                 a+ + l+++d++ iDEi ++
  AHX11496.1  93 AILTNLQRNDILFIDEIHRL 112
                 55566799*********665 PP

>> DUF815  Protein of unknown function (DUF815)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   0.00012     0.072      38     116 ..      29     109 ..       9     111 .. 0.76
   2 ?    5.3   0.0     0.015       9.3     182     224 ..     165     207 ..     161     223 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00012
      DUF815  38 ealventeqfleglp....a.nnvLLwGarGtGKSslvkallneyaeegLrlievekedlkelpklvellrerperfilfvDDL 116
                 ++++en + f++ ++    a  ++L++G  G GK +l + + ne++++   +   +   l++  ++ ++l + +++ ilf+D +
  AHX11496.1  29 KHVIENLQIFIDSAQrrndAlDHILFYGPPGLGKTTLAHIISNELRSK---IYTTSGPLLSKAGDIAAILTNLQRNDILFIDEI 109
                 456666666665443111132689********************9986...667889999999999999999999999999975 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.015
      DUF815 182 LsdRFGlwlgFykldqeeYleiveklakklglelekeeleeeA 224
                 L dRFG+++  +  + +e +e++++  +kl++++e++ + e A
  AHX11496.1 165 LRDRFGITMRLEFYTIDELVELLREASDKLSVRIEEDGIVELA 207
                 78******999999999**************999987666555 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.0   0.00016     0.096       7      32 ..      51      76 ..      47     100 .. 0.76
   2 ?    4.3   0.1     0.078        47      88     107 ..      97     115 ..      85     131 .. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00016
      AAA_22  7 ilvvtGesGtGKTtllrrlleqldee 32
                +++ +G++G GKTtl+  + ++l   
  AHX11496.1 51 HILFYGPPGLGKTTLAHIISNELRSK 76
                7899************9999998433 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.078
      AAA_22  88 aravielliiDEaqhlrsee 107
                 + ++  +l iDE+++l + +
  AHX11496.1  97 NLQRNDILFIDEIHRL-PST 115
                 4444578*********.533 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.0   0.0     0.001      0.62       7      51 ..      27      76 ..      21      85 .. 0.78
   2 ?    6.7   0.0     0.011       6.4     130     150 ..      98     116 ..      86     155 .. 0.82

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.001
                HHHHHHHHHT......TTS.....EEEEEESTTSTHHHHHHHHHHHH-S. CS
      ResIII  7 yQeeaienlleklkskrdk.....rglikmaTGtGKTlvaaklierllkk 51
                 Q+++ienl   ++s +++     ++l+  + G GKT +a  +  +l++k
  AHX11496.1 27 GQKHVIENLQIFIDSAQRRndaldHILFYGPPGLGKTTLAHIISNELRSK 76
                799999999977766333334567*************9998888888776 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.011
                 TTT-SEEEEETGGGTTS.TTT CS
      ResIII 130 rdrfdviiiDEaHrlgakksw 150
                  +r+d+++iDE Hrl +  ++
  AHX11496.1  98 LQRNDILFIDEIHRLPS--TV 116
                 56899**********98..33 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   0.0   0.00015     0.092      59     109 ..      51     102 ..      30     156 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00015
                 EEEEEESSTSTHHHHHHHHHHHSSSEEEE.ESSSSSSSHSSSEEEEESSSSS CS
         MCM  59 nvllvgdpgtaKsqlLkyveklapravyt.sgkgssaagLtaavvrdeetge 109
                 ++l+ g pg++K++l + +++ +   +yt sg   s+ag  aa+  + + ++
  AHX11496.1  51 HILFYGPPGLGKTTLAHIISNELRSKIYTtSGPLLSKAGDIAAILTNLQRND 102
                 9*******************99999999626788999998888876655554 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.0   9.1e-06    0.0054      14      83 ..      18      87 ..      14     109 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 9.1e-06
       Rad17 14 kPekaeelavhkkkieevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelgiklrewlnpvslk 83
                +P+ +e+    k+ ie+++ ++++    +     +L  GP+G gk+t  +++s el  k+   + p++ k
  AHX11496.1 18 RPQSMEKFVGQKHVIENLQIFIDSAQRRNDALDHILFYGPPGLGKTTLAHIISNELRSKIYTTSGPLLSK 87
                6888888888999999999999998888887788999********************9999998888755 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   0.1   0.00021      0.13      48     121 ..      50     113 ..      39     125 .. 0.77
   2 ?    1.0   0.0      0.51   3.1e+02      77      99 ..     174     196 ..     170     206 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00021
   IstB_IS21  48 enivllGpsGvGKshlaialgveavraglsvlfvrvedLveelkrarrdgklaralkrllkvdllilDdlgllp 121
                 + i++ Gp+G GK+ la  ++ e      s ++++   L++      + g +a +l++l++ d+l +D++  lp
  AHX11496.1  50 DHILFYGPPGLGKTTLAHIISNELR----SKIYTTSGPLLS------KAGDIAAILTNLQRNDILFIDEIHRLP 113
                 67999************99887653....445777766664......467788888888888888888876655 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.51
   IstB_IS21  77 svlfvrvedLveelkrarrdgkl 99 
                 +  f+++++Lve l+ a ++ ++
  AHX11496.1 174 RLEFYTIDELVELLREASDKLSV 196
                 678************99988766 PP

>> AAA_3  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.9   0.0    0.0011      0.63       1      26 [.      51      76 ..      51      82 .. 0.91
   2 ?    4.6   0.0     0.046        28      64      90 ..     102     128 ..      93     157 .. 0.87

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.0011
       AAA_3  1 hvllegvPGlaktllvkalakaldle 26
                h+l+ g PGl+kt+l++ +++ l  +
  AHX11496.1 51 HILFYGPPGLGKTTLAHIISNELRSK 76
                9******************9998766 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.046
       AAA_3  64 nllladeinrappktqsalleameerq 90 
                 ++l+ dei r p+ ++  l  ame+  
  AHX11496.1 102 DILFIDEIHRLPSTVEEVLYPAMEDYC 128
                 7999*******************9865 PP

>> Bac_DnaA  Bacterial dnaA  protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.2   0.2   9.9e-05     0.059      28     107 ..      43     110 ..      21     124 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 9.9e-05
                 HSTTT.S--EEEE-SSSSSHHHHHHHHHHHHHHHSSSS-EEEEEHHHHHHHHHHHHHTT-HHHHHHHHTT-SEEEEE-GG CS
    Bac_DnaA  28 eapgkkynPlfiygevGlGktHLlkaignevlenapelrvvYltaeeFlnelvkalrdkkaeefkeklrkvDvLliDDiq 107
                 +  + + + +++yg+ GlGkt L + i+ne++++       Y t+   l+++       +++++  +l+++D+L iD+i+
  AHX11496.1  43 QRRNDALDHILFYGPPGLGKTTLAHIISNELRSKI------YTTSGPLLSKA------GDIAAILTNLQRNDILFIDEIH 110
                 5555677889*****************99988763......55555555433......4445555555556666666665 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   5.9e-05     0.035       1      35 [.      52      88 ..      52     133 .. 0.71
   2 ?   -1.3   0.0         5     3e+03      12      60 ..     278     322 ..     275     325 .] 0.74

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5.9e-05
      AAA_18  1 IlltGtpGvGKttlakeLskrlgf..gvnlrdvaken 35
                Il  G+pG GKttla+ +s++l +   + ++ ++++ 
  AHX11496.1 52 ILFYGPPGLGKTTLAHIISNELRSkiYTTSGPLLSKA 88
                8999**************9998434544444444444 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 5
      AAA_18  12 ttlakeLskrlgfgvnlrdvakenglllevdpealdeskrldedkldkl 60 
                  t+a ++s++    + + +++    + +++ +  +++ ++l ++ ld+l
  AHX11496.1 278 KTIASAISEK---EDSIEEMIEPYLIKIGFLHR-TPRGRKLSKKALDYL 322
                 6999999999...68888888887777777777.777777777777766 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   0.00016     0.094      14      67 ..      52     109 ..      47     185 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 0.00016
                 EEEEESTTSSHHHHHHHHTTSS--....SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  14 vaivGenGaGKStLlkllagllkp....teGeilldgkdlkeqeleslrkeigvlpqe 67 
                 + + G+ G GK+tL+ +++++l+     t+G +l +  d+  + ++  r+ i ++ + 
  AHX11496.1  52 ILFYGPPGLGKTTLAHIISNELRSkiytTSGPLLSKAGDIAAILTNLQRNDILFIDEI 109
                 5689****************99887777777776667777766666666666666555 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00029      0.18       5      21 ..      52      68 ..      50      79 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00029
      AAA_24  5 iliyGpsgiGKTtlake 21
                il yGp+g GKTtla  
  AHX11496.1 52 ILFYGPPGLGKTTLAHI 68
                889***********975 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   0.00033       0.2      34      65 ..      50      81 ..      34     101 .. 0.86
   2 ?   -2.6   0.0       5.7   3.4e+03     145     169 ..     145     169 ..     140     176 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00033
       AAA_7 34 kpvllvGptGtGKtviikdllkkldkekylsl 65
                 ++l++Gp G GKt++++ + ++l ++ y++ 
  AHX11496.1 50 DHILFYGPPGLGKTTLAHIISNELRSKIYTTS 81
                589*******************9998877765 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 5.7
       AAA_7 145 eikdvqlvaamgppgggrneitpRl 169
                 ++ + +lvaa +  g   n++  R+
  AHX11496.1 145 NLAKFTLVAATTRIGMLSNPLRDRF 169
                 5677888888888888888888887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00024      0.15       3      26 ..      52      75 ..      50      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00024
                EEEEC-TTTCHHHHHHHHHHHHCT CS
       NACHT  3 vilqGeaGsGKTtLlqklalawae 26
                ++  G++G GKTtL++ +  ++++
  AHX11496.1 52 ILFYGPPGLGKTTLAHIISNELRS 75
                7889*************9999886 PP

>> AAA_17  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00041      0.25       1      31 [.      55      85 ..      55     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00041
                EE-TTSSHHHHHHHHHHHHTEEEEEHHHHHH CS
      AAA_17  1 lGgPGsGKgtqceklvekygfthlsaGdllr 31
                +G+PG GK+t++  +  ++  ++++++  l 
  AHX11496.1 55 YGPPGLGKTTLAHIISNELRSKIYTTSGPLL 85
                7******************999998865444 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   0.00055      0.33       2      22 ..      52      72 ..      52      90 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00055
      AAA_33  2 vllvGlpGsGKstlaerllkk 22
                +l+ G+pG GK+tla+ + ++
  AHX11496.1 52 ILFYGPPGLGKTTLAHIISNE 72
                6899**********9866655 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00057      0.34      19      49 ..      49      80 ..      26      84 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00057
                TEEEEEEESTTSSHHHHHHHHHHHTT--.--- CS
        TsaE 19 gdvilLeGdLGaGKTtlvrglakalgve.evk 49
                 d il++G+ G GKTtl++ + ++l  +   +
  AHX11496.1 49 LDHILFYGPPGLGKTTLAHIISNELRSKiYTT 80
                356******************99998766554 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.8   0.0     0.014       8.2      11      32 ..      50      71 ..      40      86 .. 0.76
   2 ?    2.8   0.0      0.23   1.4e+02      98     137 ..      96     135 ..      78     143 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.8 bits;  conditional E-value: 0.014
      AAA_19 11 kvllvtaGpGtGKTrvlkhiva 32
                +++l  ++pG GKT++ + i +
  AHX11496.1 50 DHILFYGPPGLGKTTLAHIISN 71
                568899********86555444 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.23
      AAA_19  98 kklqeeellivDEfqdvdelqyrLlkallgekkklllvGD 137
                 ++lq++++l++DE+  +  +  ++l   +++    ++vGD
  AHX11496.1  96 TNLQRNDILFIDEIHRLPSTVEEVLYPAMEDYCLDIIVGD 135
                 4688888********9996666666655545443478888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (325 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       618  (0.0344693); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        81  (0.00451782); expected 17.9 (0.001)
Passed Fwd filter:                        30  (0.00167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              30  [number of targets reported over threshold]
# CPU time: 0.57u 0.29s 00:00:00.85 Elapsed: 00:00:00.43
# Mc/sec: 2255.54
//
Query:       AHX11497.1  [L=46]
Description: hypothetical protein NHE_0558 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       198  (0.0110436); expected 358.6 (0.02)
Passed bias filter:                      173  (0.00964917); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 371.07
//
Query:       AHX11498.1  [L=892]
Description: oxoglutarate dehydrogenase (succinyl-transferring), E1 component [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-58  196.9   0.0    6.2e-58  195.4   0.0    1.8  2  Transket_pyr     Transketolase, pyrimidine binding domain
    1.3e-49  168.8   0.0      2e-49  168.2   0.0    1.2  1  E1_dh            Dehydrogenase E1 component
      7e-41  139.5   0.0    1.1e-40  138.8   0.0    1.3  1  OxoGdeHyase_C    2-oxoglutarate dehydrogenase C-terminal
    6.5e-06   25.6   0.3    1.7e-05   24.3   0.3    1.6  1  2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0      0.74   3.3e+03      82     112 ..     324     351 ..     302     354 .. 0.64
   2 !  195.4   0.0   1.4e-61   6.2e-58       2     178 .]     559     753 ..     558     753 .. 0.98

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 0.74
                   HHHHGGGHHGGHHHHHCHHHHHT--EEEEES CS
  Transket_pyr  82 gdFangAqiyadqairsgeakgklkvgvvtr 112
                   + F+   q ++++ ++ +e+++++++g v++
    AHX11498.1 324 AAFSG--QGVVYESMI-LESLQQYQSGGVLH 351
                   23444..889999999.99999999986665 PP

  == domain 2  score: 195.4 bits;  conditional E-value: 1.4e-61
                   EEEHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGT...............TEGEEE--S-HHHHHHHHHHHHHHCT.TEEEEEEEEH CS
  Transket_pyr   2 kiawrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqg...............egrvidsgisEqavlgfavGaalagp.llviveaqFg 82 
                    i+w ++e +a+a+ll+e+ +++l+g+D+++gtfs+r+++l+ q+               +  v+ s++sE+++lgf++G++l +p +lv++eaqFg
    AHX11498.1 559 NIDWGNGESLAFASLLNEGISIRLTGQDCKRGTFSHRHAVLFSQStgeelcllntlsdsaKIDVVTSPLSEYGALGFEYGYSLLKPkKLVLWEAQFG 655
                   69*********************************************************************************************** PP

                   HHHGGGHHGGHHHHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTT..EEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEEC. CS
  Transket_pyr  83 dFangAqiyadqairsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipg..lkvvrPsdpaetkhllrrairredrkPvvlrlpksllrh 177
                   dFangAqi++dq i+sge k+  ++g+v++lp+g++++Gpeh+sa+ e+fl+l ++  ++++++++pa+ +h+lrr++ ++  +P++++ pksllrh
    AHX11498.1 656 DFANGAQIMIDQYISSGEIKWLSRTGLVLLLPHGYEGQGPEHSSARVERFLQLAAEnnMRIINCTTPANFFHALRRQVLSDVVRPLIVFSPKSLLRH 752
                   ****************************************************998777**********************99**************8 PP

                   T CS
  Transket_pyr 178 k 178
                   k
    AHX11498.1 753 K 753
                   5 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   0.0   4.4e-53     2e-49       9     296 ..     179     490 ..     172     493 .. 0.87

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 4.4e-53
                 HHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TT..SEEEES.S--HHHHHHT..T--HHHHHHHHTT-T............TTSSGT..T-..- CS
       E1_dh   9 vedaldalykrkkrigfyhlsagqealkvgiaaaleke..Dliite.YReagvllar..glsleeilaeltgkv............kgkggs..rh.el 87 
                 +e++l++++k  kr++++ + a   a++ +i++a   +  D+++ + +R++ ++ ++  g + ++++ae++g +            k++ g+   h  +
  AHX11498.1 179 LEEFLNIKFKGGKRFSLEGCDAALVAMEAIIEVAAISGhtDVLLGMsHRGRLNFAVNifGKKYKALFAEFAGGApfpaefavsgdvKYHFGAscTHkSF 277
                 6889999**********************999876544459999777******966522777******************6666665554441123334 PP

                 E..BTT..BEEE-SSTTTH..HHHHHHHHHHHHHHTS---EEEEEEGGG.TT-HHHHHHHHHHHHTT--E...EEEEEEESEETTEEHHHH-S---GGG CS
       E1_dh  88 myaekesrilggngivgaq..vplvaGialaakiegkkevailliGDgA.anqGdvyealnlaalwklpv...ifvveNNkygisTeaekasaskelad 180
                   +++ s ++  +++++++   p++ G a+a++ eg ++  +l++GD+A ++qG vye++ l +l +++    ++v++NN++g++T++++a++ + ++ 
  AHX11498.1 278 LSHTEISAMML-HNPSHLEavDPVLLGYARAMQDEGMTVFPVLFHGDAAfSGQGVVYESMILESLQQYQSggvLHVIVNNQIGFTTPPQYARKQPFPSF 375
                 44444443333.33333333378888******************************************97777************************** PP

                 ..TTTTS-EEEEETTSHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHH CS
       E1_dh 181 rargvgipglrVdgnDplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeieke 279
                  +  + ip+++V+++ p+av++++  A e+++++++ ++i++v+YR++gH+e+D+p +++ + +++ + ++k ++  + e+L+++gv+s   + + +  
  AHX11498.1 376 LGESFDIPIFHVNADNPEAVLYVALLASEFRSKFNKSAVIDIVSYRRYGHNEMDEPKFTQ-PVMYDVIASHKRVVDLYSEQLIQEGVISAADVAARKGG 473
                 ************************************************************.**********************************9999 PP

                 HHHHHHHHHHHHHHS-- CS
       E1_dh 280 vrkeveeavkkaeskke 296
                  r   e +++k++++k 
  AHX11498.1 474 FRDLLETELNKSKEYKP 490
                 99999999999999864 PP

>> OxoGdeHyase_C  2-oxoglutarate dehydrogenase C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.8   0.0   2.5e-44   1.1e-40       2     152 .]     757     890 ..     756     890 .. 0.95

  Alignments for each domain:
  == domain 1  score: 138.8 bits;  conditional E-value: 2.5e-44
  OxoGdeHyase_C   2 SsleelaegtsFqrvledeeeealkepekvkrvvlcsGkvyydLlkerekkekekdvaivriEqlyPfpfeelkeelekYpnakelvWvQeEpkNq 97 
                    S+l+++++g sF++v+ d+++     +++++rv++csGkvyydLl+e ++    +++ +vriEqlyPfp eel e+++ +++ +el+W+QeEpkN+
     AHX11498.1 757 STLSDFTDG-SFKNVIYDRTK-----RDSIRRVIFCSGKVYYDLLAELNS----SEILLVRIEQLYPFPKEELLEVVKIHKD-AELLWCQEEPKNM 841
                    99*******.********998.....689*****************9994....589*************************.7************ PP

  OxoGdeHyase_C  98 GawsfveprletvlkekkkkkkklryvgreasaspAtGskkvhkkeqealleeaf 152
                    Gaw fv+p +e+ ++      +klryvgr+a+a+++ G ++ h   q+al++ a+
     AHX11498.1 842 GAWFFVAPLFEDYCS------RKLRYVGRAAAAATSEGFMNDHVISQNALVRGAL 890
                    **************7......45***************************99875 PP

>> 2-oxogl_dehyd_N  2-oxoglutarate dehydrogenase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.3   3.9e-09   1.7e-05      16      35 ..      20      39 ..      14      41 .. 0.92

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 3.9e-09
  2-oxogl_dehyd_N 16 YeayleDPsSVdesWrayFk 35
                      ++yl+ P+SVd+sWra+F+
       AHX11498.1 20 QQSYLDSPNSVDPSWRAFFE 39
                     789****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (892 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       286  (0.0159518); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.23s 00:00:00.84 Elapsed: 00:00:00.38
# Mc/sec: 7010.57
//
Query:       AHX11499.1  [L=187]
Description: tRNA threonylcarbamoyl adenosine modification protein, Sua5/YciO/YrdC/YwlC family [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.6e-44  149.2   0.0    9.6e-44  149.0   0.0    1.0  1  Sua5_yciO_yrdC  Telomere recombination
     0.0086   16.0   0.2      0.013   15.4   0.2    1.2  1  Haemagg_act     haemagglutination activity domain
  ------ inclusion threshold ------
      0.019   14.0   0.0      0.023   13.8   0.0    1.1  1  Clusterin       Clusterin


Domain annotation for each model (and alignments):
>> Sua5_yciO_yrdC  Telomere recombination
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.0   0.0   1.6e-47   9.6e-44       2     179 .]       8     181 ..       7     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 149.0 bits;  conditional E-value: 1.6e-47
                     HHHTTSEEEEE-SSSEEEEEETTSHHHHHHHHHHHTSHCCC--EEEESSCCCCCCCC-TC--HHHHHHHHCT-SSSCEEEEE..E-TS-HHHHTT CS
  Sua5_yciO_yrdC   2 alrkGgivaiptetvYgLacdatneeaverlreiKgrpsdkplavlvasledlkklaeseveeealkllerfwPGpitlllkrskeklpkevapg 96 
                     +lr Gg++++ptetvY+Lacda+n  a  r++++K+r+ +k+l+v+v +++ +++lae  ++e +  l++r+ PGp+t++++r+++  ++     
      AHX11499.1   8 FLRIGGVIIFPTETVYALACDASNYHAKLRIYRLKQRNIKKNLPVMVWNFSWISRLAE--LTEYQSSLIRRYSPGPVTFIVPRKDT--SHLRFHF 98 
                     6899*****************************************************8..**********************8555..5555566 PP

                     TTEEEEEE-SSHHHHHHHHHCTS-EEEEES-STTS-S-SSHHHHHHHC-TTSECB-SS---SSS---EEEETTSSTSSECEXX CS
  Sua5_yciO_yrdC  97 lktvGvrlPdtplarlLlealgeplvaTSanlsgepsitdaeeveeelgeivdlildggeiavgvdstVvdltegkpkilRrG 179
                      ++++vr+Pd+++a+++l+ +++p+ aTS+n+s + ++t+ + ++  ++++vd+i+  ++   g++s++vd++e+ +  +RrG
      AHX11499.1  99 PRKIAVRIPDSKIALRILQLFNRPICATSVNISSKVPTTNFTRIDGYIRKRVDYIIGDNQGVSGTASSIVDISESCIVPMRRG 181
                     79***********************************************************************9999999998 PP

>> Haemagg_act  haemagglutination activity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.2   2.1e-06     0.013      59     111 ..     126     175 ..     110     182 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 2.1e-06
                  TTSEEEEEE-SSS-EEEECEEEEEECSCEEEEE-TT-EEEECCEEECECEEEE CS
  Haemagg_act  59 aasvilnrVtggspSkIqGaievlgakanlflaNpnGiifggnatiniggsfv 111
                  +  +i ++V  ++  +I+G+i+   +++++++   +G++  +++ ++i+ s +
   AHX11499.1 126 TSVNISSKVPTTNFTRIDGYIR---KRVDYIIGDNQGVSGTASSIVDISESCI 175
                  566899****************...9**********************99876 PP

>> Clusterin  Clusterin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   3.8e-06     0.023     322     366 ..      30      74 ..      20     115 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3.8e-06
   Clusterin 322 qqYdelLqivqehmedtsslleklneqFgWVselanqtqekenif 366
                  +Y   L+i++ +  +  + l  +  +F+W+s+la+ t+ + ++ 
  AHX11499.1  30 SNYHAKLRIYRLKQRNIKKNLPVMVWNFSWISRLAELTEYQSSLI 74 
                 579999*******************************98877654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (187 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1406.52
//
Query:       AHX11500.1  [L=265]
Description: metallo-beta-lactamase superfamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.1e-26   91.8   0.0    4.8e-26   91.5   0.0    1.1  1  Lactamase_B_2  Beta-lactamase superfamily domain
    3.2e-08   33.8   0.0    6.7e-08   32.8   0.0    1.8  1  Lactamase_B    Metallo-beta-lactamase superfamily


Domain annotation for each model (and alignments):
>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5   0.0   5.3e-30   4.8e-26       2     201 .]      46     233 ..      45     233 .. 0.93

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 5.3e-30
                    EEEES--TTHHHHHTCGGS--SSS--..SEEEEE-SS--HHHHGGGGCCCC...C--EE.EEEEEEHHHHHHCCTTCGHHHCHTT........TTE CS
  Lactamase_B_2   2 riLiDagpdlrqqalralqPvelrdelppidaVllthaHyDHlaglltlre...lrpkk.lplyapkgvlavleanfvylaleee........pav 85 
                    r+LiD++pdlr qa         r++++++d V++th H+DH+ag+  l     + +++ +++++++ +++++++  +yl+++ +        + +
     AHX11500.1  46 RLLIDTSPDLRLQAI--------RENFSSVDQVFYTHIHFDHTAGIHELSSftpIDERRsIRVLGDEFTISHIQQVYSYLFRQSHiggapwkrCYL 133
                    89********99944........55699***********************666444447**************************9999999999 PP

                    EEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S---HHHHHHHCT-SEEEEE-S-SSTTHHHHHHT---S CS
  Lactamase_B_2  86 nvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyipeeigerlggadllllditayeddemirhmgHltp 181
                    +++ +   e+f  g  ++++ ++p  h+  +         +G +++   ++++y++D+  ipe++ e ++ + l ++ i +++ ++    + H+++
     AHX11500.1 134 EARIVPYYEEFFAG--DISCMIFPQTHGNIN--------SCGIILD---RKFVYCTDVRLIPEKALEIMRSCSLEVFIIECFDYEK---AHAHSNL 213
                    99999999999999..5789********999........*******...9*********************999999999999999...99***** PP

                    TSHHHHCTTSSSSEEEEESB CS
  Lactamase_B_2 182 eeaveaaadlgakrlvliHi 201
                    +ea+e ++ + +kr++l+H+
     AHX11500.1 214 DEALEYIEIVAPKRAFLTHM 233
                    *******************8 PP

>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.0   7.4e-12   6.7e-08       8      75 ..      37      97 ..      31     232 .. 0.79

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 7.4e-12
                 EEEEEETTCEEEES--SCHHHHHHHHHHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCC CS
  Lactamase_B  8 syliegdggviLiDtGtsteaaraalelaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgav 75
                 s+l+e   + +LiDt  + + + +       + +   vd v++TH H+DH++g ++l + t++  +  
   AHX11500.1 37 SVLVESCSSRLLIDTSPDLRLQAI-------RENFSSVDQVFYTHIHFDHTAGIHELSSFTPIDERRS 97
                 78999***************9995.......8999**********************99888877655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       504  (0.0281109); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.26s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1962.64
//
Query:       AHX11501.1  [L=67]
Description: feS assembly protein IscX [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.1e-28   99.6   0.6    1.2e-28   99.4   0.6    1.0  1  Fe-S_assembly  Iron-sulphur cluster assembly
  ------ inclusion threshold ------
       0.18   11.9   0.0       0.18   11.9   0.0    1.0  1  PsbP           PsbP


Domain annotation for each model (and alignments):
>> Fe-S_assembly  Iron-sulphur cluster assembly
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.4   0.6   1.4e-32   1.2e-28       1      64 []       1      64 [.       1      64 [. 0.99

  Alignments for each domain:
  == domain 1  score: 99.4 bits;  conditional E-value: 1.4e-32
  Fe-S_assembly  1 lkWtdseeIAiaLyekypdvdpltvrFtdLhewvleLpefdddpeksnEkiLEaIqmaWleeae 64
                   +kW+d+eeIA aL+++y d d++++rFtdL++w+++L++f ++pe+++EkiLEaIq+aW+ e+e
     AHX11501.1  1 MKWSDIEEIAVALEDQYGDKDNINLRFTDLRDWIVSLEGFVGSPEACSEKILEAIQAAWISERE 64
                   9************************************************************985 PP

>> PsbP  PsbP
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.18      29      77 ..       8      58 ..       1      67 [] 0.82

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                TEEEEEEESS-TTSEEEEEEEE-STT.--CHHH.--HHHHHHHHHHHCCCH CS
        PsbP 29 gadvvFrdeiesdenvsVvispvskd.ksledl.Gspeevaerlvkqvlas 77
                   v+ +d+   + n+++ ++++++   sle + Gspe+++e++++ ++a+
  AHX11501.1  8 EIAVALEDQYGDKDNINLRFTDLRDWiVSLEGFvGSPEACSEKILEAIQAA 58
                458999*******************99****977***********988854 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.32u 0.27s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 513.05
//
Query:       AHX11502.1  [L=205]
Description: ribosomal protein S4 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.8e-15   56.2   0.4    7.6e-15   55.6   0.4    1.3  1  Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
    7.7e-14   51.1   0.1    1.3e-13   50.4   0.1    1.4  1  S4            S4 domain
  ------ inclusion threshold ------
      0.045   13.6   0.0      0.072   12.9   0.0    1.3  1  S4_2          S4 domain


Domain annotation for each model (and alignments):
>> Ribosomal_S4  Ribosomal protein S4/S9 N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.6   0.4   1.3e-18   7.6e-15       4      83 .]       6      92 ..       4      92 .. 0.97

  Alignments for each domain:
  == domain 1  score: 55.6 bits;  conditional E-value: 1.3e-18
                  S-CHHHHCHCTS-STSSS......S-S-SSTTTTS.-----CHCHHHHHHHHHHHHHT-SHHHHHHHHHHHHHCCSHHHHHHHHHHH CS
  Ribosomal_S4  4 gpkckllRrvgfklflkg......reyppGqhgkr.rkklseYgkqlrekqklkrrYgllekqfrryfkearrirGktgenLlqlLE 83
                  + k++++R+++ +l++++      r+y pGqhg++  kk+s++ kq+      + +Y + +kqf ++f +a r +G+t +nL+ lLE
    AHX11502.1  6 RRKFRVSRQMKASLWGSQkdpvhkRNYGPGQHGRSpIKKISDFYKQNAAQRAFRTYYVIGKKQFSNIFAKAYRGKGNTNDNLVSLLE 92
                  6799************99*******************************99999999999**************************9 PP

>> S4  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.4   0.1   2.1e-17   1.3e-13       1      48 []      93     140 ..      93     140 .. 0.98

  Alignments for each domain:
  == domain 1  score: 50.4 bits;  conditional E-value: 2.1e-17
                 EEHHHHHHHTTSSSSHHHHHHHHHTTTEEETTEEE--TT-EE-TTCEE CS
          S4   1 rRLdkvlarlglassrreArqlIehGrVlVNGkvvkdpsyrVkpgDvi 48 
                 rRL  +l+r+g+++++  Arql++h++V+VN+++v+  s+++k+gDv+
  AHX11502.1  93 RRLSSILYRSGMVPTIFAARQLVSHKHVTVNNRIVNVCSFELKEGDVV 140
                 79********************************************98 PP

>> S4_2  S4 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   1.2e-05     0.072      12      61 ..      97     146 ..      94     149 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1.2e-05
        S4_2  12 qlLKlaglvesGgeaKafiaegeVkvNGevetrRgkKlraGdvVeidget 61 
                  +L   g+v +  +a+++++ ++V+vN+ + +     l +GdvV+i +  
  AHX11502.1  97 SILYRSGMVPTIFAARQLVSHKHVTVNNRIVNVCSFELKEGDVVQIRDRA 146
                 55556667777779*******************************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       529  (0.0295053); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1613.59
//
Query:       AHX11503.1  [L=313]
Description: D-ala D-ala ligase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-22   79.1   0.0    4.2e-22   78.7   0.0    1.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    6.2e-16   58.7   0.2    7.9e-15   55.2   0.2    2.2  1  Dala_Dala_lig_N  D-ala D-ala ligase N-terminus
    6.3e-07   29.6   0.1    4.9e-06   26.7   0.0    2.3  2  ATP-grasp_3      ATP-grasp domain
     0.0087   15.6   0.0      0.015   14.8   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
  ------ inclusion threshold ------
      0.014   14.5   0.0       0.15   11.2   0.0    1.9  2  TTL              Tubulin-tyrosine ligase family
      0.027   14.2   0.0       0.12   12.1   0.0    1.9  1  ATPgrasp_Ter     ATP-grasp in the biosynthetic pathway with T
      0.037   13.6   0.0      0.047   13.3   0.0    1.1  1  DUF1444          Protein of unknown function (DUF1444)
      0.052   12.8   0.0      0.085   12.1   0.0    1.3  1  ATPgrasp_ST      Sugar-transfer associated ATP-grasp


Domain annotation for each model (and alignments):
>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.7   0.0   1.9e-25   4.2e-22      39     202 ..     139     296 ..     115     298 .. 0.88

  Alignments for each domain:
  == domain 1  score: 78.7 bits;  conditional E-value: 1.9e-25
                      EEEEESSSSTTTTEEEESSGGGHHHHHHHHHTT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SS.SSS-HHHHHC.TT-EEESS---- CS
  Dala_Dala_lig_C  39 vfVKpareGSSvGvskveseeelkeaieeafkydekvlvEeaiegreievavlgneklevsevgeivvkk.gfydyeakysddkaqlevpakle 131
                       + Kp +eGSS  +  v  e++l+   e+   +d  v+ Ee+i+g e+ va l     +v+   e  +++ ++  y+aky++  a+ +   +++
       AHX11503.1 139 YVLKPTNEGSSRNIVVVDGESHLT---EQNYPFDGPVMLEEFISGYELSVAFLS---GRVLGGLELELNGsEYCSYDAKYKKGFAEWVPIKNIP 226
                      578*****************9997...57899*********************9...899999999998857789*****999999999999** PP

                      HHHHHHHHHHHHHHHHHTT--SEEEEEEEE.ETTTEEEEEEEESS---STTSHHHHHHHCTT--HHHHHHHH CS
  Dala_Dala_lig_C 132 keveekiqelalkaykaldlrGlaRvDffl.teegeivlnEvNtlPGfTeiSlfpklakasGlefkkLvdql 202
                      +ev+++  +l  ++ ++l++rG +R Df + ++e ++v+ EvNt+PG+T +   +k+++++ +  +++v+++
       AHX11503.1 227 DEVYQSALTLTENICNILHCRGAVRADFKYdDKESKLVILEVNTCPGMTILPKIAKACANMEI--DQVVQEI 296
                      ******************************88999**************99999999987655..5666665 PP

>> Dala_Dala_lig_N  D-ala D-ala ligase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.2   3.5e-18   7.9e-15       2     101 ..      10      90 ..       9      92 .. 0.90

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3.5e-18
                      EEEEEE-SSTTHHHHHHHHHHHHHHCHCCTEEEEEEEE-TTS-EHHHHHHHHTTHHHTCCCCHCCCTCE--SEEEEE-TTTTTTSSHHHHHHHH CS
  Dala_Dala_lig_N   2 iavlfGGkStEhevSlvsaksvlkaldkekyeviligitkegkwkkkaekleskekkklkkeeekekkaeldvvfpvlhGkngEDGtlqgllel 95 
                      +a+l+GG+S E+++Sl + + v  ++ +  + v++i+++      ++                ++  + ++d++f+++hG ngE+G +qg+le+
       AHX11503.1  10 VALLYGGSSPERDISLLTKEVVEASIVRLGHGVLPIDVAD----ISA---------------ARTIPTLKCDLAFMAMHGHNGENGCIQGMLEM 84 
                      89************************8888********99....433...............34456899************************ PP

                      TT--BS CS
  Dala_Dala_lig_N  96 lgipyv 101
                       gipy+
       AHX11503.1  85 SGIPYT 90 
                      *****9 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.2e-09   4.9e-06      27     156 ..     129     270 ..     100     275 .. 0.68
   2 ?   -0.2   0.0       0.4   8.9e+02      49      78 ..     276     305 ..     270     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.2e-09
                  SS--...SSSEEEEESS-------B--SS--TTE.............EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TEEE.E..EEES- CS
  ATP-grasp_3  27 leee...ekklvvKprdGaggesvrvveekeeaeaaieeve......lvqefieGkplSvsllsdgekvlvlavnrqliekaekefvya.G..nvtpi 112
                  l+++   +kk+v+Kp + + +  ++vv+ + +++++ +         ++ efi+G +lSv +ls g     l +  +  e ++ + +y+ G  + +pi
   AHX11503.1 129 LQRKvlyPKKYVLKPTNEGSSRNIVVVDGESHLTEQ-N--YpfdgpvMLEEFISGYELSVAFLS-GRVLGGLELELNGSEYCSYDAKYKkGfaEWVPI 222
                  33336669**********999999999998666532.2..13357779****************.555555666555566666666665231133444 PP

                  ...---HHHHHHHHHHHHHTTSTT--EEEEEEEEESS...SEEEEEEES CS
  ATP-grasp_3 113 ...etelkeevvelaeevvekleglaGyvGvDlvlkd..eepyviEvNP 156
                     + e  +++ +l e++++ l  ++G v  D+ + d  ++++++EvN 
   AHX11503.1 223 kniPDEVYQSALTLTENICNIL-HCRGAVRADFKYDDkeSKLVILEVNT 270
                  0004444556666667777777.99**********99878899*****6 PP

  == domain 2  score: -0.2 bits;  conditional E-value: 0.4
                  --SS--TTE.......EEEE---SEEEEEE CS
  ATP-grasp_3  49 vveekeeaeaaieevelvqefieGkplSvs 78 
                  +  +  +a+a +e +++vqe +e  ++ v 
   AHX11503.1 276 ILPKIAKACANMEIDQVVQEIMEDVDYGVA 305
                  5556678899999999*****998888776 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   6.5e-06     0.015     126     178 ..     218     270 ..     202     272 .. 0.90

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.5e-06
                  EEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEES CS
  CPSase_L_D2 126 evAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNt 178
                  e  P + + de +q   + + ++++ ++ +ga   +f +d k+++ +++EvNt
   AHX11503.1 218 EWVPIKNIPDEVYQSALTLTENICNILHCRGAVRADFKYDDKESKLVILEVNT 270
                  5679999*********************************************8 PP

>> TTL  Tubulin-tyrosine ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.0     0.074   1.7e+02      55      92 ..     126     162 ..     115     179 .. 0.76
   2 ?   11.2   0.0   6.7e-05      0.15     214     283 ..     225     294 ..     204     301 .. 0.83

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.074
                 HHHHTTTS--S-B----SS---XX------BSSTHHHH CS
         TTL  55 aefveeaekeesntwIvKpsasarGkgirvfnkledik 92 
                 +e+++++  +++ ++++Kp+++  +++i+v++  + + 
  AHX11503.1 126 EEILQRKVLYPK-KYVLKPTNEGSSRNIVVVDGESHLT 162
                 445555555555.99***************99888776 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 6.7e-05
                 XXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXX CS
         TTL 214 iiktilaaeveasrlnvqrlkncfelyGvDili.denlkpwLlEvNasPdlksttkldaelkeeliddvln 283
                 i +++ ++ + + ++n+++  +c+   ++D+   d++ k  +lEvN+ P ++   k  +   ++ id+v++
  AHX11503.1 225 IPDEVYQS-ALTLTENICNILHCRGAVRADFKYdDKESKLVILEVNTCPGMTILPKIAKACANMEIDQVVQ 294
                 55556666.688999****************9966789*************99888888888887887776 PP

>> ATPgrasp_Ter  ATP-grasp in the biosynthetic pathway with Ter operon
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.3e-05      0.12       4      86 ..     171     272 ..     169     300 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.3e-05
  ATPgrasp_Ter   4 allvmeyLegpEySvDvlaek..........gevlaav.pRrKekgglq.....elekd..eelielaerlaeefgldglvnvQvrededg..pkLL 80 
                   ++++ e+++g+E Sv  l+++          g++++   + +K+ g  +     ++ ++  ++++ l+e++ + +++ g v   +++d+++  +++L
    AHX11503.1 171 PVMLEEFISGYELSVAFLSGRvlgglelelnGSEYCSYdAKYKK-GFAEwvpikNIPDEvyQSALTLTENICNILHCRGAVRADFKYDDKEskLVIL 266
                   67999999999999999999889999999998887765144555.33334446566444337899999*******************998867899* PP

  ATPgrasp_Ter  81 EiNpRa 86 
                   E+N+ +
    AHX11503.1 267 EVNTCP 272
                   ***966 PP

>> DUF1444  Protein of unknown function (DUF1444)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.0   2.1e-05     0.047      19      76 ..     252     309 ..     235     313 .] 0.85

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
     DUF1444  19 vtfsfdrekdtlriedketkkgvtislkeii.akyeekkekaidevveyveealkalke 76 
                  +f++d ++++l i + +t  g+ti l++i+ a  + + +++++e++e v+ +++a+++
  AHX11503.1 252 ADFKYDDKESKLVILEVNTCPGMTI-LPKIAkACANMEIDQVVQEIMEDVDYGVAAMES 309
                 679*********************9.66665155666889**************99986 PP

>> ATPgrasp_ST  Sugar-transfer associated ATP-grasp
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   3.8e-05     0.085     220     271 ..     225     277 ..     211     294 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 3.8e-05
  ATPgrasp_ST 220 lqiPnweevlelaakaaeklpglgylGwDivlde.ekgplllElNarpglaiv 271
                  +    ++ +l+l+ ++ + l++ g++  D+  d+ e ++++lE+N+ pg++i 
   AHX11503.1 225 IPDEVYQSALTLTENICNILHCRGAVRADFKYDDkESKLVILEVNTCPGMTIL 277
                  44457999**********9***********9976156899**********995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      406  (0.0226449); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.43
# Mc/sec: 2188.52
//
Query:       AHX11504.1  [L=238]
Description: cell division FtsQ family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.8e-09   35.9   0.1      5e-08   33.1   0.1    2.2  2  POTRA_1   POTRA domain, FtsQ-type
    2.3e-08   34.9   0.1    4.5e-08   33.9   0.1    1.5  1  FtsQ      Cell division protein FtsQ


Domain annotation for each model (and alignments):
>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   5.6e-12     5e-08       4      69 .]      48     113 ..      46     113 .. 0.97
   2 ?   -0.0   0.0      0.12   1.1e+03       7      33 ..     117     144 ..     114     163 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 5.6e-12
                 -EEEEES-SS--HHHHHHHHHTTSTT-GGGS-HHHHHHHHHH-TTEEEEEEEEETTTEEEEEEEC- CS
     POTRA_1   4 kqvevsGnkhlsseeiikalgiekgtslfsldleaieqrleklpwvksasVrrqwPntleitveEr 69 
                  ++++sG ++l  + + k ++ +k++s++ + ++ i++ l+k +wv  a+V  ++Pn + i + E+
  AHX11504.1  48 TDIRISGSNNLRLDSVHKMMENYKDRSIIAIPISGIRKELLKQKWVSGATVIMKLPNIIMISIDEH 113
                 579************************************************************997 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.12
                 EEES-SS--HHHHHHHHHTTS.TT-GGG CS
     POTRA_1   7 evsGnkhlsseeiikalgiek.gtslfs 33 
                  + Gn+ + ++++++ + i   +++ f+
  AHX11504.1 117 AIFGNTKIVADDLRALIPIDAeEEKKFT 144
                 6889999999999999888776555554 PP

>> FtsQ  Cell division protein FtsQ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.9   0.1     5e-12   4.5e-08      43     117 .]     157     230 ..     117     230 .. 0.73

  Alignments for each domain:
  == domain 1  score: 33.9 bits;  conditional E-value: 5e-12
                 HHHHHCCS-HHHHH....S-SEE-SS-TTEEEE-T.TS-EEEEES....TTHHHHHHT-CCHHHC............CCCT CS
        FtsQ  43 vlevlaelpeelkp...leiseialserrrwqlvlddgvevklgreelaedleeklarlvkilpqlrlgre...ieyiDLR 117
                    +l+ l+++l +   +++++i+  ++rrw+l++++g+ +kl++    ++l+ +l+r +kil++     +   ++ iDLR
  AHX11504.1 157 TSILLKTLKTKLDKgtlDKLASIEEIADRRWNLTFKNGTVIKLPE----KNLDLALNRVNKILQKN-P--DllgLKNIDLR 230
                 44455666666666777799999999*******************....56777***********7.3..23468999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       686  (0.038262); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.38
# Mc/sec: 1876.15
//
Query:       AHX11505.1  [L=41]
Description: hypothetical protein NHE_0567 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       131  (0.0073066); expected 358.6 (0.02)
Passed bias filter:                      109  (0.00607954); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 346.62
//
Query:       AHX11506.1  [L=180]
Description: GTP cyclohydrolase I family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      9e-44  149.0   0.0    9.9e-44  148.9   0.0    1.1  1  GTP_cyclohydroI  GTP cyclohydrolase I
     0.0025   17.9   0.0     0.0039   17.3   0.0    1.3  1  QueF             QueF-like protein


Domain annotation for each model (and alignments):
>> GTP_cyclohydroI  GTP cyclohydrolase I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.9   0.0   1.1e-47   9.9e-44       2     152 ..       6     157 ..       5     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 148.9 bits;  conditional E-value: 1.1e-47
                      HHHHHHHHHHTT--TTSTTTTTHHHHHHHHHHHHTGGGGS-G.GGGGSSEEETT--S-EEEEEEEEEEEETTT--EEEEEEEEEEE-TTEEE-H CS
  GTP_cyclohydroI   2 eeavreiLealgedpereglketpkRvakayeelfkgleedpkekvlkkvfeeekdemvlvkdiefsSlCeHHllpfigkahvaYiPkkkviGl 95 
                      e+++r +++a+g+dp+r +lk+tp+ + + + ++f+g+++++ +++++ + +  ++++v++kdi+f+S+CeHH+lp+ g+++v+Y+P+  ++ +
       AHX11506.1   6 EDDIRGFIAAIGDDPDRRELKDTPRLLLEILTKCFAGYAHNSLDSLITPMESCCTESLVVLKDIPFFSFCEHHILPISGNISVGYVPDAFITSI 99 
                      578999************************************777777777778999************************************* PP

                      HHHHHHHHHHHSSEE-HHHHHHHHHHHHHHHH--SEEEEEEEEEEHHHHSS.TT--TT CS
  GTP_cyclohydroI  96 SklaRivdvvarrlqvQErlteqiadaleevlkpkgvavvieaehlCmtmr.gvkkke 152
                      + ++R+v++++rrlq+QEr+++qia+al++vl+pkgv+v+ +a+h+Cm+   g+ +++
       AHX11506.1 100 GSIKRLVHACTRRLQMQERICTQIATALDRVLSPKGVIVYATARHMCMMHNdGIFDAS 157
                      ***********************************************98641444443 PP

>> QueF  QueF-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.3   0.0   4.3e-07    0.0039       4      60 ..      84     140 ..      81     145 .. 0.95

  Alignments for each domain:
  == domain 1  score: 17.3 bits;  conditional E-value: 4.3e-07
        QueF   4 atlvirYvpdkkvvelkslklYlisfrnrgifhEevvnrilddlvealkPkwlevvg 60 
                 +++ + Yvpd+ +    s+k+ + +  +r +++E +  +i++ l ++l+Pk + v++
  AHX11506.1  84 GNISVGYVPDAFITSIGSIKRLVHACTRRLQMQERICTQIATALDRVLSPKGVIVYA 140
                 6899***********************************************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      334  (0.018629); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.36
# Mc/sec: 1508.85
//
Query:       AHX11507.1  [L=272]
Description: ATP synthase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.2e-60  203.3   0.0    6.9e-60  203.1   0.0    1.0  1  ATP-synt  ATP synthase


Domain annotation for each model (and alignments):
>> ATP-synt  ATP synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  203.1   0.0   3.9e-64   6.9e-60       2     277 ..       4     270 ..       3     272 .] 0.84

  Alignments for each domain:
  == domain 1  score: 203.1 bits;  conditional E-value: 3.9e-64
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTHHHHCE..HHHHTT.....T..SSG.S...SSEEEEEEE--SSSSSTTHHHH CS
    ATP-synt   2 lkeikrRiksvkstkkItkAmkmVaaaklrkaqealeaarpyaekleevleal..akreee.....ekhpllke..eekkvllivitSDrGLcGgfNsn 91 
                 lk++  Ri+sv+stkkIt+  +m+a++klr++++al aa++y++++   l +l     +e      +k     +   + + +l v++SD+GLcGg+Ns+
  AHX11507.1   4 LKSLLLRINSVNSTKKITRVTQMIATSKLRHSKAALAAAHRYKDEVLGSLYRLgrF--AEAgipsnSK-----SdcAAGREVLFVLSSDKGLCGGYNSS 95 
                 789999*********************************************99431..2223332211.....222345789***************** PP

                 HHHHHHHHHHHHHTTTETEEEEESHHHHHHHHHSS.EHHTTCE-TS.S--HHHHHHHHHHHHSHHHTTSBSEEEEEEEEECCTSEEEEEEEEESS.... CS
    ATP-synt  92 vikkaeklieelkkegevklvvvGkkgreyfkrkvevqleftgvsk.kptfeeaseiaeeildlyeegeideveivynkfksaisqeptvekllp.... 185
                 ++k+ +    +l+ +++v+++ +Gkk++     + ++  ++ +v + + +f+ + +++ ++ d++       ++i+y++f +a++ +p+  ++      
  AHX11507.1  96 ITKYFRMIFPDLS-RRRVSFCFIGKKVAL----SSKFLVDTMDVLEsEMDFASVIDLITTAGDEV------TFSILYTRFFNAMTMHPELLRIPTrdsf 183
                 *****44445543.3368**********9....33444444444444899999999999998866......99********************994433 PP

                 T...HCS..SSTSEESS.HCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
    ATP-synt 186 lekeeekkekseyefepdeeevleellpeylasliyrallesaasEqaaRmtaMdnAtknakelidkltleyNraRQaaITqELieIvsGae 277
                 +      +e++   +ep+++e+++ l+ +y+ +++y++l e+++sE+ +Rm aMd+Atkna+++ d+l+++yNr RQ++IT+EL+e+vsGae
  AHX11507.1 184 I-----FHESHMCGLEPERDELFAFLYGKYVCAQLYECLKEAKVSENMSRMFAMDAATKNAQDVADDLKRLYNRGRQEKITRELVEVVSGAE 270
                 1.....455666799**99************************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       515  (0.0287244); expected 358.6 (0.02)
Passed bias filter:                      413  (0.0230353); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2289.01
//
Query:       AHX11508.1  [L=449]
Description: hypothetical protein NHE_0570 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
       0.01   15.7   5.0       0.01   15.7   5.0    3.3  3  KASH_CCD        Coiled-coil region of CCDC155 or KASH
      0.011   16.2   0.4      0.032   14.7   0.4    1.8  1  YicC_N          YicC-like family, N-terminal region
      0.014   14.9  15.4       0.24   10.9   4.7    2.2  2  HMMR_N          Hyaluronan mediated motility receptor N-termi
      0.027   14.9  11.5      0.049   14.1   2.8    2.5  3  Fez1            Fez1
       0.03   13.9  16.9        3.1    7.3  14.9    3.6  2  Filament        Intermediate filament protein
       0.18   12.4   6.5       0.78   10.4   0.0    3.8  3  SlyX            SlyX
       0.92    8.8  12.6       0.54    9.6   5.5    3.1  3  GAS             Growth-arrest specific micro-tubule binding
        1.2    9.1  20.3        3.4    7.7   1.8    3.8  3  CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein C
        1.7    8.7   9.0         11    6.1   0.5    3.5  3  DUF1664         Protein of unknown function (DUF1664)
        2.4    8.6   4.9         10    6.7   0.3    3.6  2  DUF4140         N-terminal domain of unknown function (DUF414
        4.5    7.5  15.5       0.19   12.0   1.4    3.5  3  TMF_TATA_bd     TATA element modulatory factor 1 TATA binding
        5.8    7.5  14.1        1.8    9.1   0.6    2.9  2  DUF16           Protein of unknown function DUF16


Domain annotation for each model (and alignments):
>> KASH_CCD  Coiled-coil region of CCDC155 or KASH
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.39   5.8e+02      65      88 ..     121     144 ..     110     148 .. 0.82
   2 ?   15.7   5.0   6.8e-06      0.01      78     165 ..     199     286 ..     194     319 .. 0.90
   3 ?   -2.8   7.7       3.1   4.7e+03      96     143 ..     345     391 ..     306     409 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.39
    KASH_CCD  65 leeEleelkalvkeleEkrarlka 88 
                 ++  +e+l+++ k++ E+  +l+ 
  AHX11508.1 121 ISGPNEDLRQTCKSTPEESGSLHH 144
                 566789*********999988875 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 6.8e-06
    KASH_CCD  78 eleEkrarlkaqnkqlekenqsLiakiesLqeenikllaekdelkkklkeLlkekaeLkkqlheleellaekealleektkqieeLkl 165
                 ++ E+ + l  + +++ +e+ sL a +++++ee+    +e+d ++  +  L++e  eL+k+l+++ +  a+   +++  t++i+eLk+
  AHX11508.1 199 KIREELNFLGIELSKIRQERRSLGAAVNKIDEELSSPVTEQDGMHVIMVLLCEEVKELRKKLQSVYAENAKMRDEICANTAEIQELKA 286
                 5667777777888999**********************************************9998888888888999********96 PP

  == domain 3  score: -2.8 bits;  conditional E-value: 3.1
    KASH_CCD  96 enqsLiakiesLqeenikllaek....delkkklkeLlkekaeLkkqlhele 143
                 +     ++i++++e+n+ +  e+    ++ ++ +k L+ +++eL++q +++e
  AHX11508.1 345 N-----QQIKKIEEDNKLNYEEIialsSMIHSNKKSLSVQIDELRMQQQSFE 391
                 2.....3455555555444444322225556666777777777777777766 PP

>> YicC_N  YicC-like family, N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.4   2.2e-05     0.032      36     119 ..     294     375 ..     291     397 .. 0.72

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2.2e-05
      YicC_N  36 lpeelraleeeirelike.rlsRGkvevsvsleseeeeekalkvneellkaylealkelaeelgaeelslaellrlpgvle.eeee 119
                 l  +l ++ ++i+el ke ++ RGk+e+ +s+++++e++ + ++n + l    +++k+++e   +++l+++e+++l+ +++ ++++
  AHX11508.1 294 LDPSLLHCNHQIEELTKEcSFLRGKLELEISFRDSQEKKLRETINSATL-VTNQQIKKIEE---DNKLNYEEIIALSSMIHsNKKS 375
                 5566777788888888873599***********9887777777777754.45677777754...4568999999999999412333 PP

>> HMMR_N  Hyaluronan mediated motility receptor N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   4.7   0.00016      0.24     158     287 ..     203     335 ..     194     341 .. 0.81
   2 ?    7.8   5.9    0.0014         2     228     317 ..     332     415 ..     322     418 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
      HMMR_N 158 klnsLsleLmklrnkleakekevsvkQedmeaklqvtqkn.....LeeskakvaqLkeklvslekekieekseteklleyieelsnvseqlekykldia 251
                  ln L +eL k+r+++ +    ++v  +d e    vt+++     +    ++v +L+ kl+s++ e+++ + e+   +++i+el++ s ++ek    + 
  AHX11508.1 203 ELNFLGIELSKIRQERRSL--GAAVNKIDEELSSPVTEQDgmhviMVLLCEEVKELRKKLQSVYAENAKMRDEICANTAEIQELKAPSCTVEKLDPSLL 299
                 5788899999999988887..4555778888888888877322222234689*********************************************** PP

      HMMR_N 252 qleellkekndeiesLkssLeekeqelskqvkdlne 287
                 +++  ++e  +e + L+ +Le +    + q k+l e
  AHX11508.1 300 HCNHQIEELTKECSFLRGKLELEISFRDSQEKKLRE 335
                 *****************9999887766666666555 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0014
      HMMR_N 228 klleyieelsnvseqlekykldiaqleellkekndeiesLkssLeekeqelskqvkdlnekckllekekeelvreeeekeqtlsaEleel 317
                 kl e i+    v       +++i+++ee  k + +ei  L s ++ +++ ls q+++l  + +  e ++ +  +  ++k++++++ l++l
  AHX11508.1 332 KLRETINSATLV------TNQQIKKIEEDNKLNYEEIIALSSMIHSNKKSLSVQIDELRMQQQSFEIKLGDISTSPRNKQRRRKSNLGDL 415
                 444444443333......4567************************************************99999999999999999877 PP

>> Fez1  Fez1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       6.8     1e+04      53     105 ..     120     134 ..      99     182 .. 0.51
   2 ?   14.1   2.8   3.3e-05     0.049      42     156 ..     199     331 ..     193     338 .. 0.76
   3 ?    6.4   0.5    0.0076        11      16      79 ..     345     408 ..     340     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 6.8
        Fez1  53 eikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelse 105
                 +                                      ++ + ++lr++ ++
  AHX11508.1 120 T--------------------------------------ISGPNEDLRQTCKS 134
                 3......................................33333333333332 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 3.3e-05
        Fez1  42 elrakleekeeeikeleesleektlelevcenelqrkkseaellrekvekleeelkelreelselsleeeeaalesdeakaqrqe.............. 126
                  +r++l+    e++++++++++  + ++++++el+   +e++ ++  +  l ee+kelr++l+++ +e+++++ e  ++ a+ qe              
  AHX11508.1 199 KIREELNFLGIELSKIRQERRSLGAAVNKIDEELSSPVTEQDGMHVIMVLLCEEVKELRKKLQSVYAENAKMRDEICANTAEIQElkapsctvekldps 297
                 56777888888889999999999999***********99999999999999999999999999988877776644433333333344566667777777 PP

        Fez1 127 ....aeeleelkreverlraeLkeerqkkeeqas 156
                     ++++eel++e   lr++L++e   +++q++
  AHX11508.1 298 llhcNHQIEELTKECSFLRGKLELEISFRDSQEK 331
                 8887778888888888888888888877777765 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0076
        Fez1  16 KqQLkdsqaevtqklseivalkaqlrelrakleekeeeikeleesleektlelevcenelqrkk 79 
                  qQ+k +  +     +ei+al + ++  +++l+ + +e++  ++s+e k  ++ +   + qr++
  AHX11508.1 345 NQQIKKIEEDNKLNYEEIIALSSMIHSNKKSLSVQIDELRMQQQSFEIKLGDISTSPRNKQRRR 408
                 59******************************99999999999999888888877766666553 PP

>> Filament  Intermediate filament protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3  14.9    0.0021       3.1      38     186 ..     179     367 ..     176     386 .. 0.79
   2 ?    2.8   2.5     0.048        72     184     244 ..     346     406 ..     341     411 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0021
                 XXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX................................XXXXXXXXXX CS
    Filament  38 eekksaevsklkelyekeleelrkqldeltkerarlqleldnlreeledlrkkyeke................................lnkreevEae 104
                 ee++++e+++ ++ly  el+++r++l+ l  e ++++ e+++l ++++++ + +++                                 +++r+e+ a+
  AHX11508.1 179 EEVERPENNGGNSLYVVELSKIREELNFLGIELSKIRQERRSLGAAVNKIDEELSSPvteqdgmhvimvllceevkelrkklqsvyaenAKMRDEICAN 277
                 5667788899999*********************************99999999888888999999999999999998777777777775555554433 PP

                 XXXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    Filament 105 lkalr......kdldeatlarvdLekkvesLkeelaflkkvheeEvkelqkqvs..eqvlvevdaarkldLteilkeiraqyeelaeknr 186
                  ++++        ++++  + +  ++++e+L++e++fl+   e E++   +q +   +++ +   + ++ +++i ++ + +yee+++ + 
  AHX11508.1 278 TAEIQelkapsCTVEKLDPSLLHCNHQIEELTKECSFLRGKLELEISFRDSQEKklRETINSATLVTNQQIKKIEEDNKLNYEEIIALSS 367
                 3333344466655666666666789*********************988888766555555666688999**************998664 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.048
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
    Filament 184 knreeaeewykskleelqeaaeknsealrsakeeitelrrqiqsleieleslkkqkaslea 244
                 ++ +++ee  k  +ee+   +++ +++ +s   +i elr+q qs ei+l ++  + ++ ++
  AHX11508.1 346 QQIKKIEEDNKLNYEEIIALSSMIHSNKKSLSVQIDELRMQQQSFEIKLGDISTSPRNKQR 406
                 4455666666677777777777777777777778888888888888887777666655555 PP

>> SlyX  SlyX
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.6   0.1      0.29   4.4e+02      20      55 ..     230     268 ..     223     280 .. 0.70
   2 ?   10.4   0.0   0.00052      0.78      18      58 ..     290     329 ..     288     337 .. 0.83
   3 ?   -0.5   2.3       1.3     2e+03       3      31 ..     346     374 ..     329     410 .. 0.55

  Alignments for each domain:
  == domain 1  score: 1.6 bits;  conditional E-value: 0.29
                 HHHHHHHHHHHHH...HHHHHHHHHHHHHT-XXXXXXXX CS
        SlyX  20 eeLndvvaeqqqq...idrlqrqlrllaerlkeleessg 55 
                 eeL+  v+eq+     +  l +++++l+++l+++ ++++
  AHX11508.1 230 EELSSPVTEQDGMhviMVLLCEEVKELRKKLQSVYAENA 268
                 566666666665422255677889999999988877765 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00052
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-XXXXXXXXXXX CS
        SlyX  18 tieeLndvvaeqqqqidrlqrqlrllaerlkeleessgase 58 
                 t+e+L+  + + ++qi++l++++  l+ +l ele s ++s+
  AHX11508.1 290 TVEKLDPSLLHCNHQIEELTKECSFLRGKL-ELEISFRDSQ 329
                 899***************************.6666555444 PP

  == domain 3  score: -0.5 bits;  conditional E-value: 1.3
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        SlyX   3 erleeLEiklafqedtieeLndvvaeqqq 31 
                 ++++++E+      + i +L+ ++    +
  AHX11508.1 346 QQIKKIEEDNKLNYEEIIALSSMIHSNKK 374
                 34444444444444444444444444444 PP

>> GAS  Growth-arrest specific micro-tubule binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.26   3.9e+02      63      90 ..     197     224 ..     189     239 .. 0.47
   2 ?    9.6   5.5   0.00036      0.54      43     105 ..     254     316 ..     248     358 .. 0.84
   3 ?   -2.2   4.2       1.5   2.2e+03      79     112 ..     358     391 ..     318     414 .. 0.48

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.26
         GAS  63 LkkaeeeveeLrkqlknyekdkqslknl 90 
                 L k +ee++ L  +l + ++++ sl ++
  AHX11508.1 197 LSKIREELNFLGIELSKIRQERRSLGAA 224
                 3333333333333333333333333322 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.00036
         GAS  43 ernekelseisqenkrlkepLkkaeeeveeLrkqlknyekdkqslknlkarlkelekelkdlk 105
                 ++ +k+l+ + +en ++++++ + ++e++eL++   + ek   sl + + +++el+ke + l+
  AHX11508.1 254 KELRKKLQSVYAENAKMRDEICANTAEIQELKAPSCTVEKLDPSLLHCNHQIEELTKECSFLR 316
                 67899****************************************************988665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.5
         GAS  79 nyekdkqslknlkarlkelekelkdlkwehevle 112
                 nye+  +    ++++ k+l  ++ +l++++++ e
  AHX11508.1 358 NYEEIIALSSMIHSNKKSLSVQIDELRMQQQSFE 391
                 3333333333333444444444444444444444 PP

>> CENP-F_leu_zip  Leucine-rich repeats of kinetochore protein Cenp-F/LEK1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.0   0.2    0.0038       5.6      60      95 ..     196     231 ..     191     235 .. 0.84
   2 ?    7.7   1.8    0.0023       3.4      63     109 ..     248     294 ..     235     310 .. 0.88
   3 ?    1.4   5.1      0.21   3.1e+02       8      79 ..     329     398 ..     326     412 .. 0.71

  Alignments for each domain:
  == domain 1  score: 7.0 bits;  conditional E-value: 0.0038
  CENP-F_leu_zip  60 eieelaeelreleldLvalrsekeeLekelqkkqer 95 
                     e+ +++eel+ l ++L+++r+e+ +L   ++k  e+
      AHX11508.1 196 ELSKIREELNFLGIELSKIRQERRSLGAAVNKIDEE 231
                     678999*****************9998777776665 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0023
  CENP-F_leu_zip  63 elaeelreleldLvalrsekeeLekelqkkqervseLeslnsslenl 109
                      l ee +el+ +L+++  e+ ++  e+  +  +++eL++  +++e+l
      AHX11508.1 248 LLCEEVKELRKKLQSVYAENAKMRDEICANTAEIQELKAPSCTVEKL 294
                     5778999*******************************999999986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.21
  CENP-F_leu_zip   8 vlekLKeserkadsLk.dkvenLerelemseenqekvileaEtskaevetlkeeieelaeelreleldLvalr 79 
                     +++kL+e+  +a ++  ++++++e + +      e++i          ++l  +i+el+ + + +e++L +++
      AHX11508.1 329 QEKKLRETINSATLVTnQQIKKIEEDNKLN---YEEIIALSSMIHSNKKSLSVQIDELRMQQQSFEIKLGDIS 398
                     677888887777777525688888776654...4555555555566667889999999999999999999887 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   0.0     0.028        42      83     119 ..     198     234 ..     194     239 .. 0.83
   2 ?    6.1   0.5     0.007        11      36     106 ..     218     291 ..     218     324 .. 0.70
   3 ?    3.1   0.9     0.059        89      50      77 ..     362     389 ..     336     400 .. 0.77

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.028
     DUF1664  83 keikeevtevredlseigedvesvkeavegleskler 119
                 ++i+ee++ +  +ls+i+++ +s+ +av++++++l++
  AHX11508.1 198 SKIREELNFLGIELSKIRQERRSLGAAVNKIDEELSS 234
                 5688999999999999999999999999999988875 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.007
     DUF1664  36 krslsdavesvskqleqvs...eslaatkrhLssridrvdkkldeqkeiskeikeevtevredlseigedvesv 106
                 +rsl  av+++ ++l +     + ++     L ++++++ kkl+++ +  +++++e+ +   +++e++  + +v
  AHX11508.1 218 RRSLGAAVNKIDEELSSPVteqDGMHVIMVLLCEEVKELRKKLQSVYAENAKMRDEICANTAEIQELKAPSCTV 291
                 57777777777777765432225566666777788888888888888888888888877777777776655444 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.059
     DUF1664  50 leqvseslaatkrhLssridrvdkklde 77 
                 +  +s+ +++ k+ Ls +id++  ++++
  AHX11508.1 362 IIALSSMIHSNKKSLSVQIDELRMQQQS 389
                 4567899999**********99988775 PP

>> DUF4140  N-terminal domain of unknown function (DUF4140)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.3    0.0067        10      65      95 ..     235     281 ..     157     284 .. 0.81
   2 ?   -0.0   0.5      0.81   1.2e+03      65      79 ..     354     385 ..     291     407 .. 0.62

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0067
     DUF4140  65 e................elkalraeleeledelaaledelaaaearl 95 
                 +                e+k+lr++l+++ +e a+ +de+ a  a++
  AHX11508.1 235 PvteqdgmhvimvllceEVKELRKKLQSVYAENAKMRDEICANTAEI 281
                 0333446777888888569999*****99999999999998887776 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.81
     DUF4140  65 e.................elkalraeleeled 79 
                 +                   k+l  +++el+ 
  AHX11508.1 354 DnklnyeeiialssmihsNKKSLSVQIDELRM 385
                 13333333333333333223333333333333 PP

>> TMF_TATA_bd  TATA element modulatory factor 1 TATA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.1       0.1   1.5e+02      14      57 ..     197     240 ..     183     246 .. 0.71
   2 ?   12.0   1.4   0.00013      0.19      26      82 ..     251     307 ..     242     313 .. 0.90
   3 ?   -2.2   5.0       3.1   4.6e+03      31      77 ..     344     391 ..     302     416 .. 0.75

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.1
  TMF_TATA_bd  14 verlsseirrlEgElaslkeelerleaerdeareeivklmkene 57 
                  ++++  e+  l +El+++++e  +l a  +++ ee+ + ++e +
   AHX11508.1 197 LSKIREELNFLGIELSKIRQERRSLGAAVNKIDEELSSPVTEQD 240
                  34677788888888888888888888888888888887777766 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 0.00013
  TMF_TATA_bd  26 gElaslkeelerleaerdeareeivklmkeneelkelkkeleelekeleelqeryet 82 
                   E+++l+++l+++ ae  ++r+ei + ++e +elk+ + ++e+l  +l   +++ e+
   AHX11508.1 251 EEVKELRKKLQSVYAENAKMRDEICANTAEIQELKAPSCTVEKLDPSLLHCNHQIEE 307
                  5999****************************************9988777777665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 3.1
  TMF_TATA_bd  31 lkeelerleaerdeareeivklmkene.elkelkkeleelekeleelq 77 
                  ++++++++e+  +   eei++l++  + ++k+l+ +++el+ + ++ +
   AHX11508.1 344 TNQQIKKIEEDNKLNYEEIIALSSMIHsNKKSLSVQIDELRMQQQSFE 391
                  467777777777777788888776554145566777777777666555 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.1   0.6    0.0012       1.8      35     102 ..     196     263 ..     193     266 .. 0.94
   2 ?    1.8   6.7      0.23   3.4e+02      28      76 ..     325     388 ..     282     400 .. 0.64

  Alignments for each domain:
  == domain 1  score: 9.1 bits;  conditional E-value: 0.0012
                 HHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH.......HHHHHHHHHHHHHHHHHHH CS
       DUF16  35 rLkkieakvdklgeqinkleqkvekqgekikelkveqkaqgeelnkvdetleliletLqkinkRlDsi 102
                 +L ki ++++ lg +++k+ q+ + +g+ ++++ +e      e + ++  + l+ e ++++ k+l s+
  AHX11508.1 196 ELSKIREELNFLGIELSKIRQERRSLGAAVNKIDEELSSPVTEQDGMHVIMVLLCEEVKELRKKLQSV 263
                 799***********************************999999999999999999999999999876 PP

  == domain 2  score: 1.8 bits;  conditional E-value: 0.23
                 B-.................BHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
       DUF16  28 fkds...............nkqrLkkieakvdklgeqinkleqkvekqgekikelkveqkaqge 76 
                 f+ds               ++q++kkie+  + + e+i +l   ++   + ++ +  e   q++
  AHX11508.1 325 FRDSqekklretinsatlvTNQQIKKIEEDNKLNYEEIIALSSMIHSNKKSLSVQIDELRMQQQ 388
                 5566333333333335555666666666666666666666666655444433333333333333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1186  (0.0661498); expected 358.6 (0.02)
Passed bias filter:                      529  (0.0295053); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.69u 0.26s 00:00:00.95 Elapsed: 00:00:00.42
# Mc/sec: 3190.59
//
Query:       AHX11509.1  [L=279]
Description: UDP-N-acetylenolpyruvoylglucosamine reductase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.4e-27   93.5   0.0    1.7e-26   92.7   0.0    1.4  1  MurB_C         UDP-N-acetylenolpyruvoylglucosamine reductase,
    4.3e-16   58.9   0.0    6.4e-16   58.4   0.0    1.2  1  FAD_binding_4  FAD binding domain


Domain annotation for each model (and alignments):
>> MurB_C  UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   92.7   0.0   1.9e-30   1.7e-26       2     119 ..     181     278 ..     180     279 .] 0.95

  Alignments for each domain:
  == domain 1  score: 92.7 bits;  conditional E-value: 1.9e-30
                 HHHHHHHHHHHHSHCHSTTCTCEESESB---EESHHHHHHHHEEEETTSSEEE-HHHHHHHTT-TTSEETTEEEESSSTTEEEESSS--HHHHHHHHHH CS
      MurB_C   2 ireavlelrakklmvkqpldtpsaGSfFknPivegeeaeelkeyeaeegevklsagwLIeqaglkGlrvggaqvsekhalflvNgggataadilalare 100
                 i++ +le+ +kk +++qp+  ++aGS+FknP                   v  +a++LIe+ag++G+++g+aq+se+h++f++N+g  +++++++l+r+
  AHX11509.1 181 IKSIMLEMIRKK-QESQPIFSKTAGSIFKNP-------------------VGYKAWELIEKAGFRGFSIGKAQISEQHCNFVINHGCESSENLIDLCRT 259
                 78899*******.9****999**********...................3349******************************999************ PP

                 HHHHHHHHHS----BSSEE CS
      MurB_C 101 vrkkVkekfgveLepEvvl 119
                 v+++V+ek g++L  E+++
  AHX11509.1 260 VKDGVREKLGITLDFEMRF 278
                 ****************998 PP

>> FAD_binding_4  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.4   0.0   7.1e-20   6.4e-16      26     139 .]      41     146 ..      24     146 .. 0.90

  Alignments for each domain:
  == domain 1  score: 58.4 bits;  conditional E-value: 7.1e-20
                    CEEEESSSTTEE.STTCSCCEEEEEETT.S--EEEEETTTTEEEEETTSBHHHHHHHHHHHTTECSSGGGTTCGSBHHHTTTTT-EETTEEGG--H CS
  FAD_binding_4  26 pvlvrGgGssll.gqavatggvvldlsr.lnrileideeegtatveaGvtlgdlvealaakglllglepgsgipgtvGGaiatnagGygsekyGli 119
                     + ++G+Gs++l g+    + ++l+l r +n  l+++  +g + ++a +  ++l++ +  ++ + g+e+ s ipgt+GGa+a+nag+y++e++   
     AHX11509.1  41 AFFILGAGSNILaGDR--IESIILKLGRnFNY-LSYE--DGKIIAGAAALQSNLAKLA-LENSIGGFEFFSTIPGTIGGAVAMNAGSYNCETK--- 127
                    4789********6666..7*******997887.7777..8****************99.**********************************... PP

                    HGTEEEEEEEETTSEEEEEE CS
  FAD_binding_4 120 rdnvlglevvladGevvrls 139
                     d v++++++  +Ge+++ls
     AHX11509.1 128 -DLVTSATFIADNGEIITLS 146
                    .****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (279 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2130.44
//
Query:       AHX11510.1  [L=323]
Description: putative lipoprotein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.14   11.2   9.6       0.19   10.8   9.6    1.1  1  AIP3        Actin interacting protein 3
        1.4    7.5   8.4        1.7    7.2   8.4    1.1  1  Ndc1_Nup    Nucleoporin protein Ndc1-Nup
        1.9    8.4   7.6        2.9    7.7   7.6    1.3  1  DUF4661     Domain of unknown function (DUF4661)
        3.7    6.0  12.6        4.2    5.8  12.6    1.1  1  Macoilin    Macoilin family
        7.8    4.5   9.8        9.6    4.2   9.8    1.1  1  Hid1        High-temperature-induced dauer-formation protein


Domain annotation for each model (and alignments):
>> AIP3  Actin interacting protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   9.6   5.3e-05      0.19      76     203 ..      99     229 ..      66     234 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 5.3e-05
                 XXXXXXXXXXXXXXXXXXXXXXXX...XXXXXXXXXXXXXXXXXXXXXXXX.........XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX. CS
        AIP3  76 evkkhideslaslskelkelkssiesqkaslqevserqeeaakekaseslakkelkaqlkevqslrrdLavlrqlysefkseikeslselrekakkvk. 173
                 ++++ +d+s+++ ++ +++  +++++++++ ++v+++q+    e++++s+++k+++++ +++q+ + +L   +++ +++ ++ +++ +    ++++v+ 
  AHX11510.1  99 DLEEFLDNSVETARSFVTDAVKKVQDSAEAVKNVASKQFGFDDETNKNSSRNKTKETSRTKIQQSQDELIQDKKTPDSQAQSSSNESNRNDGTVSTVEt 197
                 4667899999999*****************************9999999999***********************999999999999999988888887 PP

                 ..XXXX.XXXXXXHHHHHHHHHHHHHHHHHHH CS
        AIP3 174 ..easlastkkssnrayiekgkkkLseesdkl 203
                   ++   +++k+++r+  +k+k++Ls+ s+++
  AHX11510.1 198 ipDSGSGKVSKKKSRSTSKKSKSHLSTGSKEV 229
                 77777889999****************99986 PP

>> Ndc1_Nup  Nucleoporin protein Ndc1-Nup
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   8.4   0.00048       1.7     350     451 ..     122     231 ..     103     299 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00048
    Ndc1_Nup 350 inergqpapkaaps.....kapknkasapvkelprlsksplkkkddeifgnsltaeaspkssssskegvekalsslakspgqs.....psptarlspra 438
                 ++++ + +++ a s     ++++nk+s + ++++++s+++ ++++de+++ ++t++++++sss+ +++   ++s + + p +      ++ +++ s+++
  AHX11510.1 122 VQDSAEAVKNVA-SkqfgfDDETNKNS-SRNKTKETSRTKIQQSQDELIQDKKTPDSQAQSSSNESNRNDGTVSTVETIPDSGsgkvsKKKSRSTSKKS 218
                 333333222233.24778733333333.33344444434444446788887555555555554444444444444444433222224333333333666 PP

    Ndc1_Nup 439 rkllekaksrlls 451
                 +++l+++++++ +
  AHX11510.1 219 KSHLSTGSKEVSQ 231
                 6666666666655 PP

>> DUF4661  Domain of unknown function (DUF4661)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   7.6   0.00081       2.9      42     129 ..     143     231 ..     117     253 .. 0.82

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00081
     DUF4661  42 ktkdsgarrssgaapelsreskveqlgskrm.dslkldkavssteesgrleargaipklgsdpvdskgskregvsleeelsasgpeapv 129
                   k+s+++++++++  + ++s++e +++k++ ds+ ++ +  s ++ g + + ++ip  gs +v  k s++++ + +++ls+ + e++ 
  AHX11510.1 143 TNKNSSRNKTKETSRTKIQQSQDELIQDKKTpDSQAQSSSNESNRNDGTVSTVETIPDSGSGKVSKKKSRSTSKKSKSHLSTGSKEVSQ 231
                 4577888888888888888889999988765488888899999999999***********************99999999999999753 PP

>> Macoilin  Macoilin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.8  12.6    0.0012       4.2     267     375 ..     116     227 ..      57     264 .. 0.46

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0012
    Macoilin 267 sdskkkhehnesvdsklqekey.menkskskrlsksessgsesell..veesvkskssssssssn.knskkasagsagssnssskkhsessksvtssss 361
                 +d+ kk +++ +  +++ +k++  +++++++ + ++++++s ++++  ++e +++k++++s++++ +n+++ + g+++++++ + + s + ++++s s+
  AHX11510.1 116 TDAVKKVQDSAEAVKNVASKQFgFDDETNKNSSRNKTKETSRTKIQqsQDELIQDKKTPDSQAQSsSNESNRNDGTVSTVETIPDSGSGKVSKKKSRST 214
                 333333333322222222222112222222222222222222222200222233333333332220222222223333333333332222222111111 PP

    Macoilin 362 sknskkqklpaGks 375
                 sk+  k +l++G +
  AHX11510.1 215 SKK-SKSHLSTGSK 227
                 111.2222222222 PP

>> Hid1  High-temperature-induced dauer-formation protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.2   9.8    0.0027       9.6     602     689 ..     139     242 ..      78     256 .. 0.45

  Alignments for each domain:
  == domain 1  score: 4.2 bits;  conditional E-value: 0.0027
        Hid1 602 nssessrieesrsesrspslsevpelksslaitddeskaereksatessssqavs................qlremsekarakesaesteesrqesats 684
                  ++e ++ +++++ +++ +++ +++ ++ ++ ++  +++ ++ s+++++++ +vs                ++r++s+k++++ s++s+e s+ e++ +
  AHX11510.1 139 FDDETNKNSSRNKTKETSRTKIQQSQDELIQDKKTPDSQAQSSSNESNRNDGTVStvetipdsgsgkvskkKSRSTSKKSKSHLSTGSKEVSQIEAEGD 237
                 111111111111111111111222222222222222222222233333333333322222233333333335555566666666666666666555555 PP

        Hid1 685 kksps 689
                 k  p+
  AHX11510.1 238 KLLPT 242
                 55555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2191  (0.122204); expected 358.6 (0.02)
Passed bias filter:                      669  (0.0373138); expected 358.6 (0.02)
Passed Vit filter:                        85  (0.00474092); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.27s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 2233.07
//
Query:       AHX11511.1  [L=326]
Description: fructose-1,6-bisphosphatase, class II [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.7e-97  323.5   0.7    1.2e-96  323.3   0.7    1.0  1  FBPase_glpX   Bacterial fructose-1,6-bisphosphatase, glpX-enc
  ------ inclusion threshold ------
      0.072   13.2   0.0       0.19   11.9   0.0    1.6  2  RC-P840_PscD  Photosystem P840 reaction centre protein PscD
       0.17   12.2   1.3        5.1    7.5   0.4    2.2  2  Endotoxin_C2  Delta endotoxin


Domain annotation for each model (and alignments):
>> FBPase_glpX  Bacterial fructose-1,6-bisphosphatase, glpX-encoded
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  323.3   0.7    2e-100   1.2e-96       3     294 ..       5     294 ..       3     301 .. 0.96

  Alignments for each domain:
  == domain 1  score: 323.3 bits;  conditional E-value: 2e-100
  FBPase_glpX   3 lalelvrvteaAAlaaarlvGrgdkeaadqaAveamrkalneleikgevviGegekdeapmLyiGekvGsgegpevdiavdpleGttlvAkglpnais 100
                  + l+++ vt++AA a++++ Grg+ ++ad+ Ave+mr+a+n+++ +  vviGege+d+apmLyiGe++G+g g e+d+avdpleGt ++A+ +++ais
   AHX11511.1   5 YILDFLSVTQKAAFASYSFAGRGNSKEADRIAVETMRSAINQISATVSVVIGEGERDKAPMLYIGERLGNG-GLELDLAVDPLEGTDICADFREGAIS 101
                  6799******************************************************************6.8************************* PP

  FBPase_glpX 101 viAvaekgsllkapdvYmeKlvvgpeakgvidldapveenlkavakalgke.vedltvvvLdrpRheelieeireagarvklisdGDvaaaiaaalee 197
                  v+ ++ +gs+l apdvYmeK+ ++ e+   ++++++v++nlk++a+a+g+e   +l ++vL r+R+++lie+ir+aga+v+li+dGD++a ++ +l +
   AHX11511.1 102 VLGFGGSGSILCAPDVYMEKIYTPYEC--EVSFENTVAQNLKSIASAKGVEsAAKLIITVLKRERNQQLIEDIRKAGAKVRLITDGDISAIVSIIL-K 196
                  ***********************9998..69******************862679**********************************9999997.7 PP

  FBPase_glpX 198 sgvdvllGiGgapEGvlaAaalkclgGemqarlvprkeeereraekmgiedldkvltledLvkgddvifaatgvTdgelLkgvrfkggg..arteslv 293
                   ++d+++G+GgapEGvl+A a++ lgG+m ++l+++++e re a+k+gi dl+k +t  ++v+ +++if+atgvT+g+lL g++ ++++  a+ eslv
   AHX11511.1 197 GETDAYMGSGGAPEGVLSAIAVRNLGGTMIGKLLLQDNERREYARKLGILDLEKSYTHYEMVR-GEAIFIATGVTNGKLLAGIDDRDSStiASCESLV 293
                  789************************************************************.7999***************887665458889998 PP

  FBPase_glpX 294 m 294
                  +
   AHX11511.1 294 I 294
                  6 PP

>> RC-P840_PscD  Photosystem P840 reaction centre protein PscD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0      0.92   5.5e+03      42      77 ..      42      79 ..      14      91 .. 0.59
   2 ?   11.9   0.0   3.1e-05      0.19       8      76 ..     129     200 ..     122     208 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 0.92
  RC-P840_PscD 42 drsgklqleis..pasgrrklsptkeliekliegeiel 77
                     +++  ++s     g r  +p   + e+l +g +el
    AHX11511.1 42 SAINQISATVSvvIGEGERDKAPMLYIGERLGNGGLEL 79
                  44444433333003455566666666666666665555 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.1e-05
  RC-P840_PscD   8 pltadnqvrasksgpwsgnavhkaekyfitsakrdrsgklqleispasgrrklspt...keliekliegeie 76 
                    ++++n v ++  +  s   v  a k +it  kr+r+++l  +i  a  + +l +      +++ + +ge +
    AHX11511.1 129 EVSFENTVAQNLKSIASAKGVESAAKLIITVLKRERNQQLIEDIRKAGAKVRLITDgdiSAIVSIILKGETD 200
                   678999***********************************99*9999998887641113445555666655 PP

>> Endotoxin_C2  Delta endotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.018   1.1e+02      17      42 ..      29      55 ..      26      64 .. 0.77
   2 ?    7.5   0.4   0.00085       5.1      14      58 ..     132     176 ..     132     180 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.018
  Endotoxin_C2 17 nnptk.ikdtttqaaIdaAqalVdkvt 42
                  ++ +  i+ +t  +aI++  a+V+ v 
    AHX11511.1 29 SKEADrIAVETMRSAINQISATVSVVI 55
                  334447*****************9775 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.00085
  Endotoxin_C2  14 FtdnnptkikdtttqaaIdaAqalVdkvtdstkKaeLqadidkAq 58 
                   F++   +++k+    + +++A +l+ +v + +  ++L +di kA 
    AHX11511.1 132 FENTVAQNLKSIASAKGVESAAKLIITVLKRERNQQLIEDIRKAG 176
                   66766677***********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (326 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2439.86
//
Query:       AHX11512.1  [L=834]
Description: DNA topoisomerase I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   5.4e-120  401.2   0.7   7.2e-120  400.8   0.7    1.2  1  Topoisom_bac    DNA topoisomerase
      6e-34  115.8   0.7    1.3e-15   57.1   0.0    3.6  3  Toprim_C_rpt    Topoisomerase C-terminal repeat
    1.5e-24   86.1   0.1    6.7e-24   84.1   0.0    2.2  2  Toprim          Toprim domain
    9.2e-12   44.5   2.3    6.3e-11   41.9   0.5    2.5  2  zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
  ------ inclusion threshold ------
      0.018   15.3   0.0      0.092   12.9   0.0    2.2  2  Condensin2nSMC  Condensin II non structural maintenance of ch
       0.36   11.2   2.3       0.57   10.6   0.0    2.6  3  Fer2_BFD        BFD-like [2Fe-2S] binding domain
        0.8   10.2   2.6         30    5.1   0.1    2.7  2  Caskin-tail     C-terminal region of Caskin


Domain annotation for each model (and alignments):
>> Topoisom_bac  DNA topoisomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.8   0.7  2.8e-123  7.2e-120       1     413 []     128     556 ..     128     556 .. 0.91

  Alignments for each domain:
  == domain 1  score: 400.8 bits;  conditional E-value: 2.8e-123
  Topoisom_bac   1 einenlvdaaeaRrelDwliGinlsrlltkklkgkkvlsaGRVqtptLaliveRereienFvpeeyweveatl.kkekkeke......kkkkkkker 90 
                   +in+nlv+a+  R+ lD+l+G++ls++l++kl   +  saGRVq+++L++++eRe+ei  Fvpeeyw++++++  +++   +      + +k ++++
    AHX11512.1 128 KINDNLVQAQRLRQALDYLVGFSLSPVLWRKLP--GSKSAGRVQSVALRMLCERENEIGLFVPEEYWSIDVDIlGSAGLVIStqlshiDGEKLERTS 222
                   689***************************999..799**********************************96655555558999*999******* PP

  Topoisom_bac  91 ikdkeeaeaileklkkkeakvesvekkekkkppplpfdtttLqkeasrklglsakktlsiaqkLYe.......kaglitYpRTdstrlseeaelkai 180
                   ik+ e a++il ++++ ++++++++kke ++++  pf t+t+q++as+ lg++ kkt+s+aqkLYe       ++glitY+RTd t++  +a ++ai
    AHX11512.1 223 IKNAETAQQILDEINNLNFRIDEIKKKEVRQRASPPFITSTMQQAASTFLGFNVKKTMSLAQKLYEgvdiagvTEGLITYMRTDATYIAADA-INAI 318
                   **************5537*************6555**************************************66*****************.9*** PP

  Topoisom_bac 181 lealakkygkeylefaekllkktkkksvvknkkveaHeAIrPteelp.klkels....ddekklYelIvrrflaslmkdakyeettvkl..eveeee 270
                   ++++++++++ yl+ a+  +k +k    vkn++ eaHeAIrPt ++  + ++ +    +d+ klY+lI++r la++m+da + ++++ +  ++++++
    AHX11512.1 319 RKFIQDNFSESYLPEAPVIFK-KK----VKNAQ-EAHEAIRPT-NIFyTPQKVKayltNDQYKLYKLIWERSLACQMSDALIGTQSIVFvsQNNKYK 408
                   **************9999998.44....56999.*********.6665432222566688888**************************54458899 PP

  Topoisom_bac 271 fkasgktilekGfkkvykeekkeeeee....elpelkegeevkvkeveleekkTkppkryteasLikamekagiGtpaTraeiieklvergYverkk 363
                    +as++ +l++Gf++++ e+k+++++      + + keg  +kv+ev  ++++T+pp+ry+ea L+k +e+ giG+p+T+a++i+ l+er+Y+  k+
    AHX11512.1 409 TTASTSMVLFDGFHAAFSESKNKNKNPevadFITREKEGTLLKVNEVVSKQNFTEPPHRYSEAGLVKQLEELGIGRPSTYATVISVLQEREYASIKN 505
                   99999************888888775567766677788888******************************************************99 PP

  Topoisom_bac 364 kslvptelGkalvellekf.kdlvspelTaeleekLdeIaegkadakevld 413
                   ks++p + G+ + e+l +f +++v++++Ta+le+kLd++a+g +++ +v++
    AHX11512.1 506 KSFIPENRGRIVSEFLVHFfSKYVEYHFTADLEDKLDRVADGALEWLDVIQ 556
                   ****************7777***************************9985 PP

>> Toprim_C_rpt  Topoisomerase C-terminal repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.7   0.1   7.6e-10     2e-06       5      51 ..     648     694 ..     646     697 .. 0.93
   2 !   27.1   0.0   1.2e-09   3.1e-06       1      47 [.     698     743 ..     698     750 .. 0.89
   3 !   57.1   0.0   5.2e-19   1.3e-15       4      52 ..     760     808 ..     759     811 .. 0.95

  Alignments for each domain:
  == domain 1  score: 27.7 bits;  conditional E-value: 7.6e-10
  Toprim_C_rpt   5 gepikvkeGRfGPYvkhgkknasLpkgddvetitleeAlellaekra 51 
                   ge i+++ G++G Y+k+++kn  +p++ d+ +i  e A  l a+++ 
    AHX11512.1 648 GEDITLNRGPYGVYLKYKGKNIGIPSEVDPNSINEEFADRLGALPKV 694
                   899*********************************99999999885 PP

  == domain 2  score: 27.1 bits;  conditional E-value: 1.2e-09
  Toprim_C_rpt   1 hPetgepikvkeGRfGPYvkhgkknasLpkgddvetitleeAlella 47 
                   hP++++++k  +G++G Y+ +++k+++L+  + + ++tl +A+  ++
    AHX11512.1 698 HPKDNKEVKMGIGPYGLYLFWNGKYYNLQFSE-MYDMTLGKAIYFIE 743
                   9***************************8766.******99986665 PP

  == domain 3  score: 57.1 bits;  conditional E-value: 5.2e-19
  Toprim_C_rpt   4 tgepikvkeGRfGPYvkhgkknasLpkgddvetitleeAlellaekral 52 
                   +g ++++++GR+GPY+k+gk na++pk +d+++++le+A+ ++++k+ +
    AHX11512.1 760 EGDEVQIRSGRYGPYIKCGKINAPIPKSEDPQSLSLETAISMVEKKKSA 808
                   699*******************************************965 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.1   0.0   2.6e-27   6.7e-24       2     103 .]       3     114 ..       2     114 .. 0.95
   2 ?   -3.3   0.0       4.3   1.1e+04      43      66 ..     223     246 ..     202     247 .. 0.69

  Alignments for each domain:
  == domain 1  score: 84.1 bits;  conditional E-value: 2.6e-27
                 EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.........TTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHT..H CS
      Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildlet.........efkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawellevlk..e 89 
                 + ivE+p++ak+i ++lg ++++v++s Gh++ l+t         +fk  ye  e+  +v+  l +  k+a++++latDpDreGeai+w+l+ev+k  +
  AHX11512.1   3 VLIVESPAKAKAIGQYLG-KDFKVLSSFGHVRALPTkngsvdvndSFKMSYELTEKGATVVPQLIKDVKNASKLYLATDPDREGEAISWHLFEVFKenN 100
                 57****************.**********************999999999998899999999999999****************************999 PP

                 HHTTTEEEEEESSS CS
      Toprim  90 llenkigrvefsei 103
                  l++++ r++f+ei
  AHX11512.1 101 VLPKEVHRIVFNEI 114
                 9999********98 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 4.3
                 EEECTTTHHHHHHHHHHHHHHSEE CS
      Toprim  43 yeeiedkkkvlkalkelakradei 66 
                 +++ e+++++l++++ l  r dei
  AHX11512.1 223 IKNAETAQQILDEINNLNFRIDEI 246
                 337777888888888887777776 PP

>> zf-C4_Topoisom  Topoisomerase DNA binding C4 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.9   0.5   2.5e-14   6.3e-11       4      37 ..     601     635 ..     598     637 .. 0.93
   2 ?    1.7   0.1     0.089   2.3e+02       8      24 ..     761     777 ..     761     779 .. 0.88

  Alignments for each domain:
  == domain 1  score: 41.9 bits;  conditional E-value: 2.5e-14
                     -SSS-.-EEEEEE-SSSEEEEESST.T----EEB- CS
  zf-C4_Topoisom   4 CPkCg.gdLvlkrgkkGkFvGCsnYPeCkftkklk 37 
                     CPkCg g++ l  +++G F+GC+ YP+C+ ++++ 
      AHX11512.1 601 CPKCGaGKISLNVSRYGVFLGCTDYPDCRLVVNDH 635
                     *****************************998875 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.089
                     --EEEEEE-SSSEEEEE CS
  zf-C4_Topoisom   8 ggdLvlkrgkkGkFvGC 24 
                     g+++++++g++G ++ C
      AHX11512.1 761 GDEVQIRSGRYGPYIKC 777
                     57899*******99988 PP

>> Condensin2nSMC  Condensin II non structural maintenance of chromosomes subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   3.6e-05     0.092      24     140 ..      61     173 ..      58     177 .. 0.79
   2 ?   -3.5   0.0       4.2   1.1e+04      35      67 ..     536     567 ..     504     592 .. 0.54

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 3.6e-05
  Condensin2nSMC  24 ldtklikeilkaiksqipkleksvleaygeilfraWkkasge...lkeeieesciqdlmeaalhakrkklakklrkvLsafhsk.kkekeveeml 114
                     + ++lik++ +a k  +   ++++ ea++  lf+++k+ +     +++ +++++ ++ +++a+++         rk+ +++++  + +++++ ++
      AHX11512.1  61 VVPQLIKDVKNASKLYLATDPDREGEAISWHLFEVFKENNVLpkeVHRIVFNEITKTAVQNAITSP--------RKINDNLVQAqRLRQALDYLV 147
                     567999*******************************76653333555556666666666666666........555555555559********* PP

  Condensin2nSMC 115 vrlyepilwrsLkvanskvRanAael 140
                        ++p+lwr L  + s  R ++++l
      AHX11512.1 148 GFSLSPVLWRKLPGSKSAGRVQSVAL 173
                     ************99999988888775 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 4.2
  Condensin2nSMC  35 aiksqipkleksvleaygeilfraWkkasgelk 67 
                      +++++  + +  le++ +++   W++ s +++
      AHX11512.1 536 DLEDKLDRVADGALEWL-DVIQDFWSNFSAKVR 567
                     44555555555544444.555566666665543 PP

>> Fer2_BFD  BFD-like [2Fe-2S] binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       3.2   8.1e+03       6      19 ..     112     125 ..     112     136 .. 0.76
   2 ?   -2.5   0.1       2.8   7.1e+03       9      29 ..     228     247 ..     225     252 .. 0.69
   3 ?   10.6   0.0   0.00022      0.57       9      42 ..     573     605 ..     570     607 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 3.2
    Fer2_BFD   6 egvtegeIrdairr 19 
                 +++t+  + +ai++
  AHX11512.1 112 NEITKTAVQNAITS 125
                 57899999999954 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 2.8
    Fer2_BFD   9 tegeIrdairraglttveevk 29 
                 t+++I d i ++    ++e+k
  AHX11512.1 228 TAQQILDEI-NNLNFRIDEIK 247
                 789999999.43246677776 PP

  == domain 3  score: 10.6 bits;  conditional E-value: 0.00022
    Fer2_BFD   9 tegeIrdairraglttveevkrrtkagtgCggCr 42 
                    eI dai++  l + + + +  k g+gC +C 
  AHX11512.1 573 PIAEILDAINK-ALIDQKLISKDIKIGDGCPKCG 605
                 5679*****55.5********************7 PP

>> Caskin-tail  C-terminal region of Caskin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.1   0.1     0.012        30      28      49 ..     218     239 ..     205     241 .. 0.79
   2 ?    4.2   0.4     0.023        60       7      30 ..     791     814 ..     786     827 .. 0.73

  Alignments for each domain:
  == domain 1  score: 5.1 bits;  conditional E-value: 0.012
  Caskin-tail  28 essssaaevksaknILdDIgnM 49 
                   +++s++++++a++ILd I n+
   AHX11512.1 218 LERTSIKNAETAQQILDEINNL 239
                  34469999***********985 PP

  == domain 2  score: 4.2 bits;  conditional E-value: 0.023
  Caskin-tail   7 tsasLaaaLkavEkkikqeesess 30 
                   s sL+ a+  vEkk ++ +  ++
   AHX11512.1 791 QSLSLETAISMVEKKKSAPKIAKK 814
                  699************888877777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (834 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       955  (0.0532657); expected 358.6 (0.02)
Passed bias filter:                      671  (0.0374254); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.73u 0.27s 00:00:01.00 Elapsed: 00:00:00.45
# Mc/sec: 5588.87
//
Query:       AHX11513.1  [L=546]
Description: hypothetical protein NHE_0575 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (546 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 4213.07
//
Query:       AHX11514.1  [L=209]
Description: tRNA methyltransferase complex GCD14 subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.7e-34  118.9   0.0    2.2e-34  118.5   0.0    1.1  1  Methyltransf_3   O-methyltransferase
    9.8e-14   52.3   0.0    1.3e-13   51.8   0.0    1.2  1  Methyltransf_24  Methyltransferase domain
    3.2e-11   43.4   0.0    4.5e-11   42.9   0.0    1.1  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
    2.3e-06   27.5   0.0      4e-06   26.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    5.7e-05   22.9   0.0      8e-05   22.4   0.0    1.2  1  GCD14            tRNA methyltransferase complex GCD14 subunit
    0.00085   20.0   0.0     0.0015   19.2   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
     0.0047   16.1   0.0     0.0065   15.6   0.0    1.2  1  Fibrillarin      Fibrillarin
  ------ inclusion threshold ------
      0.016   14.7   0.0      0.023   14.3   0.0    1.2  1  Methyltransf_15  RNA cap guanine-N2 methyltransferase
      0.023   14.4   0.0      0.034   13.8   0.0    1.2  1  CmcI             Cephalosporin hydroxylase
      0.047   13.3   0.0      0.077   12.6   0.0    1.3  1  Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F


Domain annotation for each model (and alignments):
>> Methyltransf_3  O-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  118.5   0.0   1.2e-37   2.2e-34       8     211 ..      18     208 ..      13     209 .] 0.92

  Alignments for each domain:
  == domain 1  score: 118.5 bits;  conditional E-value: 1.2e-37
                     .--HHHHHHHHHTTTST.TGGGS--HHHHHHHHHHHHHHT--EEEEE--TTSHHHHHHHTTS-TT-EEEEEES-HHHHHHHHHHHHHTT-GGGEE CS
  Methyltransf_3   8 rehellkeLreatakktdlsemevsvdegqfLslLvklvnakrvleiGvftGyslLatalalPeDGkilaididreayeialkfiqkagvaekie 102
                     +e  ll+++re+t   +  + m++++ eg+ L+lL+k+ + k ++e+G+  Gys + +a ++ ++G++ +i++++e+++ia + ++      +i+
      AHX11514.1  18 GECGLLRKIREETFSDK-RKFMQIGRIEGKILELLIKMNSVKTIVEVGTLAGYSTIWMAKTVGPEGRVYTIEKNPEHAQIASQNFRDF---TQIK 108
                     5677899*******999.99*************************************************************9988764...68** PP

                     EEES-HHHHHHHHHTSSS---EEEEEE-S-GGGHHHHHHHHHHTEEEEEEEEEE-TTGGGGGG-SS--SHHHHH.....HHHHHHHHTT-TTEEE CS
  Methyltransf_3 103 liegdalkvLeelvkdkklpefDfifvDaDkssyvnyyeklleLvkvGgliaiDntLWeGkvveeddeeakalreyravllelnkklaeDprvei 197
                     li+gda++ L+el++ ++   fD++f+Da+ks y++y   + + +k Ggli+ DntL +G+    +     + r + + + ++n +l++ ++ + 
      AHX11514.1 109 LIVGDAKTKLDELIDFSP---FDMMFIDAEKSGYPEYLCWAEKNIKSGGLIVADNTLSFGESSFAN-----KGR-LWDSIDQFNSELSNPDKYDS 194
                     **************9996...***************************************765443.....333.457899************** PP

                     EEE-SBT-EEEEEE CS
  Methyltransf_3 198 sllsvgDGitLvrk 211
                     +++   +G+t+++k
      AHX11514.1 195 VIIQTENGMTIALK 208
                     ***********988 PP

>> Methyltransf_24  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   51.8   0.0   7.5e-17   1.3e-13       1     106 []      61     161 ..      61     161 .. 0.92

  Alignments for each domain:
  == domain 1  score: 51.8 bits;  conditional E-value: 7.5e-17
  Methyltransf_24   1 vEiGvysGvstlwllralrrngagrlvavdhdpgaeeaaalareaglddr..vrlikadseealasla.agsiDllfiDgghaaeavledleal 91 
                      vE+G+ +G+st+w+++++   g  r+++++++p   e+a++a + +++d+  ++li++d++  l +l   +++D++fiD++  ++ + e+l+++
       AHX11514.1  61 VEVGTLAGYSTIWMAKTVGPEG--RVYTIEKNP---EHAQIASQ-NFRDFtqIKLIVGDAKTKLDELIdFSPFDMMFIDAE--KSGYPEYLCWA 146
                      8*****************9998..5********...88888888.77776569************9997789*******76..999999***** PP

  Methyltransf_24  92 lprlapggvvlfdDi 106
                      ++ +++gg+++ d++
       AHX11514.1 147 EKNIKSGGLIVADNT 161
                      ************986 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.9   0.0   2.5e-14   4.5e-11      63     170 ..      45     157 ..      36     162 .. 0.87

  Alignments for each domain:
  == domain 1  score: 42.9 bits;  conditional E-value: 2.5e-14
                 HHHHHHTT.--TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHHCTTCSEEEEES-GGGTTGG...G-SEEEEEESSBBSS--H CS
        PCMT  63 alalelle.lkkgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkkldlenvivvvgDGrkGyee...kaPYdaihvgaaapeiPe 157
                 +++lell  ++ ++ ++evG+ +Gy t  +a+ vg++grv +ie+ +e ++ a++n +  d ++++++vgD ++  +e   ++P+d +++ a     Pe
  AHX11514.1  45 GKILELLIkMNSVKTIVEVGTLAGYSTIWMAKTVGPEGRVYTIEKNPEHAQIASQNFR--DFTQIKLIVGDAKTKLDElidFSPFDMMFIDAEKSGYPE 141
                 678898866***********************************************98..6778999999999887643338***************** PP

                 HHH...HTEEEEEEEE CS
        PCMT 158 ali...dQLkeGGrlv 170
                  l    + +k+GG +v
  AHX11514.1 142 YLCwaeKNIKSGGLIV 157
                 9864446788888776 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.2e-09     4e-06       4      82 ..      57     134 ..      54     171 .. 0.82

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.2e-09
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdiee.leklledekfDlilsne 82 
                       ++++++G+ +G+ t+ +a+++gp+++v+ i+ ++e  + A +n +   ++ +++ +gd+ + l++l+  ++fD+++ ++
       AHX11514.1  57 VKTIVEVGTLAGYSTIWMAKTVGPEGRVYTIEKNPEHAQIASQNFR--DFTQIKLIVGDAKTkLDELIDFSPFDMMFIDA 134
                      57899***************************************88..9*************8998666699****9984 PP

>> GCD14  tRNA methyltransferase complex GCD14 subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4   0.0   4.4e-08     8e-05      37      89 ..      53     105 ..      40     120 .. 0.84

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 4.4e-08
       GCD14  37 elkpGsvvvesGtGsgslshaiartvaPtGhlftfefheqraekareefrehe 89 
                 +++    +ve Gt +g  +  +a+tv+P G+++t+e   + a+ a ++fr+  
  AHX11514.1  53 KMNSVKTIVEVGTLAGYSTIWMAKTVGPEGRVYTIEKNPEHAQIASQNFRDFT 105
                 34444569*********999*****************************9854 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   8.1e-07    0.0015       1      70 [.      60     132 ..      60     153 .. 0.85

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 8.1e-07
                      EEEET-TTSHHHHHHHCTST.SSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBC.CGBSS..STTTEEEEEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlg.kakvtgvDiseemleaareraeeegl.nvefvqgda.edlpf..edgsfDlvvs 70 
                      ++++G+  G  t+++ak +g +++v+ ++ ++e  ++a +++++  + ++++++gda ++l++  + + fD++++
       AHX11514.1  60 IVEVGTLAGYSTIWMAKTVGpEGRVYTIEKNPEHAQIASQNFRD--FtQIKLIVGDAkTKLDEliDFSPFDMMFI 132
                      789****************66*********************65..44*********655763235557888776 PP

>> Fibrillarin  Fibrillarin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.0   3.6e-06    0.0065      67     152 ..      53     138 ..      38     159 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 3.6e-06
                  S--TTSEEEEESTTTSHHHHHHHHHHTTTSEEEEEESSHHHHHHHHHHHTTSTTEEEEES-TTSGGGGTTTS--EEEEEEESSSTT CS
  Fibrillarin  67 pikkgskvLYlGaasGttvsHvsDivgeegvvyavefsprvlrelievakkRknivPileDArkPekYralvekvDvifaDvaqpd 152
                  ++++ + ++ +G+ +G +   ++  vg+eg+vy++e  p   +   +  ++ + i  i++DA++  +     +  D++f D  ++ 
   AHX11514.1  53 KMNSVKTIVEVGTLAGYSTIWMAKTVGPEGRVYTIEKNPEHAQIASQNFRDFTQIKLIVGDAKTKLDELIDFSPFDMMFIDAEKSG 138
                  4455578999*******************************999999999999*********987766666668899999977665 PP

>> Methyltransf_15  RNA cap guanine-N2 methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   1.3e-05     0.023       5      77 ..      61     132 ..      57     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.3e-05
  Methyltransf_15   5 lDlfsGaGGnviqfalv...fekviaieinleklacaqhNaevYgvsdkitlvlgdvfellaklklekikvdlvfl 77 
                      + + + aG  +i +a++     +v++ie+n+e+ ++a +N + +    +i+l++gd ++ l +l   +  +d++f+
       AHX11514.1  61 VEVGTLAGYSTIWMAKTvgpEGRVYTIEKNPEHAQIASQNFRDF---TQIKLIVGDAKTKLDELIDFSP-FDMMFI 132
                      55556688899999998666459*********************...9*********999887644333.566665 PP

>> CmcI  Cephalosporin hydroxylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   1.9e-05     0.034      33      94 ..      57     114 ..      46     119 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 1.9e-05
        CmcI  33 PdliietGiahGGsalfsasllallkskrkvlaididireknrqaieahplasrieliegss 94 
                  ++i+e+G+  G s +++a+   +++ +++v +i+    e+ + a +  +  ++i+li g++
  AHX11514.1  57 VKTIVEVGTLAGYSTIWMAK---TVGPEGRVYTIEK-NPEHAQIASQNFRDFTQIKLIVGDA 114
                 579**************886...56899*******9.7778888888889999999999876 PP

>> Methyltr_RsmB-F  16S rRNA methyltransferase RsmB/F
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   4.3e-05     0.077       8      91 ..      56     138 ..      49     142 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 4.3e-05
                      TT-EEEESS-TTSHHHHHHHHHTTTTSEEEEEESSCCCHHHHHHHHHHTT--SEEEEES-CT.CCHHHHCC..EEEEEEEE--CC CS
  Methyltr_RsmB-F   8 eeetilDlcaaPGgKTthiaelmknkgtvvAvdankeRlkrvaenlkrLgvtntivleaDar.kidkvlggelfDriLlDaPCsg 91 
                        +ti+++ +  G  T ++a+ + ++g+v+ +++n e ++   +n + + +   +++ +Da+ k d+ +  + fD + +Da  sg
       AHX11514.1  56 SVKTIVEVGTLAGYSTIWMAKTVGPEGRVYTIEKNPEHAQIASQNFRDFTQI--KLIVGDAKtKLDELIDFSPFDMMFIDAEKSG 138
                      556788888888999*******************************987665..7777777516677777799*******98776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      456  (0.0254337); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 1792.84
//
Query:       AHX11515.1  [L=861]
Description: aconitate hydratase 1 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-168  562.0   0.0   1.4e-168  561.7   0.0    1.1  1  Aconitase      Aconitase family (aconitate hydratase)
    2.2e-43  147.7   0.1      5e-43  146.6   0.0    1.7  2  Aconitase_C    Aconitase C-terminal domain
  ------ inclusion threshold ------
      0.054   12.7   0.0       0.09   12.0   0.0    1.2  1  Acyl_transf_2  Acyl transferase


Domain annotation for each model (and alignments):
>> Aconitase  Aconitase family (aconitate hydratase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  561.7   0.0  2.4e-172  1.4e-168      13     461 .]      56     528 ..      41     528 .. 0.94

  Alignments for each domain:
  == domain 1  score: 561.7 bits;  conditional E-value: 2.4e-172
   Aconitase  13 g..iayvpdrvllqdvtgvqalvdlaaareavrrlggtlatidhlvpvdlvidhsv.....gaeealeknledefernkeryefLksaakaf.girvvp 103
                 g  i+y p+rvl+qd+tgv+a+vdla+ r+av++ gg+++ +++++pvdlvidhs+     g+++++ +n ++ef+rn ery+ Lk+a+ af ++rvvp
  AHX11515.1  56 GftIDYYPSRVLMQDFTGVPAIVDLASLRDAVSANGGDPRNVNPKIPVDLVIDHSIqvdsyGKSSSAGENKRKEFQRNIERYKLLKWAQGAFqNFRVVP 154
                 2458999*****************************************************9999999******************************** PP

   Aconitase 104 pgqGIvHqvnlEy.............glalpgktvvgtDSHTtmigglGvlaiGvGgieaeavllgqplelkipkvvgvkltGklkegvtakDlvlavi 189
                 pg GI+Hq+nlEy              +a+p+ t+vgtDSHTtm ggl vl++GvGgieae+v+lg+ +++ ip+v+g  l+Gklk+gvt++Dlvl+++
  AHX11515.1 155 PGMGICHQINLEYlsrvvctkaegraVIAYPD-TLVGTDSHTTMSGGLSVLGWGVGGIEAESVMLGEAISMVIPEVIGLGLKGKLKPGVTSTDLVLHIT 252
                 *******************999855449****.****************************************************************** PP

   Aconitase 190 gklrkkgvvgkvvEffGegvesLsledraTiaNMaaEvGAttglfpvdektleYLkatgreeaav.lveaydkaqalfelaadedaeydkvleldlstl 287
                 + lr  +vvgk+vE fGegv++Ls++draTiaNMa+E+G+t+ +f++d+ktl+YL +tg++++++ lve y+kaq  ++ + ++da++ +v++ldl ++
  AHX11515.1 253 HLLRSYNVVGKLVEVFGEGVKNLSIADRATIANMAPECGSTCNFFAPDQKTLDYLDMTGKSAEQIeLVESYTKAQTFWA-DYNHDADFIDVIHLDLGEV 350
                 *****************************************************************9************5.4466899************ PP

   Aconitase 288 epsvagpkrPqdavplselvkkefkeelekeaaekaleyklkegtklkdgkvdiaaigSCTNssnedvraaaglla.kavekglkvkpgvktsvaPGSe 385
                 +p +agpkrPqd+v + + v+++f+++       +++  +   + +l dg+v iaai+SCTN+sn++ ++aagl+a kave+gl++kp+vkts+aPGS+
  AHX11515.1 351 RPILAGPKRPQDKVLI-GAVPENFRNAY------SSI--SPLDREQLCDGSVIIAAITSCTNTSNPSAMLAAGLIArKAVEAGLTTKPWVKTSLAPGSQ 440
                 ****************.89987787655......222..2334578999************************************************** PP

   Aconitase 386 vvkayleaeGlleiLekaGfevvgagCstCignsdrle........ege...aivsssNRNFegRqgpntra.yLaSPelvvaaAlaG 461
                 vv++yl ++Gl+e+L+++Gf+vvg+gC+tCigns++l         e++   ++v+s+NRNFegR++p+++a yLaSP lvva+A+aG
  AHX11515.1 441 VVSEYLSQSGLQEYLDQLGFNVVGYGCTTCIGNSGDLLpeiseqiaEKNlttVAVLSGNRNFEGRIHPKVKAnYLASPMLVVAYAIAG 528
                 ***********************************98768877776444899***********************************9 PP

>> Aconitase_C  Aconitase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.0   0.0         3   1.8e+04      21      37 ..     122     138 ..     108     142 .. 0.55
   2 !  146.6   0.0   8.4e-47     5e-43       3     129 ..     657     786 ..     655     788 .. 0.95

  Alignments for each domain:
  == domain 1  score: -4.0 bits;  conditional E-value: 3
                  GCCGHCCHHHCCCGGTT CS
  Aconitase_C  21 tdlkipkqfegtianig 37 
                    ++ +k+f+  i++++
   AHX11515.1 122 AGENKRKEFQRNIERYK 138
                  33455555555555555 PP

  == domain 2  score: 146.6 bits;  conditional E-value: 8.4e-47
                  CCCCCTT--CHHHHSTGGGCCGHCCHHHCCCGGTTTCCCCTTTSBBSEEEETTTTEEE...EHHHHHHHHHHTT--EEEE--SSBTBS---THHHHHH CS
  Aconitase_C   3 kllklkGlttedeksnvdtdlkipkqfegtianiglgnelveekrankttdlddgeke...dvvdaaerykkegaklvviagknfGeGSSRehAAkal 97 
                   +lk+ G++++d++s+++++++++ +++gt+an++++n+++e+++ + t+++ +g +    ++++aa+ryk++g+ lvv agk++G+GSSR++AAk++
   AHX11515.1 657 EYLKELGVEPQDFNSYGARRGNHEIMMRGTFANLRIKNQMLEGQEGGYTDYFGEGGERkilSIYEAAMRYKSHGTALVVFAGKEYGTGSSRDWAAKGT 754
                  699***********************************************997765555779************************************ PP

                  HHTTEEEEEES-B-HHHHHHHHHTT-EEEEES CS
  Aconitase_C  98 rllGikaviaeSFerIfennliknglLplefk 129
                   llGikaviaeSFerI+++nl+++g+Lpl ++
   AHX11515.1 755 HLLGIKAVIAESFERIHRSNLVGMGVLPLVYA 786
                  *****************************886 PP

>> Acyl_transf_2  Acyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   1.5e-05      0.09      47     125 ..     449     533 ..     439     563 .. 0.76

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 1.5e-05
                    HHHHHHHHTTT--EEEE---B-------------HHHHHHHHHHHHHHHHHTT--.-E..EEEEETTHH...HHHHHHTTTS--S CS
  Acyl_transf_2  47 aglaeylsengfhvirydslnhvglssgeidefsmsvgkkslltvidwlkekkin.ni..gliasslsa...riayevvaeiels 125
                    +gl eyl + gf+v+ y     +g s   + e+s  +  k l tv     +++ + +i   + a  l++    +ay+++ +i++ 
     AHX11515.1 449 SGLQEYLDQLGFNVVGYGCTTCIGNSGDLLPEISEQIAEKNLTTVAVLSGNRNFEgRIhpKVKANYLASpmlVVAYAIAGNINVN 533
                    69*************************9**************9998776676655212112222222221115677777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (861 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 6025.53
//
Query:       AHX11516.1  [L=330]
Description: S-adenosyl-L-methionine-dependent methyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-49  168.6   0.1    1.2e-48  166.0   0.1    1.9  1  Methyltransf_28  Putative S-adenosyl-L-methionine-dependent m


Domain annotation for each model (and alignments):
>> Methyltransf_28  Putative S-adenosyl-L-methionine-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.0   0.1   6.7e-53   1.2e-48       2     246 ..      66     275 ..      65     279 .. 0.92

  Alignments for each domain:
  == domain 1  score: 166.0 bits;  conditional E-value: 6.7e-53
  Methyltransf_28   2 laiwlleewqalgrpskklrliElGpGkGtLmadvLrtlrkflpefyealeyhlvEaSpqlrerQknrLkekakevkkestvkslgvkveWlee 95 
                      +aiwll++w +lg+p + + + E+GpG+G +m d+L++++    +fy+a ++++vE+Sp lr+ Q+ rL  +               k++W e+
       AHX11516.1  66 IAIWLLHRWGQLGKPTE-IIIAEFGPGTGIMMLDILDAIHCS-DDFYSAVRVYMVEISPLLRKLQRGRLIAH-------------SRKICWCES 144
                      9***************8.**********************88.9**************************95.............688****** PP

  Methyltransf_28  96 lkeipeetgfilanEffDaLPihqfertedgwrellveltpekkakekefrltlspsetdplsevlpklskrlkaleegsrieispeaealled 189
                      ++eipe + +ilanEffDaLPi+qf+  +++++e  ++ +         f+ t +++e+ +   ++       +    g+ ie + + ++++ +
       AHX11516.1 145 INEIPESKILILANEFFDALPIDQFIFLDEEFFENKITAD---------FHVTPEKTEE-RFTGMF-------S---HGDIIEKNFKGREVAAS 218
                      **************************99999888877666.........7777666555.333333.......3...8**************** PP

  Methyltransf_28 190 iaerlakegGaaLiiDYgesssepngtLrairkhklvdpleepGevDltadvDFtal 246
                      + er+++ gG +L+iDYg++ ++  +t++a+r+hk+ d++++ Ge+D+t  vDF+ l
       AHX11516.1 219 MIERITRCGGGVLVIDYGHAFGVRRSTIQALRSHKFSDIFQNIGEADITHEVDFSFL 275
                      *******************99*********************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (330 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       466  (0.0259914); expected 358.6 (0.02)
Passed bias filter:                      453  (0.0252663); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.39
# Mc/sec: 2554.12
//
Query:       AHX11517.1  [L=779]
Description: valine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   4.3e-105  352.2   0.7   3.3e-103  346.0   0.7    2.7  1  tRNA-synt_1    tRNA synthetases class I (I, L, M and V)
    8.2e-26   90.6   1.1    2.2e-15   56.3   0.0    3.2  3  tRNA-synt_1g   tRNA synthetases class I (M)
      2e-24   86.3   0.3    4.5e-24   85.1   0.3    1.6  1  Anticodon_1    Anticodon-binding domain of tRNA
    2.1e-09   37.2   0.0    1.9e-08   34.0   0.0    2.1  2  tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
    0.00048   19.6   0.0       0.82    9.0   0.0    2.5  2  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain
  ------ inclusion threshold ------
      0.024   13.6   0.0        2.8    6.7   0.0    2.4  2  tRNA-synt_1f   tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  346.0   0.7  1.1e-106  3.3e-103       4     599 ..      19     550 ..      16     553 .. 0.93

  Alignments for each domain:
  == domain 1  score: 346.0 bits;  conditional E-value: 1.1e-106
  tRNA-synt_1   4 ekWeeedvfkkelekekekkefilvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefr 101
                  ekW++++v++ +   ++  + f++  +PP + GslHiGh++     d++ ry+rm+Gk+v y  G+D  Gl++e  vek+  ++         ++ef+
   AHX11517.1  19 EKWKHSGVYDFS---KDGDDIFSIDTPPPTISGSLHIGHVFSYCHTDFIARYQRMRGKNVFYSAGFDNNGLPTERLVEKTHKIRI----RATEQHEFI 109
                  89********99...677999**********************************************************964444....467789*** PP

  tRNA-synt_1 102 ekvrewkaeyaeeirkqvkrlGvsvDfdreylTldkeleeavkevfvrladkgliyrgkklvnwstklktalselEveykdkkdalihvafpladkee 199
                    + ++ ++ + e ++ +  +  s+D++  y T ++      ++ f +l++kgliyr k +v w++  +ta++++Eve k+ ++++ ++ f  +d+++
   AHX11517.1 110 RLCDAISEQKILEFKSLFDSIALSLDWSFSYQTNSEACRRLSQKSFLNLYKKGLIYRKKMPVLWDVIDQTAIAQAEVEEKEFESQMNYIIFSSEDGRK 207
                  *********************************************************************************************99999 PP

  tRNA-synt_1 200 vklviaTTtPeTllgdtavavnpeldyvitkeklilaeallkslvkkesekkiledergkeLegkevelplvnrkipiiaddyvdkeaGtGvVkiaPa 297
                    l++aTT+Pe l+g +a+  np                                der++ L+gk++  pl + kipii d+ v  e+GtG+V +   
   AHX11517.1 208 --LEVATTRPELLPGCVALLCNPS-------------------------------DERYRCLNGKYAFTPLFDVKIPIICDESVLVEKGTGLVMCCTF 272
                  ..**********************...............................9****************************************99 PP

  tRNA-synt_1 298 hdedDyevgkkynlevinildedgtlteeaaefeglkvfdarkkvveelkekglllkaekiehsvpfcerskkpiiyrateqWfvrvkeladaalkav 395
                   de D +  ++y+l++  ++d  g+++         kv+dark ++e l+ kgll ++eki+h+v ++ers+  ++  +t qW++rv + ++++  +v
   AHX11517.1 273 GDEMDIKWWQQYDLPLREVVDRYGKIDAL----GQRKVEDARKYILECLDSKGLLKRQEKITHNVKCAERSGGKLEIISTYQWYIRVLDYKEELKVKV 366
                  9***********************99764....55799************************************************************ PP

  tRNA-synt_1 396 ekvqfvpkskekryaswleniq.dWciSRqrwWGhriplfvsketeevvvreelkelvagreeeeaekkalekeakdklkkekgelekdedvlDvWFs 492
                  +++ ++p++ + ++++w+  i+ dWciSRqr+ G+r+p+++++etee+   ee++   +                 d + ++  ++++d+dvlD+W  
   AHX11517.1 367 KEIDWIPEKMRIKIEQWIDGIKwDWCISRQRYLGVRVPVYYDEETEEILLPEEVDLPIN----------------GDPILRNGRRYRQDTDVLDTWAT 448
                  ********************988***********************9999222211111................22233455689************ PP

  tRNA-synt_1 493 SgswpfstlgypeedteelkkffpadmlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltl 590
                  S+++p    +     +  ++ f  +++  +   iir W    il s    +++P+++++++g  ++++  KmSKs+gN+idp+++i+ +gad++R++ 
   AHX11517.1 449 SSLTPQINHD-----SIAVAPFRRMSLRPQAHEIIRTWAFYTILRSFLEYQKTPWERIMISGWCLASDKSKMSKSKGNTIDPVQLISDHGADIVRYWS 541
                  ****987666.....34455556899999********************************************************************9 PP

  tRNA-synt_1 591 ilsdvgrdi 599
                  +++  g d+
   AHX11517.1 542 ASAGLGCDT 550
                  988777665 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.3   0.0   7.4e-19   2.2e-15       3     136 ..      39     187 ..      37     209 .. 0.80
   2 !   11.6   0.1   2.8e-05     0.084     167     240 ..     333     409 ..     305     416 .. 0.79
   3 !   19.9   0.0   8.5e-08   0.00025     311     384 ..     497     568 ..     478     573 .. 0.74

  Alignments for each domain:
  == domain 1  score: 56.3 bits;  conditional E-value: 7.4e-19
                   EEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHT...TS-HHH......HHHHHHH....HHHHHHHHTT---S CS
  tRNA-synt_1g   3 vttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAeke...gvtpee......lvekvhe....eikelfkklnisfd 86 
                   + t+ p ++g+lH+Gh+ ++  +D +aRy+r+rg++v++ +g D+ G p+e   ek     + + e      l++ ++e    e+k+lf+++ +s d
    AHX11517.1  39 IDTPPPTISGSLHIGHVFSYCHTDFIARYQRMRGKNVFYSAGFDNNGLPTERLVEKThkiRIRATEqhefirLCDAISEqkilEFKSLFDSIALSLD 135
                   667778899***************************************9886554431112222222222226777766222246888888888877 PP

                   .EE.EETTSHHHHHHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG-E CS
  tRNA-synt_1g  87 .ky.grttseehkelvqeifkklkekgliyekeieqlycpkderflpdryve 136
                    ++ ++t+se+ ++l+q+ f +l++kgliy+k++ +l+++ d++ +++ +ve
    AHX11517.1 136 wSFsYQTNSEACRRLSQKSFLNLYKKGLIYRKKMPVLWDVIDQTAIAQAEVE 187
                   434368**********************************999999988887 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 2.8e-05
                   ...........EEE.EEEEEE-GGGGHHHHHHHH.HH-TTSHHHHHHHH.HHHHT----EE-ESS-SSS-EET...TE CS
  tRNA-synt_1g 167 pksa.isgskpevketehlffklskfekklkewieeeekeleenvkkivkewlkegLkdlaisrdldwGipvP...ga 240
                    k+a  sg k e+ +t +++ ++ +++++lk  + +e    +e+++ ++++w++    d++isr+   G++vP   ++
    AHX11517.1 333 VKCAeRSGGKLEIISTYQWYIRVLDYKEELKVKV-KEIDWIPEKMRIKIEQWIDGIKWDWCISRQRYLGVRVPvyyDE 409
                   45542456677777899**************999.555568999999*******9888*******999*****76633 PP

  == domain 3  score: 19.9 bits;  conditional E-value: 8.5e-08
                   --S-EEEE--EEE.--------------HHHHHHHH-HHHHHHHHHHHS-TTS-EEE-HHHHHHHHHHHCCCHHH CS
  tRNA-synt_1g 311 lpkkvvaheyltv.egkKlSkSrgvvvkakealerldadllRYylaaeapekkDldfswedfvervNseLadklg 384
                     ++++ +++    + +K+SkS+g+ +++ +++    ad++RY+ a+ a    D+ fs + f   v ++L++k+ 
    AHX11517.1 497 PWERIMISGWCLAsDKSKMSKSKGNTIDPVQLISDHGADIVRYWSAS-AGLGCDTCFSDNVFL--VGKKLMNKIW 568
                   45788889996651667**************************9765.456677777776664..5555666555 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.1   0.3   1.5e-27   4.5e-24       1     149 [.     592     735 ..     592     739 .. 0.85

  Alignments for each domain:
  == domain 1  score: 85.1 bits;  conditional E-value: 1.5e-27
  Anticodon_1   1 drwilselnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitEelwqreeeelgk 98 
                  d wi+s+l+++++ +++a+++++++ a s l  ff++++cd+ylelvk+r y++ +    +a ++l   l+ ll+l+aPf P+itEe++   ++++  
   AHX11517.1 592 DIWIISRLAEVIEVMENAFDQCDYSHAKSTLERFFMHEYCDNYLELVKSRAYNSVD-GNISAIHALSISLSVLLKLFAPFFPYITEEIY---STLFPA 685
                  67*************************************************98654.333599**************************...456699 PP

  Anticodon_1  99 kesimlae.wpekaeelekeleeeevellkeivkairklrselkikpsselk 149
                  + s++ +  wpe+ +  +++l     + ++ i++ +r+++se  i+ ++e++
   AHX11517.1 686 DISVHSRGmWPEEINI-KPKL-ICPGSEFIHILSKVREFKSEHSISMKKEIS 735
                  9******9***75533.3333.2344445559**************999865 PP

>> tRNA-synt_1_2  Leucyl-tRNA synthetase, Domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.17   4.9e+02      13      36 ..     199     221 ..     192     231 .. 0.75
   2 !   34.0   0.0   6.4e-12   1.9e-08      84     145 ..     236     297 ..     227     313 .. 0.89

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.17
  tRNA-synt_1_2  13 efkveeseeklevfttrpdtlfGv 36 
                     f+ e+  +klev ttrp+ l G 
     AHX11517.1 199 IFSSEDG-RKLEVATTRPELLPGC 221
                    4555554.59*********99886 PP

  == domain 2  score: 34.0 bits;  conditional E-value: 6.4e-12
  tRNA-synt_1_2  84 ftglkaihPitgekipiwvanyvlmeygtgavmavPahdqrDfeFakkynlpikqvikpede 145
                     +g +a+ P+ + kipi   + vl+e gtg vm++   d+ D +++++y+lp+++v+   ++
     AHX11517.1 236 LNGKYAFTPLFDVKIPIICDESVLVEKGTGLVMCCTFGDEMDIKWWQQYDLPLREVVDRYGK 297
                    6799*****************************************************97554 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00027      0.82      17      54 ..      44      81 ..      34     203 .. 0.74
   2 !    7.9   0.0   0.00057       1.7     243     282 ..     504     543 ..     487     557 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00027
                  EBTTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEB CS
  tRNA-synt_1e 17 ptvydashlGhaRslvafDilrrilqalgYdvqfvqnv 54
                  pt+    h+Gh+ s+  +D ++r+ +++g +v +   +
    AHX11517.1 44 PTISGSLHIGHVFSYCHTDFIARYQRMRGKNVFYSAGF 81
                  79999************************999986544 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00057
                   EE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
  tRNA-synt_1e 243 hnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                       l  ++ kmsks +n i   +++  + + ++R+  +s
    AHX11517.1 504 SGWCLASDKSKMSKSKGNTIDPVQLISDHGADIVRYWSAS 543
                   334577899**************************98665 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.1   0.0     0.006        18      32      62 ..      45      75 ..      33      83 .. 0.91
   2 ?    6.7   0.0   0.00095       2.8     273     308 ..     506     541 ..     494     546 .. 0.86

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.006
  tRNA-synt_1f 32 spSGliHiGnlrevltadlvaralrkrgeev 62
                  ++SG++HiG +     +d++ar  r rg++v
    AHX11517.1 45 TISGSLHIGHVFSYCHTDFIARYQRMRGKNV 75
                  68********************999999875 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.00095
  tRNA-synt_1f 273 lillkggekmssSkGnvltledwlevaepevlrfli 308
                   + l + ++kms+SkGn + + ++++    +++r+  
    AHX11517.1 506 WCLASDKSKMSKSKGNTIDPVQLISDHGADIVRYWS 541
                   66777889**************99999999999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (779 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      416  (0.0232026); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.68u 0.26s 00:00:00.94 Elapsed: 00:00:00.46
# Mc/sec: 5059.10
//
Query:       AHX11518.1  [L=313]
Description: peptide chain release factor 2 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-46  156.6   0.2    6.9e-46  156.6   0.2    1.7  2  PCRF      PCRF domain
    9.6e-40  135.1   1.1    9.6e-40  135.1   1.1    2.1  2  RF-1      RF-1 domain
  ------ inclusion threshold ------
      0.079   12.9   0.8        3.3    7.7   0.1    2.4  2  MIT_C     Phospholipase D-like domain at C-terminus of MIT


Domain annotation for each model (and alignments):
>> PCRF  PCRF domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.6   0.2   1.2e-49   6.9e-46      28     193 .]       1     165 [.       1     165 [. 0.90
   2 ?   -1.0   0.1      0.22   1.3e+03      39      59 ..     217     237 ..     191     263 .. 0.51

  Alignments for each domain:
  == domain 1  score: 156.6 bits;  conditional E-value: 1.2e-49
                 THHHHHTHHHHHHHHHHHHHTTTHHH...HT....-S-..-GG...GTHHHHHHHHHH..HHHHHT-..SSSTTSEEEEEEEE-SSTHHHHHHHHHHHH CS
        PCRF  28 skelaeleeivealeeleealedleeakelleedeelaelaee...eleelekeleeleeelkklLlpkdendeknaileiraGaGGdeaalfaedLlr 123
                 +ke +++e+ ++++++l+++l dl e+ el+ +de+ +e  +e   el +l++++++   e++ l++  +e+d++++++ei++GaGG+e++++a +Llr
  AHX11518.1   1 MKEKSNIESGLDEFRKLSAQLTDLIEMIELA-SDEDEQETIKEleiELLALQEKIKKK--EIECLFS--GEADANDCFIEIQSGAGGTESNDWAMMLLR 94 
                 6899999*******************88888.55444444433322788888888888..9**9999..****************************** PP

                 HHHHHHH.TTT-EEEEEEEEESSS.SEEEEEEEEESTTHHHHHGGG-EEEEEEEE-TTSSS--EEEEEEEE CS
        PCRF 124 mYtryae.rkgwkvevldaseeeagGikevtleiegegaYgkLkfEsGvHRvqRvpetesqgrihTStatV 193
                 mYtr+ae ++g++v+++d+ + e  Gik++tl++ g +aYg+ ++E+GvHR++R++++++++++hTS+a V
  AHX11518.1  95 MYTRWAEiQHGFQVQIIDKVDGEETGIKSCTLKLLGANAYGWAHTETGVHRLVRISPFDANAKRHTSFAKV 165
                 ******9668***********7777********************************************98 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.22
                 HHHHHHHHHTTTHHH...HT. CS
        PCRF  39 ealeeleealedleeakelle 59 
                  + ++ ++++++ +ea ++l+
  AHX11518.1 217 VQSQTSRSQHQNRAEALQMLK 237
                 333333333344444344441 PP

>> RF-1  RF-1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.6   0.7     0.089   5.3e+02      62     105 ..      14      58 ..       1      61 [. 0.61
   2 !  135.1   1.1   1.6e-43   9.6e-40       3     116 .]     175     283 ..     173     283 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.6 bits;  conditional E-value: 0.089
                 HHHHHHHHHH..HHHHHCCCCCHTTTTT-.S.-S---S.--ECEEEE CS
        RF-1  62 lerLkaklke..keleeekeeekkrrvkkekkkigtgs.sekiRtyn 105
                 +++L a+l +  + +e   +e +++ +k+   +i+  + +eki++++
  AHX11518.1  14 FRKLSAQLTDliEMIELASDEDEQETIKE--LEIELLAlQEKIKKKE 58 
                 67888888777544444555555555444..4566777677777765 PP

  == domain 2  score: 135.1 bits;  conditional E-value: 1.6e-43
                 CCCE--GGGEEEEEE---SSSSSSGCSSSCEEEEEETTTTEEEEEEECSSSHHHHHHHHHHHHHHHHHHHHHHHCCCCCHTTTTT-.S.-S---S--EC CS
        RF-1   3 ieieidekdleidtfrssGaGGQnVNktesaVrlthlptgvivvecqeeRsqekNrekAlerLkaklkekeleeekeeekkrrvkkekkkigtgsseki 101
                 i+i+idekdl+idt+r+sGaGGQ+VNktesaVr+thlp++ ivv++q++Rsq++Nr++Al++Lk+kl+e el++++++ + +r  +  ++i++g   +i
  AHX11518.1 175 ININIDEKDLKIDTYRASGAGGQHVNKTESAVRITHLPSK-IVVQSQTSRSQHQNRAEALQMLKSKLYEIELRKKQDALNLAR--NVDASISWGY--QI 268
                 789*************************************.8*************************7776666666555555..445689****..** PP

                 EEEECGCTTEEEETT CS
        RF-1 102 Rtynkkpqsrvkdhr 116
                 R+y+++p++++kd+r
  AHX11518.1 269 RSYVLHPYQMIKDLR 283
                 *************98 PP

>> MIT_C  Phospholipase D-like domain at C-terminus of MIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1   0.00055       3.3      37     101 ..      14      79 ..       6      81 .. 0.81
   2 ?    3.5   0.0     0.011        64      47      89 ..     211     251 ..     161     291 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00055
       MIT_C  37 llellvkkskklkkikLlTsede.eeedeqkenleelkesleklgielevefsstihdreirldng 101
                 + +l ++ ++    i+L + ede e+ +e + +l  l+e+++k +ie  ++ + +  d  i++++g
  AHX11518.1  14 FRKLSAQLTDLIEMIELASDEDEqETIKELEIELLALQEKIKKKEIECLFSGEADANDCFIEIQSG 79 
                 555555656667789999999996777888999999999999999999999999999999988877 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.011
       MIT_C  47 klkkikLlTsedeeeedeqkenleelkesleklgielevefss 89 
                    ki + +++ +++++++ e+l++lk++l + ++  + + + 
  AHX11518.1 211 LPSKIVVQSQTSRSQHQNRAEALQMLKSKLYEIEL--RKKQDA 251
                 4556666666666777899999*****99976554..444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (313 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1161  (0.0647554); expected 358.6 (0.02)
Passed bias filter:                      605  (0.0337442); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.24s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2323.94
//
Query:       AHX11519.1  [L=37]
Description: hypothetical protein NHE_0581 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      257  (0.0143343); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 298.91
//
Query:       AHX11520.1  [L=711]
Description: hypothetical protein NHE_0582 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
  ------ inclusion threshold ------
      0.089   12.7   5.5         93    3.0   0.0    4.7  4  Sigma54_AID     Sigma-54 factor, Activator interacting domain
       0.13   12.1   4.1        0.1   12.4   0.5    2.2  2  Bacillus_HBL    Bacillus haemolytic enterotoxin (HBL)
        5.7    7.6  16.0         10    6.8   5.7    3.5  3  HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interac
        7.8    6.6  10.7       0.38   10.9   0.3    3.3  4  TAN             Telomere-length maintenance and DNA damage re


Domain annotation for each model (and alignments):
>> Sigma54_AID  Sigma-54 factor, Activator interacting domain (AID)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.2     0.041   1.8e+02      25      37 ..     222     234 ..     222     237 .. 0.88
   2 ?    3.0   0.0     0.021        93      28      42 ..     495     509 ..     494     509 .. 0.95
   3 ?    3.0   0.0     0.021        93      28      42 ..     570     584 ..     569     584 .. 0.95
   4 ?    3.0   0.0     0.021        93      28      42 ..     645     659 ..     644     659 .. 0.95

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.041
  Sigma54_AID  25 lstlELeeeieee 37 
                  l+ +ELee++ +e
   AHX11520.1 222 LNHKELEERVAQE 234
                  799********99 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.021
  Sigma54_AID  28 lELeeeieeeleeNP 42 
                  +EL+ +ie+ +e NP
   AHX11520.1 495 AELKARIEKRSEKNP 509
                  69************9 PP

  == domain 3  score: 3.0 bits;  conditional E-value: 0.021
  Sigma54_AID  28 lELeeeieeeleeNP 42 
                  +EL+ +ie+ +e NP
   AHX11520.1 570 AELKARIEKRSEKNP 584
                  69************9 PP

  == domain 4  score: 3.0 bits;  conditional E-value: 0.021
  Sigma54_AID  28 lELeeeieeeleeNP 42 
                  +EL+ +ie+ +e NP
   AHX11520.1 645 AELKARIEKRSEKNP 659
                  69************9 PP

>> Bacillus_HBL  Bacillus haemolytic enterotoxin (HBL)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.5   2.3e-05       0.1     100     170 ..      31     106 ..      16     112 .. 0.88
   2 ?   -0.0   0.2      0.15   6.8e+02      98     130 ..     237     269 ..     224     287 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.3e-05
  Bacillus_HBL 100 kaellellekLqeeiqqnqkevkqlikeLkklklklakdsknFktdv.....deltsilagdsgvisqlqneiedl 170
                   +++  el++ L+e++++ q ++++l+  L++lk+    +  nF   +     + ++ +++  +  +++l+  ++++
    AHX11520.1  31 RKQQRELINSLEETLTTEQSKINSLSISLEQLKSVYGTEIDNFRIGApempaKPADTVIQERQQCVDTLKTLLSSV 106
                   5667799*************************************99988888999999*99999999999888876 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.15
  Bacillus_HBL  98 kdkaellellekLqeeiqqnqkevkqlikeLkk 130
                   ++k+   +l + L+e++++ +++v+++++ L+k
    AHX11520.1 237 ETKERSHKLHNLLEEHLTSSKANVDKTVAGLNK 269
                   566666666677777788888888888887765 PP

>> HIP1_clath_bdg  Clathrin-binding domain of Huntingtin-interacting protein 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.6   1.1    0.0054        24      35      78 ..      19      62 ..      14      72 .. 0.75
   2 ?   -2.9   0.0       2.4   1.1e+04      45      63 ..      87     105 ..      83     110 .. 0.69
   3 ?    6.8   5.7    0.0023        10      17      95 ..     181     270 ..     170     273 .. 0.88

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0054
  HIP1_clath_bdg 35 elerlkeeaerkleeqkeelekLkreleakraelarlkssLess 78
                    ++ ++ +++    ++q+e +++L++ l++++ ++++l  sLe+ 
      AHX11520.1 19 RVLQAAQQRGLSRKQQRELINSLEETLTTEQSKINSLSISLEQL 62
                    55566667777777888888888888888888888888888764 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.4
  HIP1_clath_bdg  45 rkleeqkeelekLkrelea 63 
                       ++e+++ +++Lk+ l +
      AHX11520.1  87 TVIQERQQCVDTLKTLLSS 105
                     5567888888888876655 PP

  == domain 3  score: 6.8 bits;  conditional E-value: 0.0023
  HIP1_clath_bdg  17 varqaqeeverekkeleeelerlkeeaerkle..........eqkeelekLkreleakraelarlkssLess.eqsgeqlssqlaaLqaE 95 
                     v +q+q e+ r+k ++ + +++  +eae+ ++          + ke  e++ +e+ +++++ ++l++ Le++ + s++++ +++a+L++E
      AHX11520.1 181 VEKQTQTEISRKKLQTLFLVKSNPKEAEHFIRkriaaespflNHKELEERVAQEFIETKERSHKLHNLLEEHlTSSKANVDKTVAGLNKE 270
                     679******************9999999887777778888888888999********************98725567899*******999 PP

>> TAN  Telomere-length maintenance and DNA damage repair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.2   0.2     0.079   3.5e+02      34      64 ..      24      54 ..       8      65 .. 0.75
   2 ?   10.9   0.3   8.4e-05      0.38      12      53 ..      88     130 ..      85     198 .. 0.79
   3 ?   -1.5   0.1      0.55   2.5e+03      87     131 ..     257     297 ..     209     311 .. 0.58
   4 ?   -2.9   0.0       1.5   6.7e+03       6      22 ..     469     496 ..     467     517 .. 0.68

  Alignments for each domain:
  == domain 1  score: 1.2 bits;  conditional E-value: 0.079
         TAN 34 tslsdlkdkawheifeaLfklvekEkeaylk 64
                +++  l+ k+ +e++++L + +++E++++ +
  AHX11520.1 24 AQQRGLSRKQQRELINSLEETLTTEQSKINS 54
                3344899999999999999999999999844 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 8.4e-05
         TAN  12 kikeRnkaldeLkhllsskrnktsls.dlkdkawheifeaLfk 53 
                  i eR++++d Lk+llss r ++s +  l+ k + ++++ L k
  AHX11520.1  88 VIQERQQCVDTLKTLLSSVRVNNSGKpILPRKRIEKVVSELEK 130
                 589*****************98777789999999988887754 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.55
         TAN  87 Rllvekavsklkrktlkalldhitqllpgpdgelleplaldyika 131
                 +  v+k+v  l+++ l  l+++ ++ l    +++++  + +++++
  AHX11520.1 257 KANVDKTVAGLNKEELTYLVNARVNRL----KNFVHLALDHVARS 297
                 334444444444444444444444444....34444444444444 PP

  == domain 4  score: -2.9 bits;  conditional E-value: 1.5
         TAN   6 rlLssskikeRnkald...........e 22 
                 ++L+ +k k R+ +++           e
  AHX11520.1 469 EALQEGKTKLRKVGIKekpftgddliaE 496
                 6799999999999998555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (711 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1097  (0.0611858); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 5202.09
//
Query:       AHX11521.1  [L=561]
Description: hypothetical protein NHE_0583 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.091   13.0   0.1       0.35   11.1   0.1    2.0  1  DUF2316   Uncharacterized protein conserved in bacteria (DUF2


Domain annotation for each model (and alignments):
>> DUF2316  Uncharacterized protein conserved in bacteria (DUF2316)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.1     2e-05      0.35      11      45 ..     344     378 ..     338     387 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 2e-05
     DUF2316  11 TkkeLqanfelsgltveevaedLnlttekvekvLe 45 
                  +++L+++ e +++t+eev ++L lt e+v ++L+
  AHX11521.1 344 STRDLREHVEGTDMTMEEVCDTLSLTAEEVRELLQ 378
                 5679****************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (561 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       692  (0.0385967); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.26s 00:00:00.82 Elapsed: 00:00:00.41
# Mc/sec: 4132.59
//
Query:       AHX11522.1  [L=699]
Description: hypothetical protein NHE_0584 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
  ------ inclusion threshold ------
        0.5   10.4   7.4      0.076   13.1   1.5    2.4  2  Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C


Domain annotation for each model (and alignments):
>> Baculo_PEP_C  Baculovirus polyhedron envelope protein, PEP, C terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.4     0.077   1.4e+03      66     103 ..      42      80 ..      35      89 .. 0.48
   2 ?   13.1   1.5   4.2e-06     0.076      33     102 ..     289     349 ..     263     355 .. 0.54

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.077
  Baculo_PEP_C  66 dtlltnLtdalnalqdtlrneLtnl.nsiltnLlssvtN 103
                   +t+l+ L+++    +++ + +L  l  +i tnL+ssv  
    AHX11522.1  42 STMLADLDTKTILANQQYSPDLALLvRNIYTNLASSVRT 80 
                   444444444444444444444444312333555555533 PP

  == domain 2  score: 13.1 bits;  conditional E-value: 4.2e-06
  Baculo_PEP_C  33 laqlatlldaietqLnalsedlksll..aeldtrldtlltnLtdalnalqdtlrneLtnlnsiltnLlssvt 102
                   +  ++tll +i ++L+++s+ l+sl+  ++            ++++ +l+++lr  L+n+ + l ++l+ vt
    AHX11522.1 289 TQRIQTLLRNILETLQQFSNTLSSLVrlPNS-----------QESVSQLSEALRHFLENVRASLRTMLTRVT 349
                   3334444444444444444444444311233...........344444445555555555555555554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (699 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       812  (0.0452898); expected 358.6 (0.02)
Passed bias filter:                      496  (0.0276647); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.68u 0.27s 00:00:00.95 Elapsed: 00:00:00.44
# Mc/sec: 4823.78
//
Query:       AHX11523.1  [L=323]
Description: biotin synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    9.2e-17   61.0   0.0    2.3e-16   59.7   0.0    1.7  1  BATS         Biotin and Thiamin Synthesis associated domain
    1.6e-12   48.1   0.0      6e-12   46.3   0.1    1.8  2  Radical_SAM  Radical SAM superfamily


Domain annotation for each model (and alignments):
>> BATS  Biotin and Thiamin Synthesis associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   2.6e-20   2.3e-16       1      85 [.     218     308 ..     218     309 .. 0.98

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 2.6e-20
                 E--B----TCCCC...........HHHHHHHHHHSTTSE.CCCTCHH-HHHHHH.HHHCCT--EEE-C---TTTGGGSESSTT-TCCCCHHHHHHTT- CS
        BATS   1 siprlrpikdtpl...........lkiiaalRlllPkag.illsgResaefrdq.lllklGansisagsktevggyaflttdgrsleedvkmleelGl 85 
                 +++ l+ i++tpl           ++++a++R+++Pk+  +l++gR s++++ q l++++G ns+++g+k       +lt+++  +++d +++ +lGl
  AHX11523.1 218 PLNKLIRISGTPLadvkevesidfVRVVALARIMFPKSYiRLSAGRDSMSDELQaLCFMAGTNSVFYGEK-------LLTSSNARPDRDDRLFSKLGL 308
                 799******************************************************************9.......*******************97 PP

>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.3   0.1   6.7e-16     6e-12       4     164 ..      48     205 ..      45     207 .. 0.84
   2 ?   -1.1   0.0      0.23   2.1e+03      33      74 ..     243     281 ..     228     307 .. 0.70

  Alignments for each domain:
  == domain 1  score: 46.3 bits;  conditional E-value: 6.7e-16
                  ESEESS--TTTSCCTT.HHHHHHHHHHHHHHHHHHHHHHHHHTT.SEEEEEESSTGGGSTTHHHHHHHHHHTCCCTEEEEEEECSSCHGHHHHHHHHH CS
                  xxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   4 trgCnlrCsfCarpet.vrregrgrslsveeileevkelkaekg.vkevilgggepllypdfvellerlaklavpgiritvetngtlpdeeklerlle 99 
                  t  C+ +Cs+C+++ +     +++  + ++ +++ +k++ ae g ++++i         +d+    ++++++  +++ +   ++ +l+++ ++e l+e
   AHX11523.1  48 TGSCPENCSYCPQSAHyNTGLKKEPLVELDHVIDAAKKA-AESGaTRFCIGAAWRGPRMKDLDLVCRMISEI--KKLGLETCASLGLLSPGQAESLKE 142
                  567*************9999999999*************.89995555555544444447777777777777..5666666666667779******** PP

                  TT-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSETEEEEEEEBTTTSHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM 100 lgvdrvslgleaaddekvlklmnrghtfeevlealeklreagikrvvdrivglpGendeeleell 164
                  +g+d +++++++  +  + +++  +  f ++l +le+ ++ag+k ++ +i+g+   n++ ++ l+
   AHX11523.1 143 AGLDFYNHNIDTSPEY-YSQII-TTRCFNDRLVTLENVTKAGMKICCGGIIGMGESNEDRIKMLV 205
                  ****************.*****.99****************************999999877665 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.23
                  HHHHHHHHHHHHTTSEEEEEESSTGGGSTTHHHHHHHHHHTC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  33 eileevkelkaekgvkevilgggepllypdfvellerlakla 74 
                  +++++++++ +   + ++ l+ g  ++ ++++ l +++  + 
   AHX11523.1 243 RVVALARIM-FP--KSYIRLSAGRDSMSDELQALCFMAGTNS 281
                  556666666.55..8999999999999999999999887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       445  (0.0248201); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 2452.30
//
Query:       AHX11524.1  [L=56]
Description: hypothetical protein NHE_0586 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       379  (0.0211389); expected 358.6 (0.02)
Passed bias filter:                      141  (0.00786435); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.28s 00:00:00.60 Elapsed: 00:00:00.41
# Mc/sec: 413.64
//
Query:       AHX11525.1  [L=361]
Description: aminotransferase class I and II family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.1e-49  168.1   0.0    3.8e-49  167.8   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
    2.9e-09   36.0   0.0    3.8e-09   35.6   0.0    1.1  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
  ------ inclusion threshold ------
      0.017   14.4   0.0      0.024   13.9   0.0    1.2  1  Beta_elim_lyase  Beta-eliminating lyase
      0.023   13.4   0.1       0.36    9.5   0.1    2.1  1  OKR_DC_1         Orn/Lys/Arg decarboxylase, major domain
       0.04   12.9   0.0      0.064   12.2   0.0    1.4  1  Aminotran_5      Aminotransferase class-V
      0.053   12.8   0.2       0.14   11.4   0.1    1.8  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.8   0.0   1.3e-52   3.8e-49       4     356 ..       1     339 [.       1     344 [. 0.94

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 1.3e-52
                    EESSSSSTTSTTSS.HHHHHHHHHHHH.HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHH...HTTT- CS
  Aminotran_1_2   4 inLgsneylgdsgk.ptlpevakaeke.galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllk...lnpgd 94 
                    +++++n+ylg+s++ + l+++       g++a+g++  +g++ +  ele+++ak  +        +eaa+++ sG++ +  +l+ ll+   l+   
     AHX11525.1   1 MDFSTNDYLGLSKSrELLEAAYSHGMNaGVGATGSRILSGNSNLFSELEQQIAKDKK--------TEAALIMNSGFQTNMTVLAGLLDksvLMERP 88 
                    799********9999999999999999******************************........99********************988889999 PP

                    EEEEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETT CS
  Aminotran_1_2  95 eilvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaY 190
                     ++ ++++++s  +++ ls++e+vry+       h+d+e+l  ++k+  +++k+tk+i++e+ + ++G++++   + kl   a++yn++l++Dea+
     AHX11525.1  89 IVFFDRLNHSSLYQAIFLSRAELVRYR-------HCDIEHLSHLIKKY-AQDKRTKFIVTETLFGMDGDIPDIHGIIKL---ARQYNAILYLDEAH 173
                    99*************************.......************95.57777**********************999...************** PP

                    TTCBSSSS.HTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 191 agfvfgsl.davatranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrr 285
                    a++v+g+    ++t +++++ ++ +i+g++sKa G+ G    yi++++ ++++l +  ++f++s+ l+++++ a+ ++ +k+ +++ +r +l +++
     AHX11525.1 174 ATGVLGNNgYGISTDFDLSNITH-VIMGTFSKAVGVFG---SYIASSKMIRRYLINKCTGFIYSTTLPPMLLGAIAKSWEKIASMSGARTELMAKA 265
                    ******98533455999999999.**************...******************************************************* PP

                    HHHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHH CS
  Aminotran_1_2 286 kelrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeel 356
                     +lr eL++   +v +s +++++l + ++e+ +el++ Ll + g  v++++++tv   ++r+Ri +   ++ee+ 
     AHX11525.1 266 SRLRMELQKRKYDVGTSATHIIPLILKEEEKTTELQRILLGK-GFRVSAVRPPTVpanTSRIRIALcTFHSEEDT 339
                    ******************************************.*************999******9555666655 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.6   0.0   1.3e-12   3.8e-09      55     198 ..      46     196 ..      35     235 .. 0.81

  Alignments for each domain:
  == domain 1  score: 35.6 bits;  conditional E-value: 1.3e-12
                      HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEE....EEEESTSSHHHHHHHHHTHHHTTCEEEEESTTSHHHHHHHCCT..TEEEEE CS
  Cys_Met_Meta_PP  55 svleeriaaLeggeaalavssGmaAiaaailallkaGde....ivvsddlYggtqrllkkvlkklgievkfvdtsdleelekaike..ntklvy 142
                      s le++ia+ +++eaal+++sG  + ++++  ll +       iv  d l  ++  +   + +   ++++++d ++l++l k+  +  +tk + 
       AHX11525.1  46 SELEQQIAKDKKTEAALIMNSGFQTNMTVLAGLLDKSVLmerpIVFFDRLNHSSLYQAIFLSRAELVRYRHCDIEHLSHLIKKYAQdkRTKFIV 139
                      579******************************9986544455999999988888888777778899********99997665543369***** PP

                      EESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTTS-.GGGGT-SEEEEETTT CS
  Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDntfaspllqr.plklgaDivvhSaTK 198
                      +Et+     +++Di+ i+kla++ ++++ +D + a+++l +       D  +  +T 
       AHX11525.1 140 TETLFGMDGDIPDIHGIIKLARQYNAILYLDEAHATGVLGNnGYGISTDFDLSNITH 196
                      *************************************88541444445555555555 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0     8e-06     0.024      29     169 ..      40     172 ..      24     217 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 8e-06
                      T--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE-EBTTTBE-HHHHHHHS--S- CS
  Beta_elim_lyase  29 gedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdlknkeaGkmdlekleaaikevg 122
                      g+++ + +Le+++a+   +eaal + +G + n   l+ ll   ++v++++p  ++fd     + ++ + l  ++  +    d+e l  +ik+  
       AHX11525.1  40 GNSNLFSELEQQIAKDKKTEAALIMNSGFQTNMTVLAGLL--DKSVLMERP-IVFFDRLNHSSLYQAIFLSRAELVRYRHCDIEHLSHLIKKYA 130
                      7888999*****************************9999..456666665.4555555555555777777777777789************88 PP

                      TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEET CS
  Beta_elim_lyase 123 aheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDgA 169
                      +  +++k+i++++      G    +  +  + ++a++y+  l lD A
       AHX11525.1 131 Q-DKRTKFIVTETLF----GMDGDIPDIHGIIKLARQYNAILYLDEA 172
                      8.7888888776554....4556788999999*******99999987 PP

>> OKR_DC_1  Orn/Lys/Arg decarboxylase, major domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.1   0.00012      0.36     103     207 ..      84     174 ..      43     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00012
                 --TTEEEEEESS--HHHHHHHHHS-EEEEEE--EB-TTS-BE---GGGGSHHHHHHHHHHSTTTGSESEEEE.ESS-TTSEEE-HHHHHHHHTTSESEE CS
    OKR_DC_1 103 ltpgdlvlvdRNcHKSiehalvlsgatPvylepernalgiiggidlkefeeetlkekikevpdakaprlavi.tnsTYdGvlynakeivdkleklsdri 200
                 l +  +v +dR +H S+ +a+ ls a+ v                 +  + e l + ik+++++k  +++v  t+   dG + +++ i++++ +++  +
  AHX11525.1  84 LMERPIVFFDRLNHSSLYQAIFLSRAELVR---------------YRHCDIEHLSHLIKKYAQDKRTKFIVTeTLFGMDGDIPDIHGIIKLARQYNAIL 167
                 555556777777777777777776665442...............2223337789999999999996666553455679999999***********999 PP

                 EEE-TT- CS
    OKR_DC_1 201 lfDeAwv 207
                 ++DeA+ 
  AHX11525.1 168 YLDEAHA 174
                 9****96 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.1e-05     0.064     119     181 ..     109     176 ..      18     189 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.1e-05
                  EEBETTSCBEGGGHHHH-.....-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
  Aminotran_5 119 ipldeegeldldelekll.....nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                  ++l +  + d+++l +l+     +++tk +       + G i +++ i+kla++++a++ +D a a g
   AHX11525.1 109 AELVRYRHCDIEHLSHLIkkyaqDKRTKFIVTETLFGMDGDIPDIHGIIKLARQYNAILYLDEAHATG 176
                  4455556666677766666666679999999999999*************************998865 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.8e-05      0.14      26     152 ..      46     178 ..      31     216 .. 0.68
   2 ?   -2.5   0.0      0.83   2.5e+03     262     308 ..     268     315 ..     249     324 .. 0.63

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.8e-05
                      HHHHHHHHHHHT-SEEEEESSHHHHHHHHHHH....TTTTTT-EEEEESSS-THHHHHHHHTT-EEE...EE-B-TTTSSB-GGGCGGG--TTE CS
  DegT_DnrJ_EryC1  26 eeFEkafaaylgvkhaiavssGtaAlhlaLra....lgvgpgdeVIvpsltFvatanavlelgakpv...fvDvdpdtynidpaaieaaitert 112
                      +e+E+++a+  +++ a+ ++sG ++++ +L        ++++  V    l+  +  +a+  + a+ v    +D++  ++ i+      a  +rt
       AHX11525.1  46 SELEQQIAKDKKTEAALIMNSGFQTNMTVLAGlldkSVLMERPIVFFDRLNHSSLYQAIFLSRAELVryrHCDIEHLSHLIKK----YAQDKRT 135
                      57777777777777777777777777777766533222336666666677777777777777777663334566665555553....455789* PP

                      EEEEEB-GGGB--...-HHHHHHHHHHCT-EEEEE-TT-TT-E CS
  DegT_DnrJ_EryC1 113 kaIlpVhlyGqva...dmdalkaiaakhglkvieDaAhAlGat 152
                      k I++  l+G      d+  + ++a++++ ++  D AhA G  
       AHX11525.1 136 KFIVTETLFGMDGdipDIHGIIKLARQYNAILYLDEAHATGVL 178
                      ****99998765511166667799***************9964 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 0.83
                      EESCGGTTSS...SEEESCEEEEEHCCHHHCHHHHHHHHHHCCEE-B-SG CS
  DegT_DnrJ_EryC1 262 aelttpketk...khawhlyavlveeeaevkrdelvealkeegigtrvhy 308
                      ++++++k++    ++a h ++++++ee+  k +el++ l  +g  +++++
       AHX11525.1 268 LRMELQKRKYdvgTSATHIIPLILKEEE--KTTELQRILLGKGFRVSAVR 315
                      3444444444443478888888888773..57778887777766666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (361 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2518.72
//
Query:       AHX11526.1  [L=222]
Description: alpha/beta hydrolase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
       0.12   12.4   0.0       0.23   11.6   0.0    1.4  1  Abhydrolase_4  TAP-like protein


Domain annotation for each model (and alignments):
>> Abhydrolase_4  TAP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   1.3e-05      0.23      33      92 ..     161     217 ..     146     221 .. 0.86

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 1.3e-05
  Abhydrolase_4  33 gaapvLllqnerDpaTPyegakklakalggavlvtvegeGHgalaagntCvdkavdaYLl 92 
                    +++p+L++++  D ++P e    ++++++g + v+ e++GH+++ +  + v k ++++L 
     AHX11526.1 161 SDIPILIIGSIDDKVVPVEL---IHDNFPGQKKVIFEKGGHNTIGKIPSLVYKEITSFLY 217
                    479**************986...799*****************99888888888988885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (222 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      283  (0.0157845); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.39
# Mc/sec: 1719.17
//
Query:       AHX11527.1  [L=59]
Description: hypothetical protein NHE_0589 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (59 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       232  (0.0129399); expected 358.6 (0.02)
Passed bias filter:                      196  (0.010932); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.25s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 488.97
//
Query:       AHX11528.1  [L=252]
Description: ubiE/COQ5 methyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.1e-15   55.7   0.0    1.8e-14   54.2   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
    2.4e-13   50.6   0.0    5.2e-13   49.5   0.0    1.5  1  Methyltransf_11  Methyltransferase domain
      8e-12   45.8   0.0    2.6e-11   44.1   0.0    1.8  1  Methyltransf_12  Methyltransferase domain
    8.3e-12   45.3   0.0    1.3e-11   44.6   0.0    1.4  1  Methyltransf_23  Methyltransferase domain
    6.2e-10   39.1   0.0    1.1e-09   38.3   0.0    1.4  1  Methyltransf_31  Methyltransferase domain
    1.6e-07   30.8   0.0    2.4e-07   30.2   0.0    1.2  1  Methyltransf_2   O-methyltransferase domain
    6.9e-06   25.7   0.0      1e-05   25.1   0.0    1.2  1  MTS              Methyltransferase small domain
    0.00013   21.7   0.0    0.00018   21.2   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00019   20.9   0.0    0.00034   20.0   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00079   19.5   0.0     0.0013   18.8   0.0    1.4  1  Methyltransf_32  Methyltransferase domain
    0.00089   18.6   0.0     0.0013   18.1   0.0    1.2  1  Rsm22            Mitochondrial small ribosomal subunit Rsm22
     0.0037   16.4   0.0     0.0055   15.8   0.0    1.2  1  DREV             DREV methyltransferase
     0.0078   16.0   0.0      0.011   15.4   0.0    1.3  1  PCMT             Protein-L-isoaspartate(D-aspartate) O-methyl
  ------ inclusion threshold ------
      0.029   14.3   0.0      0.044   13.7   0.0    1.3  1  Methyltransf_18  Methyltransferase domain
      0.033   13.4   0.0      0.046   12.9   0.0    1.2  1  Methyltransf_33  Histidine-specific methyltransferase, SAM-de
      0.045   13.5   0.0      0.064   13.0   0.0    1.3  1  Methyltransf_16  Lysine methyltransferase
      0.056   12.5   0.0       0.08   12.0   0.0    1.2  1  RrnaAD           Ribosomal RNA adenine dimethylase
       0.12   12.7   0.0       0.22   11.9   0.0    1.4  1  AdoMet_MTase     Predicted AdoMet-dependent methyltransferase


Domain annotation for each model (and alignments):
>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.2   0.0   1.8e-17   1.8e-14       1      90 [.      47     129 ..      47     134 .. 0.91

  Alignments for each domain:
  == domain 1  score: 54.2 bits;  conditional E-value: 1.8e-17
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeia 90 
                      +Ld+G+GtG lt+ l  +++++++t  Dis++m+++a  +++    +++ +qgd+++l+f++  fD++vss+alh+ s  d ++++++++
       AHX11528.1  47 ILDVGTGTGYLTKLLTSEFPESSYTINDISQSMIDKATLEIN---KEISTMQGDMDELNFPQ--FDMIVSSMALHWSS--DPKRLIEKLY 129
                      8******************99******************994...47**************6..******99999976..5557888776 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.5   0.0   5.2e-16   5.2e-13       1      85 [.      48     129 ..      48     131 .. 0.95

  Alignments for each domain:
  == domain 1  score: 49.5 bits;  conditional E-value: 5.2e-16
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHH CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeia 85 
                      LdvG+GtG+l++ l++ +  ++++  D+s+ m++ a  ++++e   ++ +++d+ +l+f+   fD++vss++lh+  dp++++++++
       AHX11528.1  48 LDVGTGTGYLTKLLTSEFpeSSYTINDISQSMIDKATLEINKE---ISTMQGDMDELNFPQ--FDMIVSSMALHWSSDPKRLIEKLY 129
                      8**************88899*********************99...577***********9..******************998775 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.1   0.0   2.6e-14   2.6e-11       1      91 [.      48     130 ..      48     132 .. 0.89

  Alignments for each domain:
  == domain 1  score: 44.1 bits;  conditional E-value: 2.6e-14
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirk 91 
                      L++G+GtG l++ l  ++p+++yt  Dis+s+i++a  +++k++   + + + ++l+        +fD++v+s +lh+  d++++++++++
       AHX11528.1  48 LDVGTGTGYLTKLLTSEFPESSYTINDISQSMIDKATLEINKEIS--TMQGDMDELNFP------QFDMIVSSMALHWSSDPKRLIEKLYS 130
                      8********************************999999999885..455566666654......**********************9985 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.6   0.0   1.3e-14   1.3e-11       6     133 ..      24     170 ..      19     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 44.6 bits;  conditional E-value: 1.3e-14
  Methyltransf_23   6 eeelsdklerllpk...lraggrvLdiGcGtGillevlrengf..svtgvDlspeaveiae.....kakkaqkdqfdeqeaaepqg....kfdl 85 
                      ++e+++   +l +k   ++ + ++Ld+G+GtG+l+++l  ++   s+t  D+s  ++++a      +++++q d+          +    +fd 
       AHX11528.1  24 QKECCHYMVKLIKKelpRFHPTSILDVGTGTGYLTKLLTSEFPesSYTINDISQSMIDKATleinkEISTMQGDMD---------ElnfpQFDM 108
                      5677766666665555589999****************66666689**************8866666666666666.........123359*** PP

  Methyltransf_23  86 IvlrevlehvpdppellrqiatllkpgGylllse.plasl.kedrllld...............w 133
                      Iv+++ l++  dp +l+ ++++      +l++s  +  sl ++++++l+               +
       AHX11528.1 109 IVSSMALHWSSDPKRLIEKLYSFSQ---VLIFSIlIQPSLqEWNEMFLKlelsspglnylscedI 170
                      **********************888...7777773344444599999994444444444333330 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.3   0.0   1.1e-12   1.1e-09       5      99 ..      45     130 ..      43     160 .. 0.88

  Alignments for each domain:
  == domain 1  score: 38.3 bits;  conditional E-value: 1.1e-12
  Methyltransf_31   5 lrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeie 98 
                      +++lD+G+GtG+lt+ l    +p++ ++  Dis+ +i +A+ +      ++++  qgd+ el+  +   +fD+i+s  +l+  +dp+  +e++ 
       AHX11528.1  45 TSILDVGTGTGYLTKLLT-SEFPESSYTINDISQSMIDKATLEIN----KEISTMQGDMDELN--FP--QFDMIVSSMALHWSSDPKRLIEKLY 129
                      579***************.5589999***************9877....56777*********..88..5******************999876 PP

  Methyltransf_31  99 r 99 
                      +
       AHX11528.1 130 S 130
                      5 PP

>> Methyltransf_2  O-methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.2   0.0   2.5e-10   2.4e-07      64     143 ..      45     121 ..      14     133 .. 0.82

  Alignments for each domain:
  == domain 1  score: 30.2 bits;  conditional E-value: 2.5e-10
                     SEEEEET-TTSHHHHHHHHH-TT-EEEEEE-HH.HHHHHHHHS-----TTEEEEES-TTTS-----SEEEEESSGGGS-HH CS
  Methyltransf_2  64 kslvDvGGGtGalakaivsayPtikvivfDlpe.VveaAkehlsageeervefvgGdffkdslPeaDaillkrvlhDwsde 143
                     +s++DvG GtG l k  +s +P+ + ++ D+++  + +A        +++++ ++Gd+ + + P+ D+i+ +  lh  sd 
      AHX11528.1  45 TSILDVGTGTGYLTKLLTSEFPESSYTINDISQsMIDKATLE----INKEISTMQGDMDELNFPQFDMIVSSMALHWSSDP 121
                     689****************************97255666555....899********************999999955553 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.1   0.0     1e-08     1e-05      24     103 ..      36     111 ..      27     128 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.1 bits;  conditional E-value: 1e-08
                 HHHCHCCTCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEEE CS
         MTS  24 letlpkelsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdlivs 103
                  + lp  +  ++lD+G+G+G+l+  l +e pe + t+ d++   ++ a  +le nk e+++++ d+ e     +fd+ivs
  AHX11528.1  36 KKELPRFHPTSILDVGTGTGYLTKLLTSEFPESSYTINDISQSMIDKA--TLEINK-EISTMQGDMDELNF-PQFDMIVS 111
                 45566657788********************************99865..666666.6999****998777.89****98 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0   1.8e-07   0.00018      16     108 ..      46     138 ..      31     159 .. 0.81

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1.8e-07
        MetW  16 rvldlGcGdGellellkeekqvdgrGle.ldeegvaec...vakGlsviqgdldkdlenfedksfdyvvlsqtlqatrnpkevldellrigrraivs 108
                  +ld+G+G G l +ll  e   +++ ++ ++++ + ++   ++k +s +qgd+d+ l nf+  +fd++v s +l    +pk+++++l   ++  i s
  AHX11528.1  46 SILDVGTGTGYLTKLLTSEFPESSYTINdISQSMIDKAtleINKEISTMQGDMDE-L-NFP--QFDMIVSSMALHWSSDPKRLIEKLYSFSQVLIFS 138
                 69*****************9999**996367888877644468899999999886.3.455..7********************9998888777665 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   3.4e-07   0.00034       9     140 ..       6     129 ..       1     134 [. 0.81

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.4e-07
                      XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEE CS
  Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinief 102
                      + + f++ +++yD   ++     h + k  ++k     +++++lDv +Gtg l+  l+++  e+   ++ Di+++m++ +   +     ++i  
       AHX11528.1   6 IMQNFDRASHSYDSASAIQKECCHYMVK-LIKKELPRFHPTSILDVGTGTGYLTKLLTSEFPES-SYTINDISQSMIDKATLEI----NKEIST 93 
                      6677999999999999998888888766.57777788899*************98887777655.57889******98766555....567999 PP

                      EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHH CS
  Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeay 140
                      +q++  eL+f +  fD++  s  l   +D ++ ++++y
       AHX11528.1  94 MQGDMDELNFPQ--FDMIVSSMALHWSSDPKRLIEKLY 129
                      9********985..999999999998888887777666 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   1.3e-06    0.0013       9      85 ..      31     101 ..      23     137 .. 0.71

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.3e-06
  Methyltransf_32   9 laelvakllkelakesgaltvvDvGaGkgYLsfvlalkekeyklkvvgi.dakeelvekae.kraeklgkkfnkrlsfa 85 
                      +++l++k l     + ++++++DvG G gYL+  l +   e++ + + i d+++++++ka  ++++++  +++ ++ + 
       AHX11528.1  31 MVKLIKKEL----PRFHPTSILDVGTGTGYLTKLLTS---EFPESSYTInDISQSMIDKATlEINKEIS-TMQGDMDEL 101
                      444555544....447899******************...64444444437888888776415555555.555666555 PP

>> Rsm22  Mitochondrial small ribosomal subunit Rsm22
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.3e-06    0.0013      22     128 ..      31     128 ..      14     142 .. 0.70

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.3e-06
       Rsm22  22 vLdelaervpdflPkslldvgegpgtalwaaselweeleevlvidaseel.leiskelaadapelkeaalrrsvirealeleeadLviisyvLlelede 119
                 +++ +++  p f P+s+ldvg g+g  +   +  ++e   ++  d s+++  + + e+ +++ +++ +       ++ l++ + d+++ s  L+    +
  AHX11528.1  31 MVKLIKKELPRFHPTSILDVGTGTGYLTKLLTSEFPESS-YTINDISQSMiDKATLEINKEISTMQGD-------MDELNFPQFDMIVSSMALHWS--S 119
                 5677999******************99999999998543.3333444443133344444444444444.......788999999999988887643..3 PP

       Rsm22 120 sreklvknl 128
                 + + l+++l
  AHX11528.1 120 DPKRLIEKL 128
                 444566666 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   5.5e-06    0.0055      91     176 ..      40     130 ..      26     142 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 5.5e-06
        DREV  91 sdqedkklldlGaGdGeitkrvaptfee.vya.telsetmrdrlkkkkynvlsale..lqetdv.kldlilclnlldrcfdplklledirs 176
                 + ++++ +ld+G+G G +tk +++ f e  y+  ++s+ m+d+      + +s+++  ++e ++ ++d+i++   l    dp +l+e ++s
  AHX11528.1  40 PRFHPTSILDVGTGTGYLTKLLTSEFPEsSYTiNDISQSMIDKATLEINKEISTMQgdMDELNFpQFDMIVSSMALHWSSDPKRLIEKLYS 130
                 4568899***************99997745652589******9988877777776545888887789****9999**********999876 PP

>> PCMT  Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.1e-05     0.011      73     120 ..      43      89 ..       8     130 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.1e-05
                 TT-EEEEES-TTSHHHHHHHHHHCTTCEEEEEESBHHHHHHHHHHHHH CS
        PCMT  73 kgarvLevGsGsGyltavlarlvgekgrvvsierikelveeakrnlkk 120
                 + +++L+vG+G+Gylt +l+  + e+   +  + +++++++a+ +++k
  AHX11528.1  43 HPTSILDVGTGTGYLTKLLTSEFPESSYTIN-DISQSMIDKATLEINK 89 
                 4578*************99998888874332.3445677777777766 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   4.4e-05     0.044      16      61 ..      45      90 ..      32     109 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.4e-05
  Methyltransf_18 16 srvaDiGtDHgylpiylvkegkakkviasDinegplekakenieka 61
                     ++++D+Gt  gyl+  l++e   ++ +  Di+++ ++ka  +i+k+
       AHX11528.1 45 TSILDVGTGTGYLTKLLTSEFPESSYTINDISQSMIDKATLEINKE 90
                     5799************************************999985 PP

>> Methyltransf_33  Histidine-specific methyltransferase, SAM-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   4.6e-05     0.046      60     116 ..      42      94 ..      19     114 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 4.6e-05
  Methyltransf_33  60 ipaatlvelGsGsseKtrlLLealeaaekeltYvplDvseeaLeealealaaeypsl 116
                      ++   +++ G G++  t+lL ++++++     Y   D+s++++++a+ ++++e++++
       AHX11528.1  42 FHPTSILDVGTGTGYLTKLLTSEFPES----SYTINDISQSMIDKATLEINKEISTM 94 
                      344599******************866....8******************9987654 PP

>> Methyltransf_16  Lysine methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   6.5e-05     0.064      28      94 ..      27      90 ..       7     130 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 6.5e-05
  Methyltransf_16 28 lvkylekklakelganelsklsvlELGsGtGlvGlavaellpeakviltDlee.llellkknielnkn 94
                      ++y+ k ++kel+  +++++s+l++G GtG     + +  pe + ++ D+++ +++  +  i+  k+
       AHX11528.1 27 CCHYMVKLIKKELP--RFHPTSILDVGTGTGYLTKLLTSEFPESSYTINDISQsMIDKATLEIN--KE 90
                     489****9999875..99*************9999999999**********9856665444443..33 PP

>> RrnaAD  Ribosomal RNA adenine dimethylase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   8.1e-05      0.08      32      94 ..      45     107 ..      30     142 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 8.1e-05
                 SEEEEES-TTTCCHHHHHCC-..SEEEEE-S-HHHHHHHHCHTTTCCCEEEE-S-CCGHHHHHHH CS
      RrnaAD  32 ltvleigpGkGilTeeLakra..kqvvvlElderLakllqkklskdeklkvvhqDflkfetpeev 94 
                 + +l++g+G+G lT+ L   +   ++++  + ++++   +   + ++ +  ++ D+ + ++p++ 
  AHX11528.1  45 TSILDVGTGTGYLTKLLTSEFpeSSYTINDISQSMIDKATL--EINKEISTMQGDMDELNFPQFD 107
                 689**************999989999999999999886655..77899999***99999999854 PP

>> AdoMet_MTase  Predicted AdoMet-dependent methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   0.00022      0.22      44      80 ..      29      65 ..      10      90 .. 0.89

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.00022
  AdoMet_MTase 44 aylivlwkktrseeketsfvdvgcgngllvyvlaaeg 80
                   y+++l kk+    ++ts+ dvg g g l  +l++e 
    AHX11528.1 29 HYMVKLIKKELPRFHPTSILDVGTGTGYLTKLLTSEF 65
                  699******************************9984 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       626  (0.0349155); expected 358.6 (0.02)
Passed bias filter:                      523  (0.0291706); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 1882.91
//
Query:       AHX11529.1  [L=204]
Description: dethiobiotin synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-41  142.2   0.2    1.9e-41  142.1   0.2    1.0  1  AAA_26    AAA domain
     0.0085   16.1   0.0      0.014   15.4   0.0    1.4  1  CbiA      CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  142.1   0.2   2.2e-45   1.9e-41       2     197 ..       2     189 ..       1     190 [. 0.93

  Alignments for each domain:
  == domain 1  score: 142.1 bits;  conditional E-value: 2.2e-45
      AAA_26   2 tifvtgtdtgvGKTvvslgLvralkrkgvkvgyfKPiqtgieededselikellgldqtyelpeplalsaplspelaarqegedidlekivkelekdad 100
                 ++f+tgtdt++GKT++s++++  l     + +yfKPiqtg+  d+ds++i+++++++    + +++ + +p++p++aa+++++ id++ki  +   d++
  AHX11529.1   2 SVFITGTDTNIGKTIISAWICTHL-----RYAYFKPIQTGT--DTDSDFISKVTSVP---IYESTFYFPEPIAPHIAAKNTNKVIDISKI--S-MPDNK 87 
                 69**********************.....************..7**********766...55679*************************..5.55788 PP

      AAA_26 101 ivvVEGagglgvpitee.llnadiaknlgapvilVargglgtinqllltiealrqknvrvlGvilNkvrnpe....nvetlekksgipvlGvvPylpdl 194
                  v+VEGagg++vp+      ++d++++l +p i+Va+ +lgtin++llt+ealr ++++vlGvi+N + + +    n  ++ +++++++l   Pyl+++
  AHX11529.1  88 KVLVEGAGGVLVPLHGSgIKIIDLIQSLELPAIVVASDTLGTINHTLLTLEALRARKIKVLGVIMNSTSKNKglgyNAGAINHYGSVEILMNFPYLESI 186
                 99***********87665889**********************************************766647778********************999 PP

      AAA_26 195 eap 197
                 +++
  AHX11529.1 187 TEE 189
                 875 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.6e-06     0.014       1     123 [.       3     191 ..       3     196 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.6e-06
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 ++i++t  + GKT ++a +++ l  + ++ +   +++++ +++i + ++  i +                                             
  AHX11529.1   3 VFITGTDTNIGKTIISAWICTHLRYAYFKPIQ--TGTDTDSDFISKVTSVPIYEstfyfpepiaphiaakntnkvidiskismpdnkkvlvegaggvlv 99 
                 689*********************96666444..4444445555455555555578999999************************************* PP

                 .............................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC.TS-EEEEEE--CCHCCCCH CS
                 .............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
        CbiA  55 .............................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry.gvpvlgviprdeavaeapa 123
                                              ++   l +leal+ +k   +k++gv+ n   +++       a+      y  v++l   p+ e+++e   
  AHX11529.1 100 plhgsgikiidliqslelpaivvasdtlgTINHTLLTLEALRARK---IKVLGVIMNSTSKNKGLGYNAGAINH----YgSVEILMNFPYLESITEESL 191
                 *******************99976665555555555555555443...9********98888433322222222....226666666666666666555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       409  (0.0228122); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1684.12
//
Query:       AHX11530.1  [L=454]
Description: adenosylmethionine-8-amino-7-oxononanoate transaminase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.9e-107  357.8   0.0   6.8e-107  357.6   0.0    1.0  1  Aminotran_3    Aminotransferase class-III
  ------ inclusion threshold ------
      0.016   14.4   0.0      0.055   12.6   0.0    1.9  1  Aminotran_1_2  Aminotransferase class I and II
        0.2   11.9   1.1       0.95    9.7   0.1    2.5  2  RNase_3_N      Ribonuclease III N-terminal domain


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  357.6   0.0  1.1e-110  6.8e-107       4     405 ..      19     432 ..      16     433 .. 0.96

  Alignments for each domain:
  == domain 1  score: 357.6 bits;  conditional E-value: 1.1e-110
                  TTB--SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHH CS
  Aminotran_3   4 reednlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAve 101
                  ++  +l+++it++e+  l+d  g++y+Dl+ss++v+++Gh++P ++ka+ +qa kl+ v+f+  t+e a+ l+e l + +p+ ++k+f+ ++Gs Ave
   AHX11530.1  19 EKTAPLPIAITRGENECLYDDRGNKYIDLISSWWVNLHGHSNPVIAKAIYDQALKLEQVIFADCTHELAISLCENLKASLPQTFSKFFFSDNGSTAVE 116
                  5566778******************************************************************************************* PP

                  HHHHHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGT.B-HHHHHHHHHHHHHHHHCHTCCCEEEEEE CS
  Aminotran_3 102 tAlKlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevl.keneeeeaalleelealekkkkdevaAviv 198
                  +AlK+  ++ +++++++++ +++f++++HG+t+ga+sv+ s +   + ++ fl    +++yp + +  +  e +e++ l++le+  k+ +  va++i+
   AHX11530.1 117 VALKMTLQFWQNRNQENRNIFLSFDKGYHGDTVGAMSVGIS-SDFFSSYERFLFSSQSIPYPATWIGdPDVETKEESSLKMLERFLKENSGRVAGFIL 213
                  *****************************************.999999**************987761445678899999****99************ PP

                  -S.CETTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTT.SS-EEEEEEHHHHTTS-TTS......B- CS
  Aminotran_3 199 Ep.iqgegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgG.lplsavlataevmqalapgs......hg 288
                  Ep +qg+ G+ +  pe+l+++ +l +kh+v+li+DEv+tGf rTGk+fAl+++ ++pD+++l+K+ltgG lpls +++t+e+++a+ +++      hg
   AHX11530.1 214 EPlVQGASGMRMCRPEYLERILTLLRKHEVILIFDEVMTGFYRTGKMFALDYLSITPDILCLSKGLTGGfLPLSLTITTREIYDAFLDNDfrkalvHG 311
                  **************************************************************************************8888******** PP

                  -TTTT-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTC....HHHHHHHHHCTEE-EEETTTE CS
  Aminotran_3 289 sTfgGnplacavalavleiieeekllenaqelgaalkegLeelqkky.evikevRgkGlmiaielkeeaevke....keilkkakekGvlilsaGdnv 381
                  +++++npl ca+a+a+l+++++e+ l+ ++++++  k+ L+el++++ + +k  R  G++ a++l++e+   +    k++ + ++ekG+li+++G n+
   AHX11530.1 312 HSYTANPLGCAAAIASLKLLKDENTLKAIANIEKLHKNFLSELAQSSlDCVKARRVCGTIAAFNLFSEESDYNhpivKSLKEIFLEKGLLIRPLG-NT 408
                  **********************************************99*****************99988555688888888999**********.** PP

                  EEE---TT--HHHHHHHHHHHHHH CS
  Aminotran_3 382 irllppliitdeeidelleilkka 405
                  i+l+pp++i+++ ++e+ +++ ++
   AHX11530.1 409 IYLIPPYCISQASLEEAYNKILEV 432
                  *****************9999766 PP

>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   9.2e-06     0.055     165     301 ..     226     363 ..     193     406 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 9.2e-06
                    --HHHHHHHHHHHHHTTEEEEEEETTTTCBSSSSHTHHHHGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEH..........HHHHHHHHHHHHH CS
  Aminotran_1_2 165 atleeleklldlakkynlllfvDeaYagfvfgsldavatranveeepnllivgslsKafGlaGeRvGyilgna..........avvsqlrklsrpf 250
                    + +e le +l+l +k++++l++De+  gf+ + + ++  ++ + +  + +++  lsK  Gl+G   G++  +            + +  rk+  ++
     AHX11530.1 226 CRPEYLERILTLLRKHEVILIFDEVMTGFYRTGKMFALDYLSITP--D-ILC--LSK--GLTG---GFLPLSLtittreiydaFLDNDFRKALVHG 311
                    678889*************************98776443444444..3.444..444..7777...777665556667666655555566666666 PP

                    TS.SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSTEEEEC CS
  Aminotran_1_2 251 ls.ssllqaavaaalsdallkqseleemrqrlqkrrkelrdeLaelglkvla 301
                     s ++     +aa++s +llk++++ ++ + ++k++k + +eLa+  l++++
     AHX11530.1 312 HSyTANPLGCAAAIASLKLLKDENTLKAIANIEKLHKNFLSELAQSSLDCVK 363
                    6633322333334444444445577777777888888888888777777765 PP

>> RNase_3_N  Ribonuclease III N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.7   0.1   0.00016      0.95      50      97 ..     312     354 ..     288     363 .. 0.76
   2 ?   -0.5   0.1      0.25   1.5e+03      16      38 ..     421     443 ..     418     452 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.7 bits;  conditional E-value: 0.00016
                 HHHCSHHHHHHHHHHHHHHTT--THHHHHHHHHHH--TT--S-SSTTS CS
   RNase_3_N  50 palsRykLklAaelksleelgklplleeisnyeskfkssdskPilsel 97 
                 ++ +   L +Aa + sl+ l+ +++l+ i n e+ +k+      lsel
  AHX11530.1 312 HSYTANPLGCAAAIASLKLLKDENTLKAIANIEKLHKN-----FLSEL 354
                 566677899*************************9998.....45555 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.25
                 HHHHHHHHHHHH---HHHHHHHH CS
   RNase_3_N  16 klvesykriielspnlktyeeal 38 
                  l e+y++i+e+   ++  +++ 
  AHX11530.1 421 SLEEAYNKILEVITSIHHSKKVS 443
                 57788999988877766655554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (454 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3474.15
//
Query:       AHX11531.1  [L=99]
Description: hypothetical protein NHE_0594 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       917  (0.0511462); expected 358.6 (0.02)
Passed bias filter:                      489  (0.0272742); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 798.13
//
Query:       AHX11532.1  [L=257]
Description: cytochrome c oxidase, subunit II [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.6e-53  178.6   0.1    7.9e-53  177.5   0.0    1.6  2  COX2         Cytochrome C oxidase subunit II, periplasmic dom
    2.3e-26   91.7   0.8    4.2e-26   90.9   0.8    1.4  1  COX2_TM      Cytochrome C oxidase subunit II, transmembrane d
     0.0048   15.2   0.2      0.006   14.9   0.2    1.0  1  Dpy19        Q-cell neuroblast polarisation
  ------ inclusion threshold ------
      0.038   13.5   0.1      0.047   13.2   0.1    1.1  1  Sulf_transp  Sulphur transport
      0.043   12.1   0.5      0.056   11.7   0.5    1.1  1  DUF2070      Predicted membrane protein (DUF2070)


Domain annotation for each model (and alignments):
>> COX2  Cytochrome C oxidase subunit II, periplasmic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0       1.1     4e+03      56      84 ..      53      81 ..      42      88 .. 0.75
   2 !  177.5   0.0   2.2e-56   7.9e-53       1     120 []     122     241 ..     122     241 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 1.1
        COX2 56 irllvtaedvlhsfavpslgvkvdavpGr 84
                + ++v +   l +++v  +  k + vp +
  AHX11532.1 53 MLFIVVSVSALLTYTVIRFNKKRNPVPSK 81
                45677778888888888888888888865 PP

  == domain 2  score: 177.5 bits;  conditional E-value: 2.2e-56
        COX2   1 ltikaiGhqwywsyeytdfedlefdsylvpeedleegelrllevdnrvvlpvetkirllvtaedvlhsfavpslgvkvdavpGrlnqvsllidreGvfy 99 
                 +t+k +Ghqwyw+y y+d+ +++fds l ++ +l  ge rll+vdn +vlpv+t+ir+++t++dv+hs+avp+lg+k d++pGrln++++ i++eGv+y
  AHX11532.1 122 MTVKIVGHQWYWTYSYPDHGEITFDSNLKNDGELVAGEPRLLAVDNYLVLPVDTNIRIQITSDDVIHSWAVPALGLKKDSIPGRLNETWVKIKNEGVYY 220
                 89************************************************************************************************* PP

        COX2 100 GqcselcGvnhssmpivveav 120
                 GqcselcGv+h +mpi+v+av
  AHX11532.1 221 GQCSELCGVLHGFMPIAVKAV 241
                 ******************997 PP

>> COX2_TM  Cytochrome C oxidase subunit II, transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.9   0.8   1.2e-29   4.2e-26       2      89 .]      24     110 ..      23     110 .. 0.97

  Alignments for each domain:
  == domain 1  score: 90.9 bits;  conditional E-value: 1.2e-29
     COX2_TM   2 atpaglgfqdaasplmeeleelhdyilliltlililVlyilvlilvefrrrknkitakylvhgqeiEiiWTiiPalililialpSlkl 89 
                 +  ++lgfq++asp me ++++h+++l+i+++i++ V+ +l++ +++f++++n++++k   h++ +Ei+WT+iP  i+i ia+pSl++
  AHX11532.1  24 PHAWQLGFQESASPVMEYINNFHNKMLVIMLFIVVSVSALLTYTVIRFNKKRNPVPSK-RSHNTLLEIVWTLIPLCIVIGIAFPSLRV 110
                 678*****************************************************99.99*************************86 PP

>> Dpy19  Q-cell neuroblast polarisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.2   1.7e-06     0.006     246     339 ..      31     133 ..       5     144 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 1.7e-06
       Dpy19 246 lihllslllafvlqfgnsmlllslllsvllslllilvlqrkvkskr..........lllklillllklllsialtlilkllikkvlsveddehifkllk 334
                 +    s ++ ++ +f n+ml++ l+++v++s+ll+  +  ++++kr          +ll+++++l+ l+++i +++    ++k+  ++ + e  +k++ 
  AHX11532.1  31 FQESASPVMEYINNFHNKMLVIMLFIVVSVSALLTYTV-IRFNKKRnpvpskrshnTLLEIVWTLIPLCIVIGIAFPSLRVLKYEEQIPESEMTVKIVG 128
                 55667889999**********************99999.6666666789999999988999999999*****999998888888889999999999999 PP

       Dpy19 335 akfal 339
                 +++ +
  AHX11532.1 129 HQWYW 133
                 99866 PP

>> Sulf_transp  Sulphur transport
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.1   1.3e-05     0.047      88     195 ..       2     110 ..       1     152 [. 0.66

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 1.3e-05
  Sulf_transp  88 ralitllffilgavalltgilsswleqllest..vskeslyetlglsplllialllliallllvkelrkeklqeaeklektslakklfrkpwslvlga 183
                  r l+ +lf++l  +a++ ++ ++   ql +++  +  ++  + ++ ++l++++++++ + +ll ++  + + ++++   + +  ++l++  w+l+   
   AHX11532.1   2 RKLVLILFLVLPIFAFGEQVGQPHAWQLGFQEsaSPVMEYINNFHNKMLVIMLFIVVSVSALLTYTVIRFNKKRNP-VPSKRSHNTLLEIVWTLIPLC 98 
                  5677788888888999999998877776665411555777777777777665555555555555555444444444.3444445899*********** PP

  Sulf_transp 184 vllgllavlawl 195
                  +++g+ +    +
   AHX11532.1  99 IVIGIAFPSLRV 110
                  ****98766444 PP

>> DUF2070  Predicted membrane protein (DUF2070)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.5   1.6e-05     0.056      27      88 ..      38     103 ..       3     119 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.6e-05
     DUF2070  27 ligllaflssklfgillfglpalvaflltlpvlrilggr..ltykrs...lflalltelivviisll 88 
                 ++++++   +  + ++++++   v++llt+ v+r+ ++r  +++krs   l+  + t+++++i++ +
  AHX11532.1  38 VMEYINNFHN-KMLVIMLFIVVSVSALLTYTVIRFNKKRnpVPSKRShntLLEIVWTLIPLCIVIGI 103
                 3344443333.4556666666789**************99999999999444455555666664444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       975  (0.0543812); expected 358.6 (0.02)
Passed bias filter:                      723  (0.0403257); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.38
# Mc/sec: 2009.82
//
Query:       AHX11533.1  [L=518]
Description: cytochrome c oxidase, subunit I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   5.4e-148  493.4  66.6   6.4e-148  493.2  66.6    1.1  1  COX1      Cytochrome C and Quinol oxidase polypeptide I


Domain annotation for each model (and alignments):
>> COX1  Cytochrome C and Quinol oxidase polypeptide I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  493.2  66.6  3.6e-152  6.4e-148       1     432 []      22     467 ..      22     467 .. 0.97

  Alignments for each domain:
  == domain 1  score: 493.2 bits;  conditional E-value: 3.6e-152
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCT.....-HHCHHHHHHHHHHHHHHHHHHHH.CHHHHHHHHHHHHCTSS-S-HHHHHHHHHHHHHHHHHH CS
        COX1   1 kigllylilalvlllvggllgllirlqlafp.....dletynqlrtlHgnlmiflfatpf.ilgfgnylvplllgardlafprlnalsfwlvvlgvvll 93 
                 +ig+ly+il++v ++vggl++ll+r ql+       + + yn+ +t+H+++m+f++++p+ ++gfgn++vp+++ga+d+afpr+n++sfw+++++++++
  AHX11533.1  22 DIGTLYIILSIVGGIVGGLFSLLMRSQLMHIdvfggNYQLYNVSVTAHAVIMVFFMIMPAlVGGFGNWFVPIMIGAPDMAFPRMNNISFWMLFFSLIVV 120
                 5899************************9655555677************************************************************7 PP

                 HHHHH..CSS-STTTTTTTC.........SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCGS-HHHHHHHHHHHHHHHHCHHHHHHHHHCHH CS
        COX1  94 llsll..gaattgwteYapls........evdlwllglllvvvssllgainfivtilkrrapgmtvaklplfvwavlatailillalpvlalallllll 182
                 +ls +  +++ tgwt Y+pls         +dl++++l+l+++ss+lgainfi+ti+++rapgm ++k+plfvw++l+ta+l+l+++pvla  l++ll+
  AHX11533.1 121 VLSAFigEGPGTGWTVYPPLSgikfhpdvSIDLAIFSLHLAGLSSILGAINFITTIINMRAPGMGMFKMPLFVWSILITAVLVLIVMPVLAGVLTMLLA 219
                 777776877****************************************************************************************** PP

                 HHHCT.-SSSC...E-HHHHHHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHTSCCCTHHHHHHHHHHHHHHCCCCGGGGTTTSSS-HHHHHHHHHHHHH CS
        COX1 183 drslg.kffsp...gdplldqhlfWffgHpeVyililpalgivyyilpkfagrplfsyklsvlafililflsflvwaHHlfttglpewlkalgsvfsll 277
                 dr++g  ff++   gdpll+qhlfWffgHpeVyi+ilpa+giv++i+++f+++p+f+y  +v+a+ +i++++  vwaHH+fttg++  + a+++v+++l
  AHX11533.1 220 DRNFGtAFFEVaggGDPLLYQHLFWFFGHPEVYIVILPAFGIVSEIVSTFSKKPVFGYIGMVAAMTIIGIIGCFVWAHHMFTTGVSYNTLAYFTVATML 318
                 *********8899************************************************************************************** PP

                 THHHHHHCCCHHHHCCTTS-CHCHHHHHHHHHHHHHHHHHHHHHHHHTSHHHHHHHTTBHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHSB--HHHHH CS
        COX1 278 iavPsglkvfnwlatlwrgsirfktpmlfflgfavlfiigGltGvllalpsvnyvvhntywvvaHfHlvllgavvfllfaaiyyllpkltgrmlserla 376
                 + vP+g+kvf+w+at+w+gsi++ktpmlf+lgf++lf++gG+tG+ l++ +++ ++h+ty+vv+HfH+v+  av+f++ aa+yy++ k+ gr+++e l+
  AHX11533.1 319 VGVPTGIKVFSWIATMWGGSIDLKTPMLFALGFILLFVLGGVTGIALSNSALDKMLHDTYYVVGHFHYVMSIAVLFVVYAAFYYWIGKISGRQYNELLG 417
                 *************************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHHHHHTTHBSSSST--SCCCCHHHCHHHHHHHHHHHHH CS
        COX1 377 klhfwllfiGlvlmflpmhilGllgmprraadyksfletvpelqplnvlrtiggvl 432
                 k+hf++++i+++++flp h+lGl+gmprr+ dy       +++ p+n ++++g++l
  AHX11533.1 418 KVHFYVTLIAVNITFLPHHFLGLAGMPRRVPDY------PDAFIPWNYISSVGAFL 467
                 *********************************......469***********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1074  (0.059903); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.65u 0.28s 00:00:00.93 Elapsed: 00:00:00.46
# Mc/sec: 3420.39
//
Query:       AHX11534.1  [L=302]
Description: protoheme IX farnesyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-55  187.1  31.2    3.5e-55  187.1  31.2    1.4  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  187.1  31.2   1.9e-59   3.5e-55       3     240 ..      30     268 ..      28     284 .. 0.89

  Alignments for each domain:
  == domain 1  score: 187.1 bits;  conditional E-value: 1.9e-59
        UbiA   3 ipalvg..lalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallglla 99 
                 ++a+ g  la+ +g +++l+ + l++++t+  ++aa alN+++D +iDa m rt+nRP+++Gr+s   al f+++l++l+++++a+ +n+l+all+l+a
  AHX11534.1  30 FTAITGvvLAYFSGYTTSLSSAMLAIVCTATGSGAAGALNMWYDNDIDAVMLRTRNRPIPQGRVSQLFALEFGLILAVLSVGIMAIAVNLLSALLLLVA 128
                 677778656777778888899999999999********************************************************************* PP

        UbiA 100 llly.vvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvlGrkaarillallla 197
                 ++ y vvYt ++lKrrt +++v+gg+a+++pp++gwaav++s+ ++ ++l+l++fl+t ++++a +l+  ++++ +gi++lpv+ G k+++i+ +l + 
  AHX11534.1 129 IFYYsVVYT-IWLKRRTSQNIVIGGAAGAFPPMIGWAAVSNSVGIESIILFLIIFLWTPPHFWALALKSSQDYKSVGIPMLPVTSGVKVTKIQ-ILCYS 225
                 *********.**********************************************************************************6.43444 PP

        UbiA 198 vllla..llllllalllllylllalllaalallraarlvrrrdak 240
                 vllla  +l ++l+  + +y++ al+l+ ++l++a+ ++ ++  +
  AHX11534.1 226 VLLLAtsILPYVLMFAGVIYAVTALILGFIFLYYAVAVYLDD--N 268
                 444445666888888899999999999999999977666544..3 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (302 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1180  (0.0658152); expected 358.6 (0.02)
Passed bias filter:                      343  (0.019131); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.44
# Mc/sec: 2067.93
//
Query:       AHX11535.1  [L=173]
Description: ubiquinol-cytochrome c reductase, iron-sulfur subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.4e-13   50.6   0.1    2.3e-13   49.9   0.1    1.4  1  Rieske      Rieske [2Fe-2S] domain
    3.2e-08   32.8   0.1    9.2e-08   31.3   0.0    1.8  2  UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit T


Domain annotation for each model (and alignments):
>> Rieske  Rieske [2Fe-2S] domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.9   0.1   2.6e-17   2.3e-13      27      86 ..      97     152 ..      41     156 .. 0.73

  Alignments for each domain:
  == domain 1  score: 49.9 bits;  conditional E-value: 2.6e-17
                 EEEE-T..TS-EEEEESC-TTTT-BCGGSEEETT.EEE-TTT--EEETTSBEEE-TTHHHEE CS
      Rieske  27 vvlrde..dgevyAlsdvCtHrgaplsegkidekgvleCpcHgwaydadGkvikgPaprpla 86 
                  v   +  ++++ ++++vCtH+g+ + ++     g++ CpcHg+ yd++G+v++gPap++l 
  AHX11535.1  97 RV---QhgKENWLVVVGVCTHLGCVPISNPD---GTFFCPCHGSYYDTSGRVVAGPAPANLV 152
                 22...13388999************988555...79**********************9975 PP

>> UCR_Fe-S_N  Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.0     1e-11   9.2e-08       9      41 .]       4      36 ..       2      36 .. 0.93
   2 ?   -2.6   0.0      0.39   3.5e+03      13      19 ..      38      44 ..      38      47 .. 0.79

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1e-11
  UCR_Fe-S_N  9 ptRRDFLyiATgavgaVGaaaaawPfidqmnPs 41
                ++ RDF++++T a+g+ Ga  a wP+ +++ P+
  AHX11535.1  4 KKKRDFIITTTIAFGTGGAVVATWPLLKSFGPA 36
                677**************************9995 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.39
  UCR_Fe-S_N 13 DFLyiAT 19
                D+L +AT
  AHX11535.1 38 DVLAAAT 44
                8899998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.41
# Mc/sec: 1253.03
//
Query:       AHX11536.1  [L=408]
Description: cytochrome b [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.5e-75  252.5  17.4    5.2e-75  251.4  17.4    1.5  1  Cytochrome_B     Cytochrome b/b6/petB
    3.4e-43  147.6  10.7    3.4e-43  147.6  10.7    2.3  2  Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
    9.7e-40  135.0   2.6    9.7e-40  135.0   2.6    3.7  3  Cytochrom_B_C    Cytochrome b(C-terminal)/b6/petD
  ------ inclusion threshold ------
        8.2    6.2   9.1         25    4.6   0.0    3.7  3  TRAM1            TRAM1-like protein


Domain annotation for each model (and alignments):
>> Cytochrome_B  Cytochrome b/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.4  17.4   1.2e-78   5.2e-75       2     189 .]      33     220 ..      32     220 .. 0.99

  Alignments for each domain:
  == domain 1  score: 251.4 bits;  conditional E-value: 1.2e-78
  Cytochrome_B   2 vsllvpsnlsiiynlGsllllvlvlqiltGvalafyytptvtlaflsvqyilrdvnfGwlirsvhangasllflllylhifrglllgglkktrelvW 98 
                   v++ vp n++ ++n+G l++l lv+qiltG++la++y p+ ++af+sv++i rdv fGwlir+ h++gas++f+++y+hifrgl++g++k++rel W
    AHX11536.1  33 VDYRVPININPLWNFGVLAGLSLVIQILTGIFLAMHYDPNAANAFTSVEHITRDVSFGWLIRYSHQVGASMFFVVVYVHIFRGLYYGSYKEPRELLW 129
                   78999******************************************************************************************** PP

  Cytochrome_B  99 viGvillllvivtafiGyvLpwdqmsyWavtvitnllsaiPviGstlvellwgsvsvddatLtrffslhfllPflllillllhllllhktg 189
                   ++Gv ++l++++taf+GyvLpw+qms+Wa+tvitn  saiP++G+ + +++wg+++v++ tL++ff+lh+l+Pf+++++++lhl +lh++g
    AHX11536.1 130 ILGVAIFLVMMATAFLGYVLPWGQMSFWAATVITNFFSAIPLFGESITQWIWGGFAVGSPTLNKFFALHYLFPFIIVAIVILHLAALHRFG 220
                   ****************************************************************************************986 PP

>> Cytochrom_B_N_2  Cytochrome b(N-terminal)/b6/petB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.0   0.1      0.17   7.6e+02      20      66 ..      35      85 ..      25      95 .. 0.67
   2 !  147.6  10.7   7.6e-47   3.4e-43       2     167 ..     103     269 ..     102     271 .. 0.96

  Alignments for each domain:
  == domain 1  score: 0.0 bits;  conditional E-value: 0.17
  Cytochrom_B_N_2 20 YkkpReln..WiiGvllllltllegflGysLp..ddllsvtalrvgagiis 66
                     Y+ p ++n  W  Gvl  l  +++ ++G  L   +d  +++a + +++i+ 
       AHX11536.1 35 YRVPININplWNFGVLAGLSLVIQILTGIFLAmhYDPNAANAFTSVEHITR 85
                     555555544489999888888888888877651156667777766666665 PP

  == domain 2  score: 147.6 bits;  conditional E-value: 7.6e-47
  Cytochrom_B_N_2   2 imiiliyvHmlrvfftGaYkkpRelnWiiGvllllltllegflGysLpddllsvtalrvgagiissvPvvgtwlvellfGgelpgeallsrlya 95 
                      ++++++yvH++r +++G+Yk+pRel Wi+Gv ++l++++++flGy+Lp+ ++s++a +v++++ s++P+ g+ + ++++Gg  +g+ +l++++a
       AHX11536.1 103 MFFVVVYVHIFRGLYYGSYKEPRELLWILGVAIFLVMMATAFLGYVLPWGQMSFWAATVITNFFSAIPLFGESITQWIWGGFAVGSPTLNKFFA 196
                      799******************************************************************************************* PP

  Cytochrom_B_N_2  96 lHilllpalllalivahlllvekkgqtpsr..rkeknvvgeplvpvnavkmlllflvlvallialalinPvpll 167
                      lH  l+p++++a++++hl+ +++ g++++   + +++++ +p++p+ ++k+++ ++++++++ +++++ P  l+
       AHX11536.1 197 LHY-LFPFIIVAIVILHLAALHRFGSNNPSgiEVKSDSETVPFHPYHTAKDFVTVVLFFIVFSGFLFFAPDYLG 269
                      ***.**********************99975667788889*****************************98766 PP

>> Cytochrom_B_C  Cytochrome b(C-terminal)/b6/petD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   5.1       2.3     1e+04      68      68 ..     103     103 ..      15     167 .. 0.54
   2 ?   -1.4   0.0      0.63   2.8e+03      66      89 ..     203     226 ..     188     236 .. 0.66
   3 !  135.0   2.6   2.2e-43   9.7e-40       1     103 []     276     377 ..     276     377 .. 0.99

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 2.3
                    H CS
  Cytochrom_B_C  68 l 68 
                    +
     AHX11536.1 103 M 103
                    1 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.63
                    HHHHHHHHHHHHHHHHHHTS-SSC CS
  Cytochrom_B_C  66 kvllallvvsfvvLgylGvqppee 89 
                     +++a++++++++L  +G+++p++
     AHX11536.1 203 FIIVAIVILHLAALHRFGSNNPSG 226
                    345556666666666677766665 PP

  == domain 3  score: 135.0 bits;  conditional E-value: 2.2e-43
                    B--TTC--TT----GGGHHHHHHHHCSSSHHHHHHHHHHHHHGGGCHHHH---SSSSSTT-.HHHHHHHHHHHHHHHHHHHHHTS-SSCCHHHHHH CS
  Cytochrom_B_C   1 panplktPahIaPeWYflpfYaiLraipakllGvvamgaaivilfllpwldrskvksiryrkplakvllallvvsfvvLgylGvqppeevavllsq 96 
                    +a+pl+tP+hI+PeWYflpfYaiLraip+kl+Gvva++ a++il+l+pwld+skvks ryr p++k ++++++++fv+L +lG +++ e+++++s+
     AHX11536.1 276 EADPLVTPQHIVPEWYFLPFYAILRAIPSKLGGVVALFSAVLILVLVPWLDTSKVKSGRYR-PIFKKFFLAFLCNFVFLVWLGGREAIEPYITMSR 370
                    69***********************************************************.********************************** PP

                    HHHHHHH CS
  Cytochrom_B_C  97 iatvlyF 103
                    +at++yF
     AHX11536.1 371 LATLYYF 377
                    ******9 PP

>> TRAM1  TRAM1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.6   0.0    0.0056        25      38      49 ..      24      35 ..      22      37 .. 0.93
   2 ?    2.8   3.3      0.02        91       3      41 ..     193     259 ..     191     271 .. 0.62
   3 ?   -3.0   0.0       1.3   5.9e+03      34      50 ..     350     366 ..     345     367 .. 0.76

  Alignments for each domain:
  == domain 1  score: 4.6 bits;  conditional E-value: 0.0056
       TRAM1 38 vftflRaflmey 49
                +f+flR+f+ +y
  AHX11536.1 24 IFSFLREFIVDY 35
                79********99 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.02
       TRAM1   3 kFifLsynvpl............................sansetglYgkGlkDlafvffyvivftf 41 
                 kF++L+y  p                             ++++ + + ++  kD+++v+ ++ivf++
  AHX11536.1 193 KFFALHYLFPFiivaivilhlaalhrfgsnnpsgievksDSETVPFHPYHTAKDFVTVVLFFIVFSG 259
                 66666666663444444444555555555666666664322333333356789************97 PP

  == domain 3  score: -3.0 bits;  conditional E-value: 1.3
       TRAM1  34 fyvivftflRaflmeyv 50 
                 f ++v+ + R+++  y+
  AHX11536.1 350 FVFLVWLGGREAIEPYI 366
                 88899999999886665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (408 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       801  (0.0446762); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.54u 0.28s 00:00:00.82 Elapsed: 00:00:00.45
# Mc/sec: 2739.43
//
Query:       AHX11537.1  [L=256]
Description: cytochrome C1 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.4e-92  308.6   0.0    2.8e-92  308.4   0.0    1.0  1  Cytochrom_C1     Cytochrome C1 family
     0.0025   18.1   0.0     0.0053   17.1   0.0    1.6  1  Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
  ------ inclusion threshold ------
      0.065   14.4   0.2       0.14   13.3   0.2    1.8  1  Cytochrom_C      Cytochrome c
       0.14   11.8   0.0       0.25   11.1   0.0    1.3  1  Cytochrom_C550   Cytochrome c-550 domain


Domain annotation for each model (and alignments):
>> Cytochrom_C1  Cytochrome C1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  308.4   0.0   6.3e-96   2.8e-92       1     218 [.      33     246 ..      33     247 .. 0.99

  Alignments for each domain:
  == domain 1  score: 308.4 bits;  conditional E-value: 6.3e-96
  Cytochrom_C1   1 wsfegifgkfDkaqlqRGlqvykevcsaCHslklvafrnLaelglteeevkalaaeyevkdgpddegemfeRpgkpaDklpspyaneeaaraangga 97 
                   wsf+gifg+fD++++qRGl+vy++vc++CHsl++++fr+L ++g+t e++k++a+ey+++dgpdd+ge+++Rpg ++D++  py n++aa+aan+g+
    AHX11537.1  33 WSFDGIFGTFDRQSIQRGLKVYQQVCASCHSLNRISFRHLLDIGFTPEQAKNIASEYQITDGPDDNGEYYQRPGVLSDYFAPPYSNRQAAEAANNGS 129
                   9************************************************************************************************ PP

  Cytochrom_C1  98 lppDLsllvkArkggadYiyslLtgYeeppagvevkegqyyNkyfpggviamakpLsdgqveyedgtpatveqmakDvtaFLaWaaepklearkklg 194
                   +ppDLsl+++Ar +g++Y+yslLtg++ +++    +eg++yN+yf +g++ama+pLsd+ v+y+dgt+atv+qma Dv++FL+W+ae ++e+rk+lg
    AHX11537.1 130 YPPDLSLIARARMNGPNYLYSLLTGFTGEES----DEGLHYNPYFITGKLAMAPPLSDDLVTYDDGTQATVNQMAFDVVNFLHWTAEYEMERRKSLG 222
                   **************************88665....99************************************************************ PP

  Cytochrom_C1 195 lkvilfllilavllylvkrkiwak 218
                   lkvi fll+l +l+++++++iw +
    AHX11537.1 223 LKVIGFLLVLLTLSWISNKRIWGD 246
                   **********************76 PP

>> Cytochrome_CBB3  Cytochrome C oxidase, cbb3-type, subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.1   0.0   1.2e-06    0.0053       3      40 ..      47      85 ..      45     103 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.1 bits;  conditional E-value: 1.2e-06
  Cytochrome_CBB3  3 aaaGaalykknCasCHgkggag.pslagrdwepdalvdi 40
                     +++G ++y++ CasCH  +     +l + +++p++ ++i
       AHX11537.1 47 IQRGLKVYQQVCASCHSLNRISfRHLLDIGFTPEQAKNI 85
                     78999***********97666666666667777666665 PP

>> Cytochrom_C  Cytochrome c
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   3.1e-05      0.14       2      19 ..      48      65 ..      47     132 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 3.1e-05
                 --HHHHHHTTGGGTB-SS CS
  Cytochrom_C  2 arGkelftanCaaCHgve 19
                 +rG +++++ Ca+CH+++
   AHX11537.1 48 QRGLKVYQQVCASCHSLN 65
                 7999***99*******97 PP

>> Cytochrom_C550  Cytochrome c-550 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   5.5e-05      0.25      15      42 ..      36      63 ..      21      68 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 5.5e-05
                    TS-EEEEEHHHHHHHHHHHHHHTHHHHG CS
  Cytochrom_C550 15 egetvtlseeqlkkgkklFeaeCaqCHv 42
                    +g   t+ ++ +++g k++++ Ca+CH 
      AHX11537.1 36 DGIFGTFDRQSIQRGLKVYQQVCASCHS 63
                    566678999******************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       509  (0.0283898); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1876.73
//
Query:       AHX11538.1  [L=501]
Description: protein-export membrane protein SecD [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.7e-17   62.3  14.8    7.1e-17   61.4  14.8    1.4  1  SecD_SecF  Protein export membrane protein
    0.00015   21.1   0.0    0.00034   20.0   0.0    1.6  1  Sec_GG     SecD/SecF GG Motif
     0.0009   18.3  19.4     0.0015   17.5  19.4    1.3  1  MMPL       MMPL family
     0.0023   15.7  17.9     0.0042   14.8  17.9    1.3  1  ACR_tran   AcrB/AcrD/AcrF family


Domain annotation for each model (and alignments):
>> SecD_SecF  Protein export membrane protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4  14.8   1.6e-20   7.1e-17      14     182 ..     324     489 ..     315     495 .. 0.85

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 1.6e-20
                 EEEEEEEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHTTSSSHHHHHHHHHHHHHH CS
   SecD_SecF  14 ekisvetvgpsvskelaekavlallialvliliyvalrFewrvalaaiialvhDviitvgvlsllgievdlatvaalLtiiGYSvndtvvvfdrvrenl 112
                 ++i+  ++gps++ + +  a  + ++a+vl+++++ ++++  ++l a ial+  +i++++ l l++  ++l  +a+l+  iG  v+ +v++f+r+re++
  AHX11538.1 324 NVIEQRVIGPSLGAKSTSLAKKSGILAVVLVILFMLFAYRI-YGLIAAIALIMNLILLLAGLTLIEATLTLPGIAGLILTIGMAVDANVLIFERIREEF 421
                 6788999********************************97.68888889999*********************************************9 PP

                 HH--SS-HHHHHHHHHHHHHHHHHHTT.HHHHHHHHHHHHHHTTTTHHHHHHHHHHTSTTTTTHHHHHHHH CS
   SecD_SecF 113 rkkkratlkeiinlslnqtLtrtilts.lttllvvvallllggdslkdfalallvGlivgtyssifiaspl 182
                  k  +  l + i ++ ++    ti  s +ttl ++++++++g++ +k+fa++l +G+i+ ++ss+f  + +
  AHX11538.1 422 AK--TGVLSNSIMKGFEHAKA-TIFDSnITTLAAALIMIIIGSGPIKGFAVTLSLGIITSIFSSVFATKVM 489
                 99..34444444444444433.5554316688899999****************************76654 PP

>> Sec_GG  SecD/SecF GG Motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   7.7e-08   0.00034       5      27 ..      30      52 ..      29      53 .. 0.92

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 7.7e-08
                HC--EE-TTTS-EEEEEEEE-TT CS
      Sec_GG  5 tkGlNLGlDFtGGthielqfdqp 27
                ++++ +GlD++GG+ i++  dq+
  AHX11538.1 30 GRKISMGLDLRGGVSITMSMDQA 52
                68999****************97 PP

>> MMPL  MMPL family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5  19.4   3.4e-07    0.0015     153     291 ..     349     482 ..     334     486 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.4e-07
        MMPL 153 lvvilviLlivyrSlvaallplltvvvsllaalglvlilalllglelstfvlgll.vvlliavGtDYallLvsRyreelaagedreeaviravastgkv 250
                 l+v+lviL++++   +  ++ l+ +++  ++ + l+l+la l  +e + + +g++  +l+i+ ++D ++l++ R+ree a+     +++++ +  +  +
  AHX11538.1 349 LAVVLVILFMLF---AYRIYGLI-AAI--ALIMNLILLLAGLTLIEATLTLPGIAgLILTIGMAVDANVLIFERIREEFAKTGVLSNSIMKGFEHAKAT 441
                 344444444444...22233322.223..3334455688899999999999999626788******************999888889************ PP

        MMPL 251 vtaaGltvaiamlgLvvarlpvlaqvGvaialGvlvdvliv 291
                 ++ + +t  +a l + ++  + +++++v+++lG++ +++ +
  AHX11538.1 442 IFDSNITTLAAALIMIIIGSGPIKGFAVTLSLGIITSIFSS 482
                 ***********************************999865 PP

>> ACR_tran  AcrB/AcrD/AcrF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8  17.9   9.4e-07    0.0042     333     486 ..     343     490 ..     335     500 .. 0.81

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 9.4e-07
                 HHHHHHHHHHHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHHHHHTT--BCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHH CS
    ACR_tran 333 VvktLleaivLvvlvvflFLqnlratlipaiavPlsllgtfavlkalgfslNlltLfgLvlAiGlvvDdAiVvvEnierkleeegekpleaalksmkei 431
                  +k+ ++a+vLv+l ++ F       li aia+ + l++ +a l +++ +l l  + gL l iG+ vD  + + E i ++ +++g    + ++k+ +  
  AHX11538.1 343 AKKSGILAVVLVILFML-FAYR-IYGLIAAIALIMNLILLLAGLTLIEATLTLPGIAGLILTIGMAVDANVLIFERIREEFAKTG-VLSNSIMKGFEHA 438
                 57888889998888764.4333.358*********************************************************55.5578999****99 PP

                 HHHHHHHHHHHHHHCTGGGGSBHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHH CS
    ACR_tran 432 qgalvaialvllavflPilflgGveGklfrqfaltivlaillsvlvaltltPalc 486
                 + ++  + ++ la+ l ++++g   G + + fa+t++l i+ s++ ++  t ++ 
  AHX11538.1 439 KATIFDSNITTLAAALIMIIIGS--GPI-KGFAVTLSLGIITSIFSSVFATKVMM 490
                 99999999888888877766653..444.78999999999999999987776544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (501 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1105  (0.061632); expected 358.6 (0.02)
Passed bias filter:                      559  (0.0311785); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.41
# Mc/sec: 3709.45
//
Query:       AHX11539.1  [L=404]
Description: hypothetical protein NHE_0602 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
     0.0031   17.6   0.0     0.0053   16.9   0.0    1.3  1  Thioesterase   Thioesterase domain
  ------ inclusion threshold ------
      0.025   14.3   0.0      0.056   13.1   0.0    1.6  1  PGAP1          PGAP1-like protein
      0.048   13.5   0.0      0.071   13.0   0.0    1.3  1  Abhydrolase_3  alpha/beta hydrolase fold
      0.073   12.9   0.0       0.12   12.2   0.0    1.4  1  Lipase_3       Lipase (class 3)
       0.08   12.6   0.0       0.12   12.0   0.0    1.3  1  Abhydrolase_1  alpha/beta hydrolase fold


Domain annotation for each model (and alignments):
>> Thioesterase  Thioesterase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   0.0   1.5e-06    0.0053      43     105 ..     131     193 ..     119     211 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.5e-06
                   HCTTCHHHHHHHHHHHHHHH-SSSSEEEEEETHHHHHHHHHHHHHHHCT-SEEEEEEESCCCC CS
  Thioesterase  43 pplesieelaaeyaealrqiqpegPyalfGhSlGgllAfevArqLesqGlavkslflidssap 105
                    +l+++e+l  +     r+ +    ++l G SlGg++  ++A++Le+ G+  + l+   +++ 
    AHX11539.1 131 VLLKNLEALLRSSQYYGRKYNRSNDLVLYGKSLGGMVSTKLAAKLEESGERCAKLITLVAPPN 193
                   5666777777777777788888999******************************98877765 PP

>> PGAP1  PGAP1-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   1.6e-05     0.056      80     131 ..     143     194 ..      70     200 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.6e-05
       PGAP1  80 lslysssekeptsviliGHSmGGivaraaltlknyikqsvntiltlasPhal 131
                  + y  + ++ ++++l G S+GG+v+  ++   +   +   +++tl +P ++
  AHX11539.1 143 SQYYGRKYNRSNDLVLYGKSLGGMVSTKLAAKLEESGERCAKLITLVAPPNM 194
                 244678889999**************8877777778999*******999765 PP

>> Abhydrolase_3  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0     2e-05     0.071      69     112 ..     152     195 ..      95     215 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2e-05
                    TTCEEEEEEETHHHHHHHHHHHHHHHTT---EEEEEEESE-SST CS
  Abhydrolase_3  69 dpsrivlaGdSaGGnlaaavalrardegepkvagqvliyPvtdl 112
                      + +vl G+S GG  ++ +a ++ ++ge   + + l+ P ++ 
     AHX11539.1 152 RSNDLVLYGKSLGGMVSTKLAAKLEESGERCAKLITLVAPPNMK 195
                    56789***********************999*********5433 PP

>> Lipase_3  Lipase (class 3)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   3.4e-05      0.12      32     111 ..     105     197 ..      62     214 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 3.4e-05
                 T-EEEHHHHHHHH........S-HHHHHHHHHHHHHHHTT........-EEEEEEEETHHHHHHHHHHHHHHHTT-SS---EEEEEES----B-HH CS
    Lipase_3  32 ggkvhsgfleaye........eslreqvlkelkrllekyp........eysivvtGHSLGgalAlLaaldlvengenekkkvtvvtfGqPrvgnke 111
                  g  h+  ++ ++         +  e +lk+l+ ll++ +        +  +v+ G SLGg +++ +a+ l e ge   + ++++t+ +P  + ++
  AHX11539.1 105 YGCAHRAVYRYMGgklslsnlVQQSEVLLKNLEALLRSSQyygrkynrSNDLVLYGKSLGGMVSTKLAAKLEESGE---RCAKLITLVAPPNMKYA 197
                 444455555555566666555233333445555555555555566666789************************5...57777777777666555 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   3.4e-05      0.12      74     110 ..     155     193 ..      95     208 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.4e-05
                    SEEEEEETHHHHHHHHHHHHH...GGGEEEEEEESECSSC CS
  Abhydrolase_1  74 kltlvGhSmGGmialayaaey...perVkalvllgaidpa 110
                     l+l G S+GGm+++ +aa+     er+++l++l a +p+
     AHX11539.1 155 DLVLYGKSLGGMVSTKLAAKLeesGERCAKLITLVA-PPN 193
                    57899****************************999.333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (404 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       775  (0.0432261); expected 358.6 (0.02)
Passed bias filter:                      606  (0.0338); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 2947.45
//
Query:       AHX11540.1  [L=227]
Description: 3-demethylubiquinone-9 3-O-methyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-20   71.8   0.0    8.5e-20   71.2   0.0    1.3  1  Methyltransf_11  Methyltransferase domain
    1.3e-18   67.4   0.0    1.7e-18   67.0   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
      9e-16   58.4   0.0    1.6e-15   57.5   0.0    1.4  1  Methyltransf_25  Methyltransferase domain
    7.2e-13   49.1   0.0    1.2e-12   48.5   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    4.2e-12   46.1   0.0    5.7e-12   45.7   0.0    1.3  1  Methyltransf_31  Methyltransferase domain
    1.7e-08   34.3   0.0    2.1e-08   34.0   0.0    1.1  1  NodS             Nodulation protein S (NodS)
    1.9e-08   34.0   0.2    2.5e-08   33.7   0.2    1.1  1  PrmA             Ribosomal protein L11 methyltransferase (Prm
    1.3e-05   24.8   0.0    2.1e-05   24.1   0.0    1.4  1  MTS              Methyltransferase small domain
    1.5e-05   24.1   0.0    2.2e-05   23.5   0.0    1.2  1  Methyltransf_9   Protein of unknown function (DUF1698)
    1.7e-05   24.3   0.0      3e-05   23.5   0.0    1.3  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    0.00016   21.1   0.0    0.00024   20.5   0.0    1.2  1  CMAS             Mycolic acid cyclopropane synthetase
    0.00018   21.2   0.0    0.00025   20.7   0.0    1.2  1  MetW             Methionine biosynthesis protein MetW
    0.00035   19.7   0.0     0.0004   19.6   0.0    1.2  1  DREV             DREV methyltransferase
    0.00055   19.4   0.1    0.00078   18.9   0.1    1.2  1  TehB             Tellurite resistance protein TehB
      0.001   18.6   0.0     0.0015   18.1   0.0    1.2  1  Methyltransf_PK  AdoMet dependent proline di-methyltransferas
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.017   15.1   0.0    1.2  1  Methyltransf_32  Methyltransferase domain
      0.055   13.1   0.0      0.095   12.3   0.0    1.3  1  TPMT             Thiopurine S-methyltransferase (TPMT)


Domain annotation for each model (and alignments):
>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   71.2   0.0   8.1e-23   8.5e-20       1      96 []      52     144 ..      52     144 .. 0.97

  Alignments for each domain:
  == domain 1  score: 71.2 bits;  conditional E-value: 8.1e-23
                      EEET-TTSHHHHHHHHTTSEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrgarvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpgGll 94 
                      LdvGcG+G+l+e+l + g+ v+++D+s+e +k+a e+++++   v+++ a++ +  ++d++fD++++ ev++hv+dp++++k +  +L pgG++
       AHX11540.1  52 LDVGCGGGILSEELSSLGGIVTAIDPSEESVKAAMENSKGN---VTYINASLDEAVIRDKQFDIICIMEVIEHVNDPMEFVKLCSGMLAPGGKI 142
                      8******************************9998888887...89***********************************************9 PP

                      EE CS
  Methyltransf_11  95 vi 96 
                      ++
       AHX11540.1 143 FF 144
                      87 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.0   0.0   1.6e-21   1.7e-18      21     162 ..      46     195 ..       6     197 .. 0.80

  Alignments for each domain:
  == domain 1  score: 67.0 bits;  conditional E-value: 1.6e-21
  Methyltransf_23  21 raggrvLdiGcGtGillevlrengfsvtgvDlspeaveiae..kakkaqkdqfdeq....eaaepqgkfdlIvlrevlehvpdppellrqiatl 108
                        g+ +Ld+GcG Gil+e+l+  g  vt++D+s+e v+ a   +    +   ++ +    ea   +++fd+I+ +ev+ehv dp e ++    +
       AHX11540.1  46 VVGKAILDVGCGGGILSEELSSLGGIVTAIDPSEESVKAAMenS----KGNVTYINasldEAVIRDKQFDIICIMEVIEHVNDPMEFVKLCSGM 135
                      55779****************************99888774442....2222322211113334788*************************** PP

  Methyltransf_23 109 lkpgGylllseplasl....kedrllldwlylvpagrhi..sffsarslkelleeaGlev 162
                      l+pgG +++s+ ++          ++++ l l p+ +h+   f   ++l++ + +aGle+
       AHX11540.1 136 LAPGGKIFFSTLNKTIksflFGIVAAEYLLDLLPRKTHSwqAFLKPSTLNKFFLNAGLEI 195
                      ************99877777455555555556666666666999**************98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.5   0.0   1.6e-18   1.6e-15       1      97 []      51     140 ..      51     140 .. 0.94

  Alignments for each domain:
  == domain 1  score: 57.5 bits;  conditional E-value: 1.6e-18
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHEE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvLk 94 
                      +Ld+GcG G l+++l+  +  + vt++D+see ++aa e+ +    nv+++++++++    d++fD+++++ +++h++d+   +++k ++ +L 
       AHX11540.1  51 ILDVGCGGGILSEELSSLG--GIVTAIDPSEESVKAAMENSK---GNVTYINASLDEAVIRDKQFDIICIMEVIEHVNDP--MEFVKLCSGMLA 137
                      8***************995..9*****************993...49***********************877***9965..59********** PP

                      EEE CS
  Methyltransf_25  95 pgG 97 
                      pgG
       AHX11540.1 138 PGG 140
                      **9 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   1.1e-15   1.2e-12       1      99 []      52     142 ..      52     142 .. 0.91

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 1.1e-15
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDlvvasnvlhhlkdirevldnirklLk 94 
                      L++GcG G l+++l     +  +t++D+s++++++a e  + +  + n+ ++  ++ +       +fD++ + +v++h++d+ e+++ +  +L+
       AHX11540.1  52 LDVGCGGGILSEELSSL--GGIVTAIDPSEESVKAAMENSKGNVTYINASLDEAVIRDK------QFDIICIMEVIEHVNDPMEFVKLCSGMLA 137
                      8****************..**************88888888888777777777777764......***************************** PP

  Methyltransf_12  95 pgGrl 99 
                      pgG++
       AHX11540.1 138 PGGKI 142
                      ***86 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.7   0.0   5.4e-15   5.7e-12       4     114 ..      48     159 ..      45     206 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.7 bits;  conditional E-value: 5.4e-15
  Methyltransf_31   4 glrvlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileei 97 
                      g+ +lD+GCG G l+ el ++   ++ v+ iD see+++ A en++     nv+   ++  e+   + d++fD+i+  ev+ +++dp ++ +  
       AHX11540.1  48 GKAILDVGCGGGILSEELSSL---GGIVTAIDPSEESVKAAMENSK----GNVTYINASLDEAV--IRDKQFDIICIMEVIEHVNDPMEFVKLC 132
                      6789***************66...467****************977....45555555544444..77788*********************** PP

  Methyltransf_31  98 ervlkpggilliedpr..........l 114
                      +  l pgg +  ++ +          +
       AHX11540.1 133 SGMLAPGGKIFFSTLNktiksflfgiV 159
                      ***********9999966555555552 PP

>> NodS  Nodulation protein S (NodS)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.0   0.0     2e-11   2.1e-08      37     168 ..      41     168 ..       3     176 .. 0.76

  Alignments for each domain:
  == domain 1  score: 34.0 bits;  conditional E-value: 2e-11
        NodS  37 lslaqgsiadalevGcaaGalterlapyckrltvvdvveeaiararervkesshiswivsdvqq.fstdekfdlivvaevlyyiedvaelraavrnlvs 134
                 ls ++     +l+vGc  G l+e+l+ +   +t +d  ee+++ a e  k   ++++i + + + +  d++fd+i + ev+ +++d +e+   v+    
  AHX11540.1  41 LSNSDVVGKAILDVGCGGGILSEELSSLGGIVTAIDPSEESVKAAMENSKG--NVTYINASLDEaVIRDKQFDIICIMEVIEHVNDPMEF---VKLCSG 134
                 233333335689******************************999998877..88888888865256799***********999999886...778889 PP

        NodS 135 llapdgqlvfGsardavcrrw.GhvaGaetvlall 168
                 +lap+g++ f s+ +++ +++   ++ ae +l+ll
  AHX11540.1 135 MLAPGGKIFF-STLNKTIKSFlFGIVAAEYLLDLL 168
                 ******9766.666666666513456677777776 PP

>> PrmA  Ribosomal protein L11 methyltransferase (PrmA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7   0.2   2.4e-11   2.5e-08     155     259 ..      41     145 ..      29     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 2.4e-11
        PrmA 155 leklvkegeevlDvGtGSGiLaiaaakLgakkvvavDiDevAvkvakeNaelNkveaklevalseellkeekadvi.vaNILaevl..ielaedikklv 250
                 l +    g+ +lDvG+G GiL+   + Lg   v+a+D  e +vk+a eN + N +  +    l e +++++++d+i +  ++ +v   +e+++  + ++
  AHX11540.1  41 LSNSDVVGKAILDVGCGGGILSEELSSLGGI-VTAIDPSEESVKAAMENSKGNVTYINA--SLDEAVIRDKQFDIIcIMEVIEHVNdpMEFVKLCSGML 136
                 5555667899*******************75.99*******************887777..4678888899***9944555555533367788888888 PP

        PrmA 251 keggllilS 259
                 ++gg + +S
  AHX11540.1 137 APGGKIFFS 145
                 888888877 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.1   0.0     2e-08   2.1e-05      31     102 ..      47     114 ..      26     152 .. 0.75

  Alignments for each domain:
  == domain 1  score: 24.1 bits;  conditional E-value: 2e-08
                 TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGCEEEEE-STTTTSTTS-EEEEE CS
         MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleanklevevvasdvleeveekkfdliv 102
                   + +lD+GcG G+l+ +l +      vt++d + +++++a en + n   +++   +++  + +k+fd+i 
  AHX11540.1  47 VGKAILDVGCGGGILSEELSSLGGI--VTAIDPSEESVKAAMENSKGNVTYINASLDEAV--IRDKQFDIIC 114
                 6778****************98877..9****************9999865544444333..3477899885 PP

>> Methyltransf_9  Protein of unknown function (DUF1698)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.1e-08   2.2e-05     112     220 ..      44     147 ..      30     153 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.1e-08
                     .--TT-EEEEET-TTSHHHHHHHHCT-SEEEEE---HHHHHHHHHHHCCTTTTSSEEEE---G.GGS-T---EEEEEEES-GGG-S-HHHHHHHH CS
  Methyltransf_9 112 sdlkgrtildvGcgnGyhlwrmvgegaklvvGidPselfliqfeavrkllgedqrahllplgi.eqlpeleafdtvfsmGvlyhrrsPldhllql 205
                     sd+ g++ildvGcg G      ++    +v  idPse  +    a+++  g+    + +  ++ e + + + fd++  m v+ h + P++ +   
      AHX11540.1  44 SDVVGKAILDVGCGGGILSEE-LSSLGGIVTAIDPSEESVK--AAMENSKGNV---TYINASLdEAVIRDKQFDIICIMEVIEHVNDPMEFVKLC 132
                     6899**********9986655.556667999*****97653..3555555543...444445515666799************************ PP

                     HCTEEEEEEEEEEEE CS
  Methyltransf_9 206 kdqlvkgGelvletl 220
                        l  gG++ + tl
      AHX11540.1 133 SGMLAPGGKIFFSTL 147
                     *********999887 PP

>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   0.0   2.8e-08     3e-05      32     158 ..      30     151 ..      24     177 .. 0.77

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.8e-08
                      HHHHHHHHHHH..--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEEEE--TTT-TTS-T-EEEEEEE CS
  Ubie_methyltran  32 hrlWkkfvekl..vavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinieflqanaeeLpfeddsfDvvtvs 123
                      h++ k  ++ +  +++  g+ +lDv +G g l+ +ls+     g v+ +D +e+ +k     ++e++k n+ +++a+  e    d+ fD++ + 
       AHX11540.1  30 HKMNKLRIQYIlsNSDVVGKAILDVGCGGGILSEELSSL---GGIVTAIDPSEESVK----AAMENSKGNVTYINASLDEAVIRDKQFDIICIM 116
                      55555544444114566799**********998888765...467889999987765....56889999************************* PP

                      S-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE---- CS
  Ubie_methyltran 124 fGlrnvtDklkaLkeayrvlkpGGrlvvlefskve 158
                        +  v D  + +k    +l pGG+++   + k +
       AHX11540.1 117 EVIEHVNDPMEFVKLCSGMLAPGGKIFFSTLNKTI 151
                      *************************9876655543 PP

>> CMAS  Mycolic acid cyclopropane synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0   2.3e-07   0.00024      54     169 ..      40     149 ..      23     165 .. 0.76

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2.3e-07
                 HHTTTT--TT-EEEEES-TTSHHHHHHHHHH--EEEEEES-HHHHHHHHHHHHTS-SSS-EEEEES-GGG-----SEEEEES-GGGTSGGGHHHHHHHH CS
        CMAS  54 ileklelkpGmtlLdiGcGWGslvrraverydvkvvglTlSkeqaklakkrvdeldlerkvevklldyedldekvdrvvsvgafehvgkenydtffkkl 152
                 il   ++  G+ +Ld+GcG G l  +  +  +  v ++  S+e  k a ++ +   +  ++  +l +    d+++d +  ++++ehv      +f+k +
  AHX11540.1  40 ILSNSDV-VGKAILDVGCGGGILS-EELSSLGGIVTAIDPSEESVKAAMENSKGNVTYINA--SLDEAVIRDKQFDIICIMEVIEHVND--PMEFVKLC 132
                 4554444.599********66555.556666999*********999988876655554444..4444444468*************975..469***** PP

                 HHHS-TT-EEEEEEEEE CS
        CMAS 153 kkllkedGllllhtits 169
                 + +l ++G +   t+ +
  AHX11540.1 133 SGMLAPGGKIFFSTLNK 149
                 ********998887765 PP

>> MetW  Methionine biosynthesis protein MetW
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.0   2.3e-07   0.00025      15      95 ..      49     129 ..      37     145 .. 0.85

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 2.3e-07
        MetW  15 srvldlGcGdGellellkeekqvdgrGleldeegvaecvakGl.sviqgdldkdlenfedksfdyvvlsqtlqatrnpkevl 95 
                   +ld+GcG G l e l    ++    ++ +ee+v+++++    +v   ++  d +  +dk+fd++ +   +  +++p e +
  AHX11540.1  49 KAILDVGCGGGILSEELSSLGGIV-TAIDPSEESVKAAMENSKgNVTYINASLDEAVIRDKQFDIICIMEVIEHVNDPMEFV 129
                 579**************8866665.68***********97543278888888888999***************999998755 PP

>> DREV  DREV methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   3.8e-07    0.0004      82     187 ..      35     145 ..      10     205 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 3.8e-07
        DREV  82 laiekespasdqedkklldlGaGdGeitkrvaptfeevyatelset.mrdrlkkkkynvlsale.lqe...tdvkldlilclnlldrcfdplklledir 175
                 l i+    +sd   k +ld+G G G +++ +++    v a + se+ ++  ++  k nv  ++  l+e    d ++d+i  +++++   dp+++++   
  AHX11540.1  35 LRIQYILSNSDVVGKAILDVGCGGGILSEELSSLGGIVTAIDPSEEsVKAAMENSKGNVTYINAsLDEaviRDKQFDIICIMEVIEHVNDPMEFVKLCS 133
                 567777789***********************9988888887775414555666666665555444441115889********************9999 PP

        DREV 176 salepngrviva 187
                  +l+p g++  +
  AHX11540.1 134 GMLAPGGKIFFS 145
                 999999998766 PP

>> TehB  Tellurite resistance protein TehB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   7.4e-07   0.00078      32     103 ..      49     117 ..      25     136 .. 0.79

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 7.4e-07
                 -EEEEES-TTSHHHHHHHHTT-EEEEEES-HHHHHHHHHHHHHTT-TTEEEEE--GGG----S-EEEEEEES CS
        TehB  32 gkvldlgcgqgrnslylsllgydvtawdknensiafleeikekenlknistalydineaklderydfilstv 103
                   +ld+gcg g  s  ls lg  vta+d  e+s++   e ++k n++ i+++l +  ++  d+++d+i    
  AHX11540.1  49 KAILDVGCGGGILSEELSSLGGIVTAIDPSEESVKAAME-NSKGNVTYINASLDE--AVIRDKQFDIICIME 117
                 3579******************************98765.578888888877543..334477888876554 PP

>> Methyltransf_PK  AdoMet dependent proline di-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.4e-06    0.0015      55     158 ..      47     143 ..      22     155 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.4e-06
  Methyltransf_PK  55 evkvaldcGaGiGrvtknlLlkllskvDlvepvekflekakeelaeekkkvgkvyvvglqeftPeegrYdliWiqWcvghLtDedlvaflkrck 148
                        k +ld+G+G G ++++ L +l + v  ++p e+ +++a     e++k    +++ +l+e +  ++++d+i i  ++ h+ D   ++f+k c 
       AHX11540.1  47 VGKAILDVGCGGGILSEE-LSSLGGIVTAIDPSEESVKAAM----ENSKGNVTYINASLDEAVIRDKQFDIICIMEVIEHVNDP--MEFVKLCS 133
                      34789******9988887.5789999999999999998887....5577888999**************************886..8******* PP

  Methyltransf_PK 149 kalkpnGliv 158
                        l+p+G i 
       AHX11540.1 134 GMLAPGGKIF 143
                      *******886 PP

>> Methyltransf_32  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.1   0.0   1.6e-05     0.017      26      82 ..      48     100 ..      27     123 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.6e-05
  Methyltransf_32  26 altvvDvGaGkgYLsfvlalkekeyklkvvgidakeelvekaekraeklgkkfnkrl 82 
                       + ++DvG+G g Ls  l++    ++  v++id +ee v++a++  +    ++n++l
       AHX11540.1  48 GKAILDVGCGGGILSEELSS----LGGIVTAIDPSEESVKAAMENSKGNVTYINASL 100
                      5789****************....69**************99987776555555555 PP

>> TPMT  Thiopurine S-methyltransferase (TPMT)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0     9e-05     0.095       9      90 ..      18      98 ..      15     118 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 9e-05
                HHHTT--TT-.-SS--HHHHHHHHT.T-S--EEEEEET-TT-HHHHHH-BTTEEEEEE-S-HHHHHHHHHHHTTSGGGGGEEE CS
        TPMT  9 rweeeqipfh.qeevnpllkkfldalkakaglrvlvPlCGkaldlvwlAeqgrevvGvelselAvekffeeanlepkvkelsg 90
                 w++ +  f+ ++++n+l  +++ +++   g+ +l  +CG+++    l++ g  v +++ se  v++++e+   + +v+++++
  AHX11540.1 18 EWHKPHGSFEmLHKMNKLRIQYILSNSDVVGKAILDVGCGGGILSEELSSLGGIVTAIDPSEESVKAAMENS--KGNVTYINA 98
                57777777773588999999**99999999999999*******************************65544..445555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       436  (0.0243181); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 1749.55
//
Query:       AHX11541.1  [L=311]
Description: 3-oxoacyl-[acyl-carrier-protein] synthase 3 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-31  108.8   1.6    2.8e-31  107.5   0.0    2.5  4  ACP_syn_III_C    3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    6.7e-28   96.4   3.2    1.5e-27   95.2   3.2    1.6  1  ACP_syn_III      3-Oxoacyl-[acyl-carrier-protein (ACP)] synth
    1.1e-06   28.2   0.3    1.9e-06   27.4   0.3    1.4  1  Thiolase_N       Thiolase, N-terminal domain
     0.0012   18.9   0.1      0.003   17.6   0.1    1.6  2  Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal 
     0.0017   17.8   1.1     0.0034   16.9   1.1    1.5  1  Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal 
  ------ inclusion threshold ------
      0.045   13.3   0.1      0.078   12.5   0.1    1.4  1  Diphthami_syn_2  Diphthamide synthase


Domain annotation for each model (and alignments):
>> ACP_syn_III_C  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       2.4   7.2e+03       6      17 ..      69      80 ..      67      95 .. 0.75
   2 ?   -2.1   0.1       1.5   4.5e+03      72      88 ..     112     128 ..      83     130 .. 0.80
   3 ?   -2.6   0.0       2.2   6.6e+03      67      83 ..     151     167 ..     143     170 .. 0.76
   4 !  107.5   0.0   9.4e-35   2.8e-31       4      90 .]     225     311 .]     222     311 .] 0.97

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 2.4
                   --GGG-SEEEE- CS
  ACP_syn_III_C  6 ltpedidalvph 17
                   +++edida+v  
     AHX11541.1 69 FSVEDIDAIVVA 80
                   678999998865 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.5
                    EEEEEEETTTEEEEEEE CS
  ACP_syn_III_C  72 vllvgfGaGltwgaall 88 
                    ++ +gf  Gl++ +a++
     AHX11541.1 112 AACSGFLYGLSIVSAMV 128
                    56678888888888876 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 2.2
                    -TT-EEEEEEEETTTEE CS
  ACP_syn_III_C  67 kpgdlvllvgfGaGltw 83 
                    k+ ++++l+g GaG   
     AHX11541.1 151 KDRNTCILFGDGAGAAL 167
                    66778899999999765 PP

  == domain 4  score: 107.5 bits;  conditional E-value: 9.4e-35
                    TT--GGG-SEEEE-SSSHHHHHHHHHHHT--GGGB--THHHH-B-GGGHHHHHHHHHHHTTSS-TT-EEEEEEEETTTEEEEEEEE- CS
  ACP_syn_III_C   4 agltpedidalvphqanlriidavakklglpeekvvvnldeyGntsaasiplaLdeaveegklkpgdlvllvgfGaGltwgaallrw 90 
                    +g+++++id++v+hqan+riid v +k+g+++ kv+v++d+y+ntsaasip++Ld++ +e+ lk+gd++ll+++G+G+t+g +++++
     AHX11541.1 225 SGISAQEIDYFVMHQANIRIIDLVSEKIGIDPYKVIVTVDKYANTSAASIPITLDHLNNEKILKKGDKLLLTAMGGGFTYGVMIVEY 311
                    799*********************************************************************************985 PP

>> ACP_syn_III  3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   95.2   3.2   5.1e-31   1.5e-27       1      68 [.     108     175 ..     108     185 .. 0.93

  Alignments for each domain:
  == domain 1  score: 95.2 bits;  conditional E-value: 5.1e-31
                  EEEE-GGGHHHHHHHHHHHHHHTTS-SEEEEEEEEEGGGCS-TTTHHHHTTB-EEEEEEEEEEESSSS CS
  ACP_syn_III   1 fDlnaaCsgfvyalsvAdaliesgaakrvLvigaetlskilDwkdrstavlfGDGAgAvvleaseeeg 68 
                  fD+naaCsgf+y+ls+++a++++g++++vL++ga+++s+i+Dwkdr+t++lfGDGAgA++++a+e  g
   AHX11541.1 108 FDINAACSGFLYGLSIVSAMVAAGKVSKVLLVGADAMSSIVDWKDRNTCILFGDGAGAALISAGEVGG 175
                  9**************************************************************87555 PP

>> Thiolase_N  Thiolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.4   0.3   6.5e-10   1.9e-06      17     123 ..      45     152 ..      35     196 .. 0.86

  Alignments for each domain:
  == domain 1  score: 27.4 bits;  conditional E-value: 6.5e-10
                 TTTTS-HHHHHHHHHHHHHHHHT.S-GGGCCEEEEEHSSCTTSTSCHHHHHHHHTTS-TTSEEEEEEHGGGHHHHHHHHHHHHHHTTSHSEEEEEEEEE CS
  Thiolase_N  17 slkdlsaeeLlaealkallekag.vdpeevdevivGnvlqagegqniarqaalkagipeevpavtvnkvcsSglkavalaaqsiaageadvvvagGvEs 114
                  + +  +++L+ +a  ++l+ ++  + e++d ++v++  ++    ++a+ ++ k+ i +++ +  +n +cs  l ++  +  ++aag+++ v+++G+  
  AHX11541.1  45 IVDEEDVSDLALNASLKCLNGVQdFSVEDIDAIVVATCTASKRIPAVANILQGKLSIKRQILSFDINAACSGFLYGLSIVSAMVAAGKVSKVLLVGADA 143
                 5566778899999999999999999************************************************************************** PP

                 STTS-EEET CS
  Thiolase_N 115 msnaptaes 123
                 ms     ++
  AHX11541.1 144 MSSIVDWKD 152
                 **8765555 PP

>> Chal_sti_synt_C  Chalcone and stilbene synthases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0       1.7     5e+03      81     107 ..      93     119 ..      82     130 .. 0.65
   2 !   17.6   0.1     1e-06     0.003      33     144 ..     205     306 ..     191     310 .. 0.78

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1.7
  Chal_sti_synt_C  81 klekekleasrkvlseyGnvssatvly 107
                      ++ + kl + r++ls   n + +  ly
       AHX11541.1  93 NILQGKLSIKRQILSFDINAACSGFLY 119
                      444567777777777666665555555 PP

  == domain 2  score: 17.6 bits;  conditional E-value: 1e-06
  Chal_sti_synt_C  33 dlPekieenieeflkklleklGieefndlfwivhPGGpaildrleaklklekekleasrkvlseyGnvssatvlyvldelrdkelkkklattge 126
                       + e   +++   ++k+++  Gi+  +  ++++h     i+d + +k+++++ k+ ++   + +y n s+a++   ld+l ++++ kk ++   
       AHX11541.1 205 KVFEAAVKKLTTEINKAFDVSGISAQEIDYFVMHQANIRIIDLVSEKIGIDPYKVIVT---VDKYANTSAASIPITLDHLNNEKILKKGDKL-- 293
                      4555556667777899********9999999***********************9987...679****************996655554433.. PP

  Chal_sti_synt_C 127 gkewGlllafGPGltiet 144
                           ll a+G G+t   
       AHX11541.1 294 -----LLTAMGGGFTYGV 306
                      .....4444555544444 PP

>> Chal_sti_synt_N  Chalcone and stilbene synthases, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.9   1.1   1.1e-06    0.0034      86     224 ..      38     171 ..      22     172 .. 0.83

  Alignments for each domain:
  == domain 1  score: 16.9 bits;  conditional E-value: 1.1e-06
  Chal_sti_synt_N  86 psldarleivnaevlklgkeaalkalkewGr.Pkskithlvfvs.ssevelPGadlklakklGlrpsvkrvmlyflGcygGatvlrlakdiaen 177
                      + +++r  +  ++v +l+ +a+lk+l+      +++i  +v  + ++  ++P     l  kl ++ ++  + +    c+g   +l +   +   
       AHX11541.1  38 TGIKTRYIVDEEDVSDLALNASLKCLNGVQDfSVEDIDAIVVATcTASKRIPAVANILQGKLSIKRQILSFDI-NAACSGFLYGLSIVSAMVAA 130
                      678899999999**************987543789**9998765256789************99999998887.578***************** PP

  Chal_sti_synt_N 178 nkGarvlvvaseitvlgfrgPskdrlddlvGaalfGdGaaaviiGad 224
                       k ++vl+v ++   ++     kdr        lfGdGa a++i a+
       AHX11541.1 131 GKVSKVLLVGADA--MSSIVDWKDR----NTCILFGDGAGAALISAG 171
                      *********9985..3333333444....45679*********9875 PP

>> Diphthami_syn_2  Diphthamide synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   2.6e-05     0.078      24      67 ..     218     262 ..     200     290 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 2.6e-05
  Diphthami_syn_2  24 sevesLvs.visenkesymfhvvnvhlvellaesvGiplikleta 67 
                      ++  + vs +  ++ + + +h  n+++++l++e +Gi+  k  ++
       AHX11541.1 218 INKAFDVSgISAQEIDYFVMHQANIRIIDLVSEKIGIDPYKVIVT 262
                      45555554145556678899*****************98887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       599  (0.0334096); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.26s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2357.53
//
Query:       AHX11542.1  [L=342]
Description: fatty acid/phospholipid synthesis protein PlsX [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.5e-91  305.0   0.8    6.3e-91  304.8   0.8    1.0  1  FA_synthesis  Fatty acid synthesis protein


Domain annotation for each model (and alignments):
>> FA_synthesis  Fatty acid synthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  304.8   0.8   3.5e-95   6.3e-91       3     321 ..       7     331 ..       5     333 .. 0.96

  Alignments for each domain:
  == domain 1  score: 304.8 bits;  conditional E-value: 3.5e-95
                   EEEESS-STTTTHHHHHHHHHHHHH-.TTEEEEEEE-HHHHHTT--S....--TT.EEEEE--B---TTS-HHHHHHH-TTBHHHHHHHHHHTTS-S CS
  FA_synthesis   3 iavdamGgdhgpeevvkgvelaakea.ddleivlvGdkeeiepllkk..eeeakskleivhaedviemeekpvaavrkkkdssmavalelvkegead 96 
                   +a+d+mGgd +p e++ g+++ +    d + + l+Gd   +e +l++  +  + ++ ei+h++d++++++kp+ avr  k+ssm++a++ v+e    
    AHX11542.1   7 VALDVMGGDNAPDEIIFGASRYLMRHpDSVFFRLFGDGPSLERCLSHslNLVLLKNSEIIHTDDIVSSNDKPSLAVRGRKGSSMYRAVQDVREMISH 103
                   89*******************987661557888**************7777788999**************************************** PP

                   EEEE-S-HHHHHHHHHHCT-B-TT-SS-EEE-EE--TTS-EEEE-SSS-TT--HHHHHHHHHHHHHHHHHTS--SS-EEEEEESSSSTT-SSHHHHH CS
  FA_synthesis  97 alvsaGntgAlmalallrlgrikgierpalavllPtvsgktvlLDvganvdckpkeLvqfalmGsvyaesvlgvdsprvglLniGeeevkgndlvkq 193
                    +vsaGntgA m+ +++ lg+++ i rpa++++lP+++g++v+LD+gan +c ++ L qfa mG ++a+ +lg ++p v+lLniG ee+kg+d +k+
    AHX11542.1 104 CVVSAGNTGAFMGISKILLGMLDDIYRPAIVTTLPSKKGEVVVLDLGANLECSSEVLYQFAFMGAAFAKAALGTENPSVALLNIGVEENKGTDAIKE 200
                   ************************************************************************************************* PP

                   HHHHHHT-T...TSEEEEEEEGGGCCCTS-SEEE--HHHHHHHHHHHHHHHHHHHHHHHHHHTTT----------HHCHHHHHHHH-GGGC--EEEE CS
  FA_synthesis 194 tfellkaie...sieflGnvegrdildgkvdvivcdgftgNvilktaegvakavksllkeelkkslasklgalllskalkrlkkkldykeyggavll 287
                   +f++lk+ +      f G++e  d+l g+vdv+v dgftgN++lktaeg+ + +k+ + ++ k+s++s+++  +lsk+lk   +k++++  +ga+l+
    AHX11542.1 201 AFHMLKEKSeasRFDFRGYIEPADMLGGNVDVVVSDGFTGNIMLKTAEGIYHLIKEGIVSATKASFLSRIAGCILSKNLKGSMAKFNPDLRNGAMLI 297
                   ******987665789********************************************************************************** PP

                   TBSS-EEE--TT--HHHHHHHHHHHHHHHHTTHH CS
  FA_synthesis 288 GlkgvvikshgkankkaikaaIrqakelvetqvi 321
                   Gl+g  +k+hg+++ +a+ +aI +a++lve++ +
    AHX11542.1 298 GLNGIAVKAHGSSDRNAFSNAIMVAANLVENDLN 331
                   ******************************9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       304  (0.0169558); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.47u 0.21s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2543.92
//
Query:       AHX11543.1  [L=853]
Description: hypothetical protein NHE_0608 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (853 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       662  (0.0369234); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.67u 0.30s 00:00:00.97 Elapsed: 00:00:00.43
# Mc/sec: 5905.94
//
Query:       AHX11544.1  [L=172]
Description: NADH-quinone oxidoreductase, E subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.3e-59  200.2   0.0    1.5e-59  200.0   0.0    1.0  1  2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin


Domain annotation for each model (and alignments):
>> 2Fe-2S_thioredx  Thioredoxin-like [2Fe-2S] ferredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  200.0   0.0   8.2e-64   1.5e-59       1     145 []      25     172 .]      25     172 .] 0.98

  Alignments for each domain:
  == domain 1  score: 200.0 bits;  conditional E-value: 8.2e-64
                      HHHHHTTS-..-GGGGHHHHHHHHHHH.HSS--HHHHHHHHHHHTS-HHHHHHHHTTSSSS-SS---SEEEEEE-SHHHHTTTHHHHHHHHHHH CS
  2Fe-2S_thioredx   1 ikeiiakyp..ekrsaliplLklvQee.egwlpeealeevaellgvppaevyevatFYsmfnlkpvgkyviqvCtttpCalrgseeilealekk 91 
                      +++i+a+yp  +krsa++plL+lvQe+ e+w+p +a++++a+ll++p+++vyeva+FYsmfn++pvgky iqvC+ttpC+lrg+++i +a+ k+
       AHX11544.1  25 VEQILARYPssHKRSAVLPLLHLVQEQnENWIPIAAMDYIAQLLDMPVIRVYEVASFYSMFNTAPVGKYLIQVCRTTPCWLRGADRICNAIAKE 118
                      589************************889**************************************************************** PP

                      HT--TT-B-TTSSEEEEEES--S-GGGSSEEEESSSSEEES-HHHHHHHHHHHH CS
  2Fe-2S_thioredx  92 lgikagettadgkftleeveClGaCanaPvvqindevyedltpekveeileklk 145
                      l i++g+ t+dgkf+l eveClGaC+naPv+qin++++e+l++++v ++++klk
       AHX11544.1 119 LSIRVGQSTEDGKFSLVEVECLGACVNAPVIQINNDYFEELDEKSVIRLISKLK 172
                      **************************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (172 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       380  (0.0211947); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 1270.69
//
Query:       AHX11545.1  [L=460]
Description: phosphotransferase enzyme family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-28   99.0   0.1    3.6e-28   98.1   0.1    1.4  1  ABC1      ABC1 family
    3.7e-05   23.8   0.0    5.2e-05   23.3   0.0    1.3  1  APH       Phosphotransferase enzyme family
    0.00016   21.1   0.1    0.00032   20.1   0.0    1.5  2  Pkinase   Protein kinase domain


Domain annotation for each model (and alignments):
>> ABC1  ABC1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.1   6.1e-32   3.6e-28       2     118 ..      85     200 ..      84     201 .. 0.97

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 6.1e-32
        ABC1   2 elgkkleeiFaefdeePiAaASiaqVhrAklksgeeVavKvqrpgvkkriksDlellkllakllkkflkelrldleelvdefskslleEldferEAkna 100
                 e+++k+e++F+ ++eeP+A+ASiaq+h+A++ sg+ Va+Kv +p+++k +k+D+++  ++a++++ fl++ + +l  +++ f+ s+  Eld++ EA++ 
  AHX11545.1  85 EFSSKVEDLFSWISEEPVASASIAQIHKATTLSGDVVAIKVLKPNIEKIFKRDIRIAFFVARIFSCFLSKRF-NLIPILKRFTASVNCELDLKMEAASL 182
                 7899*************************************************************9998888.8************************* PP

        ABC1 101 ekfrenfaklkevkvPkv 118
                 +++r+n + ++ev +P+v
  AHX11545.1 183 SEMRDNSRYDTEVIMPRV 200
                 ****************99 PP

>> APH  Phosphotransferase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.3   0.0   8.8e-09   5.2e-05     165     197 ..     244     274 ..     162     277 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.3 bits;  conditional E-value: 8.8e-09
                 -EEEE-SS-SGGGEEEC..TTEEEEE---TT-E CS
         APH 165 ptvllHgDlhpgNllvdpddgrvtGviDfedag 197
                 + ++ HgD+hpgN+ v+p+ ++v G++Df+ +g
  AHX11545.1 244 RNGFFHGDIHPGNIFVTPG-NKV-GLVDFGIVG 274
                 67899************66.776.*****9776 PP

>> Pkinase  Protein kinase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.1   0.0       1.4   8.1e+03      16      34 ..     111     128 ..     106     134 .. 0.73
   2 !   20.1   0.0   5.4e-08   0.00032     111     153 ..     239     281 ..     189     307 .. 0.86

  Alignments for each domain:
  == domain 1  score: -4.1 bits;  conditional E-value: 1.4
                 EEEEETTTTEEEEEEEEEC CS
     Pkinase  16 ykaveketgkivAvKkikk 34 
                  ka+ + +g+ vA+K++k 
  AHX11545.1 111 HKAT-TLSGDVVAIKVLKP 128
                 5555.57889999999985 PP

  == domain 2  score: 20.1 bits;  conditional E-value: 5.4e-08
                 HHHHHHTTEE-SS-SGGGEEEETTTEEEE-SGTTSEESSSSCS CS
     Pkinase 111 leylHskgiiHrDlKpeNiLidekgelKitDFGlakelesssk 153
                 ++ ++++g++H D+ p Ni++   +++ ++DFG++ ++++++k
  AHX11545.1 239 FKQVYRNGFFHGDIHPGNIFVTPGNKVGLVDFGIVGRIDKKTK 281
                 567899****************9999***********999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (460 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       473  (0.0263818); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.27s 00:00:00.80 Elapsed: 00:00:00.44
# Mc/sec: 3123.42
//
Query:       AHX11546.1  [L=196]
Description: hypothetical protein NHE_0611 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
  ------ inclusion threshold ------
        0.1   12.8   0.1       0.15   12.2   0.1    1.3  1  Rhabdo_NV  Rhabdovirus Non-virion protein


Domain annotation for each model (and alignments):
>> Rhabdo_NV  Rhabdovirus Non-virion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   8.3e-06      0.15      12      74 ..     115     180 ..     103     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 8.3e-06
   Rhabdo_NV  12 alrealryknevaghgfsfddgdlvwr...eeddatwrrlcdvvnalisskrmqrvlymdlsitkg 74 
                 a +   r kn  a + f + dgd+ w    e+d+ + + +   + a++ +k  +    +dl   kg
  AHX11546.1 115 AKKGECRVKNPSASYVFDVLDGDIAWLknvEDDENAIKSMKSDIYAVVVAKSRKGTCSLDLYSLKG 180
                 4556789*******************5333566777888888888888888888888888877776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      457  (0.0254894); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1540.21
//
Query:       AHX11547.1  [L=105]
Description: bacterial DNA-binding family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-18   66.4   0.8    2.4e-18   66.1   0.8    1.1  1  Bac_DNA_binding  Bacterial DNA-binding protein
    1.7e-07   31.3   0.0    2.2e-07   31.0   0.0    1.1  1  HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1
    2.2e-06   27.8   0.2    2.6e-06   27.6   0.2    1.0  1  HU-HIG           HU domain fused to wHTH, Ig, or Glycine-rich
    0.00011   22.0   0.0    0.00016   21.5   0.0    1.3  1  HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
    0.00011   22.3   0.0    0.00016   21.7   0.0    1.4  1  HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
  ------ inclusion threshold ------
      0.023   14.6   0.4      0.029   14.3   0.4    1.1  1  DUF2987          Protein of unknown function (DUF2987)
      0.044   13.3   0.1      0.044   13.3   0.1    1.1  1  NA37             37-kD nucleoid-associated bacterial protein


Domain annotation for each model (and alignments):
>> Bac_DNA_binding  Bacterial DNA-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.1   0.8   9.5e-22   2.4e-18       4      88 ..      16     100 ..      13     102 .. 0.96

  Alignments for each domain:
  == domain 1  score: 66.1 bits;  conditional E-value: 9.5e-22
                      HHHHHHHHTT----HHHHHHHHHHHHHHHHHHHHTT-EEEETTTEEEEEEEE--BS-B-TTT--B--B--EEEEEEEE-HHHHHH CS
  Bac_DNA_binding   4 keLieeiaektgltkkdakrvveafldtikeaLkkgekvelsgFGtfkvkerkartgrnpkTgekvkiparkvvkFkpskelkea 88 
                       +Li+ +ae + + k +ak +++a+ + i ++Lkk++++++++ Gt++v+++ka t  +pkT+++vk +++ ++kF++s+ +k  
       AHX11547.1  16 VDLINIVAEGASIPKGQAKHAINALYEYIYDSLKKKKSIRIPKVGTLSVVKKKATTYCDPKTKQMVKQAETERIKFTISSVIKGD 100
                      59****************************************************************************9988865 PP

>> HU-CCDC81_euk_1  CCDC81 eukaryotic HU domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.0   0.0   8.4e-11   2.2e-07      20      85 ..      29      96 ..      22     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 31.0 bits;  conditional E-value: 8.4e-11
  HU-CCDC81_euk_1 20 tteqllliWdalgeyieeqlekgkgvhipnfGtFtfeapdldlkadknellrdkklr..rPvFvvdek 85
                     ++ q + +++al eyi++ l+k+k++ ip+ Gt ++ +++ ++++d +++++ k+ +  r  F ++  
       AHX11547.1 29 PKGQAKHAINALYEYIYDSLKKKKSIRIPKVGTLSVVKKKATTYCDPKTKQMVKQAEteRIKFTISSV 96
                     56788899*************************************99999988888877888887765 PP

>> HU-HIG  HU domain fused to wHTH, Ig, or Glycine-rich motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.2     1e-09   2.6e-06      29     120 ..      10     103 ..       6     105 .] 0.88

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1e-09
      HU-HIG  29 kgtvdfeeLceeiskrstlsrgdvkavldaledelkeaLadGerVeLgelGyFslslks.kgved.ekevransikkkkinfrpgkklkkelkk 120
                 k+ v+  +L++ +++  ++++g+ k ++ al + + ++L++ ++++++++G++s+  k  ++  d + +   ++ + ++i+f++++ +k  lk+
  AHX11547.1  10 KEVVKSVDLINIVAEGASIPKGQAKHAINALYEYIYDSLKKKKSIRIPKVGTLSVVKKKaTTYCDpKTKQMVKQAETERIKFTISSVIKGDLKS 103
                 666788899*********************************************99988544444377778999999************99997 PP

>> HU-CCDC81_bac_2  CCDC81-like prokaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.0   6.1e-08   0.00016       3      53 ..      18      68 ..      18      84 .. 0.93

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 6.1e-08
  HU-CCDC81_bac_2  3 LansiaeaegisyeeAlqkiekeveelkqeLeeegrveleniGeLslneeg 53
                     L+n +ae   i+  +A ++i+   e + + L++++++ ++++G+Ls+ +++
       AHX11547.1 18 LINIVAEGASIPKGQAKHAINALYEYIYDSLKKKKSIRIPKVGTLSVVKKK 68
                     899******************************************987665 PP

>> HU-CCDC81_euk_2  CCDC81 eukaryotic HU domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   6.3e-08   0.00016      10      67 ..      22      77 ..      12      85 .. 0.87

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.3e-08
  HU-CCDC81_euk_2 10 laaaaglsrdvVescvqetfqalgdllrngknvelefkgiGvLsirnrkvkmkFyesf 67
                     +a  a++++ +++++++++   + d l+++k++++  + +G+Ls+ ++k++   +++ 
       AHX11547.1 22 VAEGASIPKGQAKHAINALYEYIYDSLKKKKSIRI--PKVGTLSVVKKKATTYCDPKT 77
                     7888***************************9886..67********99998888775 PP

>> DUF2987  Protein of unknown function (DUF2987)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.4   1.2e-05     0.029       5      61 ..      37      92 ..      33      97 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 1.2e-05
     DUF2987  5 leleYsgfYsrlkkvnkedyelvelafylkdketkelCkiekaeietekkeepltvt 61
                ++  Y+  Y+ lkk +    ++v +   +k+k t + C  +  +++++ ++e +++t
  AHX11547.1 37 INALYEYIYDSLKKKKSIRIPKVGTLSVVKKKAT-TYCDPKTKQMVKQAETERIKFT 92
                66679******************98665555555.*****************99987 PP

>> NA37  37-kD nucleoid-associated bacterial protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.1   1.7e-05     0.044     185     250 ..       9      84 ..       1     103 [. 0.65

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.7e-05
        NA37 185 tkkllkave...dfakkeeldkaekqelrkrvveylkeqleegesvdleel......aeelfkdnpee.....kefvkee 250
                 tk+++k v+    +a+    +k +++ + ++++ey+++ l+ ++s+++ ++           k+ ++      k+ vk++
  AHX11547.1   9 TKEVVKSVDlinIVAEGASIPKGQAKHAINALYEYIYDSLKKKKSIRIPKVgtlsvvK----KKATTYcdpktKQMVKQA 84 
                 5555555541104556666789*****************************8755531....222222322345555553 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (105 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 786.78
//
Query:       AHX11548.1  [L=242]
Description: DNA-binding regulatory, YebC/PmpR family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-73  247.4   0.2    1.5e-73  247.2   0.2    1.0  1  Transcrip_reg  Transcriptional regulator
  ------ inclusion threshold ------
      0.066   14.2   0.1       0.25   12.3   0.1    2.0  2  Rotamase       PPIC-type PPIASE domain
      0.093   13.1   0.1       0.25   11.7   0.0    1.8  2  YcgL           YcgL domain


Domain annotation for each model (and alignments):
>> Transcrip_reg  Transcriptional regulator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  247.2   0.2   2.4e-77   1.5e-73       1     239 [.       5     237 ..       5     238 .. 0.95

  Alignments for each domain:
  == domain 1  score: 247.2 bits;  conditional E-value: 2.4e-77
                    .XCHHCCCCCCHCCCCHHHHHHHHHHHHHHHHHTHH-S-GGG-HHHHHHHHHHHHTT--HHHHHHHHHHCCSTS.TS.--EEEEEEEEE.....TT CS
  Transcrip_reg   1 skWsnikhkKaandakkgklftklakeItvaakeeggpDpesNprLraaiekakkanvpkdnIeraIkkgagekseganyeevtyegyg.....pg 91 
                    s+++nikh+K+a+dakk+k ftkl +e++vaa++ g pDp+ NprLr+a+++a+++++pkd+Ie+a k ++++ +++++y+e++y + g     p+
     AHX11548.1   5 SQYANIKHRKGAQDAKKAKKFTKLRRELVVAARS-GIPDPAFNPRLRSALANARRQGLPKDKIEAAFKSASNK-TDADDYQEIYYMASGsgemwPN 98 
                    78*******************************6.99**********************************96.57789*******9997777788 PP

                    TEEEEEEEEES-HHHHHHHHHHHHHHTT-EEE-TTSSGGGEEEEEEEEEECCHCT-HHHHHHHHHHHHTESEEEEETTTC.EEEEEEGGGHHHHHH CS
  Transcrip_reg  92 gvavivealTdnknrtaaevrsifsknggnlgesgsvsflFerkgvivveekeeevdedelleaaieaGaeDveedeeeevievitepedlaavkk 187
                    g++v+v+alT+nknrta+evr+i+sk+g  +   +  sf+F+r g++++ ++  +vd d+l+e a+e+Ga Dv++  e++ ++v+ + ed++++++
     AHX11548.1  99 GISVVVDALTNNKNRTASEVRHILSKFGFVF---AELSFMFDRLGLFSY-AE--SVDLDRLIEFALEIGALDVKK--ENKRHNVYSNKEDFSRIAD 186
                    *******************************...89*************.54..6*******************9..557899************* PP

                    HHHHTTT---SEEEEEEEESS-EE--HHHHHHHHHHHHHHHTSTTEEEEEES CS
  Transcrip_reg 188 aLeeagglevesaeleyipkeeveldeeeaekleklidaLeeldDVqnvytN 239
                    +L+++ + ++e ++l+++pk++  +++e +++lek+++aLee+dDVqnvyt 
     AHX11548.1 187 ELSKE-FGDCEYSGLVWVPKSPQIASKEVQQNLEKMLEALEENDDVQNVYTS 237
                    **988.4579**********998889************************97 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.84     5e+03      50      50 ..      79      79 ..      49     125 .. 0.58
   2 ?   12.3   0.1   4.2e-05      0.25      27      87 ..     172     237 ..     162     241 .. 0.77

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.84
                H CS
    Rotamase 50 a 50
                a
  AHX11548.1 79 A 79
                2 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 4.2e-05
                 CCTCCCHHHHHHHHCCC-.-CHHHCCTTEEEC.....EETTTS-CCCHHHHCCS-CT-B-S-EEET CS
    Rotamase  27 eqlksgedtFeelArkySddknsakngGdlgw.....vekgqlppefekaafslkkGeisepvetk 87 
                  ++ s++++F+++A + S++ +  +  G +       ++++++++++ek++++l++++ ++ v t+
  AHX11548.1 172 HNVYSNKEDFSRIADELSKEFGDCEYSGLVWVpkspqIASKEVQQNLEKMLEALEENDDVQNVYTS 237
                 556677777*********99887777776542333446666***************9988888776 PP

>> YcgL  YcgL domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.8   0.0         3   1.8e+04      54      67 ..     114     127 ..     111     128 .. 0.74
   2 ?   11.7   0.0   4.2e-05      0.25       7      61 ..     169     220 ..     164     229 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.8 bits;  conditional E-value: 3
        YcgL  54 daekVlaaLeeqGf 67 
                 +a++V++ L++ Gf
  AHX11548.1 114 TASEVRHILSKFGF 127
                 56788888888887 PP

  == domain 2  score: 11.7 bits;  conditional E-value: 4.2e-05
        YcgL   7 skkeetYLYvekkddfsevPeeLlesfGkpefvmeleLskerkLaradaekVlaa 61 
                 +k++++Y   ++k+dfs++ +eL ++fG+ e    + + k+ ++a++++++ l++
  AHX11548.1 169 NKRHNVY---SNKEDFSRIADELSKEFGDCEYSGLVWVPKSPQIASKEVQQNLEK 220
                 5555555...678*******************99999999999998877654443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (242 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1138  (0.0634726); expected 358.6 (0.02)
Passed bias filter:                      786  (0.0438396); expected 358.6 (0.02)
Passed Vit filter:                        69  (0.00384851); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.26s 00:00:00.73 Elapsed: 00:00:00.41
# Mc/sec: 1785.41
//
Query:       AHX11549.1  [L=548]
Description: chaperonin GroL [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.5e-89  300.9  19.1    2.2e-89  300.3  19.1    1.3  1  Cpn60_TCP1  TCP-1/cpn60 chaperonin family
     0.0047   16.3   3.2     0.0063   15.8   0.9    1.9  2  TraH        Conjugative relaxosome accessory transposon prote


Domain annotation for each model (and alignments):
>> Cpn60_TCP1  TCP-1/cpn60 chaperonin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  300.3  19.1   2.5e-93   2.2e-89       5     489 ..      26     525 ..      22     527 .. 0.93

  Alignments for each domain:
  == domain 1  score: 300.3 bits;  conditional E-value: 2.5e-93
                 HHCCSSTTXXEEEEEETTSEEEEEXSHHHHHHCSXXXSHH....HHHHHHHHHHCCCCCTTCHHHHHHHHHHHHHHHHHHHHCTXXHHHHHHHHHHHHH CS
  Cpn60_TCP1   5 vkttlGPkGmdKmlvnkggkvvvTnDGatilkeleiehPa....akllveaaesqdeevGDGTttvviLageLleeaekliaagvhpttiiegyekale 99 
                   +tlGP G+ ++  +++g + vT+DG ++++ l+ e+      ++ll +a ++ +e++GDGTtt+++L+g+++++a+k+iaa     +++ g+++a++
  AHX11549.1  26 AGVTLGPEGRPVIMSKSYGGPEVTKDGYKVINALKPEDEKvakiVELLNQATSQANEKAGDGTTTATMLVGNMIKNAHKHIAAQRSRMKLKAGMKRARD 124
                 578*********************************9876666688999************************************************** PP

                 HHHHHHHHHXEEBXSCSTT.HHHHHHHHHHCTTSSXXSTHHHHHHHHHHHHHCHCCCSEECSCCCEECCCCEECEC...TTSEEESEEEESS--SST.. CS
  Cpn60_TCP1 100 kaleaLkeiaveisseekdreeLlkvartslsskltskeaeelsklvvdAvklieenekeldlgrikvvkieggsl...edselveGlvldkgvlsp.. 193
                 ++++++++ia++i+se    ee+++va++s++++       e+++ +++A+          ++g+ +v+++e+g+     + ++v+G+v+d+g++sp  
  AHX11549.1 125 AVVKHIQSIAKKIDSE----EEIAQVASISANGN------SEIGNKIAEAM---------NKVGKEGVITVEEGKGleeFSVSVVKGMVFDRGYVSPyf 204
                 **************99....9*************......99*********.........799********99998743445667************** PP

                 .....TSSCEEECEEEEEESS-BS--HHCCHHHCCCCSCCHHHHHHHHHHHHHHHHHHHHHHTTECEEEESS-B-HHHHHHHHHCT-EEE-S-...... CS
  Cpn60_TCP1 194 .....dmpkklenakvllldvsLeiektetkttvvlsdaeeleklekaeekqleellekiiksgvnvvvcqkgiddlalhflakngilalrrv...... 281
                      +m  +++n+++l+ +++L+  ++                        +  lle i++s++ vv+++++++ +al+ l+ +++++  ++      
  AHX11549.1 205 itnseKMIVEFDNPYILIANKKLSSIQP------------------------MVSLLETIVRSNRAVVIIAEDVEGEALTSLVLSKMRGSLKAcavkap 279
                 **887788888*****************........................***************************************999***** PP

                 .....-HHHHHHHHHHHT--EBSCG......GGGGCGC-EEEEEEEECCETTCCEEEEE...................................CESSS CS
  Cpn60_TCP1 282 .....kkkdlerlakatGatavssl......edltpeelGtakkveeekigsekttiie...................................evksg 334
                      + ++le++ ++tGa+ + s       e+lt e+lGtak++    i++++tti++                                     + g
  AHX11549.1 280 gfgdrRAEMLEDIRILTGARSLVSDdigvtvESLTVEDLGTAKSI---IISKDSTTIVDgngskdaisarvnqiktqiekttsdydkeklqerlAKLAG 375
                 ****999*************8888779******************...***********88888888887777777776666666655555544239** PP

                 SXEEEEEEESTCCCHHHHHHHHHHHHHHHHHHHHHHEEEETTTCHHHHHHHHHHCCCCTSXCCHHHHHHHHHHHHTHHHHHHHHHCTSXHHHHHHHHHH CS
  Cpn60_TCP1 335 kiatillrgatdtvldeieraiedAlnvvknaiedekvvpGGGatelelakklkeyaksvsgeeqlaieafakALevipktLaeNaGldpievlaklra 433
                 ++a+++++gat+++++e+++++edAl+++++a+e e++vpGGGat+l + k l e+ +s++++eq +i++++ AL++++ ++ eNaG d+  ++ +l++
  AHX11549.1 376 GVAVLKVGGATEVEVKERKDRVEDALHATRAAVE-EGIVPGGGATLLNAIKVL-EELSSDDDDEQAGINIVKAALKAPISQIVENAGEDASVIVHNLLE 472
                 **********************************.******************.888999*************************************** PP

                 HHHTTXTTEEEETTTTCEEECCCCTXEEEHHHHHHHHHHHHHHHHHHHCEEEEEXX CS
  Cpn60_TCP1 434 ahnkgekelgidvesgeiidlveagvvDplkvkrqalksAteaastiLrideiika 489
                    +++++  +d+++ +++d+++ag++Dp+kv+r al+sA+++as + ++++ i++
  AHX11549.1 473 ---SKDINRIFDARKLQYVDAFKAGIIDPAKVVRVALESAVSVASVLVTTEALIVD 525
                 ...566699*******************************************9987 PP

>> TraH  Conjugative relaxosome accessory transposon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.9     7e-07    0.0063      86     220 ..      52     189 ..      49     200 .. 0.80
   2 ?    0.1   0.0     0.042   3.8e+02     174     234 ..     333     387 ..     295     516 .. 0.60

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 7e-07
        TraH  86 gyaFqlALqtlspqlgkvikklqakaqalnqlqinsCeaAqglvkglapekktkakqsiceeagsksglfsdvaearsecstegqadsvlakassdpal 184
                 gy +  AL+  +++++k+++ l++++++ n+   +  ++A+ lv+++ +     a ++i+++  s ++l +++ +ar  + +   ++s+++k +s++++
  AHX11549.1  52 GYKVINALKPEDEKVAKIVELLNQATSQANEKAGDGTTTATMLVGNMIK----NAHKHIAAQ-RSRMKLKAGMKRARDAVVK--HIQSIAKKIDSEEEI 143
                 7777889999***********************************7775....455555444.677888999*******988..689999999888888 PP

        TraH 185 kdqgevvee.....gnlvwkalkkkglt.....sgdkelaellmsl 220
                 ++ +++  +     gn + +a++k g       +  k l+e+  s+
  AHX11549.1 144 AQVASISANgnseiGNKIAEAMNKVGKEgvitvEEGKGLEEFSVSV 189
                 8887777755688999999999998877666665556666666665 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.042
        TraH 174 vlakassdpalkdqgevveegnlvwkalkkkgltsgdkelaellmslvGtviikenaadgk 234
                 + + +      kd   +  + n +   ++k+++   +++l+e l  l G v + + +  ++
  AHX11549.1 333 IVDGN----GSKDA--ISARVNQIKTQIEKTTSDYDKEKLQERLAKLAGGVAVLKVGGATE 387
                 32222....22333..444467777777777776555667777777777777743333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (548 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1052  (0.0586759); expected 358.6 (0.02)
Passed bias filter:                      534  (0.0297841); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.44
# Mc/sec: 3741.23
//
Query:       AHX11550.1  [L=98]
Description: 10 kDa chaperonin [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.2e-30  104.5   1.0    2.4e-30  104.4   1.0    1.0  1  Cpn10     Chaperonin 10 Kd subunit


Domain annotation for each model (and alignments):
>> Cpn10  Chaperonin 10 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.4   1.0   1.4e-34   2.4e-30       2      92 ..       5      94 ..       4      95 .. 0.97

  Alignments for each domain:
  == domain 1  score: 104.4 bits;  conditional E-value: 1.4e-34
                -EE-TTEEEEEESGG-TTS-TT----HHHHHSEEEEEEEEE-T........TS-TTS--T-EEEEEGGGTSS-GG---.EEEEEGGG--EE CS
       Cpn10  2 ikplgdrVlvkraeeeekteggiilpdsakekpeqGvVvaVGegarnekgedvplevkvgdkVlfpkyagtkvkvdgkeylilkekdIlav 92
                +k+l+d+Vl+k  +ee+  ++gi++pdsak+kp+ GvVvaVG+ga+n++g+  p+ vk+gd Vl++k+ag++v++dg ey+++ke+dI+av
  AHX11550.1  5 LKMLHDQVLIKP-QEEQDGASGIYIPDSAKKKPTIGVVVAVGQGAKNSNGTFDPVCVKEGDVVLYRKWAGSEVEHDGVEYVVMKESDIIAV 94
                689*********.68899************************************************************************8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       342  (0.0190752); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 797.01
//
Query:       AHX11551.1  [L=319]
Description: hypothetical protein NHE_0616 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
  ------ inclusion threshold ------
      0.022   15.0   0.0      0.038   14.2   0.0    1.4  1  RNase_P_Rpp14  Rpp14/Pop5 family


Domain annotation for each model (and alignments):
>> RNase_P_Rpp14  Rpp14/Pop5 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   2.1e-06     0.038      18      73 ..     175     234 ..     126     250 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 2.1e-06
                    -...HHHHHHHHHHHHHHHHHHHHHHH--...EEEEEETTTTEEEEEEEGGGHHHHHHHH CS
  RNase_P_Rpp14  18 e...ksllkairesvqelfGdyglgklgs.slsvkyfspatstaiiRcsresyrlvwaaL 73 
                    +   +++l+ i  s++el   + +  +++ s ++k++s+++++ iiRc  ++++ v+ ++
     AHX11551.1 175 AeslSTILDSISPSINELCRSIITLDTQKiSSHIKQYSDSEGLLIIRCLMKYCNAVLEII 234
                    33468999999999999999999999999889********************99998765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (319 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       602  (0.0335769); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.21s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2548.23
//
Query:       AHX11552.1  [L=588]
Description: surA N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    2.1e-25   89.4   1.3    2.1e-25   89.4   1.3    3.0  4  SurA_N_3    SurA N-terminal domain
    5.6e-16   58.7   3.0      1e-15   57.9   0.2    2.6  3  SurA_N_2    SurA N-terminal domain
    6.6e-11   43.1  10.6      0.012   16.4   0.5    4.4  3  Rotamase_2  PPIC-type PPIASE domain
  ------ inclusion threshold ------
      0.019   15.1   1.1      0.058   13.5   0.5    2.2  2  SurA_N      SurA N-terminal domain
      0.047   13.9   0.1       0.89    9.8   0.0    2.8  2  HTH_17      Helix-turn-helix domain


Domain annotation for each model (and alignments):
>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.4   1.3     6e-29   2.1e-25      16     158 ..      12     155 ..       3     158 .. 0.92
   2 ?    3.1   0.0      0.02        71      96     120 ..     231     255 ..     227     291 .. 0.88
   3 ?   -3.9   0.1       2.8     1e+04      84     106 ..     465     487 ..     451     494 .. 0.67
   4 ?   -3.5   0.0       2.2   7.8e+03      74      93 ..     564     585 ..     550     587 .. 0.52

  Alignments for each domain:
  == domain 1  score: 89.4 bits;  conditional E-value: 6e-29
    SurA_N_3  16 illgliilaFvlwGvgsylsgsg.nsvakVngekIsraefqqayrrqleqlrqqlggnldaelldelglrqqvldqlidealllqeakklglsvsdeev 113
                  +l+l+ila++ + +++ l +++ + va+V+ ekI+ + f ++yr+  + ++++++  l++++l+e+g+ ++vl +li+e++++q  k+++l++ d+  
  AHX11552.1  12 SVLVLVILALLGTAINGALIERNsDVVASVGREKITVDAFLSEYRKSERYIQSMFNFGLSSSQLKEMGVGRMVLTNLIQEKVIAQLLKRMNLHIHDSIA 110
                 57888888888788888555555367************************************************************************* PP

    SurA_N_3 114 akeiasipaFqedGkFdkerYkqlLaangltpeefeaslredlll 158
                  ++i++++ F +d+kF++++++++L +n lt++e+ ++++++++ 
  AHX11552.1 111 IDKIKRNELFLDDNKFSRAKLENFLDRNDLTEREYIEKVKQEIAK 155
                 ******************************************986 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.02
    SurA_N_3  96 lllqeakklglsvsdeevakeiasi 120
                 + +q++kk+ +sv+d+ev+k+ +s 
  AHX11552.1 231 ISEQTVKKELISVTDSEVQKKFESL 255
                 568999*************998776 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 2.8
    SurA_N_3  84 rqqvldqlidealllqeakklgl 106
                 ++q+  +l +e+l+++  +++ +
  AHX11552.1 465 QEQIAFRLLQEKLVSNNHREQTI 487
                 45555666666666666666655 PP

  == domain 4  score: -3.5 bits;  conditional E-value: 2.2
    SurA_N_3  74 daellde..lglrqqvldqlid 93 
                  +el+++  ++++ +v ++li+
  AHX11552.1 564 LSELIQTavNEFKVKVTNNLIK 585
                 4444444445555555555554 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.2   2.8e-19     1e-15      15     145 .]      13     135 ..       4     135 .. 0.91
   2 ?   -0.4   0.0      0.27   9.5e+02      98     120 ..     231     253 ..     229     270 .. 0.84
   3 ?   -2.2   0.0      0.92   3.3e+03      97     118 ..     566     587 ..     554     588 .] 0.81

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 2.8e-19
    SurA_N_2  15 iiglallaFilgdlfgvgsylfssssnevaeVnGekIslqefqqaveearqqlqqqlgenfdeseedeaqlreqvldqlvseklleqeaeklGltvsde 113
                 +++l++la +    + +++ l +++s++va+V+ ekI++++f  ++++ ++ +q++++  +++s+ +e+ + ++vl++l++ek+++q +++++l++ d+
  AHX11552.1  13 VLVLVILALL---GTAINGALIERNSDVVASVGREKITVDAFLSEYRKSERYIQSMFNFGLSSSQLKEMGVGRMVLTNLIQEKVIAQLLKRMNLHIHDS 108
                 2456666666...45566788999*************************************************************************** PP

    SurA_N_2 114 elqdaiqgnpaikqsFqpetGkFdkeklkqfl 145
                    d i+ n+     F   + kF+++kl++fl
  AHX11552.1 109 IAIDKIKRNEL----FL-DDNKFSRAKLENFL 135
                 ***********....**.************97 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.27
    SurA_N_2  98 lleqeaeklGltvsdeelqdaiq 120
                 + eq ++k  ++v+d+e+q+  +
  AHX11552.1 231 ISEQTVKKELISVTDSEVQKKFE 253
                 5689999999*******998665 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 0.92
    SurA_N_2  97 klleqeaeklGltvsdeelqda 118
                 +l++ ++++++++v+++ ++d+
  AHX11552.1 566 ELIQTAVNEFKVKVTNNLIKDL 587
                 6888889999999998888876 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.2   3.0   1.7e-05     0.061       1      47 [.     202     267 ..     202     345 .. 0.54
   2 !   16.4   0.5   3.4e-06     0.012      46     120 ..     365     453 ..     321     454 .. 0.72
   3 !   14.3   0.0   1.5e-05     0.054      44     113 ..     474     543 ..     455     547 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.7e-05
  Rotamase_2   1 vteaevkayYeankdefskpegktlelavvkdq.vaaeaa...lalakag...............a 47 
                 +teae+ ++Y++nk  f + e++t e+a+  +q v++e++   + +++++               +
  AHX11552.1 202 PTEAELLSFYNENKGGFIGEEYRTAEYATISEQtVKKELIsvtDSEVQKKfeslqlgkryyvdyiE 267
                 8*************************9999988444555544433333333333333335555542 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 3.4e-06
  Rotamase_2  46 g......aekdfaalakgnskkaadlg.ifesa.......snlpeelakaafalkpgevsgpvetdngyyivkvtevkpakvppfeevk 120
                 +      +++d+++l+ ++++k + +g i +++        n++ +l++++f+ ++g   ++v  +n   i+ vt+v+pa+ +pfe+v+
  AHX11552.1 365 QigedlaSGADWETLKEKYGIKLQRVGpIGKDSrdkegnaINIDGNLLEEIFKKEKGIQHELVSPANELIIFSVTSVEPAAEQPFEKVR 453
                 155555566899999999999988888633333334444455555********999977789**************************9 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 1.5e-05
  Rotamase_2  44 kagaekdfaalakgnskkaadlgifesa....snlpeelakaafalkpgevsgpvetdngyyivkvtevkpakv 113
                 +   ek + +  ++++++   +++++s+    +  ++++++++f+l++g++++++e+++ ++i kv e++++++
  AHX11552.1 474 Q---EKLVSNNHREQTIDLYRPDVSKSKrlhyE-YSDDFIAEIFNLSVGDTTKLFESEKYFFIGKVLEKRKPEP 543
                 3...33566677777777777777777755532.455*******************************887544 PP

>> SurA_N  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.5   1.6e-05     0.058      43     113 ..      81     154 ..      37     158 .. 0.87
   2 ?   -2.2   0.0       1.2   4.2e+03      55      77 ..     231     253 ..     229     266 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
      SurA_N  43 erqvlerlilekiqlqeaektgirvddeelnqaiae...iAkeNkltldqlraalaedGlsydefreqiRkEii 113
                  r vl  li ek+ +q  +++++++ d+     i++      +Nk + ++l++ l+++ l+  e+ e++++Ei+
  AHX11552.1  81 GRMVLTNLIQEKVIAQLLKRMNLHIHDSIAIDKIKRnelFLDDNKFSRAKLENFLDRNDLTEREYIEKVKQEIA 154
                 5789***********************8655555442335689*****************************97 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.2
      SurA_N  55 iqlqeaektgirvddeelnqaia 77 
                 i  q+ +k  i+v+d+e+++  +
  AHX11552.1 231 ISEQTVKKELISVTDSEVQKKFE 253
                 66788888889999999887665 PP

>> HTH_17  Helix-turn-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.22   7.8e+02      13      50 ..     105     138 ..     103     139 .. 0.76
   2 ?    9.8   0.0   0.00025      0.89       8      44 ..     226     269 ..     225     271 .. 0.90

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.22
      HTH_17  13 vsrstvyrlirrgelpaakiGrrwriprsdleewlekr 50 
                 +++s + + i+r+el ++      +++r+ le +l+++
  AHX11552.1 105 IHDSIAIDKIKRNEL-FLDD---NKFSRAKLENFLDRN 138
                 555566677888888.8877...7899*******9987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00025
      HTH_17   8 AelLgvsrstvy.rlir......rgelpaakiGrrwriprsdle 44 
                 Ae+  +s++tv  +li+      ++++  + +G+r++++  ++e
  AHX11552.1 226 AEYATISEQTVKkELISvtdsevQKKFESLQLGKRYYVDYIEFE 269
                 88999*******77**7778888****999************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       721  (0.0402142); expected 358.6 (0.02)
Passed bias filter:                      422  (0.0235373); expected 358.6 (0.02)
Passed Vit filter:                        47  (0.00262145); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.60u 0.24s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4163.37
//
Query:       AHX11553.1  [L=402]
Description: poly A polymerase head domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.4e-31  107.4   0.0    1.1e-30  106.6   0.0    1.4  1  PolyA_pol        Poly A polymerase head domain
    2.7e-08   33.4   0.4      1e-07   31.6   0.4    2.0  1  PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polym
  ------ inclusion threshold ------
      0.047   13.5   0.3       0.14   12.0   0.3    1.8  1  CdvA             CdvA-like coiled-coil domain


Domain annotation for each model (and alignments):
>> PolyA_pol  Poly A polymerase head domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.6   0.0   1.9e-34   1.1e-30       2     125 ..      26     146 ..      25     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 106.6 bits;  conditional E-value: 1.9e-34
                 EEETHHHHHHHTT---CEEEEEECS-HHHHHHHHHHHHT-EEEEETTTTCCCCEECCEEEEECCEECEEEEEE---SSHHH...HHHHHHCTSSBGGGS CS
   PolyA_pol   2 ylvGGaVRDlllgkepkDvDlatdaapeelakllrkkvkeallsgeefqtiavlekkqllevatfRlekdesdarnpesekstesleeDlkrRDftiNa 100
                 ++vGG+VRD +lg++  D+D+at+ +pee  ++lr +  +a+ +g +++t + l +++++e++t+R + +++  r+  ++ +te+++eD+krRDft Na
  AHX11553.1  26 RFVGGCVRDSILGRKISDFDIATTLEPEEAMSILRANSFTAIPTGLKHGTFTTLVGSRSVEITTLRKDLECDG-RHA-TVMFTENWKEDAKRRDFTFNA 122
                 89**************************************9999**********************9996655.554.68999**************** PP

                 -EEECTTTCEE-TTSHHHHHHTTEE CS
   PolyA_pol 101 laynlnkgkvlDlfgGikdLkskvi 125
                 l+++  +g+v+D+f G++dLk +++
  AHX11553.1 123 LYMD-IDGNVYDYFSGLEDLKYRRL 146
                 ****.6789************9886 PP

>> PolyA_pol_RNAbd  Probable RNA and SrmB- binding site of polymerase A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.4   1.7e-11     1e-07       7      57 ..     181     231 ..     176     237 .. 0.93

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 1.7e-11
  PolyA_pol_RNAbd   7 eTaaairklaplLkkispeRifeEllKlLlsghpeaglelLretgLlkylf 57 
                      e+++a +k++++++ +s eRi+ E+lKlL++++   +le +   ++l+ +f
       AHX11553.1 181 EILEACEKYKEQINLLSGERIQAEMLKLLSYDNFLSTLEAMQSAKVLERVF 231
                      889********************************************9998 PP

>> CdvA  CdvA-like coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   2.4e-05      0.14      45      84 ..     290     331 ..     276     338 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 2.4e-05
        CdvA  45 lkkrlkeledqikslekalan..lkisyasGEidEeaYksai 84 
                 l++++++l+   ++l k lan  lki ya ++i++++Y++ +
  AHX11553.1 290 LENHIASLQTTASRLGKDLANklLKILYAENKINDKEYQQFS 331
                 788999999999999999999889***************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       614  (0.0342462); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.37
# Mc/sec: 3278.72
//
Query:       AHX11554.1  [L=299]
Description: hypothetical protein NHE_0619 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.16   12.4   0.1       0.33   11.3   0.1    1.5  1  DUF4413   Domain of unknown function (DUF4413)
       0.23   11.3   1.4        8.1    6.3   0.6    2.3  2  DUF4268   Domain of unknown function (DUF4268)
       0.98    9.3   5.8        1.6    8.6   5.6    1.4  1  Myc_N     Myc amino-terminal region


Domain annotation for each model (and alignments):
>> DUF4413  Domain of unknown function (DUF4413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   5.5e-05      0.33      16      77 ..     109     176 ..     106     196 .. 0.68

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
     DUF4413  16 levkkllkewakseddlls.kmaekmqe....kfdkywkksnlllaiaviLDPryKl.kyvefalkki 77 
                 lev+++l+++ ++ ++ ++ +++ km+     k  k + k  l+++iav +DP+++  +  +  +k +
  AHX11554.1 109 LEVERDLEDEQEEIEEEINvDILAKMSSarqkKDAKEILKRLLICMIAVRMDPKCRAgETAQSNVKHA 176
                 578888888877744433335555555532226666667999**************977777766654 PP

>> DUF4268  Domain of unknown function (DUF4268)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.3   0.0     0.012        70      57      89 ..      26      58 ..      10      66 .. 0.81
   2 ?    6.3   0.6    0.0013       8.1      60      89 ..     103     132 ..      95     158 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.3 bits;  conditional E-value: 0.012
     DUF4268 57 IskkdeeenkeifekLkeqkeeieeelgeeleW 89
                ++ ++ +  ++++++++ q+ +i++++g +l+ 
  AHX11554.1 26 LDGAESDYYQRFYKYFYLQQAKIARMCGLPLHI 58
                55667788899*****************99976 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0013
     DUF4268  60 kdeeenkeifekLkeqkeeieeelgeeleW 89 
                 k++e   e+ + L++++eeieee+++++  
  AHX11554.1 103 KEKESELEVERDLEDEQEEIEEEINVDILA 132
                 67899999999**************97754 PP

>> Myc_N  Myc amino-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   5.6   0.00027       1.6     225     272 ..      97     144 ..      76     176 .. 0.78

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00027
       Myc_N 225 dskalssseedvlsesdeeeeeeeeeeeeidVVtvekrrssskrkevs 272
                   + + +++e++l+ +++ e+e+ee eeei+V  + k  s+ ++k++ 
  AHX11554.1  97 RDQVRLKEKESELEVERDLEDEQEEIEEEINVDILAKMSSARQKKDAK 144
                 334555566667777788888889*************99888887755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (299 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1135  (0.0633053); expected 358.6 (0.02)
Passed bias filter:                      579  (0.032294); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.43
# Mc/sec: 2079.00
//
Query:       AHX11555.1  [L=210]
Description: 3,4-dihydroxy-2-butanone 4-phosphate synthase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.3e-55  186.6   0.0    3.7e-55  186.4   0.0    1.0  1  DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase


Domain annotation for each model (and alignments):
>> DHBP_synthase  3,4-dihydroxy-2-butanone 4-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  186.4   0.0   2.1e-59   3.7e-55       2     192 .]       7     200 ..       6     200 .. 0.95

  Alignments for each domain:
  == domain 1  score: 186.4 bits;  conditional E-value: 2.1e-59
                    HHHHHHHT.T--EEEESSTTTT-BEEEEEEGGG--HHHHHHHHHHB-S--EEEEEHHHHHHTT--BSSSS-SS..TT---BB--EEESST-SSS-S CS
  DHBP_synthase   2 eaiealka.GkfvivvDdedrenegdLiiaAekvtpekvafmirhasGlicvalteeradeLeLplmveened..khktaftvsvdaaegttTGIs 94 
                    e++++lk+  k+ ++vD+ +renegd++++ + +t e ++f ++h++G+ cv++tee +++LeL l+ ++  d  ++  +f  +++a+eg+tTGIs
     AHX11555.1   7 EILQELKEkRKPFVLVDSGNRENEGDIVVPVQLLTREIMNFAVTHCRGVPCVCVTEELCKKLELTLLRRSGIDdvPNVARFVTTIEAREGVTTGIS 102
                    677777752689*******************************************************996554348999***************** PP

                    HHHHHHHHHHHH-TT--GGGEEEEEEEEEEEE-TTGGGTS-SHHHHHHHHHHHTTS-SBEEEEEBB-TTSCB-BHHHHHHHHHHHT-EEEEHHHHH CS
  DHBP_synthase  95 aaDRalTirkladpkakpedfrrPGhvfplrareggvleRrghTEaavdLarlaglkpaavicellnddgtmarrdeleefakkhglkiitiedli 190
                     aDR +T+  l++++ +++df++PGhvfpl+  ++g++ R ghTE +  +a lag+kp ++ice+l+++g++ar++ l+ef kkh+l i++i+ l 
     AHX11555.1 103 VADRVRTMGLLVQDNVTKDDFVSPGHVFPLMIDKDGLEARLGHTEGSATFACLAGFKPESMICEILDEQGDSARLPYLTEFIKKHDLRITSIDILH 198
                    ********************************************************************************************9998 PP

                    HH CS
  DHBP_synthase 191 ey 192
                    +y
     AHX11555.1 199 RY 200
                    77 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1652.27
//
Query:       AHX11556.1  [L=794]
Description: ftsK/SpoIIIE family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-65  220.6   0.7    4.2e-65  219.5   0.7    1.6  1  FtsK_SpoIIIE     FtsK/SpoIIIE family
    2.8e-26   91.6   0.0    6.6e-26   90.4   0.0    1.7  1  FtsK_alpha       FtsK alpha domain
    4.5e-25   87.2   0.1    1.2e-24   85.9   0.1    1.8  1  FtsK_gamma       Ftsk gamma domain
    2.4e-05   24.1   7.5    3.7e-05   23.5   3.5    2.2  2  FtsK_4TM         4TM region of DNA translocase FtsK/SpoIIIE
    2.5e-05   23.4   0.0     0.0099   14.8   0.0    2.3  2  AAA_10           AAA-like domain
    7.3e-05   23.1   0.0    0.00034   20.9   0.0    2.1  1  AAA_22           AAA domain
    0.00042   19.8   1.3        4.9    6.5   0.2    3.5  3  TniB             Bacterial TniB protein
    0.00063   18.9   0.0     0.0012   18.0   0.0    1.4  1  T2SSE            Type II/IV secretion system protein
    0.00095   19.0   0.6     0.0047   16.7   0.6    2.1  1  DEAD             DEAD/DEAH box helicase
     0.0012   19.0   2.5     0.0027   17.8   0.1    2.7  4  DUF87            Helicase HerA, central domain
  ------ inclusion threshold ------
      0.026   13.5   0.0      0.093   11.6   0.0    1.8  2  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.039   13.7   0.1       0.13   12.0   0.1    1.9  1  AAA_29           P-loop containing region of AAA domain
        4.8    7.5  13.6       0.31   11.3   7.3    2.1  2  DUF4064          Protein of unknown function (DUF4064)
        9.3    5.3  14.6        1.2    8.2  10.0    1.7  2  ABC2_membrane_3  ABC-2 family transporter protein


Domain annotation for each model (and alignments):
>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  219.5   0.7   3.3e-68   4.2e-65       2     243 .]     412     631 ..     411     631 .. 0.94

  Alignments for each domain:
  == domain 1  score: 219.5 bits;  conditional E-value: 3.3e-68
                   HHHHHTSHHHHT---TTEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHHHHHHTT--TTTEEEEEE-TTSSSCGGGTT-TTBSS.S- CS
  FtsK_SpoIIIE   2 LlevleskkfrtessqlpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLilSlatthtPeeVqliliDykgvelsalediphllsvav 98 
                   L+e+les+ ++++   lp+algk+isg+p+v+dl km+ hllvaG+tgsGKS+a+n++ilSl+++ +P+e +li++D+k++els ++diphlls +v
    AHX11556.1 412 LRELLESEVYKDQNIVLPIALGKNISGEPIVADLTKMP-HLLVAGTTGSGKSVAINAMILSLIYRLEPHECKLIMVDPKMLELSIYDDIPHLLS-PV 506
                   7899999*******************************.*******************************************************.** PP

                   B-SHHHHHHHHHHHHHHHHHHHHHHHHTT-SSHHHHHHHHHHHHHTT---B-TT-......................-----------B-----EEE CS
  FtsK_SpoIIIE  99 atdperalraleeLvkemeeryalfreagvrsiaaydgeiaedpldifgdvflvlDnyddlaaeneritsLsnqgpsygvhvlvtagrelekrpslv 195
                   +tdp++a+ al+++vkeme+ry+l+ +  vr+i++y+++++e +++ +    l+            +  + +   p  g ++   +  +l+k+p +v
    AHX11556.1 507 VTDPKKAVVALKWVVKEMERRYKLMTKLAVRNIERYNKKAEEFIKNNK----LF------------EYEEAVGIDPTTGEKLTQMKSIQLKKLPLIV 587
                   ******************************************999943....22............112234456899999999999********** PP

                   EEEC-HHHHHHHHHHH....HHHHHHHHHHHCGGGTEEEEEEES---T CS
  FtsK_SpoIIIE 196 vivderieLrlaapkdssvlvedaivRlarkgraaglHlllatqrlsv 243
                   v+vde+++L+l+a+k+    +e+ i+Rla+++ra+g+H ++atqr+sv
    AHX11556.1 588 VVVDEMADLMLVAGKE----IETSIQRLAQMARASGIHIIMATQRPSV 631
                   ****************....**************************96 PP

>> FtsK_alpha  FtsK alpha domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.4   0.0   5.2e-29   6.6e-26       1     101 []     307     404 ..     307     404 .. 0.96

  Alignments for each domain:
  == domain 1  score: 90.4 bits;  conditional E-value: 5.2e-29
  FtsK_alpha   1 LPsldlLeeeekekkkedeeelekkaklieetleefgieakvveisvGPvvtqyevepapgvkvskiaaleddlalaLaaksirieapipGksvvGiev 99 
                 +PsldlL++ + +  ++  e++  +a++++++le+f+i++k+veisvGP+vt ye++pa+g+k s+i++l+ d+a++++a s ri ++ipG++++Gie+
  AHX11556.1 307 IPSLDLLKRGNPS--QKCAEDTLGRAENLKKVLEDFKIDCKIVEISVGPIVTLYELQPAAGIKSSSIISLSTDVARTMSAVSARI-SIIPGRNAIGIEL 402
                 6***********9..6777788889************************************************************.9************ PP

  FtsK_alpha 100 Pn 101
                 Pn
  AHX11556.1 403 PN 404
                 *9 PP

>> FtsK_gamma  Ftsk gamma domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.9   0.1   9.4e-28   1.2e-24       3      61 ..     735     793 ..     733     794 .] 0.97

  Alignments for each domain:
  == domain 1  score: 85.9 bits;  conditional E-value: 9.4e-28
  FtsK_gamma   3 eDelfeeavelvveegkaStSllQRrlriGYnRAarlidqLeeeGiVgpaegskpReVl 61 
                  D+l+++ave++ +++k+S+S++QR+l+iGYn+Aa+l++++eeeGiV+p++++++R++l
  AHX11556.1 735 FDSLYNQAVEIIKRDNKVSISYIQRKLSIGYNKAAKLVEKMEEEGIVSPPNQAGKRNIL 793
                 69********************************************************9 PP

>> FtsK_4TM  4TM region of DNA translocase FtsK/SpoIIIE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.5   3.5   2.9e-08   3.7e-05       2     134 ..      12     131 ..      11     133 .. 0.74
   2 ?    2.2   0.1       0.1   1.3e+02      65     110 ..     136     187 ..     135     199 .. 0.66

  Alignments for each domain:
  == domain 1  score: 23.5 bits;  conditional E-value: 2.9e-08
    FtsK_4TM   2 rllkEllgllllllalflllaLlsYspdDpswstsgsaaaavhNwgGrvGAwladlllslfGlsawllvvlllawglrllrrkslerrllrllgallll 100
                 ++++ l+g+   l +lfl++  l  +p+++s++ +++   + +N +  +G+++a +++ ++Gl+ +ll ++l++ ++ +   k  e+++l +l++ll +
  AHX11556.1  12 NITHILFGITYRLGLLFLIVCGLISNPEEASFNVAVE---KSRNEMLFLGSFVATFCMNFLGLGFYLLCLFLIFSAAFS---K--EKKVLSILFILLSI 102
                 5677888899888999988887777*******99985...56************************9988887765432...3..23344454444444 PP

    FtsK_4TM 101 lasaalfalrlasledelpggaGGvlGrllaaal 134
                 +++   ++l+  s e+ l g+ GGv+G l+a+ l
  AHX11556.1 103 VVL---AKLTP-SEEW-LFGSYGGVIGSLIAKHL 131
                 444...44333.4466.45899********9987 PP

  == domain 2  score: 2.2 bits;  conditional E-value: 0.1
    FtsK_4TM  65 sawllvvlllawglrllrrksle......rrllrllgalllllasaalfalr 110
                 +++++++ +l+++ r+++  +l+      ++++rll  +++++ s   f +r
  AHX11556.1 136 AVYWCIAGMLLIVTRIFNLLTLRrirkilKKIYRLLKTVIVAIWSKRKFDFR 187
                 689*******999999998555533222255666666666666665555554 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.0   7.7e-06    0.0099      19      68 ..     446     499 ..     431     532 .. 0.80
   2 !    6.2   0.0    0.0032       4.1     243     312 ..     587     659 ..     573     667 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 7.7e-06
      AAA_10  19 tnasasliiGdlGnGKSvlakllvlyisllg....gkaliiDpkkerekfketl 68 
                 t+ ++ l+ G +G GKSv ++ ++l +  +      k++++Dpk  +   +  +
  AHX11556.1 446 TKMPHLLVAGTTGSGKSVAINAMILSLIYRLepheCKLIMVDPKMLELSIYDDI 499
                 77899****************998776655345559*******97666665555 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0032
      AAA_10 243 vvifDEawiftssaeGkkllkelvR...iGRsynaavylvtqsad.DvlkeelknniglklaFretdkeeikkv 312
                 vv++DE   +  +a Gk+++ ++ R   + R+    ++++tq ++ Dv    +k n+++++ F  t k + + +
  AHX11556.1 587 VVVVDEMADLMLVA-GKEIETSIQRlaqMARASGIHIIMATQRPSvDVITGVIKANFPTRISFAVTSKIDSRTI 659
                 67788887776664.88888877773325699999*******9765*****************98887666655 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.0   2.6e-07   0.00034       7     130 ..     450     627 ..     446     633 .. 0.87

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 2.6e-07
      AAA_22   7 ilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsst.sskdllrellralglelka.................................. 70 
                 +l+v G +G+GK++ ++ +  +l   +  e ++ +++ v+++ ++ s  d   +ll+ +  + k+                                  
  AHX11556.1 450 HLLVAGTTGSGKSVAINAMILSL--IYRLEPHECKLIMVDPKMLElSIYDDIPHLLSPVVTDPKKavvalkwvvkemerryklmtklavrnierynkka 546
                 799*******************9..23444489999999999999988888999999888888889999999999999999999999************ PP

      AAA_22  71 ..................erlsseellealeqalraravielliiDEaqhlr...s...eealeeLrsllnlsrkgvqliLvGt 130
                                    + + e l ++   +l++     ++++DE+  l+       e+ ++ L +++    +g+++i++ +
  AHX11556.1 547 eefiknnklfeyeeavgiDPTTGEKLTQMKSIQLKKLPL-IVVVVDEMADLMlvaGkeiETSIQRLAQMAR--ASGIHIIMATQ 627
                 ***************************************.**********988863345666666666666..99999998765 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.0    0.0039         5      33      53 ..     446     466 ..     442     471 .. 0.89
   2 !    6.5   0.2    0.0038       4.9     104     169 ..     569     634 ..     532     636 .. 0.87
   3 ?    3.3   0.0     0.037        47       2      32 ..     754     786 ..     753     794 .] 0.72

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0039
        TniB  33 krmpnlllvGdsnnGKtmive 53 
                 ++mp+ll++G +  GK++ ++
  AHX11556.1 446 TKMPHLLVAGTTGSGKSVAIN 466
                 79***************9987 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0038
        TniB 104 vskleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGteealral 169
                  +kl+q+    l++l + v+++DE+ +l+    ++ ++ ++ l ++ +   i i+++  +  ++++
  AHX11556.1 569 GEKLTQMKSIQLKKLPLIVVVVDEMADLMLVAGKEIETSIQRLAQMARASGIHIIMATQRPSVDVI 634
                 45777888889*****************************************99998777777666 PP

  == domain 3  score: 3.3 bits;  conditional E-value: 0.037
        TniB   2 iayiradrwigyprakeilerLee..Lleypkr 32 
                 i yi+++  igy++a++++e++ee  +++ p++
  AHX11556.1 754 ISYIQRKLSIGYNKAAKLVEKMEEegIVSPPNQ 786
                 789*******************64224444444 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   9.5e-07    0.0012      58     153 ..     374     472 ..     346     499 .. 0.75

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 9.5e-07
       T2SSE  58 akldiseerplqdarlp.ekgvrlrvvllPvvagealviR.kksakeltlddlgaeealkekia.evlrkavrerglilvsGgTgsGKttllyallkei 153
                  + d+++    ++ar++   g +  ++ lP  + e + +R   +++ ++ ++++   al ++i+ e + + +++   +lv+G+TgsGK++ ++a++  +
  AHX11556.1 374 LSTDVARTMSAVSARISiIPGRNAIGIELPNKHREVVLLReLLESEVYKDQNIVLPIALGKNISgEPIVADLTKMPHLLVAGTTGSGKSVAINAMILSL 472
                 56778888888888888766777777888888888899995444455566777777777776652445555688889****************987554 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.6   3.6e-06    0.0047      15     153 ..     449     615 ..     421     632 .. 0.54

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 3.6e-06
                 CEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS..............................-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEE.. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..............................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.. RF
        DEAD  15 gdvlvaaeTGsGKTlaflipvlqivyetkgktg..............................pkalivePtreLaeqtlnnlkkfkkyidlrvlli.. 81 
                  ++lva+ TGsGK+ a    +l+ +y+   +++                              pk  +v  ++  ++++ +++k ++k   l v  i  
  AHX11556.1 449 PHLLVAGTTGSGKSVAINAMILSLIYRL--EPHecklimvdpkmlelsiyddiphllspvvtdPKKAVV-ALKWVVKEMERRYKLMTK---LAVRNIer 541
                 5678*********************985..333123444444444444444444443333333222222.244444444444444444...33332211 PP

                 ETTSSH.HHHHHHH...HTTCSEEEEEHHHHHHHHHCTSSHCTTEEE..EEEET.HHHHHHTTTHHHHHHHHHHSHHHC CS
                 xxxxxx.xxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxx.xxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  82 iggvaa.rdqlskl...dngvdivvgtpgrlddllstgklnlsqvrf..lVlDE.adrlldqgfsdfinrilnqlpqit 153
                 ++++a+   + +kl   ++ v i  +t ++l +    ++++l+++ +  +V+DE ad +l    +++i++ +++l+q+ 
  AHX11556.1 542 YNKKAEeFIKNNKLfeyEEAVGIDPTTGEKLTQ---MKSIQLKKLPLivVVVDEmADLMLVA--GKEIETSIQRLAQMA 615
                 332222112222222112335555555555555...56688898865448899955666665..777777777776554 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.9   3.7e+03     110     144 ..     276     308 ..     222     362 .. 0.66
   2 !   17.8   0.1   2.1e-06    0.0027      13      60 ..     440     488 ..     430     489 .. 0.76
   3 ?   -1.8   0.0       2.2   2.8e+03     158     183 ..     532     560 ..     512     590 .. 0.66
   4 ?   -2.1   0.0       2.6   3.3e+03     143     178 ..     696     767 ..     690     783 .. 0.54

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.9
       DUF87 110 dkpaaav.qrsvleealdqakakeekeklssdepve 144
                 +++++++ ++s++++a + ak   + ++ ++++ ++
  AHX11556.1 276 TTHNTSReKKSIFQKAREAAK---LGGSGKVRSTIP 308
                 334444424444444444443...444444444444 PP

  == domain 2  score: 17.8 bits;  conditional E-value: 2.1e-06
       DUF87  13 pvyldlnklvtrHlAilgsTGsGKSntvavLleelle...kkgatililDp 60 
                 p+  dl k+   Hl++ g+TGsGKS  +  ++ +l+     +  +++++Dp
  AHX11556.1 440 PIVADLTKM--PHLLVAGTTGSGKSVAINAMILSLIYrlePHECKLIMVDP 488
                 778888889..9***************998888887667444458888887 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 2.2
       DUF87 158 rklknqaiarlldkledllrkggsf...s 183
                  kl+ + i+r+++k e++++++++f    
  AHX11556.1 532 TKLAVRNIERYNKKAEEFIKNNKLFeyeE 560
                 57778889999999999999999993221 PP

  == domain 4  score: -2.1 bits;  conditional E-value: 2.6
       DUF87 143 veklleelk....................................kekeelrklknqaiarlldkledllrk 178
                 vek+ e+l+                                    + +e ++++++ +i+ +++kl+   +k
  AHX11556.1 696 VEKIVEHLRksgipeydcsitleensdestaictsvgddfdslynQAVEIIKRDNKVSISYIQRKLSIGYNK 767
                 555555555444455444444444444444444455555555554555566666666666666666655555 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   7.3e-05     0.093      15      39 ..     448     472 ..     435     510 .. 0.77
   2 ?   -1.6   0.0      0.78   9.9e+02     245     281 ..     586     628 ..     571     633 .. 0.72

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 7.3e-05
  TrwB_AAD_bind  15 tqhilivGttGsGKtqalekllrai 39 
                      h+l++GttGsGK++a+++++ ++
     AHX11556.1 448 MPHLLVAGTTGSGKSVAINAMILSL 472
                    469**************99988654 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.78
  TrwB_AAD_bind 245 lWfflDElpaLgrl......eelksllaegRkfGgavvlglqs 281
                    + +++DE+++L  +       ++++l++ +R  G+ ++++ q 
     AHX11556.1 586 IVVVVDEMADLMLVagkeieTSIQRLAQMARASGIHIIMATQR 628
                    5677899998876633222236888899999999999999986 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1    0.0001      0.13      24      44 ..     450     470 ..     437     475 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
      AAA_29  24 atlltGpsGsGKSTllDAiqa 44 
                   l++G++GsGKS  + A++ 
  AHX11556.1 450 HLLVAGTTGSGKSVAINAMIL 470
                 5899*************9975 PP

>> DUF4064  Protein of unknown function (DUF4064)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   7.3   0.00024      0.31      13     101 ..      19     105 ..       8     106 .. 0.69
   2 ?   -1.2   0.4       1.9   2.5e+03      69     101 ..     115     154 ..     114     156 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00024
     DUF4064  13 gilgillglllllflfllssgefsqelteeqalsgedasavl..eflstllivlgvialiaivlgivgalllkknkkvsGilfiiaailsl 101
                 gi++ l+ l+l+++ ++++ +e s++     a++ + +++    +f+ t+ + ++ +++ ++ l+++++   +k kkv  ilfi+ +i++l
  AHX11556.1  19 GITYRLGLLFLIVCGLISNPEEASFNV----AVEKSRNEMLFlgSFVATFCMNFLGLGFYLLCLFLIFSAAFSKEKKVLSILFILLSIVVL 105
                 445555555666664444444444333....3333333333366999999999999999999999999999999**************987 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 1.9
     DUF4064  69 liaivlgivgalllk..knkk.....vsGilfiiaailsl 101
                 l+ +  g++g+l+ k  k ++     ++G l+i++ i+ l
  AHX11556.1 115 LFGSYGGVIGSLIAKhlKYPRavywcIAGMLLIVTRIFNL 154
                 6666678888888884444447888888888888877766 PP

>> ABC2_membrane_3  ABC-2 family transporter protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.2  10.0   0.00092       1.2     216     280 ..      24     103 ..      13     124 .. 0.80
   2 ?   -2.0   0.1       1.1   1.5e+03      28      84 ..     721     782 ..     714     789 .. 0.64

  Alignments for each domain:
  == domain 1  score: 8.2 bits;  conditional E-value: 0.00092
  ABC2_membrane_3 216 vyllqlllilll......afgl........gipfgnlglll.llfllfglayialgyllsslfknsetaqilifivilll 280
                      ++ll+l+++ l+       f++        +++ g++++++  +fl  g+ +++l++ +s++f++++++ +++fi++++ 
       AHX11556.1  24 LGLLFLIVCGLIsnpeeaSFNVaveksrneMLFLGSFVATFcMNFLGLGFYLLCLFLIFSAAFSKEKKVLSILFILLSIV 103
                      455555555555555554555599*****999999****99999**9*********************998887777643 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.1
  ABC2_membrane_3  28 ddentpiavvdedn.sslsqqlvealeaspsve..lvyevds..eeeakkalkngdidgilv 84 
                      +de+t i+    d+ +sl++q ve+++ +++v+  ++++  s   ++a k++++ + +gi+ 
       AHX11556.1 721 SDESTAICTSVGDDfDSLYNQAVEIIKRDNKVSisYIQRKLSigYNKAAKLVEKMEEEGIVS 782
                      44444443333333578999999999999998888555555556777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (794 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1207  (0.0673211); expected 358.6 (0.02)
Passed bias filter:                      816  (0.0455129); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.77u 0.30s 00:00:01.07 Elapsed: 00:00:00.42
# Mc/sec: 5665.68
//
Query:       AHX11557.1  [L=133]
Description: hypothetical protein NHE_0622 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      197  (0.0109878); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1023.75
//
Query:       AHX11558.1  [L=264]
Description: acetyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-08   33.8   0.1    5.4e-08   33.1   0.1    1.3  1  Acetyltransf_1   Acetyltransferase (GNAT) family
      8e-08   32.6   0.4    1.4e-07   31.8   0.4    1.4  1  Acetyltransf_7   Acetyltransferase (GNAT) domain
    2.8e-06   27.3   0.0    5.3e-06   26.4   0.0    1.4  1  Acetyltransf_10  Acetyltransferase (GNAT) domain
     0.0022   18.2   0.0     0.0036   17.5   0.0    1.2  1  Acetyltransf_6   Acetyltransferase (GNAT) domain
  ------ inclusion threshold ------
      0.032   13.9   0.1       0.19   11.4   0.0    2.3  2  Amidase02_C      N-acetylmuramoyl-l-alanine amidase
      0.037   14.7   0.0      0.073   13.7   0.0    1.5  1  Acetyltransf_3   Acetyltransferase (GNAT) domain
      0.047   13.7   0.0      0.087   12.8   0.0    1.4  1  FR47             FR47-like protein
      0.094   12.8   0.1       0.61   10.2   0.0    2.2  2  Acetyltransf_4   Acetyltransferase (GNAT) domain
       0.11   12.5   0.0        2.1    8.3   0.0    2.3  2  PriA_3primeBD    3′ DNA-binding domain (3′BD)


Domain annotation for each model (and alignments):
>> Acetyltransf_1  Acetyltransferase (GNAT) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   2.7e-11   5.4e-08       5     117 .]     132     240 ..     127     240 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 2.7e-11
                     HHHHHHHTHHHHHHHHHHH...HHHHHHSTTC..EEEEEEETTEEEEEEEEEEEETTSTTEEEEEEEEESGGGTTSSHHHHHHHHHHHHHHHTTE CS
  Acetyltransf_1   5 vellvesffppnedaseee...feesfsleae..gllvaeedgeliGfisllkipdekggvayieslaVspeyrgkGlGsaLlealeerareegi 94 
                     +++l       ++++se +   f+ + + + +  +++++ +d e++G ++++  ++    va  +    + +yrg+G+G +++ + +  ++e g+
      AHX11558.1 132 FDWLSSRI---FCHRSELVsisFRGIERADSNrlRFFLVFKDAEIVGVCGFYLENQ----VACFYADGLDYKYRGQGIGAQMILQRIVLVKELGC 219
                     55555443...444444444456666555555578888******************....999999999************************** PP

                     SEEEEEEETTEHHHHHHHHHTTE CS
  Acetyltransf_1  95 kkivlaveedndaairlYeklGF 117
                     + + +++   n  + +lY+k+GF
      AHX11558.1 220 TSVIAHC--INPISAGLYKKMGF 240
                     9965544..48899****88**9 PP

>> Acetyltransf_7  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.8   0.4     7e-11   1.4e-07       4      75 ..     163     241 ..     160     242 .. 0.73

  Alignments for each domain:
  == domain 1  score: 31.8 bits;  conditional E-value: 7e-11
                     EEEEEEETTEEEEEEEEEEESTCTEEEE...E-GGGTTSSHHHHHHHH.....TTSEEEEEEEEE.THHHHHHHHHHTTEE CS
  Acetyltransf_7   4 evfVaeddgkivGfialslldaeitrla...VdpeyrgkGiGraLlea.....aekgiileqlel.naekaikfYeklGFe 75 
                     ++f++ +d +ivG ++++l++ +  +++    d +yrg+GiG +++       +e g++ + ++  n+  ++++Y+k+GF+
      AHX11558.1 163 RFFLVFKDAEIVGVCGFYLEN-QVACFYadgLDYKYRGQGIGAQMILQrivlvKELGCTSVIAHCiNP-ISAGLYKKMGFR 241
                     689999*******99999987.555566566899***********95423443227776223344244.7789*******7 PP

>> Acetyltransf_10  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.0   2.7e-09   5.3e-06      26     111 ..     157     245 ..     149     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 2.7e-09
  Acetyltransf_10  26 ieegealllvaeeggkivGvielrdgshisllf...VdpeyrgqGigkaLleaveeeaekdgikleltvnasp.yavpfYeklGFkavge 111
                       ++++  +++++++ +ivGv++ + +++++ ++    d +yrgqGig++++ + +  +++ g   ++ ++  +    ++Y+k+GF+++g+
       AHX11558.1 157 ADSNRLRFFLVFKDAEIVGVCGFYLENQVACFYadgLDYKYRGQGIGAQMILQRIVLVKELGCT-SVIAHCINpISAGLYKKMGFRMLGS 245
                      4678899****************8888888776344688******************9888777.555555444************9876 PP

>> Acetyltransf_6  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.8e-06    0.0036      66     130 ..     157     221 ..     151     223 .. 0.92

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.8e-06
  Acetyltransf_6  66 aargalrlyvlrldgrpvAvalglrsgdrlyywlggydpelaklspgllllweliedaaeeGlrr 130
                     a++++lr++ +  d ++v+v+  +  +++++++  g d+ +++ ++g  ++++ i   +e G+++
      AHX11558.1 157 ADSNRLRFFLVFKDAEIVGVCGFYLENQVACFYADGLDYKYRGQGIGAQMILQRIVLVKELGCTS 221
                     6799**********************************************999998888888875 PP

>> Amidase02_C  N-acetylmuramoyl-l-alanine amidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   9.7e-05      0.19      18      40 ..      47      69 ..      45      70 .. 0.91
   2 ?   -2.0   0.0       1.5   3.1e+03      13      28 ..     246     259 ..     243     261 .. 0.73

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 9.7e-05
  Amidase02_C 18 fiTeptsdteLdkitawLDrkgW 40
                 f + + +++eL+ i ++LD + W
   AHX11558.1 47 FCSSVVQENELKTILEYLDERQW 69
                 567899****************9 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.5
  Amidase02_C  13 dGltYfiTeptsdteL 28 
                  +Gl Y  +ep+ +teL
   AHX11558.1 246 LGLYY--SEPRGNTEL 259
                  56666..788888887 PP

>> Acetyltransf_3  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.7e-05     0.073      50     138 .]     158     241 ..     132     241 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.7e-05
  Acetyltransf_3  50 eeegyg.waivlkdtgviGsvglrdleeedeeaelgymlapsfwgkGyateavralleyafeelglerlvavidkeNeaSirvleklGfe 138
                     +++ +  +++  kd +++G++g++  ++    +     l+ +++g+G++  +  + + ++ +elg + ++a++   N+ S+ +++k+Gf+
      AHX11558.1 158 DSNRLRfFLV-FKDAEIVGVCGFYLENQVA--CFYADGLDYKYRGQGIGAQMILQRIVLV-KELGCTSVIAHC--INPISAGLYKKMGFR 241
                     3344552555.578868*******766653..8888889999*************99999.899899777766..7************96 PP

>> FR47  FR47-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   4.4e-05     0.087      12      79 ..     176     242 ..     167     246 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 4.4e-05
                 EEEEEEE-TTSSEEEEEE-GGG-SSSHHHHHHHHHHHHHHHS-S-EEEEEETT-HHHHHHHHHHT-EE CS
        FR47  12 laawilrkdggelgalqvlpehrrrGlgsrlvkalakeiaergktvllvvvasNtpsirlyeklGfek 79 
                 +++  l++++   +a  ++ + r++G g +++ + +  + e g t++ ++   N  s  ly+k+Gf+ 
  AHX11558.1 176 VCGFYLENQVACFYADGLDYKYRGQGIGAQMILQRIVLVKELGCTSV-IAHCINPISAGLYKKMGFRM 242
                 566677888888888889999***************99999999875.5677899***********96 PP

>> Acetyltransf_4  Acetyltransferase (GNAT) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.9   0.0       6.9   1.4e+04      31      44 ..      51      64 ..      47      74 .. 0.63
   2 ?   10.2   0.0   0.00031      0.61      41     139 ..     154     245 ..     144     252 .. 0.70

  Alignments for each domain:
  == domain 1  score: -3.9 bits;  conditional E-value: 6.9
  Acetyltransf_4 31 vssveefekfleal 44
                    v +  e++++le+l
      AHX11558.1 51 VVQENELKTILEYL 64
                    45556667777765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00031
  Acetyltransf_4  41 lealdsekeyvflvaesdrivGyaylgqfkkrakdwkaelsvylaerdnnkeglgrelidaleqvlkeqnienllaeiaspnensiqfhkalGFe 135
                     +e+ ds   ++flv+++ +ivG +    ++    + ++     l + + + +g+g ++i   +   ke + ++  a  +  n +s+ ++k++GF+
      AHX11558.1 154 IERADSNRLRFFLVFKDAEIVGVCGFY-LEN---QVACFYADGL-DYKYRGQGIGAQMILQRIVLVKELGCTSVIAHCI--NPISAGLYKKMGFR 241
                     555566677788888888888887766.333...3344444444.3566777777666655555558888888888888..778*********** PP

  Acetyltransf_4 136 lvgi 139
                     ++g 
      AHX11558.1 242 MLGS 245
                     *997 PP

>> PriA_3primeBD  3′ DNA-binding domain (3′BD)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0      0.11   2.1e+02      49      66 ..      51      68 ..      10      89 .. 0.86
   2 ?    8.3   0.0    0.0011       2.1      57      92 ..     113     148 ..     103     151 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.11
  PriA_3primeBD 49 eveeeklkpieevldeep 66
                    v+e++lk i+e lde++
     AHX11558.1 51 VVQENELKTILEYLDERQ 68
                   456899********9865 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0011
  PriA_3primeBD  57 pieevldeepllteellelaewlaeyylaplgevlk 92 
                    +i++ ++  p+ ++e+l+l++wl+++ ++   e ++
     AHX11558.1 113 KIDSSVELIPIENSEQLKLFDWLSSRIFCHRSELVS 148
                    6777788889999****************9988775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       478  (0.0266607); expected 358.6 (0.02)
Passed bias filter:                      442  (0.0246528); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.49u 0.21s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 2002.50
//
Query:       AHX11559.1  [L=147]
Description: hypothetical protein NHE_0624 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       406  (0.0226449); expected 358.6 (0.02)
Passed bias filter:                      299  (0.0166769); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 1201.30
//
Query:       AHX11560.1  [L=1073]
Description: pyridine nucleotide-disulfide oxidoreductase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.5e-12   47.4   0.0    1.4e-11   44.2   0.0    2.4  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    1.1e-05   25.1   1.8    4.5e-05   23.2   0.3    2.8  3  Fer4_20        Dihydroprymidine dehydrogenase domain II, 4Fe-
     0.0015   19.0   0.4        5.2    7.7   0.0    4.4  5  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
  ------ inclusion threshold ------
      0.061   12.4   0.7        4.9    6.1   0.0    2.7  3  FAD_binding_2  FAD binding domain
       0.08   12.1   0.0        2.5    7.2   0.0    2.6  3  K_oxygenase    L-lysine 6-monooxygenase (NADPH-requiring)
      0.083   12.1   0.0       0.35   10.1   0.0    2.0  2  FAD_binding_3  FAD binding domain
       0.15   11.3   0.2         26    3.9   0.0    3.0  3  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
       0.18   10.9   0.0        1.1    8.2   0.0    2.2  2  GIDA           Glucose inhibited division protein A


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.2   0.0   6.2e-15   1.4e-11       2     244 ..     345     681 ..     344     690 .. 0.69
   2 ?   -2.5   0.0       1.1   2.4e+03       2      29 ..     871     901 ..     870     925 .. 0.62

  Alignments for each domain:
  == domain 1  score: 44.2 bits;  conditional E-value: 6.2e-15
                  SEEEE--SHHHHHHHHHHHHHTS-EEEEE......TTHCHHHCSHHHHCHHHHHHHHHHHHH.......................HHHHCHHHHCCCC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxx.......................xxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlve......legtclnggcllskallgvaedaeias.......................evvkklnqgiell 70 
                  +v++ G GpAG+++a++l + g+ v+ v+      l          ++k +   +++ e ++                                +++ 
   AHX11560.1 345 RVLISGTGPAGFTLAHYLLNDGHTVIAVDgakiepL----------PTKYVGLGGKNFELIEnvndlyenlderivygfggvseyG------ITVRWN 426
                  89999***********************54444444..........5555555555554444455555555599***997555441......333333 PP

                  HCCTCEEEE...ESC.EEEEETEEEC.......TCEEEEEESEEEE---E.EE-BCTCTTC.............TTBEECCSECHHHHHHCCSS-T.. CS
                  xxxxxxxxx...xxx.xxxxxxxxxx.......xxxxxxxxxxxxxxxxx.xxxxxxxxxx............xxxxxxxxxxxxxxxxxxxxxxx.. RF
  Pyr_redox_2  71 lgeevvkid...pgk.kkvklekkke.......gdeekiaydklvlAtGs.sprdlgipGv............aenvgklvrtldsaealklkllp.. 142
                  ++  ++k++    ++  ++ +   ++       +d +++ ++++ l++Gs +p++++++ v            +        +l+             
   AHX11560.1 427 KN--YLKLIrilLERrSNYRVFGGVCfgsnisaKDCRRLGFGHVALCIGSgNPNIPDVKNVltrgvrfasdflM--------NLQMS--------Gaf 506
                  33..33332111222233333333336666666999*************7689999999885444333322221........33333........223 PP

                  ...........SEEEEES-SHHHHHHHHHHHHHT-..........................................................EEEEE CS
                  ...........xxxxxxxxxxxxxxxxxxxxxxxx..........................................................xxxxx RF
  Pyr_redox_2 143 ...........krivvvGgGyiGvElAaalaklgk..........................................................evtlv 171
                               +vv+G+G+++v+ A ++  + k                                                           v ++
   AHX11560.1 507 kvnsiatlqlhMPVVVIGAGLTAVDSATEALTYYKvqvekflqryeylsgvygcseveknwdkeekriayeflshartlretvdktqflkslgGVKII 604
                  33333365566678***************766644467888888888888888888888888888888888888888888888888888887667799 PP

                  ESSSSSS..TTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE....EEE.EEETTSCEEEESEEEE-S-EEES-HHC CS
                  xxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 172 eardrll..raldkelsaaleealekeGvevklgtsvkeidgnge....kle.vvledgeeidadlvvvavGvrpstell 244
                  ++ +r+   +a+  ++++   +    eG+e+  +t++ ei++++      ++ ++ ++  +i+a+ v++a+G rp+++l+
   AHX11560.1 605 YR-KRIQdsPAYRLNFEEL--NSAMLEGIEFIEETEPLEIIQDEYglvkAIKcLHRGKMISINARSVIIATGTRPNSSLR 681
                  99.5555477777777766..4444459***************999765555788888888****************997 PP

  == domain 2  score: -2.5 bits;  conditional E-value: 1.1
                  SEEEE--SHHH...HHHHHHHHHHTS-EEEE CS
                  xxxxxxxxxxx...xxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAG...laaaltlaqagakvtlv 29 
                  +v+ iGgG +    ++ a++++++g++v+ +
   AHX11560.1 871 KVLLIGGGLGNavlFSIAKEMKRKGCQVIYF 901
                  6778888887622235677777777777766 PP

>> Fer4_20  Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       2.5   5.6e+03      14      36 ..     200     221 ..     195     227 .. 0.68
   2 !   23.2   0.3     2e-08   4.5e-05      34     107 ..     242     311 ..     236     315 .. 0.89
   3 ?   -2.2   0.0       1.5   3.3e+03      52      87 ..     427     462 ..     423     474 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.5
                 HHHHHHHHTT----TT-HHHHCS CS
     Fer4_20  14 eeealeeAsRClqCkkapcvkgC 36 
                 e++ ++  + Cl C++++ +++C
  AHX11560.1 200 ESNSVDHTNYCLVCHTRK-KDSC 221
                 5567888899****7544.2234 PP

  == domain 2  score: 23.2 bits;  conditional E-value: 2e-08
                 HCSTT---HHHHHHHHHTT-HHHHHHHHHHH-S-HHHHH.HHS-GGGTGCCS-GGGTTB.----HHHHHHHHHHH CS
     Fer4_20  34 kgCPveidipefikkiaegnleeaakiiketnslpavcg.rvCpqeelCegaCvlekkgkepvaigklerfvada 107
                 kgCP++ +i e+ k  +eg++ +a+++++ +n++ a +g r+C     C ++C+++  ++epv++  +e  + +a
  AHX11560.1 242 KGCPLRQKISEMNKLYSEGKIIAALSVVTLDNPMCAATGhRICN---DCMRSCIYQ--KQEPVNVPGIETAILNA 311
                 79********************************9999868995...5*******5..447*****999988765 PP

  == domain 3  score: -2.2 bits;  conditional E-value: 1.5
                 T-HHHHHHHHHHH-S-HHHHHHHS-GGGTGCCS-GG CS
     Fer4_20  52 gnleeaakiiketnslpavcgrvCpqeelCegaCvl 87 
                 +n+ + ++i+ e+ s   v g vC  ++   ++C +
  AHX11560.1 427 KNYLKLIRILLERRSNYRVFGGVCFGSNISAKDCRR 462
                 566677889999999999******999999999976 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.31     7e+02       1      28 [.     345     372 ..     345     379 .. 0.89
   2 ?   -2.8   0.0       4.5     1e+04      50      63 ..     416     429 ..     389     432 .. 0.74
   3 !    7.7   0.0    0.0023       5.2       2      25 ..     520     544 ..     519     578 .. 0.84
   4 ?    4.3   0.0     0.026        58      53      77 ..     628     653 ..     592     655 .. 0.81
   5 ?   -1.6   0.0       1.8   4.1e+03       2      25 ..     872     898 ..     871     915 .. 0.58

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.31
                 EEEEECSSHHHHHHHHHHHHTTSEEEEE CS
   Pyr_redox   1 kvvvvGgGyiglElAgalaelgkkVtvv 28 
                 +v++ G G  g  lA +l + g+ V  v
  AHX11560.1 345 RVLISGTGPAGFTLAHYLLNDGHTVIAV 372
                 699***************9999988766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 4.5
                 HHHTTEEEECSEEE CS
   Pyr_redox  50 lekngievllntkv 63 
                 +++ gi+v++n++ 
  AHX11560.1 416 VSEYGITVRWNKNY 429
                 56779999999876 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.0023
                 EEEECSSHHHHHHHHHHHH.TTSEE CS
   Pyr_redox   2 vvvvGgGyiglElAgalae.lgkkV 25 
                 vvv+G+G+++++ A+++   ++ +V
  AHX11560.1 520 VVVIGAGLTAVDSATEALTyYKVQV 544
                 8*************87644255555 PP

  == domain 4  score: 4.3 bits;  conditional E-value: 0.026
                 TTEEEECSEEEEEEEEETTS.EEEEE CS
   Pyr_redox  53 ngievllntkveeiegsedg.vesvk 77 
                 +gie++ +t++ ei ++e g v+++k
  AHX11560.1 628 EGIEFIEETEPLEIIQDEYGlVKAIK 653
                 4*******************999887 PP

  == domain 5  score: -1.6 bits;  conditional E-value: 1.8
                 EEEECSSHHHHHH...HHHHHHTTSEE CS
   Pyr_redox   2 vvvvGgGyiglEl...AgalaelgkkV 25 
                 v+ +GgG+ +  l   A+++++ g++V
  AHX11560.1 872 VLLIGGGLGNAVLfsiAKEMKRKGCQV 898
                 666777766654411144445555555 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.5   0.0     0.014        31       2      30 ..     346     374 ..     345     379 .. 0.93
   2 ?   -2.4   0.6      0.84   1.9e+03       2      18 ..     520     536 ..     520     538 .. 0.86
   3 ?    6.1   0.0    0.0022       4.9     155     206 ..     626     680 ..     614     695 .. 0.77

  Alignments for each domain:
  == domain 1  score: 3.5 bits;  conditional E-value: 0.014
                    EEEE--SHHHHHHHHHHHHTTT-EEEEES CS
  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvek 30 
                    v++ G+G AG + A+ + + G++v+ v+ 
     AHX11560.1 346 VLISGTGPAGFTLAHYLLNDGHTVIAVDG 374
                    8999*********************9986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.84
                    EEEE--SHHHHHHHHHH CS
  FAD_binding_2   2 viViGsGlAGLaAAlea 18 
                    v+ViG+Gl    +A+ea
     AHX11560.1 520 VVVIGAGLTAVDSATEA 536
                    8*******988888876 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0022
                    T...EEEEESEEEEEEEECTT.EEEEEEEEETTTTCEEEEEESEEEE-----GG... CS
  FAD_binding_2 155 g...vdfqerteadeLivedg.rvtGavvenpesgrevrirakavvlatgGfgr.al 206
                    +   ++f e+te +e+i+++   v  + +   + g+   i+a+ v++atg  ++ +l
     AHX11560.1 626 MlegIEFIEETEPLEIIQDEYgLVKAIKCL--HRGKMISINARSVIIATGTRPNsSL 680
                    34459************9654267777666..********************99433 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0    0.0011       2.5     151     220 ..     467     545 ..     449     555 .. 0.80
   2 ?    1.4   0.0     0.061   1.4e+02     140     161 ..     656     677 ..     619     697 .. 0.73
   3 ?   -3.3   0.0       1.7   3.8e+03     188     208 ..     866     886 ..     834     901 .. 0.68

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0011
  K_oxygenase 151 nlvlgvG.tepkiPevleklegkervvHsseylerkee...........llakkriaVvGsGqSaaeifedllrrqkkvelk 220
                  ++ l +G ++p+iP+v + l+    v  +s++l + +            l+ +  ++V+G+G +a + + ++l+ +k v+++
   AHX11560.1 467 HVALCIGsGNPNIPDVKNVLT--RGVRFASDFLMNLQMsgafkvnsiatLQLHMPVVVIGAGLTAVDSATEALTYYK-VQVE 545
                  7888888789*****999887..67888888888886689999999998888999**********999888887655.5555 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.061
  K_oxygenase 140 aegeeeelearnlvlgvGtepk 161
                  ++g+  +++ar++++++Gt+p+
   AHX11560.1 656 HRGKMISINARSVIIATGTRPN 677
                  6789999************995 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 1.7
  K_oxygenase 188 llakkriaVvGsGqSaaeife 208
                    ++++++ +G+G   a +f 
   AHX11560.1 866 IPSGEKVLLIGGGLGNAVLFS 886
                  56789999*****98886665 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.1   0.0   0.00015      0.35       3      31 ..     345     373 ..     344     398 .. 0.87
   2 ?   -2.0   0.0      0.74   1.7e+03     115     173 ..     625     685 ..     622     779 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.1 bits;  conditional E-value: 0.00015
                    EEEEE--SHHHHHHHHHHHHTTHHEEEEE CS
  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlve 31 
                     VlI G+GpaG++la+ L + G  v+ v+
     AHX11560.1 345 RVLISGTGPAGFTLAHYLLNDGHTVIAVD 373
                    59********************9999888 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.74
                    HHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEEEEEE--GTT..-HHHHHHT CS
  FAD_binding_3 115 aeerglqvrfktevesleqdeegvtaevrdketgeeetvrakYlvGaDGgr..Stvrktlg 173
                    a  +g+++ ++te + + qde g    ++    g+   ++a+ ++ a G r  S  r++++
     AHX11560.1 625 AMLEGIEFIEETEPLEIIQDEYGLVKAIKCLHRGKMISINARSVIIATGTRpnSSLRDEVP 685
                    5667899999999999999999988888888889999999999999999753366666666 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.59   1.3e+03       2      25 ..     348     370 ..     347     379 .. 0.77
   2 ?    3.9   0.0     0.012        26     164     186 ..     517     539 ..     499     556 .. 0.79
   3 ?    3.5   0.0     0.015        34     122     194 ..     662     733 ..     609     789 .. 0.67

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.59
  Pyr_redox_3   2 IiGaGPaGlaaaielkkagledyl 25 
                  I G GPaG + a+ l + g  +++
   AHX11560.1 348 ISGTGPAGFTLAHYLLNDGH-TVI 370
                  77**********99988777.454 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.012
  Pyr_redox_3 164 gqkvvViGgknSavDaAlelvrk 186
                  +  vvViG++ +avD A+e   +
   AHX11560.1 517 HMPVVVIGAGLTAVDSATEALTY 539
                  5679**************97655 PP

  == domain 3  score: 3.5 bits;  conditional E-value: 0.015
  Pyr_redox_3 122 tyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkya....gqkvvViGgknSavDaAlelvrkgaeVtvvt 194
                  +++A++viiAtG   +Pn    +  ++ ++ ys +++++ +     +    V+G+  Sa D    + ++ ++++   
   AHX11560.1 662 SINARSVIIATGT--RPNS---SLRDEVPELYSDMENLSFFGdldpKYSGSVVGAMASAKDKYPRITERLMRIEPTS 733
                  68999*******9..6765...4444466777777776433311122345688888888877666666655555544 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.33   7.4e+02       2      18 ..     520     536 ..     519     554 .. 0.87
   2 ?    8.2   0.0   0.00051       1.1     103     150 ..     631     674 ..     620     691 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.33
                 EEEE-SSHHHHHHHHHH CS
        GIDA   2 viViGgGhAGceAAlaa 18 
                 v+ViG+G+  +  A +a
  AHX11560.1 520 VVVIGAGLTAVDSATEA 536
                 9*******999988876 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.00051
                 HHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
        GIDA 103 eklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                 e +e+++ leii++e+  ++     +k +   +   i+a++v+iatGt
  AHX11560.1 631 EFIEETEPLEIIQDEYGLVKA----IKCLHRGKMISINARSVIIATGT 674
                 568999**********99966....9999999999************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1073 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       851  (0.047465); expected 358.6 (0.02)
Passed bias filter:                      689  (0.0384294); expected 358.6 (0.02)
Passed Vit filter:                        80  (0.00446204); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.81u 0.27s 00:00:01.08 Elapsed: 00:00:00.40
# Mc/sec: 8053.25
//
Query:       AHX11561.1  [L=149]
Description: (3R)-hydroxymyristoyl-[acyl-carrier-protein] dehydratase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.2e-30  104.2   0.0    4.8e-30  104.0   0.0    1.0  1  FabA             FabA-like domain
     0.0082   16.5   0.0      0.013   15.9   0.0    1.3  1  4HBT             Thioesterase superfamily
  ------ inclusion threshold ------
      0.084   12.4   0.0       0.12   11.9   0.0    1.3  1  MaoC_dehydratas  MaoC like domain


Domain annotation for each model (and alignments):
>> FabA  FabA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.0   0.0   8.1e-34   4.8e-30       1     137 [.      16     141 ..      16     142 .. 0.93

  Alignments for each domain:
  == domain 1  score: 104.0 bits;  conditional E-value: 8.1e-34
                 ---TT.T---SEEEEEESTCTCTSS.EEEEEEE--TTSHHHHHSSTTS----HHHHHHHHHHHHHHHHHHCC---SCCEEE-EEEEEEECEEEE-S--- CS
        FabA   1 lpark.lllldrvleieeeggkfgkGlivaekdvtpnewfFqgHFpgdPvmPGvLgleamaQlvgfyllksggdegkgrarklvlfagvdevkfrgqvt 98 
                 +p+r  +l+ld+vle++ e  +     iv + dv+p+ wfFqgHFp+ P+ PGvL++e++aQ++g+y++ +  +e  +     ++fa++++vkf+++v 
  AHX11561.1  16 IPHRDpFLFLDEVLEVNRESRS-----IVCRWDVSPDAWFFQGHFPDFPITPGVLIVESLAQAAGVYAMLTVDREYHN---RPFFFASIEKVKFKRPVS 106
                 699999***********88888.....*******************************************97655555...46799************* PP

                 TT-.EEEEEEEEEEEEECCTCEEEEEEEEEETTEEEEEE CS
        FabA  99 Pgdkklvleveikkvseekrviiiadaellvdgklvyea 137
                 Pg+ +l+l+  + k   ++ + +++d+e++++g++ +ea
  AHX11561.1 107 PGA-QLRLQAVLIK---KSMNFWKFDTEASAGGEVCAEA 141
                 ***.9**9999888...9****************99987 PP

>> 4HBT  Thioesterase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   2.1e-06     0.013      15      75 ..      72     136 ..      63     140 .. 0.83

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 2.1e-06
                 HHHHHHHHHTTST....TEEEEEEEEEEEESS-BBTTCEEEEEEEEEEEESSEEEEEEEEEETTS CS
        4HBT  15 eaagaalrslggr....gilvvvvelsidflrpvrlgdeltvearvlrlgrtsavvevevrdedg 75 
                 +aag++++   +r    +  ++++  +++f+rpv +g  l+++a +++ + +  +++ e  ++++
  AHX11561.1  72 QAAGVYAMLTVDReyhnRPFFFASIEKVKFKRPVSPGAQLRLQAVLIKKSMNFWKFDTEASAGGE 136
                 56777777777777**99*****************************999999999988877765 PP

>> MaoC_dehydratas  MaoC like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     2e-05      0.12      67     104 ..      83     120 ..      59     136 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2e-05
                      HHHHSTTEGGGEEEEEEEE-S--BTTCEEEEEEEEEEE CS
  MaoC_dehydratas  67 eeelgdnvvarvgeikvrFtkpVlpgdtlkvelevvgk 104
                       +e+ ++   +  ++kv+F +pV pg +l+ +++   k
       AHX11561.1  83 DREYHNRPFFFASIEKVKFKRPVSPGAQLRLQAVLIKK 120
                      344555577788899***************99987665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      243  (0.0135535); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1188.42
//
Query:       AHX11562.1  [L=195]
Description: outer membrane family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.5e-19   69.2   7.7    5.9e-19   68.8   7.7    1.2  1  OmpH      Outer membrane protein (OmpH-like)
  ------ inclusion threshold ------
      0.039   13.7   1.3      0.071   12.9   0.1    2.0  2  SurA_N_3  SurA N-terminal domain
       0.93    8.5   6.5        1.1    8.3   6.5    1.1  1  Atg14     Vacuolar sorting 38 and autophagy-related subunit 1
        1.4    9.6   4.9        0.5   11.1   2.3    1.6  2  DUF2203   Uncharacterized conserved protein (DUF2203)
        1.8    9.4   7.3       0.28   11.8   1.2    3.0  3  M         M protein repeat


Domain annotation for each model (and alignments):
>> OmpH  Outer membrane protein (OmpH-like)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.8   7.7   1.6e-22   5.9e-19       1     138 []      24     164 ..      24     164 .. 0.86

  Alignments for each domain:
  == domain 1  score: 68.8 bits;  conditional E-value: 1.6e-22
                 TEEEE-HHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTS....-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        OmpH   1 kiavvdvqkileespegkaaqeqlekkfkklqaeleakekelqklqeelqkkakkle...keekeqelqkkeqelqqkqqqkaqelqkkqqellkpild 96 
                 kia+vdv+ i+e+sp + a  +++++k+++++a++ +++++l+++ +el +++  l+    ++k  +l ++ +  +++++++a +l+++    +++i +
  AHX11562.1  24 KIAIVDVNAIFESSPSAAALVNDIKSKQEDIRAKFVSEKEQLDAKHKELREQKGILSeesLNQKLGALFDEAASAERRAAEAASKLEAEYISKVENIGK 122
                 8************************************************8544443234444444447777777777577777999999999999**** PP

                 HHHHHHHHHHHHTT-SEEEE.GGG-S--.-GGGB-HHHHHHHH CS
        OmpH  97 kinkaikevakekgydlvldsrgavlya.ddklDiTdeVlkkL 138
                 ++++ i + a +k++dlv++ ++++ly+ +  lDiT++V+++L
  AHX11562.1 123 EVKQLIGQHAVDKKLDLVIN-SSQALYSsAGVLDITADVITAL 164
                 ********************.6677788699*********997 PP

>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.1     2e-05     0.071      12      95 ..       9      95 ..       1     106 [. 0.74
   2 ?   -1.6   0.1      0.58   2.1e+03      35      59 ..     165     189 ..     152     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 2e-05
    SurA_N_3 12 wiakillgliila.Fv..lwGvgsylsgsgnsvakVngekIsraefqqayrrqleqlrqqlggnldaelldelglrqqvldqlidea 95
                w+ ++++g++++  +   +++v++++++s++++a Vn+ k ++++++ ++  ++eql  +  +   ++ + +++  +q l  l dea
  AHX11562.1  9 WFCTLFFGVVLADgLKiaIVDVNAIFESSPSAAALVNDIKSKQEDIRAKFVSEKEQLDAKHKELREQKGILSEESLNQKLGALFDEA 95
                5555555555544332647***********99************************9998876666666666666666666666665 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.58
    SurA_N_3  35 sgsgnsvakVngekIsraefqqayr 59 
                 ++++++va V  +++ + +++++ +
  AHX11562.1 165 NEKSSNVANVSASEVAKGDLSSKKQ 189
                 4445569999888888888877665 PP

>> Atg14  Vacuolar sorting 38 and autophagy-related subunit 14
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   6.5   0.00031       1.1      68     161 ..      43     175 ..      35     194 .. 0.71

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00031
       Atg14  68 kleelksliadlrerlqelkdklsqlkkeieekkkklaklsdklk...........kRrsdleslqneleerrkkqiaklqdaik.............. 141
                  ++++ks+++d+r++    k++l+   ke++e+k  l++ s + k           +Rr+    + ++le++  ++++++ +++k              
  AHX11562.1  43 LVNDIKSKQEDIRAKFVSEKEQLDAKHKELREQKGILSEESLNQKlgalfdeaasaERRAA--EAASKLEAEYISKVENIGKEVKqligqhavdkkldl 139
                 5688999999999999999999999999999999999999988889999999998877776..788888888888888888888877777666666666 PP

       Atg14 142 ................rieqklsslssktlesrssl 161
                                  +++++++l+ k+     ++
  AHX11562.1 140 vinssqalyssagvldITADVITALNEKSSNVANVS 175
                 665554444444444444444444444444444444 PP

>> DUF2203  Uncharacterized conserved protein (DUF2203)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   2.3   0.00014       0.5       7      79 ..      39     127 ..      33     138 .. 0.64
   2 ?   -3.0   0.0       3.1   1.1e+04      38      39 ..     173     174 ..     153     194 .. 0.40

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00014
     DUF2203   7 eAnalLpllkelleelr....alrkeleeleeeleeakaeaekse..................aaeleaeleeleaei.eelveeieelGvevkdl 79 
                  A al+  +k++ e++r    +        +e+l+++++e ++++                  aa++e++ +e+++++  e+++++e++G evk+l
  AHX11562.1  39 SAAALVNDIKSKQEDIRakfvS-------EKEQLDAKHKELREQKgilseeslnqklgalfdeAASAERRAAEAASKLeAEYISKVENIGKEVKQL 127
                 5777777888777777744442.......33333333333333333444455777899999985555555555555551689************96 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 3.1
     DUF2203  38 ea 39 
                 + 
  AHX11562.1 173 NV 174
                 11 PP

>> M  M protein repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   1.2   7.9e-05      0.28       2      19 ..      61      78 ..      60      80 .. 0.88
   2 ?   -1.0   0.1       1.2   4.3e+03       5       9 ..     108     112 ..      99     113 .. 0.70
   3 ?   -4.1   0.0         5   1.8e+04       8      11 ..     186     189 ..     184     190 .. 0.52

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 7.9e-05
           M  2 akkeLEaelqeLeeelqa 19
                +k++L+a+++eL e++ +
  AHX11562.1 61 EKEQLDAKHKELREQKGI 78
                8*************9855 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.2
           M   5 eLEae 9  
                 +LEae
  AHX11562.1 108 KLEAE 112
                 45555 PP

  == domain 3  score: -4.1 bits;  conditional E-value: 5
           M   8 aelq 11 
                 +++q
  AHX11562.1 186 SKKQ 189
                 4555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (195 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1552  (0.0865637); expected 358.6 (0.02)
Passed bias filter:                      546  (0.0304535); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.22s 00:00:00.63 Elapsed: 00:00:00.36
# Mc/sec: 1644.17
//
Query:       AHX11563.1  [L=324]
Description: phospho-N-acetylmuramoyl-pentapeptide-transferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-35  122.7  17.9    1.4e-35  122.7  17.9    2.2  2  Glycos_transf_4  Glycosyl transferase family 4
  ------ inclusion threshold ------
      0.031   13.8   0.0       0.11   12.1   0.0    2.1  1  MraY_sig1        Phospho-N-acetylmuramoyl-pentapeptide-transf


Domain annotation for each model (and alignments):
>> Glycos_transf_4  Glycosyl transferase family 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  122.7  17.9   1.5e-39   1.4e-35       4     159 ..      80     246 ..      77     247 .. 0.92
   2 ?   -1.3   0.4      0.21   1.8e+03       4     129 ..     306     319 ..     250     322 .. 0.59

  Alignments for each domain:
  == domain 1  score: 122.7 bits;  conditional E-value: 1.5e-39
  Glycos_transf_4   4 llltillilllGflDDv........lglkarlKlilqilaalililtld..lslttlglllt..qvlielglilavlltllvivgvtNavNliD 85 
                      ++++i+ ++ +Gf+DD+         g+ +r+Kl+lqi+a +i+il+++  +++++l+ l++   + ++lg + ++++++l+ivgv+NavNl+D
       AHX11563.1  80 IIFGIFSYSCVGFVDDFtkikygsnAGVLPRTKLLLQIIAGTICILLIKysVHIENLTYLFFpgGHYLDLG-WCYYIFAVLFIVGVSNAVNLTD 172
                      67899999********9888888888****************99999886667777777666667899999.888899**************** PP

  Glycos_transf_4  86 GldGlaagvsiiialalvvlaavdgrsellllalallgallGfllfNrypAkvFmGDsgslflGlvlavlailg 159
                      GldGla+++ + +++ l+ +a+++++++++l++++++ga+++f++fN +pAk+FmGD+gsl+lG+++a++ail+
       AHX11563.1 173 GLDGLAISTILSALIGLLAIAVSQHNHQVMLTIIIIVGAAAAFIPFNLRPAKIFMGDVGSLALGAIIAIIAILL 246
                      ************************************************************************86 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.21
  Glycos_transf_4   4 llltillilllGflDDvlglkarlKlilqilaalililtldlslttlgllltqvlielglilavlltllvivgvtNavNliDGldGlaagvsii 97 
                      +                                                                                             
       AHX11563.1 306 FW-------------------------------------------------------------------------------------------- 307
                      22............................................................................................ PP

  Glycos_transf_4  98 ialalvvlaavdgrsellllalallgallGfl 129
                                          +++l++ +lG+l
       AHX11563.1 308 --------------------LTSLAMMILGLL 319
                      ....................223333444444 PP

>> MraY_sig1  Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   1.2e-05      0.11       4      13 .]      50      59 ..      47      59 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.2e-05
   MraY_sig1  4 TPTMGGvlIi 13
                TPT GG++I+
  AHX11563.1 50 TPTLGGLVIC 59
                *********6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1136  (0.063361); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.51u 0.22s 00:00:00.73 Elapsed: 00:00:00.40
# Mc/sec: 2423.42
//
Query:       AHX11564.1  [L=246]
Description: 3-oxoacyl-[acyl-carrier-protein] reductase FabG [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-63  212.0   0.2    9.8e-63  211.8   0.2    1.0  1  adh_short_C2     Enoyl-(Acyl carrier protein) reductase
    8.7e-54  181.9   0.5      1e-53  181.7   0.5    1.0  1  adh_short        short chain dehydrogenase
    2.2e-18   66.8   0.3      3e-18   66.4   0.3    1.3  1  KR               KR domain
    7.5e-05   22.3   0.4    0.00029   20.4   0.4    2.0  1  Epimerase        NAD dependent epimerase/dehydratase family
    0.00047   19.4   0.1    0.00072   18.8   0.1    1.2  1  Polysacc_synt_2  Polysaccharide biosynthesis protein
    0.00097   19.2   0.1     0.0017   18.4   0.1    1.4  1  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0012   18.3   0.0     0.0022   17.5   0.0    1.4  1  GDP_Man_Dehyd    GDP-mannose 4,6 dehydratase
     0.0048   16.8   0.0     0.0058   16.5   0.0    1.1  1  NAD_binding_10   NAD(P)H-binding
  ------ inclusion threshold ------
      0.026   13.9   0.1      0.048   13.0   0.1    1.4  1  ThiF             ThiF family
      0.052   14.1   0.1       0.74   10.4   0.1    2.1  2  F420_oxidored    NADP oxidoreductase coenzyme F420-dependent
       0.17   11.4   0.0       0.24   10.9   0.0    1.2  1  NmrA             NmrA-like family
        0.2   11.8   0.0       0.57   10.4   0.0    1.8  2  DUF4253          Domain of unknown function (DUF4253)


Domain annotation for each model (and alignments):
>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  211.8   0.2   6.6e-66   9.8e-63       1     233 [.      14     243 ..      14     244 .. 0.95

  Alignments for each domain:
  == domain 1  score: 211.8 bits;  conditional E-value: 6.6e-66
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGHHHHHHHHHHHTTSEEEE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HHHHHH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneeakkrveelaeelgaevlecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsreefdr 97 
                   Ga  gIG aiA+ l++ Ga++v++  nee+ k+++++ +  +a+++  D +d ++v+ l+e++++++g+lD++v nag++++  +  l ++ e ++r
    AHX11564.1  14 GASGGIGSAIARYLHSCGARLVISGTNEEKLKTLNSAIN-NDARIVLQDLSDLKNVHLLIEACKNELGGLDGMVCNAGMTDD--KLSLRMNLECWQR 107
                   8999*************************9544444444.35668*************************************..999********** PP

                   HHHHHTHHHHHHHHHHHH.HCTSC.CEEEEEEEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHCTGGGGSTTHHHHHHHH CS
  adh_short_C2  98 aldvnlyslfllakaalp.lmkeg.gsivnlssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikTlaasgikgfdelleel 192
                   ++dvnl+s f l k+a+  +m+e+ g+ivn+ssv a ++ p+++ y+a+Ka+++a+++++A+e++ kg+ +N+++pg+ikT ++++++  de  +++
    AHX11564.1 108 IIDVNLTSSFILNKHAAAlMMREKyGRIVNISSVVAVMGNPGQANYCASKAGMIAMSKSFAREFATKGVLINCIAPGFIKTSMTDKLT--DEQHSHV 202
                   ******************7788879**************************************************************8..8999*** PP

                   HHHSTTSS-B-HHHHHHHHHHHCSGGGTT--SEEEEESTTG CS
  adh_short_C2 193 earaplgrlgtpeevaeaalfLasdeasyitGqtlvvDgGl 233
                    + +p++r+g+p+e   +++fL+sd+asyitGqt++v+gG+
    AHX11564.1 203 LNGIPMKRIGEPQELCGITAFLLSDMASYITGQTFHVNGGM 243
                   ****************************************8 PP

>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   0.5   6.8e-57     1e-53       1     194 [.       8     198 ..       8     199 .. 0.98

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 6.8e-57
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEEEESCHHHHHHHHHHHHHTTSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCSHH CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvvvdrseekleevakelkeegakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfselsee 99 
                 k +l+tGas+GIG aia+ l + Ga++v+ + +eekl+++ + ++++   a ++  D++d ++v  l+e+++++lg+ld +v NAG+t ++   +++ e
  AHX11564.1   8 KRILITGASGGIGSAIARYLHSCGARLVISGTNEEKLKTLNSAINND---ARIVLQDLSDLKNVHLLIEACKNELGGLDGMVCNAGMTDDKLSLRMNLE 103
                 679************************************99999996...9************************************************ PP

                 HHHHHHHHHTHHHHHHHHHHHHHHHHCTTEEEEEEEEGGGTSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSBSSHHHHHHCTHH CS
   adh_short 100 ewervievNltgvflltravlpamlkqssGrIvnvsSvagkvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlvdTdmakelreke 194
                  w+r+i+vNlt+ f l ++++  m++++ GrIvn+sSv++ ++++g+a Y+AsKa+++++++s+a+e+a++g+ +n++aPG+++T m+ +l++++
  AHX11564.1 104 CWQRIIDVNLTSSFILNKHAAALMMREKYGRIVNISSVVAVMGNPGQANYCASKAGMIAMSKSFAREFATKGVLINCIAPGFIKTSMTDKLTDEQ 198
                 *****************************************************************************************998875 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.3     2e-21     3e-18       4     161 ..      11     165 ..       9     203 .. 0.88

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 2e-21
                 EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE---------TTT-- CS
          KR   4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAgvlrdklleemt 101
                 litG+ Gg+G ++ar l + gar lv+ + +       ++++++l++  + + ++v  D+sd ++v+ l+e++k+e + + G +  Ag+++dkl  +m+
  AHX11564.1  11 LITGASGGIGSAIARYLHSCGAR-LVISGTN-------EEKLKTLNSAiNNDARIVLQDLSDLKNVHLLIEACKNELGGLDGMVCNAGMTDDKLSLRMN 101
                 9****************998886.7777777.......34566666654778888889***************************************** PP

                 HHHHHHHHTTTTHHHHHHHHHTTT....S--SEEEEEEEHHHHH--TT-HHHHHHHHHHHHHHH CS
          KR 102 aedleqvlapKvkGawnLhelled....esldffvlfSSiagllgsagqanYaaaNaflDalae 161
                  e +++++   ++ +  L++  +     e+   +v +SS+ +++g++gqanY a  a + a+ +
  AHX11564.1 102 LECWQRIIDVNLTSSFILNKHAAAlmmrEKYGRIVNISSVVAVMGNPGQANYCASKAGMIAMSK 165
                 ******************98777666779999**********************9887766655 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.4   1.9e-07   0.00029       1      61 [.      10      73 ..      10     203 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.9e-07
                EEEETTTSHHHHHHHHHHHHCTSE.EEEEES-STTTTCHHCHHC.....EEEE--TT-HHHHHHHHH CS
   Epimerase  1 ilVtGatGfiGsalvkallekgye.vigldrlssasntarledl.....elveldltdrsalerlfk 61
                il+tGa+G iGsa++++l + g + vi  +++++ + t +   +     ++v  dl d ++++ l++
  AHX11564.1 10 ILITGASGGIGSAIARYLHSCGARlVISGTNEEKLK-TLN--SAinndaRIVLQDLSDLKNVHLLIE 73
                8*********************99677666663332.222..2233566888888888887766555 PP

>> Polysacc_synt_2  Polysaccharide biosynthesis protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.1   4.8e-07   0.00072       1      73 [.      10      75 ..      10      80 .. 0.72

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 4.8e-07
                     EEEETTTSHHHHHHHHHHHHHB-SEEEEEES-HHHHHHHHHH......-TTEEEE....E--TT-HHHHHHHT CS
  Polysacc_synt_2  1 vlvtGagGsiGselvrqilkkkpkkiillerdElklyeiekeleeelkkkklkveivpvigdvrdkerlekal 73
                     +l+tGa+G iGs++ r + ++  +++++  ++E kl ++++ ++   ++ ++   +++ + d+++ + l +a+
       AHX11564.1 10 ILITGASGGIGSAIARYLHSCG-ARLVISGTNEEKLKTLNSAIN---NDARI---VLQDLSDLKNVHLLIEAC 75
                     89***********998877765.68999************9984...34344...233455555555554444 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.4   0.1   1.1e-06    0.0017       9      79 ..       4      71 ..       1      82 [. 0.80

  Alignments for each domain:
  == domain 1  score: 18.4 bits;  conditional E-value: 1.1e-06
                  ..TT-EEEEES-.SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHHT.E.T-EEEEGCGHHHHHHT-SEE CS
  Shikimate_DH  9 slkekkvlliGa.GemaelvakhLlakgvkkvvvaNRtlerakelaeelkge.eiealkleelkellaeadvv 79
                  slk+k++l+ Ga G +++ +a++L++ g++ +v+ + + e+ k+l + ++++ +i  ++l++lk    +++++
    AHX11564.1  4 SLKDKRILITGAsGGIGSAIARYLHSCGAR-LVISGTNEEKLKTLNSAINNDaRIVLQDLSDLK----NVHLL 71
                  599********98****************9.******************554044445555554....55555 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.0   1.4e-06    0.0022       1      75 [.      11      76 ..      11      79 .. 0.83

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 1.4e-06
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHHHHT CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerllaevq 75
                   LiTG +G iGs +a++L + g + ++     s +n +++++l +     ++++ +++  Dl+D ++++ l++ ++
     AHX11564.1 11 LITGASGGIGSAIARYLHSCGARLVI-----SGTNEEKLKTLNS----AINNDARIVLQDLSDLKNVHLLIEACK 76
                   9*********************9976.....5556666777654....35678899***********99998765 PP

>> NAD_binding_10  NAD(P)H-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.9e-06    0.0058       1     113 [.      14     152 ..      14     208 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.9e-06
                     TTTSHHHHHHHHHHHHC-T-EEEEEETTHHHCHHHHCT..TTCEEEE--TT-CCHHHHHHT.......T-SEEEES---TCC....HHHH..... CS
  NAD_binding_10   1 GAtGkvGrllvkellargghevtalvRnpeklaeleae..eglevvegdvtdvedlaealk.......gadaVvsalggggk....deeg..... 77 
                     GA+G++G+++++ l + g  ++++   n+ekl+ l ++  + +++v  d++d + +   ++       g d  v+++g +++    +  +     
      AHX11564.1  14 GASGGIGSAIARYLHSCG-ARLVISGTNEEKLKTLNSAinNDARIVLQDLSDLKNVHLLIEacknelgGLDGMVCNAGMTDDklslR--Mnlecw 105
                     9****************5.9999999******9887443367778887777755544444433366669998777776666546551..255667 PP

                     ..............HHHHHHHHHHCT--EEEEEEETTTTSGCGCHHHHHH CS
  NAD_binding_10  78 ..............aknivdaakeagvkRfvlvsaigvgdevpgefgewn 113
                                    k++++ + +++  R+v +s++ +     g+ g+ n
      AHX11564.1 106 qriidvnltssfilNKHAAALMMREKYGRIVNISSVVAVM---GNPGQAN 152
                     777788888899999999999999*******999987653...3444443 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   3.2e-05     0.048      16      43 ..       5      33 ..       3      44 .. 0.92

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.2e-05
                HHTSEEEEE--.SHHHHHHHHHHHHHTTT CS
                xxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
        ThiF 16 LrdskvllvGa.GglGsellknLalsGvg 43
                L+d+++l+ Ga Gg+Gs ++++L  +G +
  AHX11564.1  5 LKDKRILITGAsGGIGSAIARYLHSCGAR 33
                99********88************99976 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.1   0.00049      0.74       6      51 ..      15      56 ..       9      76 .. 0.83
   2 ?    1.6   0.0      0.27   4.1e+02      27      80 ..     140     192 ..     124     203 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 0.00049
                   TTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC-EEE CS
  F420_oxidored  6 GaGnmgealasgllaagaqpheivvansrnpekaeelaeelgvkvt 51
                   ++G +g+a+a+ l ++g     +v+    n+ek++ l ++++ ++ 
     AHX11564.1 15 ASGGIGSAIARYLHSCG---ARLVIS-GTNEEKLKTLNSAINNDAR 56
                   5799*************...999956.9*********999986655 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.27
                    CEEEEEESSCCCHHHHHHHHC-EEECECHHHHHHH-SEEEE-S-HHHHHHHHHH CS
  F420_oxidored  27 eivvansrnpekaeelaeelgvkvtavdneeaaeeadvvvlavkpedveevlse 80 
                    ++v a   np +a++ a+++g  +++++ +   +   v++ ++ p  ++  +++
     AHX11564.1 140 SVV-AVMGNPGQANYCASKAGMIAMSKSFAREFATKGVLINCIAPGFIKTSMTD 192
                    555.66889999999999999666665555555557788888888777766554 PP

>> NmrA  NmrA-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00016      0.24       1      59 [.      10      69 ..      10     108 .. 0.72

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00016
                EEESSTTSHHHHHHHHHHHHHT-EEEEE.ES-S-SHHHHHHHHSTTEEEES-TT-HHHHH CS
        NmrA  1 IlviGaTGrqGksvvrallkaghkvral.vRdtkselakslkeaGvelvkgdlddkeslv 59
                Il++Ga+G +G++++r+l + g +  +  + ++k ++++s  ++ + +v +dl d ++++
  AHX11564.1 10 ILITGASGGIGSAIARYLHSCGARLVISgTNEEKLKTLNSAINNDARIVLQDLSDLKNVH 69
                89******************9987655414444556666666778888877766544443 PP

>> DUF4253  Domain of unknown function (DUF4253)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       4.5   6.8e+03      39      57 ..      26      44 ..      21      57 .. 0.63
   2 ?   10.4   0.0   0.00038      0.57      12      48 ..     140     176 ..     135     203 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4.5
     DUF4253 39 Weerygaelvgigfdtlel 57
                + + +ga+lv  g++  +l
  AHX11564.1 26 YLHSCGARLVISGTNEEKL 44
                4456888888777665444 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00038
     DUF4253  12 dilaylgwaGainyeltnedlvavlrsWeerygaelv 48 
                  ++a++g  G++ny+ +++ ++a+ +s++++++ + v
  AHX11564.1 140 SVVAVMGNPGQANYCASKAGMIAMSKSFAREFATKGV 176
                 6899**************************9987644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (246 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       552  (0.0307881); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1876.93
//
Query:       AHX11565.1  [L=48]
Description: hypothetical protein NHE_0630 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       306  (0.0170673); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.21s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 392.41
//
Query:       AHX11566.1  [L=150]
Description: RNase H family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.2e-45  153.4   0.0    4.7e-45  153.3   0.0    1.0  1  RNase_H   RNase H
    0.00071   19.4   0.0      0.001   18.9   0.0    1.3  1  RVT_3     Reverse transcriptase-like


Domain annotation for each model (and alignments):
>> RNase_H  RNase H
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.3   0.0   5.3e-49   4.7e-45       2     142 ..       2     142 ..       1     143 [. 0.89

  Alignments for each domain:
  == domain 1  score: 153.3 bits;  conditional E-value: 5.3e-49
                 .SEEEEEEEEEECTTTCEEEEEEECTT...EEEEEEECCCCHHHHHHHHHHHHHHH.TT.SCSEEEEEES-HHHHHHHHCCCHHHHHTTSSSETTSSBH CS
     RNase_H   2 kavvvYtDGsclgnpgeggagavlykeg.arnisapleeaqtnnraELsAvieaLk.alksdekvniytDSkYvvkgitqwvhrwkknawkttseqkpv 98 
                 +++++YtDG+c+gnpg+gg++a++ +eg  + i +  e  +tnn++EL+A+i+aL+   ++++++++ytDS+Yv+kgit+w+++w kn+w ++s++ pv
  AHX11566.1   2 EKYIIYTDGACSGNPGPGGWAAIIIQEGvGERIISGKEISTTNNQMELIAAIKALEsFEEKGQRITLYTDSNYVYKGITSWIQGWMKNRWYNSSKE-PV 99 
                 6789******************764454444444444458****************544666****************************888888.** PP

                 TTHHHHHHHHHCHCSSEEEEEE-SCCSSSTHHHHHHHHHHHHHH CS
     RNase_H  99 knkdlaellkelakkkkvqlkwvkgHaGvpkgNemaDrlAkeaa 142
                 knk+++ +l+++   +++++ wvk+H+G+ ++Ne +Dr+A+++a
  AHX11566.1 100 KNKEMWLRLHAVSLLHDIEWFWVKAHNGD-YYNEIVDRIARQEA 142
                 *********99999***************.9**********987 PP

>> RVT_3  Reverse transcriptase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   1.1e-07     0.001       2      78 ..       8      81 ..       7     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 1.1e-07
       RVT_3  2 fdgafkkksgaggagvvirds.nGevllagaeklqgkasveeAElqALlrGLqlalklgirrlvvegDsktvvqllng 78
                +dga++ + g gg++++i ++  Ge++ +g+e    ++++ + El A + +L+   + g +r+++ +Ds  v++ +++
  AHX11566.1  8 TDGACSGNPGPGGWAAIIIQEgVGERIISGKEI---STTNNQMELIAAIKALESFEEKG-QRITLYTDSNYVYKGITS 81
                79***********9999988879********88...8889999**********998887.78*********9998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (150 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       580  (0.0323498); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1213.12
//
Query:       AHX11567.1  [L=252]
Description: methyltransferase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-12   47.3   0.0      3e-12   46.7   0.0    1.2  1  Methyltransf_23  Methyltransferase domain
    2.4e-10   40.9   0.1    4.9e-10   39.9   0.1    1.6  1  Methyltransf_11  Methyltransferase domain
      1e-06   29.3   0.0    2.9e-06   27.9   0.0    1.8  1  Methyltransf_25  Methyltransferase domain
      1e-05   25.4   0.0    4.2e-05   23.4   0.0    1.9  1  Methyltransf_31  Methyltransferase domain
    1.8e-05   25.4   0.1    4.9e-05   24.0   0.1    1.9  1  Methyltransf_12  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.7   0.0   8.3e-16     3e-12      16     162 ..      26     176 ..       5     179 .. 0.79

  Alignments for each domain:
  == domain 1  score: 46.7 bits;  conditional E-value: 8.3e-16
  Methyltransf_23  16 llpk.lraggrvLdiGcGtGillevlrengf....svtgvDlspeaveiae.kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppellr 103
                      ll+k       vL +G+  G+ l  l++ ++    ++t  D+++e+ + ++ +++   +d+f     +   +kfdl+++ ++l+hv ++  +++
       AHX11567.1  26 LLEKiSGNFTDVLNLGAHRGEILLALKDAPYlrfeNITHLDMCDEMLKYVRgEKIVVADDNF-----DLGVRKFDLVISGMFLHHVNNLVDVFS 114
                      33332345559***********999*7765555589*********99999997777777777.....44558********************** PP

  Methyltransf_23 104 qiatllkpgGylllseplaslkedrllldwlylvpag.....rhisffsarslkelleeaGlev 162
                      +i++ lkp+G ++ s ++ +   ++ l++  + ++++     r++ f+  ++ ++ll++ G++v
       AHX11567.1 115 CIHETLKPDGICVASLFGPE--TLSELKQAIFNAEMDlgfvpRVSPFIHIKDAGRLLQRVGFSV 176
                      ****************9875..44445554444444444556899*****************86 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.9   0.1   1.4e-13   4.9e-10       1      95 [.      38     127 ..      38     128 .. 0.84

  Alignments for each domain:
  == domain 1  score: 39.9 bits;  conditional E-value: 1.4e-13
                      EEET-TTSHHHHHHH.HTT....SEEEEEES-HHHHHHHHHHCCHHT-EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEE CS
  Methyltransf_11   1 LdvGcGtGrlaeala.krg....arvvgvDlskemlklakekaseeglkvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLk 89 
                      L++G+ +G ++ al+        ++++ +D+++emlk+++    +e+    +vvad   + +   +fDlv+s ++lhhv+++ ++++ i+  Lk
       AHX11567.1  38 LNLGAHRGEILLALKdA-PylrfENITHLDMCDEMLKYVR----GEK----IVVADDN-FDLGVRKFDLVISGMFLHHVNNLVDVFSCIHETLK 121
                      67899999999999951.34566*************8774....443....4777766.6788888**************************** PP

                      EEEEEE CS
  Methyltransf_11  90 pgGllv 95 
                      p+G++v
       AHX11567.1 122 PDGICV 127
                      ****98 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   0.0   8.1e-10   2.9e-06       1      97 []      37     124 ..      37     124 .. 0.87

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 8.1e-10
                      EEEET-TTSHHHHHHHCTS..TSSEEEEEESSHHHHHHHHHHHHHTTTTEEEEESBCCGBSSSTTTEEEEEEEST.GGGSSHHHHHHHHHHHHH CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrl..gkakvtgvDiseemleaareraeeeglnvefvqgdaedlpfedgsfDlvvssga.lhhlsdedlekalkeiar 91 
                      vL lG+ +G+++lal ++     +++t +D+ +eml+++r +         +v++d +++++  ++fDlv+s g+ lhh++  +l ++++ i++
       AHX11567.1  37 VLNLGAHRGEILLALKDAPylRFENITHLDMCDEMLKYVRGEK--------IVVAD-DNFDLGVRKFDLVIS-GMfLHHVN--NLVDVFSCIHE 118
                      89**************9954458****************9877........45555.566666778******.78799998..899******** PP

                      HEEEEE CS
  Methyltransf_25  92 vLkpgG 97 
                       Lkp+G
       AHX11567.1 119 TLKPDG 124
                      *****9 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.4   0.0   1.2e-08   4.2e-05       7     120 ..      37     142 ..      32     171 .. 0.72

  Alignments for each domain:
  == domain 1  score: 23.4 bits;  conditional E-value: 1.2e-08
  Methyltransf_31   7 vlDlGCGtGeltfelae..elgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDlilsnevlnaladpdkileeie 98 
                      vl lG+  Ge++++l +   l++  +++ +D+  e++++ r +          + + d ++l      +kfDl++s  +l++++++ +++  i+
       AHX11567.1  37 VLNLGAHRGEILLALKDapYLRF-ENITHLDMCDEMLKYVRGE-------K-IVVADDNFDLG----VRKFDLVISGMFLHHVNNLVDVFSCIH 117
                      56666666666666665543322.3366666666666666663.......1.13445555555....279************************ PP

  Methyltransf_31  99 rvlkpggilliedpr..llaelp.a 120
                      + lkp+gi++++ +   +l+el+ a
       AHX11567.1 118 ETLKPDGICVASLFGpeTLSELKqA 142
                      **********999886677777643 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.1   1.4e-08   4.9e-05      52      98 ..      83     125 ..      38     126 .. 0.67

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 1.4e-08
  Methyltransf_12  52 elealdlldldggssfDlvvasnvlhhlkdirevldnirklLkpgGr 98 
                        ++ d     g  +fDlv++  +lhh++++ +v++ i++ Lkp+G+
       AHX11567.1  83 ADDNFD----LGVRKFDLVISGMFLHHVNNLVDVFSCIHETLKPDGI 125
                      222222....2336********************************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       460  (0.0256568); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.37
# Mc/sec: 2033.41
//
Query:       AHX11568.1  [L=157]
Description: transcription elongation factor GreA domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.6e-29   99.9   1.0      1e-28   99.2   1.0    1.3  1  GreA_GreB_N   Transcription elongation factor, N-terminal
    1.3e-28   98.7   0.9    2.7e-28   97.7   0.9    1.5  1  GreA_GreB     Transcription elongation factor, GreA/GreB, C-t
  ------ inclusion threshold ------
      0.057   12.4   0.3      0.068   12.1   0.3    1.1  1  Phage_cap_P2  Phage major capsid protein, P2 family
      0.078   12.7   0.0       0.11   12.2   0.0    1.3  1  Ten1_2        Telomere-capping, CST complex subunit


Domain annotation for each model (and alignments):
>> GreA_GreB_N  Transcription elongation factor, N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   99.2   1.0   2.3e-32     1e-28       2      71 .]       5      74 ..       4      74 .. 0.99

  Alignments for each domain:
  == domain 1  score: 99.2 bits;  conditional E-value: 2.3e-32
                 EE-HHHHHHHHHHHHHHHHXHHHHHHHHHHHHHHHSSSTSSHHHHHHHHHHHHHHHHHHHHHHHHHTEEE CS
  GreA_GreB_N  2 ylTkegyekleeeLeelktverpeiaeaikeareeGDlsENaeYdaAkeeqaeiearIreLedkLanaev 71
                 ++T+egy +l++eLe+l +v  p i++a+++are GDlsENaeY++A++eq+++e++I eLe++La+ae+
   AHX11568.1  5 PITREGYVRLKDELEHLVKVVKPSIIAAVAQARELGDLSENAEYHEARKEQSFVEGKILELESQLAKAEI 74
                 89******************************************************************98 PP

>> GreA_GreB  Transcription elongation factor, GreA/GreB, C-term
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.7   0.9     6e-32   2.7e-28       2      76 ..      81     155 ..      80     156 .. 0.98

  Alignments for each domain:
  == domain 1  score: 97.7 bits;  conditional E-value: 6e-32
                 ..SS--TT-EEEEE-.SS--EEEE----TTT-BS-SSB--TTSHHHHHHTT--TT-EE---BTTB---EEEEEEX CS
   GreA_GreB   2 pkdvVtfGstVtledldtgeeetytiVgpdeadpskgkiSveSPlGkaLlgkkvGdevevkapsgkikveIlkie 76 
                 + d+V+fG+ Vt+e+l++g  +ty+iVg+ e+++++ kiS  SP+Gka+++k+ Gd+ve+++p+g++ ++Ilk+e
  AHX11568.1  81 SGDKVKFGASVTVENLENGTSTTYQIVGNVESNIKERKISLSSPIGKAIMNKEAGDVVEIELPNGQKIYKILKVE 155
                 569***********************************************************************8 PP

>> Phage_cap_P2  Phage major capsid protein, P2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.3   1.5e-05     0.068       7      75 ..      31      99 ..      27     116 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 1.5e-05
  Phage_cap_P2  7 arlaklngveseevsekFsvepsveqkLeekiqessefLkkInvvgVdeqkGekvglgvsgliasrtdt 75
                  a++a++ ++ + + ++++  + + +  +e ki+e ++ L k  +++V++++G+kv+ g+s ++   ++ 
    AHX11568.1 31 AAVAQARELGDLSENAEYHEARKEQSFVEGKILELESQLAKAEIIDVSQLSGDKVKFGASVTVENLENG 99
                  6677777776666678888888889999******************************99887665555 PP

>> Ten1_2  Telomere-capping, CST complex subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   2.4e-05      0.11      46      95 ..      78     128 ..      41     132 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.4e-05
      Ten1_2  46 eeskqaelkvetdl.vepfearlgslyqviGelekekedgeivlrARvlrc 95 
                 ++ +++++k  +++ ve++e  + ++yq++G++e++ ++++i l + ++++
  AHX11568.1  78 SQLSGDKVKFGASVtVENLENGTSTTYQIVGNVESNIKERKISLSSPIGKA 128
                 556777888888888*********************999999999887776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       848  (0.0472977); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1188.60
//
Query:       AHX11569.1  [L=466]
Description: dihydrolipoyl dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-67  225.7   0.1    1.1e-66  225.1   0.1    1.3  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
      9e-38  128.9   0.4    6.4e-37  126.2   0.3    2.3  2  Pyr_redox_dim   Pyridine nucleotide-disulphide oxidoreductase
    2.7e-22   79.1   3.2    8.3e-18   64.7   0.0    3.1  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    4.1e-14   52.5   2.4    1.8e-09   37.3   0.0    2.2  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    1.2e-13   50.6   9.6    2.3e-06   26.6   0.4    4.3  4  HI0933_like     HI0933-like protein
    1.3e-11   44.6   0.3    4.1e-09   36.3   0.1    2.3  2  FAD_oxidored    FAD dependent oxidoreductase
    6.4e-11   42.0   8.1    1.5e-07   30.8   1.0    3.8  4  FAD_binding_2   FAD binding domain
    7.8e-11   41.7   7.8    3.6e-07   29.6   3.4    2.9  2  GIDA            Glucose inhibited division protein A
    1.9e-08   34.4   7.3    8.7e-06   25.9   0.3    3.3  3  NAD_binding_8   NAD(P)-binding Rossmann-like domain
    5.4e-08   32.8   4.2    0.00071   19.3   0.2    3.9  4  DAO             FAD dependent oxidoreductase
    9.3e-07   28.4   2.2       0.21   10.9   0.1    3.3  3  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
    1.2e-06   28.0   6.0     0.0023   17.2   0.5    3.9  4  FAD_binding_3   FAD binding domain
    2.8e-05   23.5   6.9    0.00036   19.9   0.4    2.9  3  Thi4            Thi4 family
    3.4e-05   23.1   2.2       0.12   11.4   0.8    2.6  3  Lycopene_cycl   Lycopene cyclase protein
     0.0067   16.9   0.2          5    7.6   0.0    3.2  3  XdhC_C          XdhC Rossmann domain
     0.0068   16.3   2.6      0.022   14.6   0.1    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
  ------ inclusion threshold ------
      0.025   14.1   0.0       0.18   11.3   0.0    2.0  2  DUF1609         Protein of unknown function (DUF1609)
      0.027   13.6   0.2        4.3    6.4   0.0    2.7  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
      0.037   14.5   0.3        6.5    7.3   0.0    3.0  3  NAD_binding_7   Putative NAD(P)-binding
      0.051   13.1   1.8        5.5    6.5   0.0    2.5  2  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
      0.074   12.4   0.2       0.74    9.2   0.0    2.3  2  2-Hacid_dh_C    D-isomer specific 2-hydroxyacid dehydrogenase
       0.19   10.5   1.5       0.57    9.0   0.1    2.0  2  Trp_halogenase  Tryptophan halogenase


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.1   0.1   1.3e-69   1.1e-66       1     294 []      13     331 ..      13     331 .. 0.93

  Alignments for each domain:
  == domain 1  score: 225.1 bits;  conditional E-value: 1.3e-69
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEE....TTHCHHHCSHHHHCHHHHHHHHHHHHH.........................HHHHCHHHHCCC CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxx.........................xxxxxxxxxxxx RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlve....legtclnggcllskallgvaedaeias.........................evvkklnqgiel 69 
                  +dvvviGgGpAG+ +++++aq g++v+++e    l+gtcln+gc++skall+++ ++  a+                         + vk l qgi++
   AHX11569.1  13 FDVVVIGGGPAGYVCSIKAAQLGMRVACIEkrsvLGGTCLNEGCIPSKALLHSSYAYYSARnhfaalgiecsdvklnlekmmenktKIVKDLAQGIDF 110
                  69******************************************************999999************************************ PP

                  CHCCTCEEEEESCEEEEETEEEC....TCEEEEEESEEEE---EEE-BCTCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  70 llgeevvkidpgkkkvklekkke....gdeekiaydklvlAtGssprdlgipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalak 163
                  l +++++++ +g++ ++   +++    +  e++  +++vlAtGs++  ++     e+      +l s  al+l+ +p++++vvGgG+iG+E+A+++++
   AHX11569.1 111 LFKKNKIALFRGAGSIVNGGNQKlvsiDGSETVHTKYIVLATGSESAEFPFVKCDEK-----NILSSRGALSLESVPQSMIVVGGGAIGLEMASVWSR 203
                  *************999998877789**8889*************9999944433233.....5799******************************** PP

                  HT-EEEEEESSSSSSTTS-HHHHHHHHHHHHHTTEEEEESCEEEEEEETTE.EEE.EEETTSCEEEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 164 lgkevtlveardrllraldkelsaaleealekeGvevklgtsvkeidgnge.kle.vvledgeeidadlvvvavGvrpstelleeklglelderggiv 259
                  lg +v l+e +dr+  a d e+s +l + l+k+G++++l ++++ i++ +  +++  +++++e++ a+ +++++G++p ++ l   + le +++g+i+
   AHX11569.1 204 LGTKVILIEFCDRIAAASDGEVSSYLLKSLKKQGITFHLSSRITSIESGNLvSASfQKDGKEEKVSAEKILISIGRKPYSSDL--GIELEKNSAGFIK 299
                  ********************************************99988764333567777777***************9886..677777******* PP

                  --TTSBESSTTEEE-GGGCTECCSS--HHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 260 vdeflrtnvpgiyaiGDvaggkggpelaqaAvqqG 294
                  vd++ +t+vpgiya+GDv+    gp+la++A +++
   AHX11569.1 300 VDKNFQTSVPGIYAVGDVI---PGPMLAHKAEDEA 331
                  *******************...*********9987 PP

>> Pyr_redox_dim  Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.7   1.4e+03      18      69 ..     265     315 ..     264     319 .. 0.79
   2 !  126.2   0.3   7.9e-40   6.4e-37       1     110 []     348     456 ..     348     456 .. 0.98

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.7
                    HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEET.TTTBEEEEEEEC CS
  Pyr_redox_dim  18 eeeAkaagieikvgkfpfkangralayaetkgfvKlvada.ktgkvlGahivG 69 
                    ee++ a++i i++g+ p+++     +++++ gf+K+  d+  +  v G+  vG
     AHX11569.1 265 EEKVSAEKILISIGRKPYSSDLGIELEKNSAGFIKV--DKnFQTSVPGIYAVG 315
                    88999999999999999999999999999******8..442444566666555 PP

  == domain 2  score: 126.2 bits;  conditional E-value: 7.9e-40
                    BEEEEESSSEEEEEES-HHHHHHHHSGEEEEEEEEECGHHHCHTTHTEEEEEEEEETTTTBEEEEEEECTTHHHHHHHHHHHHHTTSBHHHHHTSB CS
  Pyr_redox_dim   1 iptvvftdpevasvGlteeeAkaagieikvgkfpfkangralayaetkgfvKlvadaktgkvlGahivGpgageliqelavaikagltvedladti 96 
                    ip+v++t+pevasvG+teee+ka  +++kv kfpf+an+ra++ ++t+gfvK+++d+  + +lG+hi+G +a++li+e+ +a+++g+++ed+a+t+
     AHX11569.1 348 IPSVIYTHPEVASVGKTEEELKALDVQYKVSKFPFAANSRAKTTNDTEGFVKILVDE-HDTILGVHIIGASASSLIAEAVLAMEYGASAEDIARTC 442
                    7******************************************************98.899*********************************** PP

                    SSSSSTGGGGHCHH CS
  Pyr_redox_dim  97 hihPtlsealkeaa 110
                    h hP l+ea+keaa
     AHX11569.1 443 HSHPDLNEAVKEAA 456
                    ***********985 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.7   0.3   8.6e-05      0.07       2      35 ..      15      48 ..      14      56 .. 0.91
   2 !   64.7   0.0     1e-20   8.3e-18       2      69 ..     185     252 ..     184     263 .. 0.94

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 8.6e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                vvv+GgG  g  +   +a+lg +V ++e ++ l 
  AHX11569.1 15 VVVIGGGPAGYVCSIKAAQLGMRVACIEKRSVLG 48
                8***************************998776 PP

  == domain 2  score: 64.7 bits;  conditional E-value: 1e-20
                 EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHTTEEEECSEEEEEEEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekngievllntkveeiegs 69 
                 ++vvGgG iglE+A+++++lg kV ++e  d++  + D e+s++l ++l+k+gi+++l++++++ie  
  AHX11569.1 185 MIVVGGGAIGLEMASVWSRLGTKVILIEFCDRIAAASDGEVSSYLLKSLKKQGITFHLSSRITSIESG 252
                 79***************************************************************943 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.9   1.7e-05     0.014       1      32 [.      16      46 ..      16      53 .. 0.91
   2 !   37.3   0.0   2.2e-12   1.8e-09     113     305 .]     132     315 ..      69     315 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.7e-05
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEkgni 32
                 ++iG+GPaG  + i++ ++g+ ++  +Ek ++
   AHX11569.1 16 VVIGGGPAGYVCSIKAAQLGM-RVACIEKRSV 46
                 79*******************.799***9865 PP

  == domain 2  score: 37.3 bits;  conditional E-value: 2.2e-12
  Pyr_redox_3 113 gfevetsk.etyeAkkviiAtGefdkPnklnipGeeklvkhyskvkefhkyagqkvvViGgknSavDaAlelvrkgaeVtvvtrgseiekeesdpsys 209
                  +  v+ +  et+++k++++AtG  +  +++ ++  e + + +s      +   q ++V+Gg+  + ++A    r g +V ++   + i + +   + +
   AHX11569.1 132 QKLVSIDGsETVHTKYIVLATGS-ESAEFPFVKCDE-KNILSSRGALSLESVPQSMIVVGGGAIGLEMASVWSRLGTKVILIEFCDRIAAAS---DGE 224
                  44555554269************.999999999999.56666666544478899****************************9999888874...788 PP

  Pyr_redox_3 210 lkpdienrleelvkeekikvlfnaevkeikekeeeykvktedgkkvevkddvvla.tGykpdlsflkkslfeldedgrpvlteeteetnvpglflaG 305
                  ++ +  + l++   ++ i+++  +++++i+  +      ++dgk+ +v+ + +l+ +G kp  s l    +e+++ g+++++++  +t vpg++ +G
   AHX11569.1 225 VSSYLLKSLKK---QG-ITFHLSSRITSIESGNLVSASFQKDGKEEKVSAEKILIsIGRKPYSSDLG-IELEKNSAGFIKVDKN-FQTSVPGIYAVG 315
                  99999999987...45.*************98877778899999999999999998**********9.8888889999999976.6788*****998 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.6   0.4   2.9e-09   2.3e-06       1      36 [.      13      48 ..      13      55 .. 0.92
   2 ?    4.3   0.0     0.016        13     138     167 ..     128     157 ..      99     160 .. 0.87
   3 !   10.9   0.4   0.00017      0.14       2      34 ..     184     216 ..     183     221 .. 0.89
   4 !   12.6   0.0   4.9e-05      0.04     110     166 ..     224     281 ..     213     287 .. 0.83

  Alignments for each domain:
  == domain 1  score: 26.6 bits;  conditional E-value: 2.9e-09
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 +dv+viGgG+AG  ++i+aa+ g rV+ +ek + lg
   AHX11569.1 13 FDVVVIGGGPAGYVCSIKAAQLGMRVACIEKRSVLG 48
                 59*****************************98776 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.016
                  ETTE.EEEEE.TTEEEEESEEEE----SS- CS
  HI0933_like 138 eedgkfrvktkseeeleadklvlAtGGlSi 167
                  + +++  v+++++e+++++++vlAtG++S+
   AHX11569.1 128 NGGNQKLVSIDGSETVHTKYIVLATGSESA 157
                  45566889999****************995 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 0.00017
                  SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSS CS
  HI0933_like   2 dviviGgGaAGlmaAisaakrgkrVlllekakk 34 
                  ++iv+GgGa Gl  A   ++ g +V+l+e  ++
   AHX11569.1 184 SMIVVGGGAIGLEMASVWSRLGTKVILIEFCDR 216
                  589*************************96655 PP

  == domain 4  score: 12.6 bits;  conditional E-value: 4.9e-05
                  HHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE..TTEEEEESEEEE----SS CS
  HI0933_like 110 divdallkelkeagvklrletevksvekeedgkfrvkt.kseeeleadklvlAtGGlS 166
                  ++ + llk lk++g++++l+++++s+e+ +  + +++   +ee+++a+k+++++G + 
   AHX11569.1 224 EVSSYLLKSLKKQGITFHLSSRITSIESGNLVSASFQKdGKEEKVSAEKILISIGRKP 281
                  68899*********************99887777777745899**********99765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.3   0.1     5e-12   4.1e-09       1      42 [.      14      55 ..      14      75 .. 0.93
   2 !    6.3   0.0    0.0063       5.1       3      31 ..     186     214 ..     185     271 .. 0.93

  Alignments for each domain:
  == domain 1  score: 36.3 bits;  conditional E-value: 5e-12
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsgl 42
                  DvvV+GGgpaG+++ i Aa+ G +v+ +e+r vlGG+  +++
    AHX11569.1 14 DVVVIGGGPAGYVCSIKAAQLGMRVACIEKRSVLGGTCLNEG 55
                  9***********************************987766 PP

  == domain 2  score: 6.3 bits;  conditional E-value: 0.0063
  FAD_oxidored   3 vVvGGgpaGvaAAiaAaraGakvlLveer 31 
                   +VvGGg+ G+  A    r G kv+L+e  
    AHX11569.1 186 IVVGGGAIGLEMASVWSRLGTKVILIEFC 214
                   8*************************965 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.8   1.0   1.9e-10   1.5e-07       1      37 [.      14      50 ..      14      53 .. 0.96
   2 !    6.2   0.7    0.0056       4.5       2      43 ..     185     223 ..     184     240 .. 0.81
   3 ?    1.1   0.0      0.21   1.7e+02     142     197 ..     224     275 ..     214     282 .. 0.86
   4 !    5.8   0.0    0.0077       6.3     373     404 ..     294     320 ..     256     327 .. 0.76

  Alignments for each domain:
  == domain 1  score: 30.8 bits;  conditional E-value: 1.9e-10
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSG CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefgga 37
                   Dv+ViG+G AG++++++aa+ G +va++ek ++ gg+
     AHX11569.1 14 DVVVIGGGPAGYVCSIKAAQLGMRVACIEKRSVLGGT 50
                   9*******************************99986 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0056
                    EEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGGGG--S CS
  FAD_binding_2   2 viViGsGlAGLaAAleaaeaGlkvavvekeqefggatawsqG 43 
                     iV+G+G+ GL  A   ++ G kv+++e  ++    +a+s G
     AHX11569.1 185 MIVVGGGAIGLEMASVWSRLGTKVILIEFCDR---IAAASDG 223
                    59*************************97777...5566665 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.21
                    HHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE CS
  FAD_binding_2 142 allarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvl 197
                    ++   l++s++k g++f+ + +++++  e+g  + a ++  ++g+e+++ a ++++
     AHX11569.1 224 EVSSYLLKSLKKQGITFHLSSRITSI--ESGNLVSASFQ--KDGKEEKVSAEKILI 275
                    56677999******************..88******999..999999999998876 PP

  == domain 4  score: 5.8 bits;  conditional E-value: 0.0077
                    S-E.EEBETTSBESTTEEESSBTEEE-STCEES CS
  FAD_binding_2 373 mgG.vetdengrvldadgqpipGLYAaGevaag 404
                     +G +++d n+++       +pG YA+G v+ g
     AHX11569.1 294 SAGfIKVDKNFQT------SVPGIYAVGDVIPG 320
                    4454899999999......*********99855 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   3.4   4.4e-10   3.6e-07       1     150 [.      14     154 ..      14     173 .. 0.73
   2 !   12.5   0.1     7e-05     0.057       2      37 ..     185     219 ..     184     231 .. 0.87

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 4.4e-10
                 CEEEE-SSHHHHHHHHHHHHTT--EEEE...ES-GGGTT--SSSSEEE-T....THHHHHHHHHHHT-SHHHHHHHHEEEEEEESTTS-CCC-EEEEEE CS
        GIDA   1 dviViGgGhAGceAAlaaarlGakvlLi...thkldtiaelsCnpsiggi....akgllvrEidalggliikaadkagiqfrilNrskGpavralraqv 92 
                 dv+ViGgG AG+ ++++aa+lG++v+ i       +t+++ +C ps   +    a +   +   a   l i++ d +     +        +++ ++++
  AHX11569.1  14 DVVVIGGGPAGYVCSIKAAQLGMRVACIekrSVLGGTCLNEGCIPSKALLhssyAYYSARNHFAA---LGIECSDVKLN---L------EKMMENKTKI 100
                 79**************************87777789************99644444444444444...44555554332...2......3334443455 PP

                 -HHHHHHHHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT CS
        GIDA  93 drelyskevteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGt 150
                  ++l +    + l +++++ ++++  + ++   ++ k v  +  et+++k +v+atG+
  AHX11569.1 101 VKDLAQG--IDFLFKKNKIALFRGAGSIVN--GGNQKLVSIDGSETVHTKYIVLATGS 154
                 5555433..356667899999999999884..58888889999999999999999999 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 7e-05
                 EEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT- CS
        GIDA   2 viViGgGhAGceAAlaaarlGakvlLithkldtiae 37 
                 +iV+GgG  G+e A   +rlG kv+Li +  d+ia 
  AHX11569.1 185 MIVVGGGAIGLEMASVWSRLGTKVILI-EFCDRIAA 219
                 69************************9.66666655 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.3   1.1e-08   8.7e-06       1      36 [.      17      52 ..      17      62 .. 0.96
   2 !   10.6   0.1   0.00062      0.51       1      33 [.     187     219 ..     187     256 .. 0.81
   3 ?    0.3   0.2       1.1   8.7e+02       1      18 [.     413     430 ..     413     437 .. 0.83

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 1.1e-08
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG- CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraa 36
                   ++G+G +G v+   +a+ g +v ++ekr+ lGG + 
     AHX11569.1 17 VIGGGPAGYVCSIKAAQLGMRVACIEKRSVLGGTCL 52
                   8********************************996 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00062
                    EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSG CS
  NAD_binding_8   1 IvGaGlsGlvaAylLakagfdvlllekrdrlGG 33 
                    +vG+G+ Gl +A+  ++ g +v l+e  dr+  
     AHX11569.1 187 VVGGGAIGLEMASVWSRLGTKVILIEFCDRIAA 219
                    8*************************9999874 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 1.1
                    EE--SHHHHHHHHHHHCC CS
  NAD_binding_8   1 IvGaGlsGlvaAylLaka 18 
                    I+Ga +s+l a + La +
     AHX11569.1 413 IIGASASSLIAEAVLAME 430
                    9********999998864 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.2   8.7e-07   0.00071       1      56 [.      14      85 ..      14     128 .. 0.74
   2 ?    1.2   0.0      0.26   2.2e+02     179     207 ..     134     159 ..     102     177 .. 0.57
   3 !    8.0   0.9    0.0022       1.8       3      37 ..     186     221 ..     184     225 .. 0.90
   4 ?    2.7   0.0     0.097        79     150     201 ..     227     278 ..     220     294 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 8.7e-07
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGGGSSE.....EEEESSSSTHHS.TH.........H CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..VtllekgdiagsgaSgrns.....gllhsglrylpe.as.........e 56
                dvv+iGGG +G  +   +a+ g  V+ +ek++ +g g+  + +     +llhs+++y+   ++         +
  AHX11569.1 14 DVVVIGGGPAGYVCSIKAAQLGmrVACIEKRSVLG-GTCLNEGcipskALLHSSYAYYSArNHfaalgiecsD 85
                9******************************9999.9888888888888899999666541434555555540 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.26
                 EEEEEEECTEEE.EEEEEEEE--GGGHHHH CS
         DAO 179 vwgverttpgen.daadavVnaaGawsdll 207
                 ++ +    +g++ ++ +++V+a+G  s ++
  AHX11569.1 134 LVSI----DGSEtVHTKYIVLATGSESAEF 159
                 2222....1333334488******998744 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0022
                 EEECTSHHHHHHHHHHHHTT..EEEEESSSSTTSSGG CS
         DAO   3 viiGGGiiGlstAyeLarrg..VtllekgdiagsgaS 37 
                 +++GGG iGl  A   +r g  V+l+e  d+++ +aS
  AHX11569.1 186 IVVGGGAIGLEMASVWSRLGtkVILIEFCDRIA-AAS 221
                 8***************99999******998888.777 PP

  == domain 4  score: 2.7 bits;  conditional E-value: 0.097
                 HHHHHHHHHTT-EEEESECEEEEEEEETCEEEEE.EECT.EEEEEEEEEEE--G CS
         DAO 150 aalaraaealGveilegtevtgleeedgkvwgve.rttp.gendaadavVnaaG 201
                  +l++ ++++G+++++ +++t++e  ++ v+    ++   +e+++a+++ ++ G
  AHX11569.1 227 SYLLKSLKKQGITFHLSSRITSIES-GNLVSA-SfQKDGkEEKVSAEKILISIG 278
                 679999*****************65.223333.244333344444566776665 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.1   0.00026      0.21      30      61 ..      14      45 ..       5      50 .. 0.91
   2 !    9.7   0.0    0.0006      0.49      28      59 ..     182     213 ..     174     265 .. 0.85
   3 !    5.8   0.1    0.0089       7.3      55     128 ..     369     439 ..     358     441 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00026
                 EEEEESTSHHHHHHHHHHHHTT-EEEEEESSH CS
  AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtvlDvrp 61
                  v+viGgG aG      a++lg +V  +++r+
   AHX11569.1 14 DVVVIGGGPAGYVCSIKAAQLGMRVACIEKRS 45
                 79*************************99985 PP

  == domain 2  score: 9.7 bits;  conditional E-value: 0.0006
                  --EEEEESTSHHHHHHHHHHHHTT-EEEEEES CS
  AlaDh_PNT_C  28 pakvlviGgGvaGlqAiatakglgakVtvlDv 59 
                  p  ++v+GgG  Gl+ +++ ++lg kV +++ 
   AHX11569.1 182 PQSMIVVGGGAIGLEMASVWSRLGTKVILIEF 213
                  56789**********************99876 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.0089
                  EEEESSHHHHHHHHHTTTCECEEHCHHHHHHHHHHHH-SEEEE---BTTSS---SC-HHHHHTS-TTEEEEETT CS
  AlaDh_PNT_C  55 tvlDvrparleqleslgakfvevlksqeellaeavkeadvvigtvlipGkkaPkLvteemvksMkpgsVivDvA 128
                  ++lDv+ ++ +   + +++  ++ + +e  ++  v e d + g v+i G++a  L+ e+ v +M+ g+   D+A
   AHX11569.1 369 KALDVQYKVSKFPFAANSR-AKTTNDTEGFVKILVDEHDTILG-VHIIGASASSLIAEA-VLAMEYGASAEDIA 439
                  5566666665555555555.67788888889999999999887.7***********865.66799998777776 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.5   2.9e-06    0.0023       2      34 ..      13      45 ..      12      49 .. 0.95
   2 ?    0.0   0.0      0.48   3.9e+02     149     166 ..     139     156 ..     130     162 .. 0.84
   3 !    8.0   0.8    0.0018       1.4       5      31 ..     186     212 ..     183     221 .. 0.92
   4 ?    1.2   0.0      0.22   1.8e+02     100     156 ..     218     271 ..     213     313 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.9e-06
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESSS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekrs 34
                    dV+++G+GpaG + +   ++ G rv ++ekrs
     AHX11569.1 13 FDVVVIGGGPAGYVCSIKAAQLGMRVACIEKRS 45
                   79*****************************97 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.48
                    EEEEEEEEEEEE--GTT- CS
  FAD_binding_3 149 eeetvrakYlvGaDGgrS 166
                      etv+ kY+v a G  S
     AHX11569.1 139 GSETVHTKYIVLATGSES 156
                    446**********99988 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0018
                    EEE--SHHHHHHHHHHHHTTHHEEEEE CS
  FAD_binding_3   5 lIVGaGpaGlmlallLseaGvrvvlve 31 
                    ++VG+G  Gl  a++ s+ G +v+l+e
     AHX11569.1 186 IVVGGGAIGLEMASVWSRLGTKVILIE 212
                    79************************8 PP

  == domain 4  score: 1.2 bits;  conditional E-value: 0.22
                    EE--HHHHHHHHHHHHHHHTEEETCSEEEECCEECCCCCCCEEEECCTTEEEEEEEE CS
  FAD_binding_3 100 tvypqteleriLvehaeerglqvrfktevesleqdeegvtaevrdketgeeetvrak 156
                    ++ +  e+  +L+++++++g++++ + +++s+e  ++ v+a +  +++g+ee+v+a+
     AHX11569.1 218 AAASDGEVSSYLLKSLKKQGITFHLSSRITSIE-SGNLVSASF--QKDGKEEKVSAE 271
                    55666789999******************9765.456666665..566888889886 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.4   4.4e-07   0.00036      17      66 ..      12      60 ..       4     167 .. 0.91
   2 !    6.7   0.2    0.0045       3.7      17      48 ..     182     212 ..     167     219 .. 0.87
   3 ?   -2.6   0.1       3.2   2.6e+03      20      39 ..     411     430 ..     397     433 .. 0.81

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 4.4e-07
                EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--TTTTTTSTTBSE CS
        Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGGGawlGGqlfsa 66
                e Dvv++G+G++G  ++   a+  +++va +e++  +GG     G + s+
  AHX11569.1 12 EFDVVVIGGGPAGYVCSIKAAQL-GMRVACIEKRSVLGGTCLNEGCIPSK 60
                78****************99999.**********9999988777766555 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0045
                 EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEE CS
        Thi4  17 esDvvivGaGssGLtaayylakkpdlkvaile 48 
                  + +++vG+G+ GL  a + ++  + kv+++e
  AHX11569.1 182 PQSMIVVGGGAIGLEMASVWSRL-GTKVILIE 212
                 56789*****************9.******99 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3.2
                 EEEE--SHHHHHHHHHHHHC CS
        Thi4  20 vvivGaGssGLtaayylakk 39 
                 v i+Ga +s L a  +la +
  AHX11569.1 411 VHIIGASASSLIAEAVLAME 430
                 77999999999999988865 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.8   0.00015      0.12       1      32 [.      14      43 ..      14      49 .. 0.92
   2 ?   -3.4   0.0       4.5   3.7e+03     119     143 ..     132     156 ..     123     161 .. 0.78
   3 !   10.5   0.0   0.00028      0.23       2      36 ..     185     217 ..     184     282 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00015
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                   DvvviG+GpAg     +   a+ g++v +ie 
     AHX11569.1 14 DVVVIGGGPAGYVCSIKA--AQLGMRVACIEK 43
                   9***********999999..99********85 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 4.5
  Lycopene_cycl 119 eslvvleggrkirarlvvdarglas 143
                    ++lv ++g ++++ + +v a+g  s
     AHX11569.1 132 QKLVSIDGSETVHTKYIVLATGSES 156
                    6789999999999999999999544 PP

  == domain 3  score: 10.5 bits;  conditional E-value: 0.00028
  Lycopene_cycl   2 vvviGaGpAglslAarlteakpglkvvlieaspsl 36 
                    ++v+G+G+ gl +A     ++ g kv+lie  + +
     AHX11569.1 185 MIVVGGGAIGLEMASVW--SRLGTKVILIEFCDRI 217
                    69************999..**********988776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.0      0.03        24       1      33 [.      15      47 ..      15     155 .. 0.88
   2 !    7.6   0.0    0.0062         5       1      31 [.     185     215 ..     185     275 .. 0.88
   3 ?   -0.7   0.0       2.4     2e+03      12      94 ..     337     434 ..     330     443 .. 0.40

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.03
                EEEE--STTHHHHHHHHHHHTEEEEEEES-GGG CS
      XdhC_C  1 lvifGaghvaqalarlaaalgfrvtvvdpreef 33
                +v++G+g+ +  +   aa+lg+rv ++++r+ +
  AHX11569.1 15 VVVIGGGPAGYVCSIKAAQLGMRVACIEKRSVL 47
                689**************************9864 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0062
                 EEEE--STTHHHHHHHHHHHTEEEEEEES-G CS
      XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpre 31 
                 ++++G+g ++ ++a++ ++lg +v++++  +
  AHX11569.1 185 MIVVGGGAIGLEMASVWSRLGTKVILIEFCD 215
                 69***********************998655 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 2.4
                 HHHHHHHHHTEEEEEEES-GGGG........-GGG-TT-SE...........-EEEE--S-HHHHHHHHHHHSSS-...-SEEEESS-HHHHHHHCTTS CS
      XdhC_C  12 alarlaaalgfrvtvvdpreefa........tkerfpeade...........tavvvlthdhklDaealeaalrkk...aayigllGSrkkaarrlerl 88 
                  la   a++g+  +v+ + +e+a                 +            +++    + + D+e   ++l ++   +  + ++G+ + +   ++ l
  AHX11569.1 337 ILAGKSAHIGWIPSVIYTHPEVAsvgkteeeL--------KaldvqykvskfPFAANSRAKTTNDTEGFVKILVDEhdtILGVHIIGASASSLIAEAVL 427
                 55555555666666666666555333322220........12223333333322222223333333333333321111122344444444444444444 PP

                 .--.... CS
      XdhC_C  89 raa.gls 94 
                 + + g s
  AHX11569.1 428 AMEyGAS 434
                 4444555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.6       0.5   4.1e+02       2      30 ..      15      43 ..      14      51 .. 0.92
   2 !   14.6   0.1   2.7e-05     0.022       4      56 ..     187     239 ..     184     268 .. 0.84

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.5
                EEEE--SCCHHHHHHHHHHTT-EEEEE-S CS
     3HCDH_N  2 vaviGaGtmGagiaavfasagleVvlvdi 30
                v viG G  G      +a+ g++V  ++ 
  AHX11569.1 15 VVVIGGGPAGYVCSIKAAQLGMRVACIEK 43
                89**********************99886 PP

  == domain 2  score: 14.6 bits;  conditional E-value: 2.7e-05
                 EE--SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
     3HCDH_N   4 viGaGtmGagiaavfasagleVvlvdiseealekalekieksleklvekgklk 56 
                 v+G G +G ++a+v  + g +V l++  +++++++  ++++ l k  +k+ ++
  AHX11569.1 187 VVGGGAIGLEMASVWSRLGTKVILIEFCDRIAAASDGEVSSYLLKSLKKQGIT 239
                 9**************************************99776666666555 PP

>> DUF1609  Protein of unknown function (DUF1609)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00021      0.18     125     208 ..     221     303 ..     205     309 .. 0.86
   2 ?   -0.1   0.0      0.67   5.4e+02     171     212 ..     366     407 ..     338     412 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00021
     DUF1609 125 kvGvvevGlfkdksgesvvyhlmfkptdiekaGkvvrpsfakaddvekidedeelsdaskfvyPkgvrsevvkekdefrivwrn 208
                   G+v   l k  +++ + +hl  + t+ie+ G+ v++sf k  + ek+  ++ l  +++  y  +  +e+ k++  f  v +n
  AHX11569.1 221 SDGEVSSYLLKSLKKQGITFHLSSRITSIES-GNLVSASFQKDGKEEKVSAEKILISIGRKPYSSDLGIELEKNSAGFIKVDKN 303
                 5688888899999****************85.9******************999999999999999999999999988777776 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.67
     DUF1609 171 ekidedeelsdaskfvyPkgvrsevvkekdefrivwrnpkdt 212
                 e+++  +    +skf +  + r+ ++++++ f  +  +++dt
  AHX11569.1 366 EELKALDVQYKVSKFPFAANSRAKTTNDTEGFVKILVDEHDT 407
                 23333344456799***************9997666555555 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       1.9   1.5e+03       3      15 ..      13      25 ..      11      45 .. 0.59
   2 ?    6.4   0.0    0.0052       4.3     144     207 ..     140     198 ..     130     234 .. 0.77
   3 ?    4.0   0.0     0.027        22     138     161 ..     259     282 ..     239     296 .. 0.81

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 1.9
  K_oxygenase  3 lDligiGiGpsnL 15
                 +D++ iG Gp+  
   AHX11569.1 13 FDVVVIGGGPAGY 25
                 6777777777654 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0052
  K_oxygenase 144 eeelearnlvlgvGtepkiPevleklegkervvHsseylerkeellakkriaVvGsGqSaaeif 207
                  +e+++++ +vl++G+e +  ++++  + +++++ s  +l+ +     +++++VvG+G  + e++
   AHX11569.1 140 SETVHTKYIVLATGSESAEFPFVKC-D-EKNILSSRGALSLE---SVPQSMIVVGGGAIGLEMA 198
                  6899**********77665556663.3.36677666666665...789999******9887765 PP

  == domain 3  score: 4.0 bits;  conditional E-value: 0.027
  K_oxygenase 138 kdaegeeeelearnlvlgvGtepk 161
                   +++g+ee+++a+++++++G +p+
   AHX11569.1 259 FQKDGKEEKVSAEKILISIGRKPY 282
                  3589******************98 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0     0.085        70       6      39 ..      11      44 ..       8     109 .. 0.81
   2 ?    7.3   0.0    0.0079       6.5       8      39 ..     183     214 ..     176     278 .. 0.77
   3 ?   -1.6   0.0       4.6   3.8e+03      63      81 ..     437     455 ..     383     462 .. 0.68

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.085
  NAD_binding_7  6 kgkkvlvvGgGevAarkvrklleagakvtvvape 39
                   k+  v+v+GgG+ ++    k ++ g +v  + ++
     AHX11569.1 11 KEFDVVVIGGGPAGYVCSIKAAQLGMRVACIEKR 44
                   6789********9998777777777777776665 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0079
  NAD_binding_7   8 kkvlvvGgGevAarkvrklleagakvtvvape 39 
                    ++++vvGgG ++++ ++   + g kv+++  +
     AHX11569.1 183 QSMIVVGGGAIGLEMASVWSRLGTKVILIEFC 214
                    6799**********************997544 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 4.6
  NAD_binding_7  63 dlviaatddrelneriaea 81 
                    d++ ++ ++++lne++ ea
     AHX11569.1 437 DIARTCHSHPDLNEAVKEA 455
                    3445555556666665554 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.4   0.4     0.015        12       3      31 ..      15      43 ..      13      47 .. 0.92
   2 ?    6.5   0.0    0.0067       5.5       4      31 ..     186     213 ..     183     236 .. 0.87

  Alignments for each domain:
  == domain 1  score: 5.4 bits;  conditional E-value: 0.015
                    EEEE--STTHHHHHHHHHHCTSEEEEE-S CS
  UDPG_MGDP_dh_N  3 isviGlGYvGlvtaavlaeighevigvDi 31
                    ++viG G  G v+++  a++g+ v ++ +
      AHX11569.1 15 VVVIGGGPAGYVCSIKAAQLGMRVACIEK 43
                    89************************975 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0067
                     EEE--STTHHHHHHHHHHCTSEEEEE-S CS
  UDPG_MGDP_dh_N   4 sviGlGYvGlvtaavlaeighevigvDi 31 
                      v+G G +Gl +a v +++g +vi++  
      AHX11569.1 186 IVVGGGAIGLEMASVWSRLGTKVILIEF 213
                     69**********************9975 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.1      0.45   3.7e+02      38      67 ..      14      43 ..       5      50 .. 0.88
   2 ?    9.2   0.0   0.00091      0.74      36      68 ..     182     214 ..     163     243 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.45
                  EEEEES-SHHHHHHHHHHHHTT-EEEEESS CS
  2-Hacid_dh_C 38 tvGiiGlGrIGqavakrlkafgmkviaydr 67
                   v +iG G  G     +++++gm+v ++++
    AHX11569.1 14 DVVVIGGGPAGYVCSIKAAQLGMRVACIEK 43
                  6899*********************98875 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00091
                   TSEEEEES-SHHHHHHHHHHHHTT-EEEEESSS CS
  2-Hacid_dh_C  36 gktvGiiGlGrIGqavakrlkafgmkviaydrs 68 
                    + + ++G G+IG ++a + + +g kvi ++  
    AHX11569.1 182 PQSMIVVGGGAIGLEMASVWSRLGTKVILIEFC 214
                   567889**********************98755 PP

>> Trp_halogenase  Tryptophan halogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.0   0.1   0.00069      0.57       1      47 [.      14      58 ..      14      67 .. 0.76
   2 ?    0.4   0.2      0.28   2.3e+02       2      32 ..     185     212 ..     184     233 .. 0.83

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00069
                    EEEEE--SHHHHHHHHHHHHHTTTSSEEEEEE-SSS.---SS-EE--T CS
  Trp_halogenase  1 kivivGGGtaGwlaAaalakalkgklevtlveseei.gtvgvGeatip 47
                    ++v++GGG+aG++  +  a+ +   ++v  +e+  + g     e+ ip
      AHX11569.1 14 DVVVIGGGPAGYVCSIKAAQLG---MRVACIEKRSVlGGTCLNEGCIP 58
                    69***********998887777...89999998754255555666666 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.28
                     EEEE--SHHHHHHHHHHHHHTTTSSEEEEEE CS
  Trp_halogenase   2 ivivGGGtaGwlaAaalakalkgklevtlve 32 
                     +++vGGG  G   A++ ++ +   ++v l+e
      AHX11569.1 185 MIVVGGGAIGLEMASVWSRLG---TKVILIE 212
                     689***************999...6788888 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (466 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       530  (0.029561); expected 358.6 (0.02)
Passed bias filter:                      476  (0.0265492); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                        22  (0.00122706); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              22  [number of targets reported over threshold]
# CPU time: 0.65u 0.26s 00:00:00.91 Elapsed: 00:00:00.45
# Mc/sec: 3139.18
//
Query:       AHX11570.1  [L=371]
Description: succinyl-diaminopimelate desuccinylase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.4e-31  107.7   0.0    7.8e-31  107.4   0.0    1.1  1  Peptidase_M20  Peptidase family M20/M25/M40
    8.2e-19   67.5   0.0    1.4e-18   66.8   0.0    1.4  1  M20_dimer      Peptidase dimerisation domain


Domain annotation for each model (and alignments):
>> Peptidase_M20  Peptidase family M20/M25/M40
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0   8.7e-35   7.8e-31       1     206 [.      61     369 ..      61     370 .. 0.90

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 8.7e-35
                    EEEEES-BSSTTCGGGSSS.TTSEEETTTEEESTTTTTTHHHHHHHHHHHHHHHHHTTT-SSEEEEEEESTTSSTT.THHHHHHHHHHTTTCESEE CS
                    xxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20   1 llgsHlDvVpeeetdgwtt.pfslteedGklyGrGaddmkggvlaalealralkdegikpkgtivllfqpdEEggr.gGakallegleerekvdav 94 
                    ++++H DvVp++++  w   pf +++    +yGrG++dmkg +++++ al ++ d+  + + +i ++++ dEE ++ +G+  ++  l+   +  +v
     AHX11570.1  61 CFAGHVDVVPAADSGLWICnPFVGEVISETIYGRGVVDMKGAIASFITALFEFLDNY-DSQLNIGVILTSDEEMSSsNGMLPMIRYLR---QGGYV 152
                    589*******888878**9******999****************************6.6689***********7667********655...23333 PP

                    E.EEEEESSSBTCHSTETEEEE.......................................................................... CS
                    x.xxxxxxxxxxxxxxxxxxxx.......................................................................... RF
  Peptidase_M20  95 f.elhieepgileagklaigvv.......................................................................... 115
                    + +++++ep+  ++ + +i+++                                                                          
     AHX11570.1 153 IhDCIVGEPTCESKIGDSIKIGrrgslnvavsysgiqghvayhekannpipemldalvrlrdhkfdngneffppshceitsidvdnpstnvipgkv 248
                    34799********666667777************************************************************************** PP

                    ..............................EEEEEEEEEES..HEEECCHHHHHHHHHHHHHHHTSCEEEEEESSSBHTHHHHTTTEEEEEEE.SS CS
                    ..............................xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
  Peptidase_M20 116 ..............................kvevellegga..pvtlndsplvkalaeaaeelfgekvelivsgpggtdarffagiptvmifg.pg 178
                                                  +ve+  +++++  p+ ++  +++++l++a+ +  g + +++++g g++darf+ +i +v+ fg  +
     AHX11570.1 249 stnfnirfnnlqtvkrlkqaidsifvsrtsAVEIV-YSENPalPFLSEKTAFADKLSAAILKCSGISAQFTTKG-GTSDARFLREITNVLEFGlLN 342
                    ***************************98657777.4344312555559999**********88**********.********99989999**777 PP

                    GGCTTSTTTEEEHHHHHHHHHHHHHHHH CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M20 179 sglaHspnEyvdledlekgikvlarlle 206
                     ++aH++nE   l+d+    +++ ++l+
     AHX11570.1 343 -ETAHKVNECAPLKDILLLKEIYLEFLK 369
                    .*********************999986 PP

>> M20_dimer  Peptidase dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0   1.6e-22   1.4e-18       1     101 [.     173     273 ..     173     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 1.6e-22
                 SEB-EEEEEEEEEE-B-EEGG-TTTTB-HHHHHHHHHHCSCTTEEC.....TCCTCCCCCEECCE-C.CCCEESSEEEEEEEEEHHHHHHHHHHHHHHH CS
   M20_dimer   1 ighkGlaggkitvkgkagHsgapgagaNAieklarllaeledeegdiaeerslprttlnvtgiegGs.aknvipdeaeakidiRllpgedpeevleeie 98 
                 ig++G++ + ++  g +gH ++ +++ N+i ++ ++l +l+d+++d++ ++++p++ +++t+i+  + ++nvip++++ +++iR+++ +++++++++i 
  AHX11570.1 173 IGRRGSLNVAVSYSGIQGHVAYHEKANNPIPEMLDALVRLRDHKFDNG-NEFFPPSHCEITSIDVDNpSTNVIPGKVSTNFNIRFNNLQTVKRLKQAID 270
                 69**********************************************.****************99*******************************9 PP

                 HHH CS
   M20_dimer  99 eil 101
                 +i+
  AHX11570.1 271 SIF 273
                 876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (371 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       338  (0.0188521); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2790.01
//
Query:       AHX11571.1  [L=188]
Description: hypothetical protein NHE_0636 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       885  (0.0493614); expected 358.6 (0.02)
Passed bias filter:                      524  (0.0292264); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1409.46
//
Query:       AHX11572.1  [L=598]
Description: GTP-binding protein TypA/BipA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-52  177.5   0.0    3.4e-52  176.8   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    1.2e-22   79.7   0.0    2.2e-22   78.9   0.0    1.5  1  EFG_C        Elongation factor G C-terminus
    7.3e-08   32.5   0.1    1.3e-07   31.6   0.1    1.4  1  MMR_HSR1     50S ribosome-binding GTPase
    6.9e-05   23.2   0.3    0.00022   21.5   0.3    1.9  1  GTP_EFTU_D2  Elongation factor Tu domain 2
     0.0065   15.8   0.1      0.011   15.1   0.1    1.2  1  Septin       Septin
  ------ inclusion threshold ------
      0.011   15.1   0.0      0.022   14.2   0.0    1.4  1  SRPRB        Signal recognition particle receptor beta subuni
      0.012   15.6   0.0       0.62   10.1   0.0    2.4  2  Dynamin_N    Dynamin family
      0.098   12.8   0.2       0.38   10.9   0.2    2.0  2  EFG_II       Elongation Factor G, domain II
       0.13   11.5   0.0       0.21   10.8   0.0    1.2  1  DUF4938      Domain of unknown function (DUF4938)


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.8   0.0   1.7e-55   3.4e-52       1     193 [.       3     189 ..       3     190 .. 0.92

  Alignments for each domain:
  == domain 1  score: 176.8 bits;  conditional E-value: 1.7e-55
                 TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEE CS
    GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavl 99 
                 k+++n ++i+hvDhGKtTLt +Ll +++  ++          +D+++ E++rgiT+ s+++s++  +k+++inliDtPGH dF  ev+r ++++D ++l
  AHX11572.1   3 KKVLNTAVIAHVDHGKTTLTNNLLRQSNVLDD--------LGMDRNPLEQKRGITMFSKVASIY--YKETKINLIDTPGHSDFGGEVERIMSMADSVLL 91 
                 5789********************99998777........569*********************..********************************* PP

                 EEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHH..........HHHHHH CS
    GTP_EFTU 100 vvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvk..........tlleal 188
                 +vd++eGv+pqt+ vl  alk g+++iv++NK+Dr++ +l+e+v+e+++ +      l+  + +++ ++pv+++S+ +g++++          +lle++
  AHX11572.1  92 LVDSAEGVMPQTKFVLSKALKSGLRPIVIVNKVDRPDRRLEEVVNEISDLF------LSLDANDEQLDFPVLYASGRDGWCIRdlndpkdnliPLLETI 184
                 ************************************************999......66565566679************7776666666666899988 PP

                 HHHSH CS
    GTP_EFTU 189 vellp 193
                 +e++p
  AHX11572.1 185 MEYTP 189
                 88876 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.9   0.0   1.1e-25   2.2e-22       2      87 ..     391     476 ..     390     478 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.9 bits;  conditional E-value: 1.1e-25
                 EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE--HHHHH CS
       EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevpgdkld 87 
                  lEPi++++++ +eey g v+++l++r+G++++m++  +grv++ ++iP++ lig++ ++ s T+G+g+++  f+gY+++ g++ +
  AHX11572.1 391 KLEPIEELTVDLDEEYAGIVMETLNTRKGIMQSMDNYPGGRVRLVYHIPSRSLIGYHGQFLSDTRGTGILNKVFHGYAPYSGKIES 476
                 69*******************************************************************************99865 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.1   6.7e-11   1.3e-07       4     114 .]      10     123 ..       7     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 6.7e-11
                 EEESTTSSHHHHHHHHHT..........STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETTTTCSH CS
    MMR_HSR1   4 ivGrpNvGKStLinaltg..........ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlillvvdaseeklk 91 
                 ++ +   GK+tL n l++          ++   ++k g T   + + + +k+++i+l+DtpG  +      ++g +++++ + ad +ll+vd++ e++ 
  AHX11572.1  10 VIAHVDHGKTTLTNNLLRqsnvlddlgmDRNPLEQKRGITMFSKVASIYYKETKINLIDTPG-HS------DFGGEVERIMSmADSVLLLVDSA-EGVM 100
                 6667788**********86777766655588999999***********9999**********.44......5666666666658********66.7799 PP

                 HHHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  92 pldeeleelleeakkplilvlnk 114
                 p+ + + +   +++ + i+++nk
  AHX11572.1 101 PQTKFVLSKALKSGLRPIVIVNK 123
                 99888888877766667888887 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.5   0.3   1.1e-07   0.00022       1      74 []     213     284 ..     213     284 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.5 bits;  conditional E-value: 1.1e-07
                  EEEEEEEEEESEEETTEEEEEEC.TCTTSEE..EEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskke..ivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                  G++  g+++ G +  +  v+ +  ++    e  +  r ++l+ f++  +   + a+aG i+ai g+++a  v+dt++
   AHX11572.1 213 GRILIGKIEKGSIAANASVKAINlKG----ElvENARLTKLQIFEGMGKRNADSAQAGEIIAIAGVSEA-SVTDTIC 284
                  78899999999999999999977555....4568**********************************8.*****98 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.1   5.4e-06     0.011       6      75 ..       7      75 ..       4      94 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 5.4e-06
                EEEEEEBTTSSCCCCCCTTSSSS--.----------------S-EEEEEEEEETTCEEEEEEEE---BSSS CS
      Septin  6 tlmvvGesglGkttlintlfetdli.eeekleeasekkkktveikkkkvvieedgvklnltviDtpgfGda 75
                +  v+ +   Gkttl n l++++ + ++  ++++  ++k+ +++ +k ++i  +++k+  ++iDtpg+ d+
  AHX11572.1  7 NTAVIAHVDHGKTTLTNNLLRQSNVlDDLGMDRNPLEQKRGITMFSKVASIYYKETKI--NLIDTPGHSDF 75
                5567788899********9977655055566666568888888888888888887765..67*****8775 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   1.1e-05     0.022      10      86 ..      12      96 ..       4     102 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 1.1e-05
                -STTSSHHHHHHHHHHS..............S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETT CS
       SRPRB 10 GlsdsGKTslftrLttd..............svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDSt 86
                   d GKT+l + L+ +              + +k  + + s++a  +   k++k++liD PGh  +  ++       s + +++ +vDS+
  AHX11572.1 12 AHVDHGKTTLTNNLLRQsnvlddlgmdrnplE-QKRGITMFSKVASIY--YKETKINLIDTPGHSDFGGEVERI---MSMADSVLLLVDSA 96
                45789*******99999889999988888743.444444544444444..599*************99987655...45566677777776 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.2   0.0     0.042        85       2      22 ..       9      29 ..       8      47 .. 0.81
   2 ?   10.1   0.0   0.00031      0.62      98     168 .]      59     124 ..      32     124 .. 0.83

  Alignments for each domain:
  == domain 1  score: 3.2 bits;  conditional E-value: 0.042
                EEEEBTTTTHHHHHHHHHTS- CS
   Dynamin_N  2 avvGsqSsGKSSvlnaLlged 22
                av+ ++ +GK+++ n+Ll++ 
  AHX11572.1  9 AVIAHVDHGKTTLTNNLLRQS 29
                6888999***********876 PP

  == domain 2  score: 10.1 bits;  conditional E-value: 0.00031
                 TTS-SEEEEE---B-SSSGTTSHHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHSTTBTTEEEEEE-C CS
   Dynamin_N  98 llvkgltlvDlPGldsvnkrdqelvkeyikkadiilavtsanhdlsnsealflarevdpkgkrtivvltkl 168
                  ++ +++l+D+PG  +   +    v++++  ad +l+++++   ++  + +f+ +++ + g r iv+++k+
  AHX11572.1  59 YKETKINLIDTPGHSDFGGE----VERIMSMADSVLLLVDSAEGVM-PQTKFVLSKALKSGLRPIVIVNKV 124
                 567899*******9985444....6999999999999999888777.67788899999999**99999985 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.6   0.0       6.5   1.3e+04      43      53 ..     247     257 ..     243     260 .. 0.83
   2 ?   10.9   0.2   0.00019      0.38      11      66 ..     311     370 ..     303     378 .. 0.67

  Alignments for each domain:
  == domain 1  score: -3.6 bits;  conditional E-value: 6.5
      EFG_II  43 TketilsGmGe 53 
                 Tk +i +GmG+
  AHX11572.1 247 TKLQIFEGMGK 257
                 6778999**97 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00019
      EFG_II  11 epkskadedklsk..aLarlleE...DptlrverdeeTketilsGmGelHleivverlkre 66 
                 +p + +d dkl +   L+rll+E     ++++e   e +++ + G Gel+l +++e++++e
  AHX11572.1 311 SPLTGRDGDKLTSrvILDRLLQEvktNVSINLEEKGE-GQYEVRGRGELQLGVLIENMRKE 370
                 5566666677765334677776622244455554444.899*****************997 PP

>> DUF4938  Domain of unknown function (DUF4938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00011      0.21     142     227 ..     213     295 ..     199     314 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00011
     DUF4938 142 grlligqgergwivapadlraapdlqp...pwsrlgriliiavtgeryrqqaiaeqaarhqgiildqanrasvitaladpactalivgf 227
                 gr+lig+ e+g i a a ++a   l+      +rl ++ i    g+r  + a a +      i +     asv  +++dp++t  i  +
  AHX11572.1 213 GRILIGKIEKGSIAANASVKAIN-LKGelvENARLTKLQIFEGMGKRNADSAQAGE-----IIAIAGVSEASVTDTICDPSVTDPIAAI 295
                 9******************9874.44411156788888888888888766555443.....4556667899999999999999877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (598 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       377  (0.0210274); expected 358.6 (0.02)
Passed bias filter:                      342  (0.0190752); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4410.64
//
Query:       AHX11573.1  [L=819]
Description: DNA polymerase I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.5e-122  407.7   5.0   6.5e-122  407.2   5.0    1.2  1  DNA_pol_A     DNA polymerase family A
    1.2e-45  155.3   0.0    2.4e-45  154.3   0.0    1.6  1  5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like do
    2.6e-26   92.1   0.1    2.4e-25   88.9   0.0    2.7  2  5_3_exonuc    5'-3' exonuclease, C-terminal SAM fold
  ------ inclusion threshold ------
      0.019   15.1   0.0      0.096   12.8   0.0    2.2  2  HHH_2         Helix-hairpin-helix motif
      0.019   15.6   0.0      0.056   14.1   0.0    1.8  1  HHH_5         Helix-hairpin-helix domain
       0.03   14.6   0.4        1.5    9.3   0.0    2.9  2  IMS_HHH       IMS family HHH motif


Domain annotation for each model (and alignments):
>> DNA_pol_A  DNA polymerase family A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.2   5.0  2.2e-125  6.5e-122       2     371 ..     444     812 ..     443     814 .. 0.95

  Alignments for each domain:
  == domain 1  score: 407.2 bits;  conditional E-value: 2.2e-125
                 HHHHHHHHHHHHHHHHHHHHHHHHSS.C-STTTCCCCHHHHTCCCCS.TTSBETTS.BTTTCCHHHHHT.S..CHHHHHHHHHHHHHHHHHTTTTGGGC CS
   DNA_pol_A   2 eeleelseeleeeleeleeeiyelag.efnlnSpkqlaevLfeklklpekkktktg.ystdeevLekla.k.hplaklileyrelsklkstyvdallkl 96 
                 e+l++lsee+++el+++e++i++++g +f+l+Spkql+e+Lfek+k+p +kk ktg  std evLe+l+ + + +a+++l++r+  klks y+d+l + 
  AHX11573.1 444 EYLNNLSEEISTELQRIEKNIFDIVGeRFSLASPKQLSEILFEKMKIPVQKKLKTGlASTDGEVLESLSiQgYRIADELLKWRHNIKLKSAYIDPLINR 542
                 689***********************56****************************999*********98689************************** PP

                 C...BTTTSEE--EEESSSSSSSS-EEESS-GGGS-TTSCCHHHHHHTBCG.TTCCEEEEEEETTHHHHHHHHHCT.HHHHHHHHTTH-HHHHHHHHHC CS
   DNA_pol_A  97 i...nkktgrihtsfnqtvtatGrlsssepnlqnipirteegrriRkafvaeegghvllsaDysqiELRilAhlsgdeklieafkegeDiHsktAsevf 192
                 i   +++ +ri+t+++ t t tGrlsss+pnlqnip r    ++iR++f+ ++ +h+++ aDysqiELRilAh+++ +kl +a+ +g+D+H+ tA+++f
  AHX11573.1 543 IesgEHRANRISTTYSTTLTLTGRLSSSNPNLQNIP-R---DENIRRIFITRK-DHTFICADYSQIELRILAHIANVTKLKAALMSGTDLHTLTARQIF 636
                 *88655688**************************9.3...468********9.688****************************************** PP

                 TS.GGGHHHHHHHHHHHHHHHHHTT--HHHHHHHHTSSHHHHHHHHHHHHHHSHHHHHHHHHHHHHCCCECCEEETTCSEEEECTTT-CCHCCCHHHHH CS
   DNA_pol_A 193 gvpveevtkeqRrqaKainfGiiYGagakgLaeqlgiseeeAkefiekyferypgvksyleetleeakekgyvetllgrrrylpeiksknaalrekaer 291
                 ++  +++t+e R++aKa+nfGi+YG++++gLa+ql+is+eeA  +i +yfe+yp++k+y++ t+e+a+ +gyv+tl++r++++++i+s+n+al++ aer
  AHX11573.1 637 KT--DNITPELRNRAKAVNFGIVYGITNFGLAKQLSISKEEATLYIAQYFEEYPEIKEYMRATKETARINGYVKTLMNRKCPIRNINSTNYALKSIAER 733
                 *9..*********************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEETTEEEEEEECCCHHHHHHHHHHHHHHHHH..SSS--EEEEEEE CS
   DNA_pol_A 292 aavNapiQGsAaDiiklamikieealkeeklkarlllqvHDElvfevpeeeveevaelvkeamesave..ldvplkvevkvG 371
                 +a+NapiQG+AaDii+ ami+i e+ +       +++qvHDEl+fev+++ ++++a  +k+ me++ +  ++v lk+ ++ G
  AHX11573.1 734 SAINAPIQGTAADIIRKAMIAIAEESELL---ECMVMQVHDELIFEVEKNMLHKFALNIKTRMEESPQisMHVDLKCGTSLG 812
                 ***********************988654...67*****************************8887744567777666666 PP

>> 5_3_exonuc_N  5'-3' exonuclease, N-terminal resolvase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  154.3   0.0     8e-49   2.4e-45       2     159 .]       5     164 ..       4     164 .. 0.93

  Alignments for each domain:
  == domain 1  score: 154.3 bits;  conditional E-value: 8e-49
  5_3_exonuc_N   2 llLiDgsslifRayyal..lttsdgeptnavygflnmllklleeekpthlavvfDakkktfRhelypeYKanReetpeelkeqlplikevlealgik 96 
                   l++iD+ +++f ay+al  l t++  p++avygf+n+llk l+  kp++l+v++D++k+tfR+ ly++YKanR+++p +l++q+ l++e+++al+++
    AHX11573.1   5 LMIIDAYNFLFSAYFALpnL-THNELPVGAVYGFINILLKHLR-SKPDYLVVALDTGKSTFREVLYDAYKANRPPVPGNLTPQFSLLRECIDALNLN 99 
                   89**************9855.7788******************.68899******9889************************************** PP

  5_3_exonuc_N  97 vlevegyEADDvigtlakraeeeg..vvivsgDkDllQlvednvrvld.vkkeelldeeevaekyg 159
                    lev+g+EADDvi++l+k+ + ++  +vi+s+DkDl+Qlv++nv +++ + k+++++ +ev+ek+g
    AHX11573.1 100 SLEVHGFEADDVIASLVKKFQGSDlkIVILSTDKDLMQLVNENVYIVNpI-KNKIIGTNEVKEKFG 164
                   *******************8854345**********************64.4677*********97 PP

>> 5_3_exonuc  5'-3' exonuclease, C-terminal SAM fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.9   0.0   8.1e-29   2.4e-25       2      93 ..     166     255 ..     165     259 .. 0.94
   2 ?   -1.3   0.0       1.1   3.4e+03      54      83 ..     688     718 ..     665     731 .. 0.69

  Alignments for each domain:
  == domain 1  score: 88.9 bits;  conditional E-value: 8.1e-29
  5_3_exonuc   2 kPeqiidlkaLvGDssDnipGvpgiGektAakLlkeygsleeilenldelkekklkekLeenkeearlskkLatiktdvpleleledlklke 93 
                  P qi+d++aL+GD+sDnipGvpgiG ktAakLl+++gs+++    ++e++ ++++e+L ++ +++ lskkL+ + ++++++ +l+d+++++
  AHX11573.1 166 FPIQIADFLALIGDASDNIPGVPGIGIKTAAKLLNTFGSIDNFK--IEEISPSRIRENLLRYSDQLTLSKKLVSLADNIEIKHSLHDIRYNS 255
                 599***************************************84..6899999**********************************99876 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 1.1
  5_3_exonuc  54 kklkekLeenkeearlskkLatik.tdvple 83 
                 +++ke ++++ke+ar++  + t+  +++p+ 
  AHX11573.1 688 PEIKEYMRATKETARINGYVKTLMnRKCPIR 718
                 4588899999999999888877752446654 PP

>> HHH_2  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   3.2e-05     0.096       7      30 ..     186     209 ..     184     214 .. 0.92
   2 ?   -2.4   0.0       1.7   5.2e+03      44      57 ..     515     528 ..     500     559 .. 0.52

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.2e-05
       HHH_2   7 GIrhVGektAklLakrFksldaLk 30 
                 G++ +G ktA +L + F+s+d++k
  AHX11573.1 186 GVPGIGIKTAAKLLNTFGSIDNFK 209
                 89*******************986 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 1.7
       HHH_2  44 GeeiAqsivefFen 57 
                 G +iA++  ++ +n
  AHX11573.1 515 GYRIADELLKWRHN 528
                 44444444444333 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.9e-05     0.056       6      29 ..     186     208 ..     181     220 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.9e-05
                 TSTT--HHHHHHHHTTT--SHHHH CS
       HHH_5   6 svsGiGpktAlallsaGiesvedl 29 
                 +v+GiG ktA +ll++ ++s++ +
  AHX11573.1 186 GVPGIGIKTAAKLLNT-FGSIDNF 208
                 69**************.9999854 PP

>> IMS_HHH  IMS family HHH motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   0.0   0.00051       1.5      16      31 ..     187     203 ..     183     203 .. 0.91
   2 ?    2.4   0.1     0.081   2.4e+02       1      16 [.     332     347 ..     332     348 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00051
     IMS_HHH  16 ipGiGgklgek.LeklG 31 
                 +pGiG k+++k L+++G
  AHX11573.1 187 VPGIGIKTAAKlLNTFG 203
                 8**********999987 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.081
     IMS_HHH   1 pddvkefLwplpitki 16 
                 pd++ ++L++l+i+ki
  AHX11573.1 332 PDSITTLLEDLSIKKI 347
                 78999**********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (819 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       795  (0.0443416); expected 358.6 (0.02)
Passed bias filter:                      539  (0.030063); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.62u 0.27s 00:00:00.89 Elapsed: 00:00:00.39
# Mc/sec: 6306.64
//
Query:       AHX11574.1  [L=274]
Description: cytochrome c oxidase subunit III family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-83  281.0  20.2    1.5e-83  280.6  20.2    1.2  1  COX3      Cytochrome c oxidase subunit III
  ------ inclusion threshold ------
       0.15   12.4   3.3       0.24   11.8   0.5    2.3  2  CopD      Copper resistance protein D


Domain annotation for each model (and alignments):
>> COX3  Cytochrome c oxidase subunit III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.6  20.2   1.7e-87   1.5e-83       2     257 ..       5     271 ..       4     272 .. 0.91

  Alignments for each domain:
  == domain 1  score: 280.6 bits;  conditional E-value: 1.7e-87
                 SS------SHHHHHHHHHHHHHHHHHHHHHSS-..-HHHHHH.HHHHHHHHHHHHHHHHHHHTTT----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        COX3   2 pfhlvsaspwplvlsvalllltsalvlflhgykesstllila.llslllvmllwfrdivaeatllGehtlavqkGlklGlilfiisevllflalfwaff 99 
                 +fh++++spwp+++s a+  +++++++ ++ +   s l  ++ l+ lll  + w+rd+v+e+ +  +h+  v++Gl++G+il+i+sev++f+a+fw+ f
  AHX11574.1   5 SFHILDPSPWPIFTSAASCGVVTSAAFLMRSSP-YSGLSFFSfLFLLLLCLFCWWRDVVSEGIVDKAHNPLVRRGLRIGMILLIFSEVMFFFAFFWSLF 102
                 7*************************9999988.555555551556778899*********************************************** PP

                 HHHHS--GGGTS.......SSS-TT-----TTSHHHHHHHHHHHHHHHHHHHHHHHHTTBHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS-TTS.... CS
        COX3 100 hsalsPtvelGa.......twpPvGikavnPlevPllntiillssGvtvtyahhsliegnrkkalkgllltillavlftllqaveyleasftisd.... 187
                 ++ l P+  +         twp  Gi  +nP ++P+lnt+ill sG+t+t+ah+s++++++k++++gll t+ll+++ft lq +ey++a+f++s+    
  AHX11574.1 103 KAWLDPAYVMDGpwpttrlTWPGEGITVLNPWNIPFLNTMILLLSGATMTWAHYSVLKSDNKSVVRGLLYTMLLGLVFTCLQGYEYYHATFSLSEegyk 201
                 ****99987765122222267778**********************************************************************74444 PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--BSSB-HHHHHHHHHHHHHHHHHHHHHHHTTTTT CS
        COX3 188 gvyGsvfylatGlhglhviigtillavallrllkyhltknhhlGfeaailywhfvdvvwlflyvsvywwg 257
                 ++y s fylatG+hglhviigti++av+l+r  +  +t + hlG+e+a +ywhfvdvvwlfl+ ++yw +
  AHX11574.1 202 AIYSSNFYLATGFHGLHVIIGTIFIAVCLFRAKAGQFTPENHLGLEFATWYWHFVDVVWLFLFTILYWLS 271
                 7999***************************************************************975 PP

>> CopD  Copper resistance protein D
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.1     0.077   6.9e+02      49      89 ..      46      80 ..      19      98 .. 0.66
   2 ?   11.8   0.5   2.6e-05      0.24      15      69 ..     141     195 ..     135     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.077
        CopD 49 alllvllalaalnrfrlvprleaatgaggqalrhrlrrsaa 89
                 l+l+ll+l+++ r ++ + +       ++a +  +rr ++
  AHX11574.1 46 FLFLLLLCLFCWWRDVVSEGI------VDKAHNPLVRRGLR 80
                467777777777776666666......23333334444444 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 2.6e-05
        CopD  15 vavvlvtGvvnallrvglagllttayGrlllaKlalllvllalaalnrfrlvprl 69 
                 ++++l++G+++++ ++++    + +  r ll +++l+lv ++l ++ ++  +  l
  AHX11574.1 141 TMILLLSGATMTWAHYSVLKSDNKSVVRGLLYTMLLGLVFTCLQGYEYYHATFSL 195
                 799************88544444555566***************99999776666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (274 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       628  (0.0350271); expected 358.6 (0.02)
Passed bias filter:                      235  (0.0131073); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.35
# Mc/sec: 2365.81
//
Query:       AHX11575.1  [L=1375]
Description: DNA-directed RNA polymerase, beta' subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.2e-84  284.3   0.0    2.1e-84  283.6   0.0    1.4  1  RNA_pol_Rpb1_1   RNA polymerase Rpb1, domain 1
    1.7e-66  224.4   0.4    3.6e-66  223.3   0.2    1.7  2  RNA_pol_Rpb1_5   RNA polymerase Rpb1, domain 5
    1.1e-36  126.5   0.0    2.3e-33  115.8   0.0    2.8  1  RNA_pol_Rpb1_2   RNA polymerase Rpb1, domain 2
      3e-21   76.0   0.0    8.6e-21   74.5   0.0    1.9  1  RNA_pol_Rpb1_3   RNA polymerase Rpb1, domain 3
    3.2e-16   59.2   0.4    8.4e-16   57.9   0.4    1.7  1  RNA_pol_Rpb1_4   RNA polymerase Rpb1, domain 4
    1.6e-05   25.0   0.2       0.53   10.5   0.0    4.8  5  Peptidase_M23    Peptidase family M23
     0.0017   18.3   0.0      0.029   14.4   0.0    2.8  3  Apocytochr_F_C   Apocytochrome F, C-terminal
  ------ inclusion threshold ------
       0.01   15.7   0.0        1.1    9.1   0.0    3.4  3  Biotin_lipoyl_2  Biotin-lipoyl like
      0.036   14.3   0.3       0.12   12.7   0.3    1.8  1  YnfE             Uncharacterized YnfE-like
      0.093   12.8   0.0       0.25   11.4   0.0    1.7  1  RPN1_C           26S proteasome non-ATPase regulatory subunit


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb1_1  RNA polymerase Rpb1, domain 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  283.6   0.0   1.1e-87   2.1e-84       4     312 .]      17     343 ..      14     343 .. 0.94

  Alignments for each domain:
  == domain 1  score: 283.6 bits;  conditional E-value: 1.1e-87
                     --EEEEEE--HHHHHHH-SBB--STTSTCSTSSSSBBSSSSSSSSS-SSSSSTSTTTSSTTT.........T---..........--EEEEEECE CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.........xxxx..........xxxxxxxxxx RF
  RNA_pol_Rpb1_1   4 ikeiqfgiaspeeirkwSvvevtkaetieekslkPeegGllDerlgtidkdleCetCgkkkk.........eCeg..........hfGhieLakP 79 
                     +++i++++as ++ir++S++evtk+eti++++ kPe+ Gl++ ++++++k++eC +Cgk+kk         +C +          ++GhieLa+P
      AHX11575.1  17 FDSIKISLASADKIRALSYGEVTKPETINYRTFKPERDGLFCAKIFGPTKSYEC-LCGKYKKikysgvvceRCGVevtssrvrreRMGHIELASP 110
                     789***************************************************.**********999999888899****************** PP

                     EE-HHHHHH...........HHHHCTTCETTTTEBSS-TT.....SH....HHHHHHCSSSCC.......CCHHHHHHHHCCS-BE-SSSSB-EE CS
                     xxxxxxxxx...........xxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxx.......xxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1  80 vfhigffkl...........ilkilecvckecskllldee.....kkkllsklkkrekleelk.......krlkaieelckkinlcekCgavqpk 151
                     v+hi+f+k+           +lk +e++++++s++++d++     k+++++++++ e+++e+         +++ai++++ ++nl          
      AHX11575.1 111 VAHIWFLKSlpskictlldlTLKNVEKILYFESYVVIDPGvtafnKNDIITDESYSEAIREYGagsftamIGAEAIKHMLASLNL---------- 195
                     ****************************************99999999**************98888887788888888888877.......... PP

                     EEEETTEEEEEESSSSTSCEEEE-HHHHHHHHHCSTHHHHHHTTSBTTTB-GGGCCECCEEE--GGGS-BEESSSSSEEBECCCCHHHHHHHHHH CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 152 leeegeklkaalkkskeeekeklsaekvkkllkriededvevlgfkssgsrPewliltvlPVpPpeiRPsvqldggrrsedDlteklrdiikrNn 246
                      ee   kl+++  ++++       + k kk++k ++     v+ f  s srP ++il v+PV+Pp++RP+v+ldggr++++Dl+ ++r++i+rNn
      AHX11575.1 196 -EEMAVKLRSQAASTNS-------EVKKKKIIKTLR----LVEQFLGSDSRPVDMILDVIPVMPPDLRPLVMLDGGRFATSDLNALYRSVINRNN 278
                     .7777777777777777.......667778888888....8889999************************************************ PP

                     HHHHHHHSSSSSTCHHHHHHHHHHHHHHCC-TTSSSSSEEBSTTSSS--THHHHHTSSSSCCCCCT CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb1_1 247 rLkkaeeegapeliieeekelLQehvatlfdneisglkpatqkskrplkslsqrLkGKeGrfRgnL 312
                     rLk  +   ap++ii++e+++LQe+v++lfdn  +  k ++ ++krp ks+s++LkGK+GrfR+nL
      AHX11575.1 279 RLKSLIYLRAPSIIINNERRMLQEAVDALFDNGRRT-KIIKGSNKRPYKSISDMLKGKQGRFRQNL 343
                     *********************************998.****************************9 PP

>> RNA_pol_Rpb1_5  RNA polymerase Rpb1, domain 5
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.97   1.7e+03     150     151 ..     521     628 ..     180     707 .. 0.47
   2 !  223.3   0.2     2e-69   3.6e-66       4     265 ..     752    1298 ..     749    1300 .. 0.94

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.97
                     E.............................................................................................. CS
                     x.............................................................................................. RF
  RNA_pol_Rpb1_5 150 k.............................................................................................. 150
                     +                                                                                              
      AHX11575.1 521 Qevhptvfcapweaehafvnkkialhtrircqlefngesrlytttfgrlqllkilpegvpfdsvntmltvrdisnlvdlvykicghgktvefadk 615
                     03333333333333333333333333333444444444444444444444444444444444444444444444444444444444444444444 PP

                     ............C CS
                     ............x RF
  RNA_pol_Rpb1_5 151 ............g 151
                                 g
      AHX11575.1 616 imelgfryatlsG 628
                     4444444444441 PP

  == domain 2  score: 223.3 bits;  conditional E-value: 2e-69
                      HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTEEEETTSEEEETTS-EEESSGGGTS.............................. CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.............................. RF
  RNA_pol_Rpb1_5    4 vkefffhtmggReGLiDtAvkTaesGYlqRrlvkaledvvvkyddtvrnsggeivqflygedg.............................. 66  
                      v e+f++t+g+R+GL+DtA+kTa+sGYl+Rrlv++++d ++ ++d++   g  + + ++g+ +                              
      AHX11575.1  752 VLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDSIIVEEDCGATDGLMVRASIEGGVVimplsdsifsrvsagdivdpsdgstivrag 844 
                      78*********************************************9999999999999988****************************** PP

                      ..............................................B--TT-BHHHHHHHHHHHHHHCCCSSTTSSTCSSTSSSSS....... CS
                      ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....... RF
  RNA_pol_Rpb1_5   67 ..............................................lvepGeavGiiaaQSiGePgTQltlnTFHfaGvasknvtl....... 106 
                                                                    lv++GeavG+iaaQS+GePgTQlt++TFH++G+a++ v++       
      AHX11575.1  845 emfddasierieslgidsvrirsvltckskygicrkcygadlsnrkLVSLGEAVGVIAAQSVGEPGTQLTMRTFHVGGAATRRVESssmvafc 937 
                      ********************************************************************************************* PP

                      .SHHHHHHH.....HTT-SS-SS-EEEEEB-SSSSSCHHHCHHHHHHHSE........................................... CS
                      .xxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................................... RF
  RNA_pol_Rpb1_5  107 .Gvprlkei.....lnvskniksksltvllvdeeakelekakkvkkaiek........................................... 150 
                       G +++ +       +++ ++ s+s+++llvd+   e  + +  ++ + +                                           
      AHX11575.1  938 sGRVKFVNAnlitnRDGNYIVLSRSFELLLVDSLGIEHFQGRVQYGGTVYvkegdmvpigkkladwdlytvpiiseasgkvsyadmiegvsyn 1030
                      *999999999998888899999**********99888777776666666689999************************************** PP

                      ............................................................................................. CS
                      ............................................................................................. RF
  RNA_pol_Rpb1_5  151 ............................................................................................. 150 
                                                                                                                   
      AHX11575.1 1031 eiqdentgisnktvvdwkqgeaasnlrprveilnadgslatgqqskeaiyllplgailnvspedmveagdiiakitkestttrditgglprvi 1123
                      ********************************************************************************************* PP

                      ..........................CBTTEEEEEEEEEEEEEEETEEEEEEECS--HHHHTTSTT..TBETTTEEES...SHHHHHHHHCHH CS
                      ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxx...xxxxxxxxxxxx RF
  RNA_pol_Rpb1_5  151 ..........................gikkikrilvkeaekgkeeekelvletegvnlsevlkvee..vvdageilsn...diaeileilgie 212 
                                                  k+++++l+++ e++++  + l      v++ ++l v+e  ++ +ge l +   d++eil++lg e
      AHX11575.1 1124 klfearkgkvnavisevdgyvefakdYYKSKRKVLIRSREDSQRVYEYL------VPKGRHLIVSEgdFIRKGEPLMDgdpDLHEILRVLGLE 1210
                      **********************999877788888888777666553555......9999*99999999************************* PP

                      HHHHHHHHHHHHHHHHTTS---HHHHHHHHHHHTTTSS---SSTT...................................CHCCSSSH CS
                      xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...................................xxxxxxxx RF
  RNA_pol_Rpb1_5  213 aarkallkeiqevykvqgvsvndrHlelivdqmtkkgeivavnrs...................................Ginkaels 265 
                      a+++++++eiq vy+ qgv++n++H+e+i++ m++k+ei++ +++                                   Gi++a+l+
      AHX11575.1 1211 ALAEYMITEIQRVYRLQGVKINNKHIEVIIRKMLQKVEITDAGDTtllvgeqveksrvekineviatqglrcasytpvllGITRASLQ 1298
                      ********************************************98999888888888888888888888888888888888888766 PP

>> RNA_pol_Rpb1_2  RNA polymerase Rpb1, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.0   1.3e-36   2.3e-33       1     165 [.     345     486 ..     345     487 .. 0.87

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 1.3e-36
                     SEEESSEEEEEEEEESSS-TTEEEEEHHHHTTSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEESTTSSEEETTTT-SCHHCCTTTTSEEEEE- CS
  RNA_pol_Rpb1_2   1 GkrvdysaRsvispdpnlkldevgvPisvakkltvpeivtelnikklrklvengpevyPgasyvkredgsekklkakkrklakelekgdiverhv 95 
                     Gkrvdys+Rsvi+++p l+l++ g+P+++a  l+ p i ++l    +  +++                 ++++++++    + e++    v  +v
      AHX11575.1 345 GKRVDYSGRSVIVVGPALELHQCGLPKKIALELFKPFIYSKLELYGIAPTIK----------------TARRMVQNE----QPEVW---DVLAKV 416
                     9*********************************998877766555543332................344555555....44555...677889 PP

                     -TTSEEEEE-SSTTSGGGEEEEEEEEESSSSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHHHCSB CS
  RNA_pol_Rpb1_2  96 kdgdvvllNRqPsLhklsimahrvkvlekktlrlnlsvttayNaDFDGDemnlhlpqseearaEaeelll 165
                     +++  v+lNR+P+Lh+ls++a++  ++e+k+++l+ +v+ta+NaDFDGD+m +h+p s ea++Ea+ l++
      AHX11575.1 417 IHQHPVFLNRAPTLHRLSVQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMSVHVPLSIEAQVEARLLVM 486
                     99****************************************************************9986 PP

>> RNA_pol_Rpb1_3  RNA polymerase Rpb1, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.5   0.0   4.8e-24   8.6e-21       1     157 []     490     636 ..     490     636 .. 0.91

  Alignments for each domain:
  == domain 1  score: 74.5 bits;  conditional E-value: 4.8e-24
                     CSEETTTTEESSS--THHHHHHHHHSSTT........EEEEHHHHHHHHHHSSSCCSSSSSSSSSBESSSE....BEEHHHHHHCCCHCCCCEEE CS
  RNA_pol_Rpb1_3   1 nilspqsgkPvigivQDsllGvyllTked........vfidreeaqqllykgvgsdsktvtlrpailkpke....lwtgkqtfsrilpneinyer 83 
                     nil+p++ +P+i++++D++lGvy+l+ e+        vf  + ea++++ ++      ++ l+++i  + e     + + +tf+r+   +i++e+
      AHX11575.1 490 NILNPANSRPIIVPSKDIVLGVYYLSLEEksqevhptVFCAPWEAEHAFVNK------KIALHTRIRCQLEfngeSRLYTTTFGRLQLLKILPEG 578
                     9***************************************************......89999999999656888999***************** PP

                     ESSSSSTSEEECSSEEEES--SHHHHSSSSTTSHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCEB-TGGGG CS
  RNA_pol_Rpb1_3  84 kneekdgkvlikngelikGvidkkvvgkksqgslihvlakeygiketvrfldslqrlgfkyllqsgftigigDt 157
                        +      + n++l        +v   ++++l++ ++k +g+ +tv+f d++++lgf+y++ sg+++g +D+
      AHX11575.1 579 V--PF---DSV-NTML--------TV--RDISNLVDLVYKICGHGKTVEFADKIMELGFRYATLSGISFGKDDM 636
                     3..32...233.4444........34..699******************************************7 PP

>> RNA_pol_Rpb1_4  RNA polymerase Rpb1, domain 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.9   0.4   4.7e-19   8.4e-16       1      83 [.     665     737 ..     665     749 .. 0.88

  Alignments for each domain:
  == domain 1  score: 57.9 bits;  conditional E-value: 4.7e-19
                     HHHHCTHTCCHHHTTHCHHHHHHHHHHHHHHHHHHHHHHHHHHCSTTTSHHHHHHHCTSSS-HHHHHHHHTB-EEEEBTTBSS CS
  RNA_pol_Rpb1_4   1 ieeaerygkledlpgksleelfeakinkilnkardkagkiaskslaasNsiliMvksGaKGsiinisqiagclGqqnvegkri 83 
                     i++ e+y+k+ d+++k+++ +++++++ i+   +++        +a+ Nsi++M++sGa+Gs+ +i+q+ag++G++++++ +i
      AHX11575.1 665 ITKHEKYNKVVDAWQKCTDIVAKDMMEGISV--YEN--------VAEMNSIFMMAQSGARGSAAQIKQLAGMRGLMAKPSGEI 737
                     7899*************************99..655........2334******************************97655 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0         4   7.1e+03       6      27 ..      20      41 ..      18      47 .. 0.81
   2 ?    1.5   0.0      0.19   3.4e+02      13      42 ..     930     962 ..     919    1004 .. 0.61
   3 ?   -1.6   0.0       1.8   3.2e+03      15      32 ..    1009    1026 ..    1002    1042 .. 0.78
   4 !    6.1   0.0    0.0073        13      52      78 ..    1084    1111 ..    1065    1118 .. 0.78
   5 !   10.5   0.0   0.00029      0.53      13      69 ..    1131    1193 ..    1124    1195 .. 0.73

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 4
                   EEEEETTT-EEEESSSEEEEEE CS
  Peptidase_M23  6 idiaapkgtpVlAaadGtVvfa 27
                   i+i+ +  ++++A + G+V++ 
     AHX11575.1 20 IKISLASADKIRALSYGEVTKP 41
                   6778888899*********875 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.19
                    T-EEEESSSEEEEEEEE...ETTTEEEEEEEEC CS
  Peptidase_M23  13 gtpVlAaadGtVvfagk...kegyGnvviidhg 42 
                    +++ +A ++G+V f++    +++ Gn++++  +
     AHX11575.1 930 SSSMVAFCSGRVKFVNAnliTNRDGNYIVLSRS 962
                    556789999999888875543355888888763 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 1.8
                     EEEESSSEEEEEEEEETT CS
  Peptidase_M23   15 pVlAaadGtVvfagkkeg 32  
                     p+++ a+G+V +a+  eg
     AHX11575.1 1009 PIISEASGKVSYADMIEG 1026
                     899********9987554 PP

  == domain 4  score: 6.1 bits;  conditional E-value: 0.0073
                     ESEES.S-TTEEE-TTCEEEEEBSTSSC CS
  Peptidase_M23   52 lskis.vkegqkVkaGqvIGtvgstgrs 78  
                     l +i  v++ + V+aG++I+++ ++  +
     AHX11575.1 1084 LGAILnVSPEDMVEAGDIIAKITKESTT 1111
                     555444***************9977644 PP

  == domain 5  score: 10.5 bits;  conditional E-value: 0.00029
                     T-..EEEESSSEEEEEEEEETTTEEEEEEEECTCEEEEEEEESEES....S-TTEEE-TTCEE CS
  Peptidase_M23   13 gt..pVlAaadGtVvfagkkegyGnvviidhgdgystlyahlskis....vkegqkVkaGqvI 69  
                     g+   V++  dG V fa+++ +    v+i+  +  + +y  l        v+eg+++++G+++
     AHX11575.1 1131 GKvnAVISEVDGYVEFAKDYYKSKRKVLIRSREDSQRVYEYLVPKGrhliVSEGDFIRKGEPL 1193
                     443379999**********7777777777776666666666544323457**********986 PP

>> Apocytochr_F_C  Apocytochrome F, C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.6   4.6e+03      38      61 ..     978    1001 ..     968    1002 .. 0.84
   2 ?   -0.6   0.0      0.71   1.3e+03      31      61 ..    1073    1103 ..    1057    1107 .. 0.82
   3 !   14.4   0.0   1.6e-05     0.029       6      62 ..    1137    1195 ..    1126    1200 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.6
                      EEEESSS-BS--ST-EE-TT-BSC CS
  Apocytochr_F_C   38 etipaGpelivsegqevkagealt 61  
                       ++  G ++ v+eg+ v  g++l+
      AHX11575.1  978 GRVQYGGTVYVKEGDMVPIGKKLA 1001
                      57889999*********9998875 PP

  == domain 2  score: -0.6 bits;  conditional E-value: 0.71
                      STSEEE-EEEESSS-BS--ST-EE-TT-BSC CS
  Apocytochr_F_C   31 edgeavvetipaGpelivsegqevkagealt 61  
                      +++++ +  +p G+ l vs ++ v+ag+ ++
      AHX11575.1 1073 QQSKEAIYLLPLGAILNVSPEDMVEAGDIIA 1103
                      4455666778*****************9876 PP

  == domain 3  score: 14.4 bits;  conditional E-value: 1.6e-05
                      B-SSSEEEEEEEEEESSEEEEEE.ETSTSEEE.-EEEESSS-BS--ST-EE-TT-BSC- CS
  Apocytochr_F_C    6 kasaaGtiskiekeekggtevti.etedgeav.vetipaGpelivsegqevkagealtn 62  
                       + + G ++  ++  k + +v i ++ed++ v +  +p+G +livseg+ +++ge+l +
      AHX11575.1 1137 ISEVDGYVEFAKDYYKSKRKVLIrSREDSQRVyEYLVPKGRHLIVSEGDFIRKGEPLMD 1195
                      4455666666666666799999943455555525679******************9864 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0      0.13   2.4e+02      15      27 ..     985     997 ..     978    1003 .. 0.85
   2 ?    9.1   0.0   0.00063       1.1      16      38 ..    1088    1110 ..    1086    1114 .. 0.86
   3 ?   -1.0   0.0       0.9   1.6e+03      18      31 ..    1181    1194 ..    1178    1200 .. 0.86

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.13
  Biotin_lipoyl_2  15 qlnVkdGqrVkaG 27 
                      +++Vk+G+ V  G
       AHX11575.1 985 TVYVKEGDMVPIG 997
                      69*******9766 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00063
  Biotin_lipoyl_2   16 lnVkdGqrVkaGdvLaelDsral 38  
                       lnV   + V+aGd++a + ++ +
       AHX11575.1 1088 LNVSPEDMVEAGDIIAKITKEST 1110
                       6888889***********99866 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.9
  Biotin_lipoyl_2   18 VkdGqrVkaGdvLa 31  
                       V +G+ + +G  L+
       AHX11575.1 1181 VSEGDFIRKGEPLM 1194
                       99********9986 PP

>> YnfE  Uncharacterized YnfE-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.5e-05      0.12      25      64 ..     642     682 ..     639     696 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.5e-05
        YnfE  25 keeDlekqkeqlelYekqLkqesssd.edfDevvdavvkcA 64 
                 k e ++k +e++  Ye q +++ +++ e++++vvda  kc 
  AHX11575.1 642 KAEHVRKTNEEVKDYEFQYQEGLITKhEKYNKVVDAWQKCT 682
                 78899******************996378*******99995 PP

>> RPN1_C  26S proteasome non-ATPase regulatory subunit RPN1 C-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00014      0.25      17      50 ..    1285    1317 ..    1282    1319 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00014
      RPN1_C   17 ttPVlLaageRAELateeYiplssvLEgivilkk 50  
                   tPVlL+ + RA L+te +i+++s+ E   il++
  AHX11575.1 1285 YTPVLLGIT-RASLQTESFISAASFQETTKILTE 1317
                  6******97.**************9999888875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.78u 0.28s 00:00:01.06 Elapsed: 00:00:00.40
# Mc/sec: 10413.89
//
Query:       AHX11576.1  [L=1358]
Description: DNA-directed RNA polymerase, beta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   4.6e-150  500.0   0.0   1.2e-149  498.7   0.0    1.6  2  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6
    2.2e-29  101.4   0.0    4.2e-29  100.5   0.0    1.5  1  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3
    5.3e-29  101.2   1.3    5.9e-18   65.2   0.1    2.8  3  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2
    1.7e-25   89.7   0.0    4.3e-25   88.4   0.0    1.7  1  RNA_pol_Rpb2_1   RNA polymerase beta subunit
    1.9e-22   79.4   0.0    5.2e-22   78.0   0.0    1.8  1  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7
    1.7e-17   63.5   0.7    1.2e-16   60.7   1.1    2.2  2  RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domai
  ------ inclusion threshold ------
      0.018   14.9   0.2       0.09   12.6   0.1    2.2  2  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> RNA_pol_Rpb2_6  RNA polymerase Rpb2, domain 6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.52   1.3e+03       2      27 ..     666     691 ..     665     696 .. 0.91
   2 !  498.7   0.0  4.6e-153  1.2e-149       1     389 [.     718    1267 ..     718    1268 .. 0.98

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.52
                     HHT-SS-TTB-HHHHHHHHHHGGGB- CS
  RNA_pol_Rpb2_6   2 aklapvvehvqspriiiqaamekqal 27 
                     a+l+p+ e+ +++r ++ ++m++qa+
      AHX11576.1 666 ASLIPFLENDDANRALMGSNMQRQAV 691
                     899********************986 PP

  == domain 2  score: 498.7 bits;  conditional E-value: 4.6e-153
                      HHHT-SS-TTB-HHHHHHHHHHGGGB.-S---TTTTT---SSEEEESS----SSB-S.TTTTTS.........GGGS-SEEEEEBBBS--TTT CS
  RNA_pol_Rpb2_6    1 vaklapvvehvqspriiiqaamekqa.lgiyslnkfkrsnqktyllcinqkPlvktgdkveagqvl.dgpatekgelalGqnavVAvmsyeGY 91  
                      vak+a+vve++++++i++ ++ +++  ++ y l+kf++sn++t   ci+q+++v +g++v+ag++l dgpat++gelalG+n++VA+ms++GY
      AHX11576.1  718 VAKRAGVVEYIDAKNIVVASESKEDFwIDSYMLHKFRKSNHNT---CIHQRCVVYQGQRVKAGDILaDGPATQQGELALGRNLIVAFMSWRGY 807 
                      69****************995555532459*************...*********************************************** PP

                      TTTT-EEEBCHHHHTTTT-EEEEEE..EEE--SSSS---.-S--..--SS-GGGS-TTSB--SS-EEETT-EEE---...B-----...---- CS
  RNA_pol_Rpb2_6   92 niEDaiilnerlvdrdvftsihikeyeveardtklgeeeitrdipnvseealkkLdedGivrvgaevkegdilvgkvt.kgeteltpeekllr 183 
                      n+ED+i+++ +++++d+fts+h++ +e+ +rdt+lg+ee+trdip v ee l+ Lde Giv+vga+v++gdilvgkvt k+++ +tpeekllr
      AHX11576.1  808 NFEDSIVISSNVARDDIFTSVHLEGFECIVRDTRLGPEELTRDIPGVAEEFLHSLDEFGIVCVGASVESGDILVGKVTpKSSSPVTPEEKLLR 900 
                      ********************************************************************************************* PP

                      -------..-B---EE--TT-EEEEEEEEE............................................................... CS
  RNA_pol_Rpb2_6  184 aifgekarevkdtslrvksgeegvVdkvkvfsr............................................................ 216 
                      aifgeka +vkd+sl++++g++g+V++vk+++r                                                            
      AHX11576.1  901 AIFGEKAIDVKDSSLYLPPGVSGCVVDVKILQRrgiekvgralliekqavdsekakrdheltvlanyiysilkemlvgkvalnslngisegdv 993 
                      ********************************************************************************************* PP

                      ......................................................EE-TT--EEEEEEEEEEE---TT-BEEETTS---BBEEE CS
  RNA_pol_Rpb2_6  217 ..................................................ekgdelkagvnklvkvyvaqkRklqvGDKfasrhGqKGvvsli 259 
                                                                        + +d+l++gv ++vkv+va k++lq GDK+++rhG+KGv+s+i
      AHX11576.1  994 itetallsinredwwklsvegiasikllrqrfvdrsaeinkvyeenfekiRGDDDLAQGVLTVVKVFVAVKHTLQPGDKMSGRHGNKGVISRI 1086
                      *************************************************999999************************************** PP

                      B-TTTSEEETTS---SEEE-GGGCHHH-BTTHHHHHHHHHCCCS................................................. CS
  RNA_pol_Rpb2_6  260 lpqeDmPfledGivvDivlNPlgvPSRmtigqllEtllgkaaal................................................. 303 
                      +p eDmP+l+dG++vDi+lNPlgvPSRm++gq+lEt+lg+a                                                    
      AHX11576.1 1087 VPAEDMPYLSDGTPVDIILNPLGVPSRMNVGQILETHLGWAVYNlgkkvsklldennfpelksllfeiykndkkmmailkgmsddevlhysqs 1179
                      *****************************************9999************************************************ PP

                      ..SSS--B--TT-...-HHHHHHHHHTTS-TT-EE-EEETTTS-B-SS-EEB-EEEEEEBS--CCCS----SS--B-TTT--B-SCGG CS
  RNA_pol_Rpb2_6  304 ..egkkvdatvFdgakeeeikelLeeagleasGkevlydGrtGekleaeifvGviYylkLkhlvedKihaRstGpyslltqQPlgGka 389 
                        +g  v+a+vF+g k++ei++lL  ag + sG+evlydG+tGe+++++++vG+ Y+lkL+hlv+dKihaRs+G ysl+tqQPlgGk+
      AHX11576.1 1180 lrKGIPVAASVFEGPKTDEIERLLILAGKDPSGQEVLYDGVTGEQFDRKVTVGCKYMLKLHHLVNDKIHARSIGSYSLITQQPLGGKS 1267
                      ***************************************************************************************8 PP

>> RNA_pol_Rpb2_3  RNA polymerase Rpb2, domain 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.5   0.0   1.6e-32   4.2e-29       1      68 []     514     582 ..     514     582 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.5 bits;  conditional E-value: 1.6e-32
  RNA_pol_Rpb2_3   1 qvldrlnplselshlrrvssl.rgglskerkttevRdlhpshwGriCpveTPEGencGlvksLallarv 68 
                     q++d++nplse++h+rr+s+l +ggl++ r+++evRd+h +h+GriC  eTPEG+++Gl++sLa++a++
      AHX11576.1 514 QFMDQTNPLSEITHKRRISALgPGGLNRGRAGFEVRDVHTTHYGRICATETPEGATIGLINSLAIYAKI 582
                     89*****************************************************************98 PP

>> RNA_pol_Rpb2_2  RNA polymerase Rpb2, domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.1   0.0     8e-12     2e-08       2      74 ..     157     229 ..     156     252 .. 0.82
   2 !   65.2   0.1   2.3e-21   5.9e-18      96     190 .]     357     455 ..     352     455 .. 0.97
   3 ?   -3.4   0.1       2.4   6.2e+03     125     159 ..     929     959 ..     925     976 .. 0.63

  Alignments for each domain:
  == domain 1  score: 34.1 bits;  conditional E-value: 8e-12
                     TSCEEEEE-SSSSSE.SSSCCEECCCEEEEECCCCSTSCEEEEECTTSSSEEEHHHHHHHTT--STTHHHHHHT CS
  RNA_pol_Rpb2_2   2 sngiyvekekdknki.satvtsslisqrgsvlklekdgktliwtriskkrkipivivlkAlglvsdreIleric 74 
                      +g+ +  +k+k+   +  + + +i +rgs+l +e d k++++ ri+kkrk p+  +l+Algl s +eI++  c
      AHX11576.1 157 APGVFFDNDKAKSISgKLNYIARIIPYRGSWLDFEFDAKDILYFRIDKKRKLPVTFLLRALGL-SNKEIFSCFC 229
                     566666666666644444577788999***********************************9.669***9776 PP

  == domain 2  score: 65.2 bits;  conditional E-value: 2.3e-21
                     SSSCHHHHHHHHHCSSTTSSSCCCCCHHHHHHH......CHHHHHHHTTTTSSTTTTTSSSTCHH...HHHHHHHHHHHHHHHHTTSSSS--TTS CS
  RNA_pol_Rpb2_2  96 iqtqeealdyigkvvalrrgeearlqsareilq......krydlgeigreklnkhlglseslenkr.lkaqdilymidrLlslklgrrevDDiDh 183
                     +++ eea+  i++   +r+ge + ++sa+++++      +rydl  +gr +ln++ +l+ + en + l+ +dil  i+ L++l+ + ++vDDiDh
      AHX11576.1 357 DCSYEEAMLSIYR--VVRPGEIPSVESAEKLFEslfflpERYDLLNVGRVRLNAKFNLNHD-ENLTvLTKEDILCTIKELMNLQRDVGDVDDIDH 448
                     57789*******9..**********************************************.99999**************************** PP

                     GGGEEEE CS
  RNA_pol_Rpb2_2 184 lgnkRvr 190
                     lgn+Rvr
      AHX11576.1 449 LGNRRVR 455
                     ******8 PP

  == domain 3  score: -3.4 bits;  conditional E-value: 2.4
                     HHHHCHHHHHHHTTTTSSTTTTTSSSTCHH..HHH CS
  RNA_pol_Rpb2_2 125 eilqkrydlgeigreklnkhlglseslenkrlkaq 159
                     +ilq r   +++gr  l ++  ++ + + k    +
      AHX11576.1 929 KILQ-RRGIEKVGRALLIEKQAVDSE-KAK--RDH 959
                     5664.777899999999998777766.333..333 PP

>> RNA_pol_Rpb2_1  RNA polymerase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.4   0.0   1.7e-28   4.3e-25       2     202 ..      19     500 ..      18     501 .. 0.98

  Alignments for each domain:
  == domain 1  score: 88.4 bits;  conditional E-value: 1.7e-28
                     TTHHHHHHHHHHHHTHHHHHCTTSSECCHCSSSHCSSSCEEEEEEEEEEESCSSECTTSCEEES.HHHHHHCTSBXEEEEEEEEEEEECCCC... CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
  RNA_pol_Rpb2_1   2 LvsqqldSFnkfveqdlekiikeeaaieseeeiqssgeelelkfvsirlgkPvvdesdasereiyPkearlrnltYsaplyvklklvvyekd... 93 
                     Lv+ q dS+  f+      i   +  + s+++i+   ++ +l+fvs r+g+P++de            + +r++tY apl+  l+lvv+ ++   
      AHX11576.1  19 LVKVQKDSYFSFIGGG-GSISSIQDIFASVFPISDGYGRASLEFVSCRVGEPKHDE----------YGCIERGITYAAPLRAVLRLVVFADEsvv 102
                     7888999999999764.46777788899*****999999*****************..........99********************9888*** PP

                     ...............TCCEEEEEEEEEEEEEXBTTSTTSSSTTS.HHHHHHTTS.TTS..SSEEETTCEEEEXEEEE.................. CS
                     ...............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................. RF
  RNA_pol_Rpb2_1  94 ...............nkeeikeeevyiGelPlMlrskacvlseaseeelvelkEcpldqGGyFiinGtekvivaqek.................. 155
                                    + ++i+e+e+y+G++P+M ++                        G+F+inG e+v+v+q++                  
      AHX11576.1 103 sseksakseqnpsspSIKDIREQEIYMGDIPIMSKN------------------------GTFVINGVERVVVSQMHrapgvffdndkaksisgk 173
                     ***************9********************........................*********************************** PP

                     ............................................................................................... CS
                     ............................................................................................... RF
  RNA_pol_Rpb2_1 156 ............................................................................................... 155
                                                                                                                    
      AHX11576.1 174 lnyiariipyrgswldfefdakdilyfridkkrklpvtfllralglsnkeifscfceitecrrtqdgkwvslfvpekfkgvrlqydlintdtgev 268
                     *********************************************************************************************** PP

                     ............................................................................................... CS
                     ............................................................................................... RF
  RNA_pol_Rpb2_1 156 ............................................................................................... 155
                                                                                                                    
      AHX11576.1 269 vlkkgsrvsialakslyakglrhyfmdvevmkdmyladdllstkgefllphgtkltkehiaktefldvdllklvdlkgnymfnavlqydcsyeea 363
                     *********************************************************************************************** PP

                     ............................................................................................XHH CS
                     ............................................................................................xxx RF
  RNA_pol_Rpb2_1 156 ............................................................................................laG 158
                                                                                                                 ++G
      AHX11576.1 364 mlsiyrvvrpgeipsvesaeklfeslfflperydllnvgrvrlnakfnlnhdenltvltkedilctikelmnlqrdvgdvddidhlgnrrvrSVG 458
                     *********************************************************************************************** PP

                     HHHHHHHHHHHHHHHHHHHHHHHHHHCTSSSSSHHHHSCSHHHH CS
                     xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  RNA_pol_Rpb2_1 159 eLlaslfrvllkklerdvkerlqksleklddlmlqllvnakpit 202
                     e + ++frv+l++++r ++e++     + d++m+ +++n+k ++
      AHX11576.1 459 EFMDNQFRVGLVRMVRVIIENM--ATADFDTVMPCDMINSKILG 500
                     **********************..99**************9876 PP

>> RNA_pol_Rpb2_7  RNA polymerase Rpb2, domain 7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.0   0.0     2e-25   5.2e-22       1      84 [.    1270    1343 ..    1270    1345 .. 0.98

  Alignments for each domain:
  == domain 1  score: 78.0 bits;  conditional E-value: 2e-25
                      BBEEEEHHHHHHHHHHTBHHHHHHHHTTTTTEEEEEEESSSSSCCCEEEBTTTTCSSSEEEEEEEHHHHHHHHHHHHTTBEEEE CS
  RNA_pol_Rpb2_7    1 GGlrfGEMErdaliayGaaalLkerltikSDavevdvcgrckllaaaneCkivkseekiekveipeafklLlqeLqslgialkl 84  
                      GG+rfGEME++al++yGa   L+e+ltikSD    dv gr++++++     iv++++++  + ipe+f+++++eL++l++++++
      AHX11576.1 1270 GGQRFGEMECWALQSYGATFALQEMLTIKSD----DVVGRVNVYDS-----IVRGDNNFYYG-IPESFNVMMNELRALCLNVEF 1343
                      9******************************....***********.....***********.******************987 PP

>> RNA_pol_Rpb2_45  RNA polymerase beta subunit external 1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.7   1.1   4.6e-20   1.2e-16       1      65 []     592     657 ..     592     657 .. 0.99
   2 ?   -1.9   0.0       1.6   4.1e+03      37      55 ..    1241    1259 ..    1237    1261 .. 0.82

  Alignments for each domain:
  == domain 1  score: 60.7 bits;  conditional E-value: 4.6e-20
                      EEEEE.TEEEEEEEEEEHHHHTTSEEE-SSS-BETTSCBSSSEEEEECSSCEEEEEGGG-SEEESS CS
  RNA_pol_Rpb2_45   1 YrkVe.gkvtdevvYLtAdeEekyviAqAnapldeegrfveerVlaRrkgevelvepeeVdymDVS 65 
                      Yr V+ gk tdev YL+A +E k  i qA++ +d++g+++++ V +Rr+ e ++++++eV++ DVS
       AHX11576.1 592 YRYVRnGKITDEVTYLSAIDEIKANICQASVRVDDDGYILDDLVYCRRNYENVFIPRDEVQFADVS 657
                      9***99***********************************************************9 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 1.6
                       CBSSSEEEEECSSCEEEEE CS
  RNA_pol_Rpb2_45   37 rfveerVlaRrkgevelve 55  
                       ++v+++++aR  g + l++
       AHX11576.1 1241 HLVNDKIHARSIGSYSLIT 1259
                       799*******988887766 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.1   3.5e-05      0.09      18      31 ..     768     781 ..     765     782 .. 0.91
   2 ?   -1.8   0.0       1.1   2.8e+03      18      30 ..     868     880 ..     868     881 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 3.5e-05
  Biotin_lipoyl_2  18 VkdGqrVkaGdvLa 31 
                      V +GqrVkaGd+La
       AHX11576.1 768 VYQGQRVKAGDILA 781
                      779**********8 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.1
  Biotin_lipoyl_2  18 VkdGqrVkaGdvL 30 
                      V+ G  V+ Gd+L
       AHX11576.1 868 VCVGASVESGDIL 880
                      667999******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       535  (0.0298399); expected 358.6 (0.02)
Passed bias filter:                      501  (0.0279436); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.83u 0.29s 00:00:01.11 Elapsed: 00:00:00.45
# Mc/sec: 9140.66
//
Query:       AHX11577.1  [L=140]
Description: ribosomal L7/L12 domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.7e-17   61.2   3.5    8.7e-17   61.2   3.5    2.5  2  Ribosomal_L12    Ribosomal protein L7/L12 C-terminal domain
    5.6e-06   26.0   4.5    5.6e-06   26.0   4.5    1.9  3  Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain


Domain annotation for each model (and alignments):
>> Ribosomal_L12  Ribosomal protein L7/L12 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   1.3     0.019   1.7e+02      20      41 ..      15      36 ..       5      65 .. 0.82
   2 !   61.2   3.5   9.7e-21   8.7e-17       1      67 []      66     138 ..      66     138 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.019
                   HHHH---HHHHHHHHTTTTSTE CS
  Ribosomal_L12 20 reitglgLkeaKdlVeaapkvv 41
                   ++i +l+L+ea +l  ++ kv+
     AHX11577.1 15 QKILSLNLVEAAELAAELKKVL 36
                   6789999999999988777765 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 9.7e-21
                    EEEEEEE-TT-HHHHHHHHHHHH..--....-HHHHHHHHTTTTSTEEEEE-HHHHHHHHHHHHCTT-EEEEE CS
  Ribosomal_L12   1 fdViLksagakKiaVIKaVreit..gl....gLkeaKdlVeaapkvvkegvskeeAeeikkkLeeaGAevelk 67 
                    f++iLk +g+kK++ IKa+++i   +l    gLke Kd V+a+p +v +g++ke+A++++k L++a++e elk
     AHX11577.1  66 FTLILKGYGDKKTNAIKALKTIFkqELgqdmGLKELKDKVDAVPVDVLSGLTKEKADAYAKVLKDAECESELK 138
                    99*******************9533446666****************************************98 PP

>> Ribosomal_L12_N  Ribosomal protein L7/L12 dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.0   4.5   6.3e-10   5.6e-06       4      44 ..      12      54 ..      10      58 .. 0.88
   2 ?   -2.9   0.0      0.63   5.6e+03      19      27 ..      83      91 ..      81      93 .. 0.49
   3 ?   -2.7   0.0      0.58   5.2e+03      24      27 ..     101     104 ..      98     117 .. 0.57

  Alignments for each domain:
  == domain 1  score: 26.0 bits;  conditional E-value: 6.3e-10
                     HHHHHHHTSBHHHHHHHHHHHHHHTTHHHH..HHHHHH.HHHH CS
  Ribosomal_L12_N  4 eiieaikeltvLElseLvkalEekFGVsAA..APvavaaaaaa 44
                     ei + i +l++ E++eL  +l++ ++ +++  AP+a aa+ aa
       AHX11577.1 12 EIAQKILSLNLVEAAELAAELKKVLNLPDVsfAPAASAAPVAA 54
                     899*************************999999999866444 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 0.63
                     HHHHHHHHH CS
  Ribosomal_L12_N 19 eLvkalEek 27
                      L++ ++ +
       AHX11577.1 83 ALKTIFKQE 91
                     455555555 PP

  == domain 3  score: -2.7 bits;  conditional E-value: 0.58
                      HHHH CS
  Ribosomal_L12_N  24 lEek 27 
                      l++k
       AHX11577.1 101 LKDK 104
                      4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       613  (0.0341904); expected 358.6 (0.02)
Passed bias filter:                      412  (0.0229795); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.35
# Mc/sec: 1211.72
//
Query:       AHX11578.1  [L=176]
Description: ribosomal L10 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.9e-12   46.2   0.0    5.3e-12   45.8   0.0    1.2  1  Ribosomal_L10  Ribosomal protein L10


Domain annotation for each model (and alignments):
>> Ribosomal_L10  Ribosomal protein L10
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.8   0.0   2.9e-16   5.3e-12       3      98 ..       2      95 ..       1      97 [. 0.95

  Alignments for each domain:
  == domain 1  score: 45.8 bits;  conditional E-value: 2.9e-16
                   CCCHCCCCCCCCCCCTTSSEEEEEE-TTS-HHHHHHCCCHHHHHGCEEEEESCCCCCCCCHCCTSS.SSCGCCSSSEEEEEESS-TCHHHHCCCCC CS
  Ribosomal_L10  3 kekKeelvkelkellkkyksvvvvdyegltvaqlqelRkklrengaelkvvKntlmrrAleetgeeeklkellkgpvalvftnedpvalakvleef 98
                   +e+K +l+ +l+  l++  +v+v++++ l   ++  +R+kl + g+++ vvKn+l+r+A+ ++g +  l+e+l+g va++  n+++ +  + + +f
     AHX11578.1  2 NERKSNLLGKLESILQQR-VVIVIKVSSLACHEIFSFREKLWDLGGNINVVKNSLARIAISNSGVS-FLSEYLAGSVAFAHCNQNVPEFLRCVFKF 95
                   589************998.**********************************************7.6******************9999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      266  (0.0148363); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.35
# Mc/sec: 1516.96
//
Query:       AHX11579.1  [L=209]
Description: ribosomal L1p/L10e family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.2e-25   88.1   0.0    7.7e-25   87.8   0.0    1.1  1  Ribosomal_L1  Ribosomal protein L1p/L10e family


Domain annotation for each model (and alignments):
>> Ribosomal_L1  Ribosomal protein L1p/L10e family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.8   0.0   4.3e-29   7.7e-25       8     203 ..      20     199 ..      11     200 .. 0.88

  Alignments for each domain:
  == domain 1  score: 87.8 bits;  conditional E-value: 4.3e-29
                   SS--EEEEEEEESSS-TTSGGG--EEEEE-STSTSSCS-EEEEE-HHHHH...HHHHTT..-SEEETCHHHHHHT-HHHHHHTCCH-SEEEEEGGGH CS
  Ribosomal_L1   8 kfdesveialnlttkkpkkadqrkpgkipLphplgkevkiclitkdpqaeyakeakeagriakviglkklkkkyksfeakrkllkefdlfladdrim 104
                   kfde  ++a+++       +++ ++g+ +  h+++   +i+++  d  a      +  +  +   g+++l + +k   +k++l   ++  ++++++m
    AHX11579.1  20 KFDEALDVAVHF------VSTDSVKGSCVFNHSFD-FGRILVFSGDTAAL----HSFGD--KVSCGGEELMESIK---SKKSLVRGHKYSVSTPAMM 100
                   677777777777......33446789999999983.46999999998776....34555..66699********6...6****************** PP

                   HHHHHHCHHHHGGGT-S-ECC..CT.BTS-HHHHHHHHCTTEEEEE-TTTSEEEEEEEETTSSHHHHHHHHHHHHHHHHHTSTTT...SGSEEEEEE CS
  Ribosomal_L1 105 pllpklLGkvfgkrkkmPipvltkgtvkedvkkevekalkstvvvrldkgtclsvkvGklsftaeelaeNieavvkalvekvpkk...wkniksiyl 198
                   p+l + + +++g+r++mP  +   g v+++v  +v ++l++++ ++++k+++l++kvGkls+  ++l +N++ +++++ + +pk+    ++i+si+l
    AHX11579.1 101 PKLSR-VARILGPRGLMPDSK--YGLVTDSVVDAVSSLLSGKSIFKSNKAGVLHCKVGKLSMGFDKLRDNFQVFCESVFSIKPKSvslSNYINSISL 194
                   *****.***************..899*********************************************************************** PP

                   EETTS CS
  Ribosomal_L1 199 kttms 203
                   ++tm+
    AHX11579.1 195 SSTMG 199
                   ****8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (209 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       501  (0.0279436); expected 358.6 (0.02)
Passed bias filter:                      455  (0.0253779); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1752.88
//
Query:       AHX11580.1  [L=143]
Description: ribosomal L11, N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.2e-20   71.7   0.0    6.1e-20   70.8   0.0    1.5  1  Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
    2.9e-12   46.9   0.1    5.2e-12   46.1   0.1    1.4  1  Ribosomal_L11    Ribosomal protein L11, RNA binding domain


Domain annotation for each model (and alignments):
>> Ribosomal_L11_N  Ribosomal protein L11, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.8   0.0   6.8e-24   6.1e-20       2      65 .]       2      65 ..       1      65 [. 0.98

  Alignments for each domain:
  == domain 1  score: 70.8 bits;  conditional E-value: 6.8e-24
  Ribosomal_L11_N  2 kkvvkvvklrvpaGkAtpaPplGpaLGplGlnikkfckefnkaTkdkkglripVkitvyqdrsf 65
                     kkvv+ +klrvpaGkA+p+P++++ LGp+G+n +kfc++ n+ T+ +   ++ V++  y d++f
       AHX11580.1  2 KKVVARLKLRVPAGKASPTPAIASSLGPKGINLMKFCQACNELTGSYGSGNVRVRVLLYHDKTF 65
                     89************************************************************98 PP

>> Ribosomal_L11  Ribosomal protein L11, RNA binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.1   0.1   5.8e-16   5.2e-12       7      70 .]      76     138 ..      73     138 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.1 bits;  conditional E-value: 5.8e-16
                    HHHHHHHTXSSXXSSTTTSXXEEEEHHHHHHHHHHHGGGHTXS.SHHHHHHHHHHHHCTTTEEE CS
  Ribosomal_L11   7 ylLkkaagiekgsgkpgketvGtvslkqvyeIAkiKksdlnaalsleaavksilgtArsmGikV 70 
                      +k+ ++ ekgs+ pgk++ + +  +++ e A+  +s++n++ ++ aa+++++g + smGik+
     AHX11580.1  76 DVVKSFLQFEKGSSAPGKDILAYIDREKISEMAQELMSSMNTR-DFNAAMRTVVGKVSSMGIKI 138
                    5789999**********************************99.******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (143 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       709  (0.0395449); expected 358.6 (0.02)
Passed bias filter:                      630  (0.0351386); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1095.63
//
Query:       AHX11581.1  [L=171]
Description: transcription termination factor nusG family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-06   29.0   0.0    1.6e-06   28.5   0.0    1.3  1  NusG      Transcription termination factor nusG


Domain annotation for each model (and alignments):
>> NusG  Transcription termination factor nusG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.5   0.0   9.2e-11   1.6e-06       3      94 ..       7     101 ..       5     102 .. 0.80

  Alignments for each domain:
  == domain 1  score: 28.5 bits;  conditional E-value: 9.2e-11
                 EEEEEE-TTTHHHHHHHH.HHHCT-..EEE-SCEEEEEEETTEEECSSTTEEEEEE---CHHHHHHHCSTTEEEE-E.ETT.SSCC-EB-HHHHHHH CS
                 xxxxxxxxxxxxxxxxxx.xxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxx.xxxxxxxxxxxxxxx RF
        NusG   3 WYvlqvepgkekkvkenL.leeegl..evivPaeekveirqgkkkklfpgyifikadmndkllmairktpgVtgfvr.vgg.eskpvplseeevqni 94 
                 W vlqv++g e kv + +  +  g+  +v+ Pa  k  +   + k+++pgy+f+k+   ++ l  + +++g +g+ + + +    p  l++++++++
  AHX11581.1   7 WCVLQVRSGTESKVCDLIrSRCAGVvvDVFSPALAKLDTP--SSKRFLPGYVFVKVAPGSTFLNEVSTMRGLYGIPCkFLNqAGSPKFLTDHDIDEM 101
                 9*****************766666699******9999955..4558***********9988888888888887753212223558999999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (171 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       375  (0.0209158); expected 358.6 (0.02)
Passed bias filter:                      341  (0.0190195); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1345.83
//
Query:       AHX11582.1  [L=42]
Description: secE/Sec61-gamma subunits of translocation complex family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-07   28.7   4.0    9.6e-07   28.6   4.0    1.0  1  SecE      SecE/Sec61-gamma subunits of protein translocation 
  ------ inclusion threshold ------
       0.02   15.4   2.3       0.02   15.4   2.3    1.0  1  DUF1751   Eukaryotic integral membrane protein (DUF1751)
       0.11   12.3   2.2      0.099   12.5   2.2    1.0  1  DC_STAMP  DC-STAMP-like protein


Domain annotation for each model (and alignments):
>> SecE  SecE/Sec61-gamma subunits of protein translocation complex
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   4.0   1.6e-10   9.6e-07      16      55 .]       3      42 .]       1      42 [] 0.95

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 1.6e-10
                CCHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
        SecE 16 WPtrkEllkttvvVlvfvvimglflflvDlvfsklinlll 55
                W +rkE+++ ++ V+v + +++l+++lvD++   ++++++
  AHX11582.1  3 WSSRKEVFSFSAFVVVLTSVFALLFALVDYIAFSVVQFFY 42
                9*******************************99999986 PP

>> DUF1751  Eukaryotic integral membrane protein (DUF1751)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.4   2.3   3.4e-06      0.02      41      76 ..       2      38 ..       1      42 [] 0.89

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 3.4e-06
     DUF1751 41 lWg.skEllkFilvvnvitnllvvlltlllylvtkse 76
                +W+ +kE++ F ++v v+t++ ++l++l+ y++++  
  AHX11582.1  2 AWSsRKEVFSFSAFVVVLTSVFALLFALVDYIAFSVV 38
                699889***********************99998765 PP

>> DC_STAMP  DC-STAMP-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   2.2   1.7e-05     0.099      47      81 ..       7      39 ..       1      42 [] 0.76

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 1.7e-05
    DC_STAMP 47 kErkrllrsllkllleliivvvflavDyllywlld 81
                kE+ +   s++ ++l+ +++++f +vDy+++++++
  AHX11582.1  7 KEVFS--FSAFVVVLTSVFALLFALVDYIAFSVVQ 39
                33333..46677888999*************9997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       793  (0.04423); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.32u 0.24s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 325.40
//
Query:       AHX11583.1  [L=428]
Description: translation elongation factor Tu [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      3e-51  173.7   0.0    4.3e-51  173.2   0.0    1.2  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    7.6e-26   90.6   0.0    1.9e-25   89.3   0.0    1.7  1  GTP_EFTU_D3  Elongation factor Tu C-terminal domain
    8.1e-18   64.6   7.9    1.6e-16   60.4   4.7    2.6  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00029   20.9   0.0    0.00059   19.9   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  173.2   0.0   9.7e-55   4.3e-51       2     192 ..      14     216 ..      13     218 .. 0.86

  Alignments for each domain:
  == domain 1  score: 173.2 bits;  conditional E-value: 9.7e-55
                 CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHH.HHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEE CS
    GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgeka.eeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavl 99 
                 +++nig+ighvDhGKtTLt ++++ + +     e +  +   +D+++eEr+rgiTi++a+++++  t +++++++D+PGH+d++k++i+g++++Dga+l
  AHX11583.1  14 PHLNIGTIGHVDHGKTTLTAAITKFCAEEGGGYESEfRAYDNIDKAPEERQRGITISTAHVEYK--TPSRHYAHVDCPGHADYIKNMITGAAQMDGAIL 110
                 699*************************99977777544677**********************..********************************* PP

                 EEETTTBSTHHHHHHHHHHHHTTTE.EEEEEESCGST...HHHHHHHHHHHHHHHHHHHHHHHHH.HHTTTTTEEEEEEBTTTTB..........THHH CS
    GTP_EFTU 100 vvdaveGvepqteevlrlalkegvp.iivfiNKmDrl...kaelkeiveevkqklsrkeekleky.gekgekevpvvfgSalkge..........gvkt 183
                 vv+ ++G ++qt+e++ la+++gv  i+v iNK+D +   ++ l+ +  ++k+ l ++++ +  +   +g ++  +++gSal +            +++
  AHX11583.1 111 VVAGTDGAMQQTKEHILLAKQVGVGsIVVYINKCDSPdldDELLELVEGDIKDLL-ASHGFVLPAdNDDG-SNPAIIRGSALAALngedtdlgkgSIRK 207
                 *************************9***********995555566666888777.44444433313333.799999***9999966666666666669 PP

                 HHHHHHHHS CS
    GTP_EFTU 184 llealvell 192
                 ll a+++++
  AHX11583.1 208 LLAACDQYI 216
                 999998886 PP

>> GTP_EFTU_D3  Elongation factor Tu C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.3   0.0   4.2e-29   1.9e-25       1     111 [.     314     409 ..     314     410 .. 0.95

  Alignments for each domain:
  == domain 1  score: 89.3 bits;  conditional E-value: 4.2e-29
                  --EEECCEEEEEEESSS.....SS-BSTT-EEEEESSS-EEEEEEEEEEECCSSTTSB-BSS-SSCCSTT-CEEEEEEECCEEEE--TTTHCCCCEEE CS
  GTP_EFTU_D3   1 sikphtkfeAqvyileke...rhtpitagYrpvlyirtadvtgkvveLlskldkktekvsekkpefvkpGdnvivevelikpialekgseypqlGrFa 95 
                  si+ph++++A+++ l+ke   r+t +++gY+p++y+rt+dvtg ++ L        ++v     e+v+pGd++++ vel +pia+ekgs      rFa
   AHX11583.1 314 SITPHKRLRARIVTLTKEeggRRTGFVSGYKPQFYFRTTDVTG-TAYL------PADGV-----EIVMPGDDLEIFVELLNPIAMEKGS------RFA 393
                  699****************************************.9999......34566.....9************************......*** PP

                  EECTTCEEEEEEEEEE CS
  GTP_EFTU_D3  96 iReggrTvaaGvvtei 111
                  iRegg Tv+aG+v ei
   AHX11583.1 394 IREGGVTVGAGQVLEI 409
                  **************98 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   60.4   4.7   3.6e-20   1.6e-16       1      74 []     241     310 ..     241     310 .. 0.98
   2 !    4.6   0.0    0.0099        44      13      43 ..     401     426 ..     400     428 .] 0.86

  Alignments for each domain:
  == domain 1  score: 60.4 bits;  conditional E-value: 3.6e-20
                  EEEEEEEEEESEEETTEEEEEEC.TCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilg.ndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                  Gtv++g++++G +k Gdev+i+g  dt +k   t+ +++e+f++ ++e +ag n+Gv++++ + ed + +G++l+
   AHX11583.1 241 GTVVTGKIERGRIKIGDEVEIVGiRDT-QK---TTCTGVEMFNKLVQEGEAGFNVGVLLRGTKRED-VCRGQVLC 310
                  9**********************8887.99...*********************************.9******8 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0099
                  EETTEEEEEECTCTTSEEEEEEEEEEEEETE CS
  GTP_EFTU_D2  13 lkkGdevrilgndtskkeivtrissletfhe 43 
                  +  G+ ++i  +d++ +   ++is+l++f++
   AHX11583.1 401 VGAGQVLEI--MDSKTD---EEISKLFRFNK 426
                  557999***..999788...*********86 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.9   0.0   1.3e-07   0.00059       2      97 ..      18     126 ..      17     143 .. 0.73

  Alignments for each domain:
  == domain 1  score: 19.9 bits;  conditional E-value: 1.3e-07
                 EEEEESTTSSHHHHHHHHHT...................STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEE CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltg...................ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflaleeadlill 81 
                 ++ +G+   GK+tL  a+t+                   +ka  +++ g T+ + + ++k+  +++  vD+pG  +       +++ +    ++d ++l
  AHX11583.1  18 IGTIGHVDHGKTTLTAAITKfcaeegggyesefraydniDKAPEERQRGITISTAHVEYKTPSRHYAHVDCPGHAD------YIKNMITGAAQMDGAIL 110
                 889****************77777777888888777654589999999***********98889*********333......45666666667899888 PP

                 EEETTTTCSHHHHHHH CS
    MMR_HSR1  82 vvdaseeklkpldeel 97 
                 vv  +++ +++ +e++
  AHX11583.1 111 VVAGTDGAMQQTKEHI 126
                 8864433344443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (428 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       494  (0.0275531); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3303.60
//
Query:       AHX11584.1  [L=686]
Description: translation elongation factor G [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    3.8e-68  228.9   0.0    5.8e-68  228.3   0.0    1.3  1  GTP_EFTU     Elongation factor Tu GTP binding domain
    5.6e-40  135.9   0.0    1.2e-39  134.8   0.0    1.6  1  EFG_IV       Elongation factor G, domain IV
    4.6e-30  103.5   0.0    9.1e-30  102.6   0.0    1.5  1  EFG_II       Elongation Factor G, domain II
    1.6e-29  101.8   0.1    3.4e-29  100.7   0.1    1.6  1  EFG_C        Elongation factor G C-terminus
    9.3e-16   58.0   0.4    6.8e-15   55.2   0.1    2.5  2  GTP_EFTU_D2  Elongation factor Tu domain 2
    0.00028   20.7   0.0    0.00061   19.6   0.0    1.5  1  RF3_C        Class II release factor RF3, C-terminal domain
     0.0014   18.7   0.0     0.0027   17.8   0.0    1.5  1  MMR_HSR1     50S ribosome-binding GTPase
     0.0095   15.3   0.0      0.017   14.5   0.0    1.3  1  AIG1         AIG1 family


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  228.3   0.0   2.6e-71   5.8e-68       1     194 []       2     275 ..       2     275 .. 0.93

  Alignments for each domain:
  == domain 1  score: 228.3 bits;  conditional E-value: 2.6e-71
                 TCEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEEEE CS
    GTP_EFTU   1 krirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdFskevirglrvlDgavl 99 
                 k+irnigi++h+D+GKtT+t+r+l +tg  +  ge++e+++++D++++E+ergiTi+saa+++   ++  +in+iDtPGHvdF+ ev+r+lrvlDgav 
  AHX11584.1   2 KKIRNIGIMAHIDAGKTTTTERILLYTGVNRTIGEVHEGAATMDWMAQEKERGITITSAATTCW--WNGAKINIIDTPGHVDFTIEVERSLRVLDGAVA 98 
                 689*************************************************************..********************************* PP

                 EEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHH............................................. CS
    GTP_EFTU 100 vvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrk............................................. 153
                 v+d v Gvepq+e+v+r+a k++vp+ +f+NKmDr++a++ ++++++ +kl ++                                             
  AHX11584.1  99 VFDGVAGVEPQSETVWRQADKHNVPRLCFVNKMDRIGADFYRCADMIVNKLGANpiivqlpigssesfvgvvdlikmqavywhgddfgakfeyreipse 197
                 ***************************************************999********************************************* PP

                 ......................................HHHHHHHHHTTT.........TTEEEEEEBTTTTBTHHHHHHHHHHHSHH CS
    GTP_EFTU 154 ......................................eeklekygekge.........kevpvvfgSalkgegvktllealvellps 194
                                                       +          +         ++vpv++gSa+k++gv+tll+a+v++lps
  AHX11584.1 198 laekaalyrekllekvaetddifmeryfggeeiseaeiK----------SairagtissHFVPVLCGSAFKNKGVQTLLDAVVDYLPS 275
                 *99999999777777777777777777776666543333..........04444456668**************************96 PP

>> EFG_IV  Elongation factor G, domain IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  134.8   0.0   5.5e-43   1.2e-39       1     119 [.     472     588 ..     472     589 .. 0.98

  Alignments for each domain:
  == domain 1  score: 134.8 bits;  conditional E-value: 5.5e-43
                 TCCESCEE.SS-CCHCCCCCCCHTSSSHCCCCCEEEECCTTTTSSEEEEE--STCCCHCCCCHHHHCCCCCCTTS-TTTS--EESEEEEEEEEE--TTT CS
      EFG_IV   1 pqVayrEtirkpvkereeklkkqsggdgqyakvileiePleegsgnefvdetkggqvpkeyieavekGfqealkeGplagepvtdvkvtLldgslhevd 99 
                 pqVayrEti+k  + +++++kkq+gg+gq+akv + +eP   ++++ f+++++gg++pkeyi+ vekG+ ++ ++G+la++p+++ kvtLldg++h+vd
  AHX11584.1 472 PQVAYRETITKSYE-VDYTHKKQTGGAGQFAKVKMLFEPY-LEGEFLFESKITGGAIPKEYIPGVEKGLISVKNKGLLANYPLIGFKVTLLDGAFHDVD 568
                 8*************.************************7.6********************************************************* PP

                 C-HHHHHHHHCHHHHHHHHC CS
      EFG_IV 100 sseaafkpaarralkeallk 119
                 ss +af++aar a+kea++k
  AHX11584.1 569 SSVLAFEIAARDAFKEAAKK 588
                 *****************986 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.6   0.0   4.1e-33   9.1e-30       2      74 ..     398     470 ..     397     471 .. 0.98

  Alignments for each domain:
  == domain 1  score: 102.6 bits;  conditional E-value: 4.1e-33
      EFG_II   2 PePvislaiepkskadedklskaLarlleEDptlrverdeeTketilsGmGelHleivverlkreykvevelg 74 
                 P+Pvi++aiepks a+++k++ a  rl++EDp+l+v  +eeT++t+l GmGelHlei+++rlkre++v+v++g
  AHX11584.1 398 PDPVIEIAIEPKSAAEQEKMALAVGRLCAEDPSLKVASNEETGQTLLRGMGELHLEIILDRLKREFNVNVNVG 470
                 9*********************************************************************998 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.1   1.5e-32   3.4e-29       2      88 ..     593     678 ..     592     679 .. 0.97

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1.5e-32
                 EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-TTHHHCHHHCTTTS-EEEEEEEEEEE--HHHHHH CS
       EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeligfateLrslTkGegsfsmefsgYeevpgdklde 88 
                 ++EP+++vei++peey+g+vi+dlssrrG+i +me++ ++  +i + +Pl+ ++g+ ++Lrs T+G++++smef++Y+++p +++ e
  AHX11584.1 593 IMEPLMRVEIITPEEYTGTVIGDLSSRRGKISEMETK-GNARVISGVVPLSRMFGYVKDLRSSTQGRANYSMEFKEYAQMPDHIAAE 678
                 8************************************.*******************************************998765 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.2   0.1     3e-18   6.8e-15       1      74 []     316     383 ..     316     383 .. 0.95
   2 ?   -0.7   0.0      0.88     2e+03      31      64 ..     609     642 ..     598     644 .. 0.74

  Alignments for each domain:
  == domain 1  score: 55.2 bits;  conditional E-value: 3e-18
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtlt 74 
                  G ++++r+ysG+l   d+v +  ++++ k   +ri++++ +h++ +e+++ + aG+iva+ gl+d+  +Gdtl+
   AHX11584.1 316 GSLTFVRIYSGILSASDTVIN--STKDSK---ERIGRMLLMHANSREDIKTEMAGNIVALAGLKDT-STGDTLC 383
                  6689*****************..887777...*********************************7.******8 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.88
                  EEEEEEEEEEETEEESEEETTSEEEEEEEESSCC CS
  GTP_EFTU_D2  31 ivtrissletfhededeavaganaGvivaikgle 64 
                    t i+ l   +++  e++  +na vi ++++l+
   AHX11584.1 609 TGTVIGDLSSRRGKISEMETKGNARVISGVVPLS 642
                  4478899999999999999999999998888775 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   0.0   2.7e-07   0.00061      15      94 ..     406     485 ..     398     506 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 2.7e-07
                 EEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TSS-EEEEESSTHHHHHHHHHHHHHH---EEEEE-S--EEEEEE-SSH CS
       RF3_C  15 vrlkdplkrkqlrkgleqLaeEGavqvfkeeeageelilgaVGqLQfeVveeRlknEYgvevrleslpyslarwvesede 94 
                 ++ k + ++ ++  ++  L  E       ++e++ +++l  +G+L +e++ +Rlk+E++v+v++   ++ +   ++++ e
  AHX11584.1 406 IEPKSAAEQEKMALAVGRLCAEDPSLKVASNEETGQTLLRGMGELHLEIILDRLKREFNVNVNVGDPQVAYRETITKSYE 485
                 56667777777888888888777554445555788999999***********************9999988888866544 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   1.2e-06    0.0027       2     114 .]       7     130 ..       6     130 .. 0.71

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 1.2e-06
                 EEEEESTTSSHHHHHHHHH..............T....STEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEE CS
    MMR_HSR1   2 vaivGrpNvGKStLinalt..............g....ekaivsdkpgtTrdinegrvklkgkeielvDtpGliegaseekglgkaflalee.adlill 81 
                 ++i+ +  +GK+t   +++              g    +    +++ g T++    +  ++g +i+++DtpG ++       ++ ++++  +  d ++ 
  AHX11584.1   7 IGIMAHIDAGKTTTTERILlytgvnrtigevheGaatmDWMAQEKERGITITSAATTCWWNGAKINIIDTPGHVD-------FTIEVERSLRvLDGAVA 98 
                 6677777889999999997666555555444331322123456777799999988888899***********655.......5566666556369**** PP

                 EEETTTTCSHHHHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  82 vvdaseeklkpldeeleelleeakkplilvlnk 114
                 v+d   ++++p+ e++ +  ++++ p +  +nk
  AHX11584.1  99 VFDGV-AGVEPQSETVWRQADKHNVPRLCFVNK 130
                 ***66.779999999998888888888777776 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   7.5e-06     0.017      30      65 ..      50      85 ..       9      94 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 7.5e-06
                TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCC CS
        AIG1 30 lsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvs 65
                 +++++t ++   +  w+g kin+iDTPg +d   +
  AHX11584.1 50 EKERGITITSAATTCWWNGAKINIIDTPGHVDFTIE 85
                467899999999999**************9987765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (686 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      308  (0.0171789); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.54u 0.25s 00:00:00.79 Elapsed: 00:00:00.40
# Mc/sec: 5122.26
//
Query:       AHX11585.1  [L=173]
Description: ribosomal protein S7 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.1e-48  162.0   1.2    8.3e-48  161.8   1.2    1.0  1  Ribosomal_S7  Ribosomal protein S7p/S5e


Domain annotation for each model (and alignments):
>> Ribosomal_S7  Ribosomal protein S7p/S5e
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.8   1.2   4.6e-52   8.3e-48       1     149 []       1     149 [.       1     149 [. 0.99

  Alignments for each domain:
  == domain 1  score: 161.8 bits;  conditional E-value: 4.6e-52
                   ..XSSSSCT------SSTTSBHHHHHHHHHSBTTBHHHHHHHHHHHHHHHHHHHSS-HHHHHHHHHHHCS-SEEEEEEBSSSSBEEEEEEE-HHHHH CS
  Ribosomal_S7   1 msrrkkakkrevlpdpkynselveklinklmkdGkkslAekivygaldiieektkkdplevleeAlenvkPrvevksrrvGGatyqvpvevrpkRrq 97 
                   msrr++akkre+ +d kyns++v+k++n++mk+GkkslAekivygal+ +e++ +  ++evl++Al n++P ve++s+r GG++y++p++++ +R++
    AHX11585.1   1 MSRRNAAKKREIPADRKYNSQVVAKFMNYVMKRGKKSLAEKIVYGALERVERQLNVPAIEVLNDALANISPAVELRSFRAGGVNYRIPIPIKGERSR 97 
                   89****************************************************99***************************************** PP

                   HHHHHHHHHHHSTSSSS-HHHHHHHHHHHHHTT-SHHHHHHHHHHHHHHHTG CS
  Ribosomal_S7  98 alAlrwiieaarkrkeksmaekLaeElidAaegegaavkkreethrmAeanr 149
                    +Al wii+ a+krk++  +ekLa El+d+  ++g+a++k ee  +mAe+ r
    AHX11585.1  98 FIALGWIISEASKRKGMASEEKLALELLDVHASRGGAFRKFEENTKMAESGR 149
                   *************************************************965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       357  (0.0199119); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1414.33
//
Query:       AHX11586.1  [L=122]
Description: ribosomal protein S12 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-39  133.8   1.3    2.3e-39  133.5   1.3    1.0  1  Ribosom_S12_S23  Ribosomal protein S12/S23


Domain annotation for each model (and alignments):
>> Ribosom_S12_S23  Ribosomal protein S12/S23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  133.5   1.3   1.3e-43   2.3e-39       2     112 ..      13     121 ..      12     122 .] 0.96

  Alignments for each domain:
  == domain 1  score: 133.5 bits;  conditional E-value: 1.3e-43
                      -------S-TSSTTSSEEEEEEEEEEEE---TT--S-EEEEEEEET.TSEEEEEEE-SSS..----TT-EEEEEE--.....BTTSTTEEEEBE CS
  Ribosom_S12_S23   2 kelrkktksdalegapqkrGvvlekvtveakkPnsAlRkvvrvrLikngkevtafipgegalnfldEhdevlvrGirrkgkavkDlpGvrykvv 95 
                      k+ +k++k++al+ +p +rG++ +++t+++kkPnsAlRkv+rvrL+ +g ev a+ipgeg  ++l+Eh++v +rG+r     vkDlpGvry++v
       AHX11586.1  13 KTPVKANKVPALDRNPLRRGICSKVYTTTPKKPNSALRKVARVRLS-SGAEVIAYIPGEG--HNLQEHSVVCIRGGR-----VKDLPGVRYHIV 98 
                      5667899***************************************.*************..***************.....************ PP

                      T....S---T..SSSTTTTT--- CS
  Ribosom_S12_S23  96 k....vagvs..lkalskykkek 112
                      +    ++gv+  +k++sky+ +k
       AHX11586.1  99 RgmfdTEGVKgrKKSRSKYGVKK 121
                      *****9***999999****9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.22s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 1004.77
//
Query:       AHX11587.1  [L=675]
Description: helicase conserved domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.3e-20   72.5   0.7    5.9e-16   58.8   0.2    2.8  2  Helicase_C       Helicase conserved C-terminal domain
    3.8e-20   72.4   3.4    1.9e-19   70.1   0.6    2.3  2  DEAD             DEAD/DEAH box helicase
    5.7e-10   39.5   0.0    1.2e-09   38.4   0.0    1.6  1  ResIII           Type III restriction enzyme, res subunit
    0.00012   21.8   0.1    0.00032   20.4   0.1    1.8  1  RecG_wedge       RecG wedge domain
    0.00053   19.8   0.3     0.0013   18.5   0.1    1.7  2  AAA_30           AAA domain
     0.0018   18.6   1.3       0.16   12.3   0.2    3.0  3  AAA_22           AAA domain
  ------ inclusion threshold ------
      0.012   15.6   0.0      0.047   13.7   0.0    2.1  1  tRNA_anti-codon  OB-fold nucleic acid binding domain
      0.014   15.4   0.0      0.054   13.5   0.0    2.0  1  Flavi_DEAD       Flavivirus DEAD domain
      0.036   14.1   0.2       0.13   12.2   0.1    2.0  2  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.037   14.4   0.5       0.12   12.7   0.3    2.0  2  NADHdh-2_N       NADH dehydrogenase subunit 2 N-terminal


Domain annotation for each model (and alignments):
>> Helicase_C  Helicase conserved C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.0    0.0002      0.36       5      75 ..     296     368 ..     292     384 .. 0.87
   2 !   58.8   0.2   3.3e-19   5.9e-16       2     110 ..     451     570 ..     450     571 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.0002
                 HHHHHHHHTTTTSEEEEEESSHHHHHH.HHHHHHHT...TSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGG CS
  Helicase_C   5 allellkleeeggkilifvntidrlek.vklllekk...gikvavlhgelpqnereeileqfnkgesdvLiatdv 75 
                  + ++l+  e g+++++ ++t+  +++ ++ll+  +   +++va l g    ++++  l++ ++g+++++iat +
  AHX11587.1 296 VFFAMLNAVEAGKQTVLLSPTTVLAKQhFELLR--SlmpELEVALLIGGQVGSSKKSLLRDVQSGSIKIVIATHA 368
                 5667778899*************8877788884..34589*********************************86 PP

  == domain 2  score: 58.8 bits;  conditional E-value: 3.3e-19
                 HHHHHHHHH.HHTTTTSEEEEEESSHHHHHH.........HHHHHHHTTSTEEEESTTSTHHHHHHHHHHHHTTSSSEEEESGGGTSSSTSTTESEEEE CS
  Helicase_C   2 kleallell.kleeeggkilifvntidrlek.........vklllekkgikvavlhgelpqnereeileqfnkgesdvLiatdvaerGidipkvnlVin 90 
                 k+e+l+e l    ++g+k+  +++ i++ e+         +k+l++++  +v ++hg l++ +  e +++f++ +++++++t+v+e G+dip+++ +++
  AHX11587.1 451 KIEQLIERLkIVLKDGSKVFWVCPIIEESENiqvisikerLKMLKQHFLNEVDCIHGGLSAHKIAEKIADFRESRIKIILSTTVIEVGVDIPDADIMVI 549
                 777888887667789999*********6655555556567888888889999*********************************************** PP

                 SSSS.SSHHHHHHHHTTSSST CS
  Helicase_C  91 fdlp.rnvtsyiqriGRtgRa 110
                  d++ +++++++q +GR+gR+
  AHX11587.1 550 EDADrFGLAQLHQLRGRVGRG 570
                 ****778*************7 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.1   0.6   1.1e-22   1.9e-19       2     172 ..     261     418 ..     260     422 .. 0.81
   2 ?    2.6   0.1     0.055        98      44     132 ..     463     554 ..     446     565 .. 0.66

  Alignments for each domain:
  == domain 1  score: 70.1 bits;  conditional E-value: 1.1e-22
                 HHHHHHHHHHH......TTCEEEEEESTTSSHHHHHHHHHHHHHHHSTTSTS-EEEEEESSHHHHHHHHHHHHHHTTTSTSEEEEEET...TSSHHHHH CS
                 xxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxx RF
        DEAD   2 diQaeaiplil......gggdvlvaaeTGsGKTlaflipvlqivyetkgktgpkalivePtreLaeqtlnnlkkfkkyidlrvlliig...gvaardql 91 
                 + Q+e+i  i+      +    l+++++GsGKTla ++++l++v     + g+++++++Pt+ La+q+++ l++++ +  l+v l+ig   g+++++ l
  AHX11587.1 261 RGQEEIIVKIYslqnqtSRMIALLQGDVGSGKTLAVFFAMLNAV-----EAGKQTVLLSPTTVLAKQHFELLRSLMPE--LEVALLIGgqvGSSKKSLL 352
                 568888888886655322234569*****************999.....7899************************7..7788889945556666666 PP

                 HHHHTT.CSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHHHHHTTTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSBS.HH CS
                 xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xx RF
        DEAD  92 skldng.vdivvgtpgrlddllstgklnlsqvrflVlDEadrlldqgfsdfinrilnqlpqitcdgklqrqvivlSATlp.kd 172
                 +++++g ++iv++t+  l d      + + ++ +lV+DE +r+  +++ + i++  n+             ++++SAT+  ++
  AHX11587.1 353 RDVQSGsIKIVIATHAVLSDK-----VIFANLGLLVIDEQHRFGADQRTKLIRENTNSD------------LLLISATPIpRT 418
                 6666778*************4.....449****************98888888855544............999999997565 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.055
                 TSTS-EEEEEESSHHHHHHH.HHHHHHHTTTST...SEEE.EEETTSSHHHHHHHH....HTTCSEEEEEHHHHHHHHHCTSSHCTTEEEEEEETHHH CS
                 xxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx...xxxx.xxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  44 gktgpkalivePtreLaeqt.lnnlkkfkkyid...lrvl.liiggvaardqlskl....dngvdivvgtpgrlddllstgklnlsqvrflVlDEadr 132
                  k+g k++ v+P  e  e++ +  +k+++k ++   l+++ +i gg +a++  +k+    +++++i+++t+  +++      +++ +  ++V+  adr
  AHX11587.1 463 LKDGSKVFWVCPIIEESENIqVISIKERLKMLKqhfLNEVdCIHGGLSAHKIAEKIadfrESRIKIILSTT--VIE----VGVDIPDADIMVIEDADR 554
                 57888888888888877775356777777765556655555999999999999998544335588888776..222....223456666666666665 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0   6.9e-13   1.2e-09       2     169 ..     257     414 ..     256     416 .. 0.82

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 6.9e-13
                 -EE-HHHHHHHHHHT......TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-EEEEESSHHHHHHHHHHGGGGTGG......GEEEESSS-B--.. CS
      ResIII   2 lelreyQeeaienlleklkskrdkrglikmaTGtGKTlvaaklierllkkgkeekflflvprkslleqtleefkkflseayke..igkkvsgdkkka.k 97 
                 ++l   Qee+i ++ +  +++ +  +l++   G+GKTl  + ++ +  ++gk  ++++l p++ l +q  e ++++++e   +  ig+ v + kk+  +
  AHX11587.1 257 FSLTRGQEEIIVKIYSLQNQTSRMIALLQGDVGSGKTLAVFFAMLNAVEAGK--QTVLLSPTTVLAKQHFELLRSLMPELEVAllIGGQVGSSKKSLlR 353
                 678899********9555545555777**********************988..9**********************9987669866666666655556 PP

                 ......-SEEEEEHHHHHHTH........HHHTTT-SEEEEETGGGTTS.TTTHHHHHT---SEEEEEESS- CS
      ResIII  98 ekdstnkkilvttiqsldadseeeeeeseellrdrfdviiiDEaHrlgakkswreilekfkeavllglTATp 169
                   +s ++ki+++t   l+ +              +  +++iDE Hr+ga++  + i e+  ++ ll ++ATp
  AHX11587.1 354 DVQSGSIKIVIATHAVLSDKV----------IFANLGLLVIDEQHRFGADQRTKLIREN-TNSDLLLISATP 414
                 668889999999888887777..........888889************6666666666.556777779**9 PP

>> RecG_wedge  RecG wedge domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.4   0.1   1.8e-07   0.00032      22     162 ..      29     169 ..      16     171 .. 0.81

  Alignments for each domain:
  == domain 1  score: 20.4 bits;  conditional E-value: 1.8e-07
  RecG_wedge  22 etiedllyyfPrdyedrrkivpiseikedekvtvkgklvnvekk..k.issltiisavlsdgisqvl.LkWfnqeyikkklktlkekevlvtGlvkkge 116
                 + i dll + Pr++ +r + + + e +e+e vt+++k  ++ +k  k  +  ++      d+  +vl + +f + y++kklk  ++  +l+ G      
  AHX11587.1  29 DRIVDLLLHKPREFINRCNFKTLAESQEGELVTIEAKYESYYEKfpKfRKTKRLHKFFFRDKNDDVLeVIFFAKTYLQKKLK--MGEWYLINGKL---- 121
                 6789**********************************998775333144567788999********999************..999****9987.... PP

  RecG_wedge 117 fGaleiknPeieeitgeqere..ilPvysLtegisqkelrkivkenis 162
                   +++++ Pe     +e+++     P y L+egis+  +  +v + ++
  AHX11587.1 122 GSSYQMSHPEKILRLDEVSKLltFDPRYRLSEGISNYRFSSLVDNALA 169
                 236799999955444444432126699********9999888888776 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.5   0.1   7.1e-07    0.0013       3     114 ..     260     404 ..     258     411 .. 0.65
   2 ?   -3.3   0.0       3.4   6.1e+03      71     112 ..     524     567 ..     506     573 .. 0.65

  Alignments for each domain:
  == domain 1  score: 18.5 bits;  conditional E-value: 7.1e-07
      AAA_30   3 naeQaaaveallt....sgdrvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLae.................elgieastiakllkrl 80 
                 + +Q++++ ++ +    +++++a+l+G  G+GKt a+  +   + +ag++ ++l+pt   Ak+  e                 +    +s+ ++ll+  
  AHX11587.1 260 TRGQEEIIVKIYSlqnqTSRMIALLQGDVGSGKTLAVFFAMLNAVEAGKQTVLLSPTTVLAKQHFEllrslmpelevalliggQ---VGSSKKSLLRDV 355
                 56666666666541111556799************99888666666899************99443333444434333332221...233333333333 PP

      AAA_30  81 k...............grarlepgtllivDEagmvdtkqlaallkaaek 114
                 +               +++ +++  ll++DE    +++q ++l+++ ++
  AHX11587.1 356 QsgsikiviathavlsDKVIFANLGLLVIDEQHRFGADQRTKLIRENTN 404
                 3555555555555997544555559**************9999998665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 3.4
      AAA_30  71 stiakllkrlk..grarlepgtllivDEagmvdtkqlaallkaa 112
                 s+i+ +l+++     +++ +++++++  a   + +ql++l  ++
  AHX11587.1 524 SRIKIILSTTVieVGVDIPDADIMVIEDADRFGLAQLHQLRGRV 567
                 44444444444663467778899999999999999999987766 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.2   8.8e-05      0.16       4     112 ..     278     398 ..     275     432 .. 0.66
   2 ?   -1.1   0.0       1.2   2.1e+03      75     115 ..     452     498 ..     437     533 .. 0.67
   3 ?    3.4   0.0     0.048        87      80     126 ..     532     578 ..     487     582 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 8.8e-05
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.erpevv.....fvtlpsstsskdllrellralglelka.....erlsseellealeqalrarav 91 
                 ++ i ++ G +G+GKT+ +   + +++e+ k++   +p++v     f  l s++   +++  +  ++g+++k+     + +s + ++++ +       v
  AHX11587.1 278 SRMIALLQGDVGSGKTLAVFFAMLNAVEAGKQTVlLSPTTVlakqhFELLRSLMPELEVALLIGGQVGSSKKSllrdvQSGSIKIVIATHA-------V 369
                 6789999**********99999999887766666855555546664444555557777777777777777777654433333333333333.......1 PP

      AAA_22  92 .........ielliiDEaqhlrseealeeL 112
                           +ll+iDE +++  +++ ++L
  AHX11587.1 370 lsdkvifanLGLLVIDEQHRF-GADQRTKL 398
                 3444467999**********9.65555444 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.2
      AAA_22  75 seellealeqalrarav..ielliiDEaqhlr..s.eealeeL.rsl 115
                  e+l+e+l   l++ ++   ++ ii+E +++   s +e l+ L  ++
  AHX11587.1 452 IEQLIERLKIVLKDGSKvfWVCPIIEESENIQviSiKERLKMLkQHF 498
                 45566666666666666666777888888885443666666663333 PP

  == domain 3  score: 3.4 bits;  conditional E-value: 0.048
      AAA_22  80 ealeqalraravielliiDEaqhlrseealeeLrsllnl.srkgvqli 126
                 +++ +   +  +  +++i++a+++   ++l +Lr ++   s+k++ ++
  AHX11587.1 532 TTVIEVGVDIPDADIMVIEDADRF-GLAQLHQLRGRVGRgSKKSFCVL 578
                 555555555555699*********.********988776666666665 PP

>> tRNA_anti-codon  OB-fold nucleic acid binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   2.6e-05     0.047      12      64 ..      76     127 ..      56     142 .. 0.78

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 2.6e-05
                      EEEETTEEEEEEEETT.EEEEEEEETHHHHHHHTTS-TTSEEEEEEEEEECTTS CS
  tRNA_anti-codon  12 drsggkvifidlrDgt.griqvvlfreeatklaenlkeGdvvrvtGrvkrrpgg 64 
                       r+++++  +  rD+  + ++v++f   +t+l+++lk G ++ + G+++++++ 
       AHX11587.1  76 FRKTKRLHKFFFRDKNdDVLEVIFFA--KTYLQKKLKMGEWYLINGKLGSSYQM 127
                      588899999999****8899999999..*********************99654 PP

>> Flavi_DEAD  Flavivirus DEAD domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0     3e-05     0.054       5     105 ..     280     388 ..     276     418 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3e-05
                 -EEEEE--TTS-TTTTHHHHHHHHHHHTT--EEEEESSHHHHHHHHHHTTTS............-EEE-.------------SEEEEEHHHHHHHHHHT CS
  Flavi_DEAD   5 kltvldlhPGaGktrkvlpelvkeaierrlrtlvLaPtrvvlaemeealkgl............evryk.tsavkeektgrelvdvmchatftkrllsp 90 
                 ++ +l+   G+Gkt  v+  +++ a+e  ++t++L+Pt v ++   e l+ l            +v ++ +s++++ ++g   + ++ ha +  +++  
  AHX11587.1 280 MIALLQGDVGSGKTLAVFFAMLN-AVEAGKQTVLLSPTTVLAKQHFELLRSLmpelevalliggQVGSSkKSLLRDVQSGSIKIVIATHAVLSDKVI-- 375
                 567778888********999885.789999**********988665555543110100000000333330333333333333355555666555554.. PP

                 ------SEEEEETTT CS
  Flavi_DEAD  91 vrkknyeliimDeah 105
                     n  l+++De h
  AHX11587.1 376 --FANLGLLVIDEQH 388
                 ..3566677777766 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   7.4e-05      0.13      16      59 ..     275     323 ..     261     331 .. 0.69
   2 ?   -2.3   0.0       2.4   4.2e+03      10      39 ..     326     355 ..     317     360 .. 0.72

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.4e-05
                 HCH.TEEEEEEESTTSSHHHHH.HHHHHHTT--...----TTTTSEEEE CS
        TsaE  16 kal.gdvilLeGdLGaGKTtlv.rglakalgve...evkSPTFtlveeY 59 
                 +++ + + lL+Gd+G+GKT  v  ++++a++        SPT +l++++
  AHX11587.1 275 NQTsRMIALLQGDVGSGKTLAVfFAMLNAVEAGkqtVLLSPTTVLAKQH 323
                 333345689**********75514556666553346689***9999887 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 2.4
                 HHHHHHHCHTEEEEEEESTTSSHHHHHHHH CS
        TsaE  10 lgkklakalgdvilLeGdLGaGKTtlvrgl 39 
                 l ++l  +l+ ++l+ G++G+ K  l r +
  AHX11587.1 326 LLRSLMPELEVALLIGGQVGSSKKSLLRDV 355
                 44455555566799999****999999876 PP

>> NADHdh-2_N  NADH dehydrogenase subunit 2 N-terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.3   6.9e-05      0.12       3      63 ..     259     320 ..     257     344 .. 0.85
   2 ?   -1.4   0.0       1.8   3.2e+03      20      56 ..     332     370 ..     326     389 .. 0.63

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 6.9e-05
  NADHdh-2_N   3 ltlgliilivltyglkaptlrlatlllgivgaagll.iesqllswtqaikmlvilsglallc 63 
                 lt g   +iv +y l+  t r+  ll g vg+   l +   +l   +a k  v+ls  ++l 
  AHX11587.1 259 LTRGQEEIIVKIYSLQNQTSRMIALLQGDVGSGKTLaVFFAMLNAVEAGKQTVLLSPTTVLA 320
                 67777789***********************976551567899*************999986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 1.8
  NADHdh-2_N  20 ptlrlatlllgivgaa..glliesqllswtqaikmlvil 56 
                 p l +a+l+ g vg++  +ll + q  s+   i    +l
  AHX11587.1 332 PELEVALLIGGQVGSSkkSLLRDVQSGSIKIVIATHAVL 370
                 778888888898887522466555544444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (675 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       666  (0.0371465); expected 358.6 (0.02)
Passed bias filter:                      525  (0.0292822); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.39
# Mc/sec: 5212.30
//
Query:       AHX11588.1  [L=98]
Description: hypothetical protein NHE_0654 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (98 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      360  (0.0200792); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.37u 0.21s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 793.54
//
Query:       AHX11589.1  [L=375]
Description: proton-translocating NADH-quinone oxidoreductase, chain M family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-79  267.4  27.9    1.4e-79  267.4  27.9    1.7  2  Proton_antipo_M  Proton-conducting membrane transporter


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  267.4  27.9   7.8e-84   1.4e-79       1     292 [.      31     321 ..      31     322 .. 0.98
   2 ?   -1.8   0.4     0.078   1.4e+03     240     260 ..     349     367 ..     327     374 .. 0.77

  Alignments for each domain:
  == domain 1  score: 267.4 bits;  conditional E-value: 7.8e-84
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllv 94 
                      a+dLl++y+ +El l+p++++ig+w++k ++++A++k+fl+tl+gs+ +L++il++++ tgtle++ l   + ++l+  ++ l+ l+l+++++v
       AHX11589.1  31 ATDLLTFYIMFELSLVPIFFIIGFWGSK-NRIYAAFKIFLYTLFGSIGFLISILYIFSKTGTLELTSLTFLVPQMLSVKAQKLIWLALFFAFAV 123
                      79***********************888.***************************************************************** PP

  Proton_antipo_M  95 KsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla.vssneisqlllilaiismllgslvalaqtdiKrllAySsishlGyml 187
                      K++++p+h+Wlpda+v+aPt +s++lA++l k+g++++ir+ll+++   s e + l++ l++i+++++s++a+ qtd+K+l+AySs++h+G+++
       AHX11589.1 124 KIPMFPFHTWLPDAHVQAPTEGSVMLAGILIKLGAYGMIRILLPIFpLLSHEFETLIFSLSAIGVIYTSVIAIMQTDMKKLVAYSSVAHMGIVT 217
                      *****************************************9999989********************************************** PP

  Proton_antipo_M 188 ialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaavavsli 281
                       +l++ + +g+++ai+++++hal++++lF ++g + yer++tr+i +y+g++ + P +  v+++l ++  GlP+t+gF+++fl L ++++ +++
       AHX11589.1 218 AGLFAFNLEGLNGAIFQVVSHALISSGLFFCIGCF-YERTHTRKISEYSGIMCFAPKFGSVFVLLSFASIGLPGTSGFIGEFLSLIGLFQSNQV 310
                      ********************************777.99******************************************************** PP

  Proton_antipo_M 282 llvlavvasvl 292
                      + +l +++++l
       AHX11589.1 311 FGILCTTGVIL 321
                      ***99777665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.078
  Proton_antipo_M 240 kkmPilalvllvlllslaGlP 260
                      ++ Pi+al+llv+ll++   P
       AHX11589.1 349 EALPIFALALLVMLLGIY--P 367
                      567899999999888876..5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (375 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       720  (0.0401584); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.44
# Mc/sec: 2557.65
//
Query:       AHX11590.1  [L=457]
Description: NADH-Ubiquinone/plastoquinone (complex I), various chains family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-53  182.4  32.4    1.1e-53  182.4  32.4    2.8  2  Proton_antipo_M  Proton-conducting membrane transporter
     0.0034   16.8   7.8     0.0034   16.8   7.8    2.8  3  NADHdeh_related  NADH dehydrogenase I, subunit N related prot


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.9      0.11     1e+03     150     169 ..      68      87 ..      10     106 .. 0.65
   2 !  182.4  32.4   1.2e-57   1.1e-53       1     292 [.     109     406 ..     109     407 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.11
  Proton_antipo_M 150 llilaiismllgslvalaqt 169
                      l il+i  ++l+ ++a++q+
       AHX11590.1  68 LTILIISCVFLAQIIAVKQS 87 
                      22222233455555555554 PP

  == domain 2  score: 182.4 bits;  conditional E-value: 1.2e-57
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllv 94 
                      +++L++lyl++El++++ly+L+ +++k+ ks+eA++k++ll+ + s ++++gi+l++  +gtl +++l+ +     +s++ l+++ll+++gll+
       AHX11590.1 109 SKNLMALYLAIELQSIGLYVLASVNQKSIKSAEAGVKYVLLGTFMSAVMIYGISLIFVSSGTLAMDALFVQ-----SSSTHLIGILLFTAGLLF 197
                      78*******************************************************************99.....9***************** PP

  Proton_antipo_M  95 KsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla...............vssneisqlllilaiismllgslvalaqtdiKr 173
                      K+++ p+h W+ d y+++Pt  s+++ a+l+k+++ +++  +  ++                ss  ++++l++ +i+s+l+g+++a  q+diKr
       AHX11590.1 198 KIGATPFHAWVGDIYEGSPTLSSTFF-AVLPKISIVAVLISIASYIdphtlieahqsvaqtESSLYMRNILFLSGILSLLFGTFAAFGQSDIKR 290
                      **************************.9******99988765544333222223333323446677899************************* PP

  Proton_antipo_M 174 llAySsishlGymlialavatqygvea.aiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFl 266
                       l++ s+sh+Gy l++++++t+ +v++  +i++l+++l+++++F +++ +     k + i +++ L  ++ ++a +++vlllslaG+Pp++gF+
       AHX11590.1 291 FLGFASVSHVGYALLGIGASTSFSVTNpGFIYILIYSLTNLGIFSVVLML-----KDKVIISLSTLNSTNKFIAFTFVVLLLSLAGIPPFTGFF 379
                      *******************9999888725789***************555.....7789*********************************** PP

  Proton_antipo_M 267 skfliLeaavavslillvla.vvasvl 292
                      +k+++++++v+ + i+  l+ v++ ++
       AHX11590.1 380 AKVYVIKNLVDSGYIVSSLIaVFTGII 406
                      *****************9998998877 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.2      0.16   1.5e+03      26      52 ..      27      53 ..      11     104 .. 0.59
   2 !   16.8   7.8   3.7e-07    0.0034      90     188 ..     111     210 ..      77     215 .. 0.77
   3 ?    1.3  10.1     0.021   1.9e+02      16     188 ..     209     383 ..     207     403 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.16
  NADHdeh_related 26 tlilfvvalifvilvilskpekqveie 52
                      +++++++li + +++ s ++   ei 
       AHX11590.1 27 DILALITVLITLGVTAFSCTDASPEIL 53
                     444444444444444444444444443 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 3.7e-07
  NADHdeh_related  90 dvfnftlflaliGianiGiv..aavkkefvl..eaafnyGlvaliatlplfggaalilastGtlsifelaklagdvlliaklllvlGvvGetGv 179
                      +++  +l+la i ++ iG+   a+v+++ +   ea  +y l+    +  +  g +li  s+Gtl++  l+ ++ ++ li  ll+++G++   G 
       AHX11590.1 111 NLM--ALYLA-IELQSIGLYvlASVNQKSIKsaEAGVKYVLLGTFMSAVMIYGISLIFVSSGTLAMDALFVQSSSTHLIGILLFTAGLLFKIGA 201
                      443..45554.56777776334999999875226789****98777777777899*************************************** PP

  NADHdeh_related 180 aPfyaakae 188
                      +Pf+a   +
       AHX11590.1 202 TPFHAWVGD 210
                      ***986655 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.021
  NADHdeh_related  16 Gdivaylseftlilfvvalifvilvilskpekqveiefgkdaiklkvvsldelkirrllaivcgl....atlgavvtgdvfnftlflal..iGi 103
                      Gdi +   +++ + f+v+  + i+++l     +++ ++  +a++    + + l +r +l +   l     t  a    d+  f  f+++  +G 
       AHX11590.1 209 GDIYEGSPTLSSTFFAVLPKISIVAVLISIASYIDPHTLIEAHQSVAQTESSLYMRNILFLSGILsllfGTFAAFGQSDIKRFLGFASVshVGY 302
                      899998889999999999888888888888888888777666666666666666666664433321112466778899*****99987655999 PP

  NADHdeh_related 104 aniGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelaklagdvlliaklllvlGvvGetGvaPf..yaakae 188
                      a +Gi a   +  v +  f y l+  ++ l +f+   l+l     +s+  l  +++  + ++ ++l+l ++G   + Pf  + ak+ 
       AHX11590.1 303 ALLGIGA-STSFSVTNPGFIYILIYSLTNLGIFSV-VLMLKDKVIISLSTLNSTNK-FIAFTFVVLLLSLAG---IPPFtgFFAKVY 383
                      9999865.5677899******************75.57788888999999999887.566666666666655...555533334444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       867  (0.0483574); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.23s 00:00:00.81 Elapsed: 00:00:00.43
# Mc/sec: 3206.49
//
Query:       AHX11591.1  [L=226]
Description: biotin--[acetyl-CoA-carboxylase] ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.6e-06   26.6   0.2    8.1e-06   25.8   0.2    1.5  1  BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
    4.9e-06   26.3   0.0    1.1e-05   25.2   0.0    1.6  1  BPL_C          Biotin protein ligase C terminal domain


Domain annotation for each model (and alignments):
>> BPL_LplA_LipB  Biotin/lipoate A/B protein ligase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.8   0.2     9e-10   8.1e-06      53     127 ..      64     126 ..      12     129 .. 0.67

  Alignments for each domain:
  == domain 1  score: 25.8 bits;  conditional E-value: 9e-10
                    EESS...-CCGTHHH.HHHHHHHHHHHH.......HHTT-TTEEEETTTEEEETTEEEEEEEEEEEETTS-EEEEEE CS
  BPL_LplA_LipB  53 speqktfqnrvlely.vsllvlavlealgy.rdskpgiegipvfikwpnDlyvngrKlaGiavtstrgktlhhivig 127
                     +e           + v ++vl+v+ a+g+ +   + i+++  + kwpnD++++g+K++Gi+ +   ++ + +i i+
     AHX11591.1  64 VAE----------NIkVGEIVLKVAVAVGElI--SKWIPNV--EYKWPNDILIDGKKVSGILLEYHDNRLVIGIGIN 126
                    433..........3334444444444443211..2344444..456****************998887666666655 PP

>> BPL_C  Biotin protein ligase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.2   0.0   1.2e-09   1.1e-05       2      45 ..     179     223 ..     178     225 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.2 bits;  conditional E-value: 1.2e-09
                 TTSEEEEEETSCEEEEEEEEE-TTSEEEEEETTE..EEEESSCCE CS
       BPL_C   2 sGqeVtlededgkveGiavGIdddGaLllktddg.lqpdinsGdi 45 
                 +G+ +++  ++++v G++ +I +dGaL+l+t+   + + ++sG+i
  AHX11591.1 179 LGKLINFDANGEIVKGMFSDIASDGALILRTEYDsSEKRFYSGSI 223
                 78888999988999*****************97779999999998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (226 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       320  (0.0178482); expected 358.6 (0.02)
Passed bias filter:                      298  (0.0166211); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1678.61
//
Query:       AHX11592.1  [L=236]
Description: polyprenyl synthetase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      2e-37  128.7   0.0    2.4e-37  128.4   0.0    1.1  1  polyprenyl_synt  Polyprenyl synthetase


Domain annotation for each model (and alignments):
>> polyprenyl_synt  Polyprenyl synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   1.4e-41   2.4e-37       2     195 ..       6     187 ..       5     203 .. 0.93

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 1.4e-41
                      HHHHHHHHHHHHSSS--HHHHHHHHHHHHHSCGHHHHHHHHHHHHHHHHHHHHHHHHHHH..HTT-SEETTEE-HHHCTCHHHHHHHHHHHHHH CS
  polyprenyl_synt   2 elleealeylveagGKrlRpllvllaaealkeeeeelekaavlawivellhaasLvhDDi..mDdsetRRGqpcahrlvGnklAindgdfllar 93 
                      e+l +a++y + a+   +R+ l+l ++ +++     + +a+++a +ve++h++sL+hDD+   D+s  RR+qp++h ++ +++Ai++gd+ll++
       AHX11592.1   6 EELFDAIRYSTLAESGCIRGFLILEFSDLFN--A-PFGDALEVASAVEMIHSFSLIHDDLpaLDNSLERRNQPACHVAFSESTAILAGDALLVL 96 
                      5677889999999999***************..3.5799******************************************************* PP

                      HHHHHHHHHSTTHHHHHHHHHHHHHHHHHHHHHHHHTTTTTCCC.SHHHHHHHHHHHTHHHCHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHH CS
  polyprenyl_synt  94 afellaklfekslellelfsevllqtveGqlldleeekdddlskfsleeyleivkyKTaylfalpvalaallagasdeelealkdiglelGlaF 187
                      a++ll+++  +s  +++  s+ +l+++ Gq+ dl++ek   +s       +ei  +KT++lfal++ ++ +l++ ++++l+ l+++g+e+G +F
       AHX11592.1  97 AYQLLSHY--GS-GIIQDASKYVLEMIVGQVHDLKQEK--VIS------SSEINVMKTGALFALSCSCIGHLCNRANDDLDILRKFGYEFGRLF 179
                      ********..88.9********************6663..333......589**********************99999*************** PP

                      HHHHHHHH CS
  polyprenyl_synt 188 QiqDDylD 195
                      Q +DD+ D
       AHX11592.1 180 QAVDDITD 187
                      ******98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       437  (0.0243739); expected 358.6 (0.02)
Passed bias filter:                      369  (0.0205812); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1826.15
//
Query:       AHX11593.1  [L=272]
Description: glutamine synthetase, catalytic domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.4e-25   88.8   0.0    5.7e-25   88.0   0.0    1.3  1  Gln-synt_C  Glutamine synthetase, catalytic domain


Domain annotation for each model (and alignments):
>> Gln-synt_C  Glutamine synthetase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   88.0   0.0   3.2e-29   5.7e-25      89     279 ..      55     231 ..      47     257 .. 0.88

  Alignments for each domain:
  == domain 1  score: 88.0 bits;  conditional E-value: 3.2e-29
                 EECCEEECCCTEEEEEE.--EECHHHHHHHHHHHHHHHHHHHHTT-EEE-SSSSSTTS---BEEEEEEEEECTT.EESSB-TTSGGGB-HHHHHHHHHH CS
  Gln-synt_C  89 veashhEvatgQvEinl.kfadalkaaDnvvtfKrvvkevArkhgltatFmpKplegdnGsgmHvhlSlwdkdg.knlfadeddeyalselarhfigGl 185
                 +e++ +E ++ Q+Ei++  ++d+   + ++ +f++++k+v +       F  Kp ++++Gs+mH+h+Sl dk+  kn++a+e       +l + +igG+
  AHX11593.1  55 IERVVNEIGEKQYEISTiPTSDLTLLVREIEMFRKLTKAVSD-------FSSKPRFDQPGSAMHIHISLHDKESsKNIIASEA------KLKLFIIGGM 140
                 688999*********997888899999999999999999976.......99*********************999******98......788999**** PP

                 HHHHHHHHHHHS-SCCHHHHCS.SSTTSSSBEEEE.SS-TTCSEEEE-TSGGCSTEEEECEBTTS-HHHHHHHHHHHHHHHHHTT--------S-S CS
  Gln-synt_C 186 lkhakaltaltaptvnSYkRlv.pgyeaPvalawg.arNRsallRipaskekakrvElRlpdasaNPYLalAallaAgldGienklepgepvekdl 279
                    +ka+++++ap v+SY+R++ ++   P  + wg ++N+s ++Ri       + +E+R+++++a    ++  ++ A   Gi+n++ pgep  k+ 
  AHX11593.1 141 CSLIKASMLCFAPEVSSYRRFQyHDKFTPRFVNWGfEENKSNAIRITK-----NTIEHRVAGSDADLLEVIKSIIGAIEYGISNEIIPGEPNFKES 231
                 *********************8245678*******668********99.....89************99********************9865543 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (272 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       344  (0.0191868); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.20s 00:00:00.62 Elapsed: 00:00:00.36
# Mc/sec: 2247.61
//
Query:       AHX11594.1  [L=250]
Description: hypothetical protein NHE_0661 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    7.5e-66  221.8  25.0    8.6e-66  221.6  25.0    1.0  1  MlaE          Permease MlaE
  ------ inclusion threshold ------
      0.067   13.1   1.8       0.25   11.3   1.8    2.0  1  Fst_toxin     Toxin Fst, type I toxin-antitoxin system
       0.41   10.4   3.8      0.096   12.5   0.7    1.4  2  Trp_oprn_chp  Tryptophan-associated transmembrane protein (Tr
       0.47    8.6   3.2       0.56    8.3   3.2    1.1  1  BIV_Env       Bovine immunodeficiency virus surface protein (


Domain annotation for each model (and alignments):
>> MlaE  Permease MlaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  221.6  25.0   1.9e-69   8.6e-66       2     211 ..      35     244 ..      34     245 .. 0.99

  Alignments for each domain:
  == domain 1  score: 221.6 bits;  conditional E-value: 1.9e-69
        MlaE   2 veqlefvgvkslpivlltalftGavlalqgasqlkqfgaesllgslvalalvrelgPvltallvagrvGsaiaAelGtmrvteeidAlevmgidpikyl 100
                 ++q+ ++g+ s+p+v++ta+f+Ga+la+q++  ++ +  + +++++++++++re+gPv+++++vagrv+s iaAe+G+m+vte++d l+ + id  +yl
  AHX11594.1  35 IKQMISIGYLSIPVVAFTATFVGAILAIQSYMGFEVMQSQMMVANILTTSITREIGPVVVGIIVAGRVASTIAAEIGAMQVTEQVDLLRSLSIDVHAYL 133
                 89************************************************************************************************* PP

        MlaE 101 vvPrvlAlvialplLtviadlvgilggylvavlllgispgaylqsvqealslkdllvgllKalvfGliialiacyqGltakggaegvgrattravvtsi 199
                 v+P+v+A++i++p+L+vi+d+ gilggyl++ + ++++   y++ + ++ls  d+++g++K+l+fG++++ ++c++Gl+ +gga+gvg a+t++vv+s+
  AHX11594.1 134 VAPKVIAALISFPILAVISDVYGILGGYLIGIYKFHFNHMLYISDTVASLSYGDFMSGIVKSLFFGFLTTSVSCFNGLRSTGGARGVGFAVTNSVVVSF 232
                 *************************************************************************************************** PP

        MlaE 200 vlilvvdlvltl 211
                 vlil++++++tl
  AHX11594.1 233 VLILFMNYLITL 244
                 **********97 PP

>> Fst_toxin  Toxin Fst, type I toxin-antitoxin system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   1.8   5.5e-05      0.25       5      14 ..      89      98 ..      86      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 5.5e-05
   Fst_toxin  5 IAPivVGVil 14
                I+P+vVG+i+
  AHX11594.1 89 IGPVVVGIIV 98
                9********8 PP

>> Trp_oprn_chp  Tryptophan-associated transmembrane protein (Trp_oprn_chp)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.1       1.9   8.7e+03     124     130 ..      52      58 ..      38      66 .. 0.50
   2 ?   12.5   0.7   2.1e-05     0.096      51     137 ..      75     164 ..      71     173 .. 0.72

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.9
  Trp_oprn_chp 124 aggvlll 130
                    ++ + +
    AHX11594.1  52 TATFVGA 58 
                   2222222 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 2.1e-05
  Trp_oprn_chp  51 vllAaavAvlavrglgrrvvgvllalagagaava..alslltdpadaaraaaaaatg.vasaaaaveltawpvlalaggvllllagvlll 137
                   +++A ++ + ++r +g +vvg+++a   a +++a  ++  +t++ d+ r+ + ++++ + + +  ++l + p+la++  v  +l+g l+ 
    AHX11594.1  75 MMVANILTTSITREIGPVVVGIIVAGRVASTIAAeiGAMQVTEQVDLLRSLSIDVHAyLVAPKVIAALISFPILAVISDVYGILGGYLIG 164
                   589999******************9655554444005555566777788777443330333333444777************99999875 PP

>> BIV_Env  Bovine immunodeficiency virus surface protein (SU)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.3   3.2   0.00012      0.56     118     231 ..      55     179 ..      16     199 .. 0.70

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00012
     BIV_Env 118 magtaladadrs........svieni.tkkdikdtdpyilill.glvvilGllGviialrrsnsegilaard.avdwwlsankeiplkftvpiilissp 205
                 + g+ la ++           ++ ni t   +++  p+++ ++ +  v   +   i a++ +++ ++l +    v  +l a k i   +++pi+ + s 
  AHX11594.1  55 FVGAILAIQSYMgfevmqsqMMVANIlTTSITREIGPVVVGIIvAGRVASTIAAEIGAMQVTEQVDLLRSLSiDVHAYLVAPKVIAALISFPILAVISD 153
                 44444443333334444444344555166666699999664440444555566667799999999999765426899********************** PP

     BIV_Env 206 lagilgyfvmeryskilkgGcqlcgs 231
                 + gilg +++  y   +++   +  +
  AHX11594.1 154 VYGILGGYLIGIYKFHFNHMLYISDT 179
                 ********999888777766655555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       887  (0.0494729); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 2038.07
//
Query:       AHX11595.1  [L=247]
Description: ABC transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.5e-29  102.5   0.0    3.8e-29  101.9   0.0    1.3  1  ABC_tran      ABC transporter
      2e-06   27.9   0.4    0.00034   20.5   0.0    2.1  2  AAA_21        AAA domain, putative AbiEii toxin, Type IV TA s
     0.0019   17.7   0.0     0.0066   15.8   0.0    1.8  2  Mg_chelatase  Magnesium chelatase, subunit ChlI
     0.0045   16.9   0.0      0.007   16.3   0.0    1.3  1  RsgA_GTPase   RsgA GTPase
     0.0073   15.8   0.0      0.016   14.6   0.0    1.6  1  SMC_N         RecF/RecN/SMC N terminal domain
     0.0077   15.6   0.0      0.011   15.1   0.0    1.2  1  FtsK_SpoIIIE  FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.011   15.4   0.0      0.022   14.5   0.0    1.4  1  AAA_29        P-loop containing region of AAA domain
      0.043   13.7   0.1       0.07   13.0   0.1    1.3  1  NACHT         NACHT domain
      0.064   12.9   0.2       0.25   11.0   0.1    1.8  2  ChitinaseA_N  Chitinase A, N-terminal domain
      0.068   12.3   0.3        0.7    8.9   0.0    2.1  2  MCM           MCM P-loop domain
      0.089   11.7   0.0       0.14   11.1   0.0    1.3  1  AAA_10        AAA-like domain
       0.12   12.9   0.1       0.19   12.2   0.1    1.4  1  AAA_23        AAA domain
       0.12   12.0   0.0       0.17   11.5   0.0    1.3  1  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-bind


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.9   0.0   2.8e-32   3.8e-29       1     136 [.      20     167 ..      20     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: 101.9 bits;  conditional E-value: 2.8e-32
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGG.B-HHHCCHCEEEE-SS--S-TTSBHHHH...........HHHTC... CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxx...........xxxxx... RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlke.qeleslrkeigvlpqepqlfpeltvren...........esdee... 84 
                 +kn++++l +ge + i+G++G GKS Llk ++gl     G++l++g ++ +  e++  ++ i++ +q+++lf+ +t+ en            ++     
  AHX11595.1  20 VKNLNFDLLPGENLCIIGQSGEGKSVLLKSIIGLIPHRTGKVLINGSEVAQnVEENTKKHDISISFQNDCLFDSMTILENlcfpliyrssiPRNTAiki 118
                 58*******************************************9999994556666778************************99887633333222 PP

                 HHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  85 iekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                  ek++ k+g   l   ++k  pssLSgG+k+r+a+ara++++p+++++DEpt
  AHX11595.1 119 SEKIIPKIG---LSSAILKLYPSSLSGGMKKRIAIARAIITQPSIVFFDEPT 167
                 445555555...666999999******************************9 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.8   0.1    0.0074        10       3      69 ..      34      94 ..      33      99 .. 0.80
   2 !   20.5   0.0   2.4e-07   0.00034     231     283 ..     134     185 ..     102     201 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.8 bits;  conditional E-value: 0.0074
      AAA_21  3 vliGpNgsGKSnLLdaldllarldrdvegltdelsggggirkipslldlydpeipfefeieeflsqg 69
                ++iG  g GKS LL+ +      ++ + ++t +   +g++  +  + +++  +i++ f+ +++++++
  AHX11595.1 34 CIIGQSGEGKSVLLKSI------IGLIPHRTGKVLINGSEVAQNVEENTKKHDISISFQNDCLFDSM 94
                69***************......55578888888888888888888888888888888887777665 PP

  == domain 2  score: 20.5 bits;  conditional E-value: 2.4e-07
      AAA_21 231 elparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell..k 283
                 +l +++lS G+k+ +a++ a++ ++   s++++DEp +gL+P    r+l+++   
  AHX11595.1 134 KLYPSSLSGGMKKRIAIARAIITQP---SIVFFDEPTTGLDPITSGRILDIVvdY 185
                 578899********99999999999...**************6666666666431 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.0   4.8e-06    0.0066       7      72 ..      15      80 ..       9      88 .. 0.79
   2 ?   -0.8   0.0      0.61   8.5e+02     179     199 ..     134     154 ..     126     205 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 4.8e-06
  Mg_chelatase  7 GqeeakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvagkkeeekl 72
                  G+++  + l+     g nl ++G +G GK++l k + +l+p+ + +  ++ +++a  ++++++++ 
    AHX11595.1 15 GNRSIVKNLNFDLLPGENLCIIGQSGEGKSVLLKSIIGLIPHRTGKVLINGSEVAQNVEENTKKHD 80
                  566666666666667889***************************999999998876666666555 PP

  == domain 2  score: -0.8 bits;  conditional E-value: 0.61
  Mg_chelatase 179 erYlsklsgplldRidlqvev 199
                   + Y s lsg +  Ri +  ++
    AHX11595.1 134 KLYPSSLSGGMKKRIAIARAI 154
                   567777777777777775444 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   5.1e-06     0.007      90     130 ..      20      61 ..       3      92 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 5.1e-06
                  HHHHHHH.CTTSEEEEECSTTSSHHHHHHHHCTT-----S-- CS
  RsgA_GTPase  90 leelkel.lkdktsvlvGqSGvGKStLinallpelelktgev 130
                  +++l+   l ++  +++GqSG GKS L++++++    +tg+v
   AHX11595.1  20 VKNLNFDlLPGENLCIIGQSGEGKSVLLKSIIGLIPHRTGKV 61 
                  56666540455999******************9999999887 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   1.2e-05     0.016      27     186 ..      33     185 ..      12     218 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.2e-05
                 EEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--BTTCSSTTEEEEEEEEEETTEE...SSSSSSCEEEEEEEETTSEEEEEETTEEE-HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N  27 taivGpNGSGKsnlldAilFvLGersakklrseklsdlihkskekasvkkaeveitfdnedkk...lkiekeevsisrrvkrkgeseykingkevtkke 122
                  +i+G+ G GKs ll +i  ++ +r+ k l +   s++ +  + ++++kk +++i f+n+      +  e+  + +  r +   ++ +ki +k + k  
  AHX11595.1  33 LCIIGQSGEGKSVLLKSIIGLIPHRTGKVLIN--GSEVAQ--NVEENTKKHDISISFQNDCLFdsmTILENLCFPLIYRSSIPRNTAIKISEKIIPKIG 127
                 479***************55555555544322..233333..577889999999999887544222555555666666666667789********9999 PP

                 HHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 123 vsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkek 186
                 +s+ +   ++++++LSgG k+ +a+a       + + +++++De    LD     ++ +++   
  AHX11595.1 128 LSSAI--LKLYPSSLSGGMKKRIAIARA----IITQPSIVFFDEPTTGLDPITSGRILDIVVDY 185
                 98876..6799**********9888754....34566789999999999999998888777654 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   8.3e-06     0.011      18      60 ..      10      51 ..       2      58 .. 0.89

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 8.3e-06
                  TEEEEEEETTS-EEEEEGGGS-.SEEEE--TTSSHHHHHHHHH CS
  FtsK_SpoIIIE 18 lpvalgkeisgnplvldlkkmashllvaGatgsGKStalntLi 60
                  l va+g   + ++l +dl + + +l ++G +g GKS+ l+++i
    AHX11595.1 10 LSVAFGNRSIVKNLNFDLLPGE-NLCIIGQSGEGKSVLLKSII 51
                  678888888889999*******.*****************998 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.5   0.0   1.6e-05     0.022      18      46 ..      26      54 ..      15      68 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 1.6e-05
      AAA_29 18 eidlkgatlltGpsGsGKSTllDAiqalL 46
                ++ + ++  ++G+sG GKS ll +i+ l+
  AHX11595.1 26 DLLPGENLCIIGQSGEGKSVLLKSIIGLI 54
                555556999*************8887664 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.1   5.1e-05      0.07       3      25 ..      33      55 ..      31      62 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.1e-05
                EEEEC-TTTCHHHHHHHHHHHHC CS
       NACHT  3 vilqGeaGsGKTtLlqklalawa 25
                +++ G++G GK++Ll++++ ++ 
  AHX11595.1 33 LCIIGQSGEGKSVLLKSIIGLIP 55
                79****************97765 PP

>> ChitinaseA_N  Chitinase A, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0         1   1.4e+03      55      75 ..      59      79 ..      55      93 .. 0.73
   2 ?   11.0   0.1   0.00018      0.25      35      79 ..     189     234 ..     181     244 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 1
  ChitinaseA_N 55 akvlldgvkvaegaasakesa 75
                   kvl++g +va+   ++ ++ 
    AHX11595.1 59 GKVLINGSEVAQNVEENTKKH 79
                  589999999998777654444 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00018
  ChitinaseA_N  35 kdeaevsvewnvWsGe.agdkakvlldgvkvaegaasakesatfkv 79 
                   ++  +++v+++ W  + +++k+ ++ dg+ v+ g++++ e+++ ++
    AHX11595.1 189 EKVSSITVTHSLWCAKrISNKVAMIHDGKIVWYGDTTSLETTKNEY 234
                   56678********9862689***************99776666555 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.9   0.0   0.00051       0.7      59      84 ..      32      57 ..      13      83 .. 0.83
   2 ?    1.4   0.1       0.1   1.4e+02      13      69 ..     113     169 ..     105     198 .. 0.87

  Alignments for each domain:
  == domain 1  score: 8.9 bits;  conditional E-value: 0.00051
                EEEEEESSTSTHHHHHHHHHHHSSSE CS
         MCM 59 nvllvgdpgtaKsqlLkyveklapra 84
                n++++g +g +Ks lLk++  l+p+ 
  AHX11595.1 32 NLCIIGQSGEGKSVLLKSIIGLIPHR 57
                99*****************9998854 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.1
                 THHHHHHHHSSTTSSS-HHHHHHHHHHHH---EBBBSSSSBBCSS-EEEEEESSTST CS
         MCM  13 diieklvksiapsiyghedvkkaillqlfggvkkkledktklrgdinvllvgdpgta 69 
                 ++  k++++i+p+i  ++++ k    +l gg+kk+      ++++  +++  +p t+
  AHX11595.1 113 NTAIKISEKIIPKIGLSSAILKLYPSSLSGGMKKRIAIARAIITQPSIVFFDEPTTG 169
                 556689999999999999999999999999999999988889999999999888875 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0   9.9e-05      0.14      24      54 ..      33      63 ..      29      91 .. 0.88

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 9.9e-05
      AAA_10 24 sliiGdlGnGKSvlakllvlyisllggkali 54
                  iiG+ G+GKSvl k ++  i  + gk+li
  AHX11595.1 33 LCIIGQSGEGKSVLLKSIIGLIPHRTGKVLI 63
                579****************999999999987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00014      0.19       8      68 ..      17      86 ..      14     141 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00014
      AAA_23  8 rsf.rdqeidFskglt.lItGpNGaGKTTildAiklaLygetprlsrks.......grgfeksdveiese 68
                rs+ ++ ++d+ +g + +I+G+ G GK+ +l  i     ++t++   +        +++ +k+d++i+++
  AHX11595.1 17 RSIvKNLNFDLLPGENlCIIGQSGEGKSVLLKSIIGLIPHRTGKVLINGsevaqnvEENTKKHDISISFQ 86
                667789999996655538***************9988877664433332445555555666666665554 PP

>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   0.00012      0.17      11      38 ..      27      54 ..      19     123 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                 EBTT-EEEEEESTTSSHHHHHHHHHHHS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 11 ivqGqrtlipgafgvGktvisqslskqs 38
                 +  G++++i+g++g Gk+v+++s++   
   AHX11595.1 27 LLPGENLCIIGQSGEGKSVLLKSIIGLI 54
                 67799******************98765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       549  (0.0306208); expected 358.6 (0.02)
Passed bias filter:                      468  (0.026103); expected 358.6 (0.02)
Passed Vit filter:                        72  (0.00401584); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1885.35
//
Query:       AHX11596.1  [L=204]
Description: heme ABC exporter, ATP-binding protein CcmA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-29  101.2   0.0    8.4e-29  100.8   0.0    1.1  1  ABC_tran  ABC transporter
    4.1e-07   30.1   6.1    0.00049   20.0   0.6    2.1  2  AAA_21    AAA domain, putative AbiEii toxin, Type IV TA syste
     0.0011   18.9   0.1     0.0021   18.0   0.1    1.4  1  NACHT     NACHT domain
      0.003   18.1   1.7     0.0046   17.5   1.6    1.4  1  AAA_23    AAA domain
     0.0035   16.8   0.4          2    7.8   0.1    2.1  2  SMC_N     RecF/RecN/SMC N terminal domain
      0.004   16.9   0.1     0.0086   15.8   0.1    1.5  1  AAA_29    P-loop containing region of AAA domain
     0.0078   15.4   0.1      0.011   14.9   0.1    1.2  1  PIF1      PIF1-like helicase
  ------ inclusion threshold ------
      0.013   15.9   0.0      0.016   15.6   0.0    1.4  1  AAA_16    AAA ATPase domain
      0.042   13.6   0.0       0.11   12.3   0.0    1.5  2  AAA_30    AAA domain
      0.062   13.3   0.0       0.11   12.4   0.0    1.4  1  TsaE      Threonylcarbamoyl adenosine biosynthesis protein Ts
      0.068   11.8   0.2      0.093   11.4   0.2    1.2  1  AAA_13    AAA domain
      0.092   10.3   0.1       0.12    9.8   0.1    1.1  1  DUF3584   Protein of unknown function (DUF3584)
       0.17   11.6   2.2       0.56    9.9   1.0    2.0  2  AAA_15    AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.8   0.0   6.1e-32   8.4e-29       2     136 ..      20     156 ..      19     157 .. 0.93

  Alignments for each domain:
  == domain 1  score: 100.8 bits;  conditional E-value: 6.1e-32
                 EEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.....HHHTCHHHHHHHSTTG CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxx RF
    ABC_tran   2 knvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.....esdeeiekalsklglk 95 
                 +n+s++++ ge++ i G+nG+GK+tLl+++ag  ++ +Geil++gk++++   + +++ei ++ +++  ++e+++ en     + +++i+ + ++l+  
  AHX11596.1  20 SNISFTVNSGEILWIKGDNGSGKTTLLRIIAGIIRNFSGEILFQGKPITQ--NTLYNSEITYIGEKSACDEEYSIFENllfwaKLRDRIALLEATLEFF 116
                 79************************************************..999**************************987777777777777766 PP

                 GTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  96 elkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                 +   ++++ + ++LS G+k+rvala++ll ++k+++lDEp+
  AHX11596.1 117 N-LGRIAHVEVKKLSSGWKKRVALAKLLLFNSKIWILDEPF 156
                 6.778888888*****************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.6   3.6e-07   0.00049       4      24 ..      34      54 ..      32      90 .. 0.77
   2 !   13.2   0.6   4.2e-05     0.058     220     287 ..     112     177 ..      74     196 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 3.6e-07
      AAA_21  4 liGpNgsGKSnLLdaldllar 24
                + G+NgsGK++LL+++ ++ r
  AHX11596.1 34 IKGDNGSGKTTLLRIIAGIIR 54
                66**************99854 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 4.2e-05
      AAA_21 220 gvvflengdgqelparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllell.kelsr 287
                 ++ f+  g+   + + +lS+G k+  al+ +ll      ++ ++DEp + L+ + ++ ++el+ ++l++
  AHX11596.1 112 TLEFFNLGRIAHVEVKKLSSGWKKRVALAKLLLFNS---KIWILDEPFTYLDTESIKLFVELFeSRLEQ 177
                 666677777777888899******99*******999...9***********************744444 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.1   1.5e-06    0.0021       2      21 ..      31      50 ..      30      58 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 1.5e-06
                CEEEEC-TTTCHHHHHHHHH CS
       NACHT  2 lvilqGeaGsGKTtLlqkla 21
                +++++G++GsGKTtLl+ +a
  AHX11596.1 31 ILWIKGDNGSGKTTLLRIIA 50
                68**************9987 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   1.6   3.3e-06    0.0046      15      43 ..      22      53 ..       7      97 .. 0.77

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 3.3e-06
      AAA_23 15 idF...skgltlItGpNGaGKTTildAiklaL 43
                i F   s  +  I G+NG+GKTT+l+ i  + 
  AHX11596.1 22 ISFtvnSGEILWIKGDNGSGKTTLLRIIAGII 53
                55566555688899***********9998665 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.1    0.0015         2      26      42 ..      31      47 ..      10      57 .. 0.82
   2 !    7.7   0.0    0.0016       2.2     132     195 ..     124     183 ..      60     194 .. 0.83

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0015
                EEEEEESTTSSHHHHHH CS
                xxxxxxxxxxxxxxxxx RF
       SMC_N 26 ftaivGpNGSGKsnlld 42
                +  i G NGSGK+ ll 
  AHX11596.1 31 ILWIKGDNGSGKTTLLR 47
                56799********9986 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.0016
                 -STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 132 iskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivi 195
                 ++ + LS G k+ vala l+       + +++lDe    LD + +k ++el++++ ++  +iv 
  AHX11596.1 124 VEVKKLSSGWKKRVALAKLLLF----NSKIWILDEPFTYLDTESIKLFVELFESRLEQRGIIVL 183
                 5556899999999999877543....4569***********************99998888875 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.1   6.3e-06    0.0086      12      39 ..      19      46 ..      17      52 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 6.3e-06
      AAA_29 12 fdghtieidlkgatlltGpsGsGKSTll 39
                f++ +++++  ++  + G++GsGK+Tll
  AHX11596.1 19 FSNISFTVNSGEILWIKGDNGSGKTTLL 46
                566667777555999************8 PP

>> PIF1  PIF1-like helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   8.1e-06     0.011       5      48 ..      14      55 ..      10      63 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.1e-06
                HHHHHHHHH......HCTS-EEEEESTTSSCHHHHHHHHHHCHC CS
        PIF1  5 eQkkvfdaiieavlnekgklfFvtGsgGtgKtflwkallkklrs 48
                e  ++f +i  + + ++g++++++G  G+gKt l++ +  ++r+
  AHX11596.1 14 EDVEIFSNI--SFTVNSGEILWIKGDNGSGKTTLLRIIAGIIRN 55
                667889999..88899**************************97 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.0   1.2e-05     0.016      18      52 ..      25      58 ..      13     184 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
      AAA_16 18 rvrsgrpelvllsGesGvGKsslvrellralekd..g 52
                +v+sg  e++ + G+ G+GK++l+r ++  + ++  g
  AHX11596.1 25 TVNSG--EILWIKGDNGSGKTTLLRIIAG-IIRNfsG 58
                56666..89***************99984.4444342 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0   7.6e-05      0.11      15      45 ..      27      56 ..      21      68 .. 0.82
   2 ?   -1.8   0.0       1.6   2.2e+03      81     110 ..     134     169 ..     110     183 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 7.6e-05
      AAA_30 15 tsgdrvavltGpAGtGKttalkalreaweaa 45
                +sg  +  ++G  G+GKtt+l+ ++ ++++ 
  AHX11596.1 27 NSG-EILWIKGDNGSGKTTLLRIIAGIIRNF 56
                445.5999****************9988765 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.6
      AAA_30  81 k.....grarlepgtllivDE.agmvdtkqlaallk 110
                 k     ++  l +++++i DE    +dt++++ +++
  AHX11596.1 134 KkrvalAKLLLFNSKIWILDEpFTYLDTESIKLFVE 169
                 444445334455568888898445556666665555 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.3e-05      0.11      18      40 ..      26      50 ..      10      59 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.3e-05
                H..TEEEEEEESTTSSHHHHHHHHH CS
        TsaE 18 l..gdvilLeGdLGaGKTtlvrgla 40
                +  g+++ ++Gd G+GKTtl r +a
  AHX11596.1 26 VnsGEILWIKGDNGSGKTTLLRIIA 50
                2347889**************9887 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.2   6.8e-05     0.093      21      58 ..      34      65 ..      21      90 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 6.8e-05
      AAA_13 21 iYGwNGaGKTtLSrllrslelgetepkfangsieitng 58
                i G NG+GKTtL r+++ + +     +f +g+i ++ +
  AHX11596.1 34 IKGDNGSGKTTLLRIIAGIIR-----NF-SGEILFQGK 65
                5599************99743.....34.455555444 PP

>> DUF3584  Protein of unknown function (DUF3584)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.1   8.9e-05      0.12      22      37 ..      34      49 ..      26      50 .. 0.91

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 8.9e-05
     DUF3584 22 ieGtNaaGKTtLlrLi 37
                i+G N++GKTtLlr+i
  AHX11596.1 34 IKGDNGSGKTTLLRII 49
                89************98 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   1.0   0.00041      0.56      25      48 ..      31      54 ..      19     115 .. 0.73
   2 ?    1.2   0.1      0.17   2.3e+02     288     351 ..     120     174 ..      68     183 .. 0.68

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00041
      AAA_15 25 ltvliGkNnsGKSsilealdlFln 48
                +  + G N+sGK+++l+++  ++ 
  AHX11596.1 31 ILWIKGDNGSGKTTLLRIIAGIIR 54
                66677*************976666 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.17
      AAA_15 288 ddeelplnknGsGvqrllllillileaekkdekeeknvilliEEPEahLHpqaqkvlikllkel 351
                     ++++k +sG +  + l+ l+l+++k           +++EP ++L ++  k +++l+ + 
  AHX11596.1 120 RIAHVEVKKLSSGWKKRVALAKLLLFNSKI---------WILDEPFTYLDTESIKLFVELFESR 174
                 455678888999999998888777766655.........8889998888888888888888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       539  (0.030063); expected 358.6 (0.02)
Passed bias filter:                      465  (0.0259356); expected 358.6 (0.02)
Passed Vit filter:                        79  (0.00440627); expected 17.9 (0.001)
Passed Fwd filter:                        13  (0.000725082); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              13  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 1551.14
//
Query:       AHX11597.1  [L=147]
Description: tRNA threonylcarbamoyl adenosine modification protein YjeE [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    6.3e-28   97.3   0.0    7.6e-28   97.0   0.0    1.0  1  TsaE          Threonylcarbamoyl adenosine biosynthesis protei
    0.00072   19.5   0.1    0.00093   19.2   0.1    1.2  1  ATPase_2      ATPase domain predominantly from Archaea
  ------ inclusion threshold ------
      0.018   15.4   0.0      0.021   15.2   0.0    1.2  1  AAA_16        AAA ATPase domain
      0.059   13.4   0.0       0.11   12.5   0.0    1.4  1  AAA_5         AAA domain (dynein-related subfamily)
       0.16   11.2   0.0       0.16   11.2   0.0    1.1  1  KAP_NTPase    KAP family P-loop domain
       0.18   12.2   0.0       0.25   11.8   0.0    1.3  1  RNA_helicase  RNA helicase


Domain annotation for each model (and alignments):
>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   97.0   0.0   2.6e-31   7.6e-28       5     107 ..       8     114 ..       5     136 .. 0.84

  Alignments for each domain:
  == domain 1  score: 97.0 bits;  conditional E-value: 2.6e-31
                 HHHHHHHHHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHTT--...----TTTTSEEEEEE..SSEEEEE-TT-SSTHHHHHCTTCCCCSTSCEEEEE CS
        TsaE   5 eetealgkklakal..gdvilLeGdLGaGKTtlvrglakalgve...evkSPTFtlveeYelekeglyHfDlYRledeeeleelgleeyleeeavvlvE 98 
                 +e+++++k + + l  +++i+L+GdLG+GKT l+ ++++ +  +    v+SPT+ +v+ Y++ ++++ H+DlYR+++++el+e+gl+e+l++ +++++E
  AHX11597.1   8 TEINEVAKMIVSILgeRRIIFLYGDLGSGKTRLSGEVIRLMLGDpslIVQSPTYGIVNVYKSISNTIAHLDLYRIKSPSELYEIGLQEILQQ-SFCIIE 105
                 6788999999998877778********************885555678************999888************************55.6***** PP

                 TGGGGCCCS CS
        TsaE  99 Wpekleell 107
                 Wpe +++ +
  AHX11597.1 106 WPEIMQSGF 114
                 ***987654 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.1   3.1e-07   0.00093       7      44 ..       9      48 ..       7      72 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 3.1e-07
    ATPase_2  7 elkeleeiler..epneiyfiYGpegsGKtaLlkeiienl 44
                e++e+ +++ +  ++++i+f+YG  gsGKt+L  e+i   
  AHX11597.1  9 EINEVAKMIVSilGERRIIFLYGDLGSGKTRLSGEVIRLM 48
                7888888776444889****************99999765 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0     7e-06     0.021      10      51 ..      11      51 ..       8      99 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 7e-06
      AAA_16 10 eqLlsalervrsgrpelvllsGesGvGKsslvrellralekd 51
                ++++ ++ ++  g+ ++++l+G+ G+GK++l  e+ r + +d
  AHX11597.1 11 NEVAKMIVSIL-GERRIIFLYGDLGSGKTRLSGEVIRLMLGD 51
                55555555444.5559***************99998876666 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.0   3.6e-05      0.11       2      32 ..      27      58 ..      26      61 .. 0.92

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.6e-05
                EEEE--SSSSHHHHHHHGGGGB.S--EEEEE- CS
       AAA_5  2 vlLvGppGtgKselaerlaaal.nreveyvql 32
                ++L G+ G+gK++l+ ++ +++ +++ ++vq 
  AHX11597.1 27 IFLYGDLGSGKTRLSGEVIRLMlGDPSLIVQS 58
                69*******************99**9999985 PP

>> KAP_NTPase  KAP family P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   5.4e-05      0.16       5      44 ..      10      48 ..       7     113 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 5.4e-05
  KAP_NTPase  5 asaladilseptlatpivvgLygkWGsGKssllnkledel 44
                ++ +a+++++  l++  ++ Lyg  GsGK+ l  ++++ +
  AHX11597.1 10 INEVAKMIVSI-LGERRIIFLYGDLGSGKTRLSGEVIRLM 48
                7899*****66.8*******************99988887 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   8.3e-05      0.25       1      62 [.      27      83 ..      27     103 .. 0.69

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 8.3e-05
  RNA_helicase  1 iwlyGpsgeGKStlakeLakallkklklkkkdsvysrnpeddfwdgYt.gqevvvidDfgqvk 62
                  i+lyG+ g GK++l+ e+++ +l++      +s+++++p+  +++ Y+   + +   D++++k
    AHX11597.1 27 IFLYGDLGSGKTRLSGEVIRLMLGD------PSLIVQSPTYGIVNVYKsISNTIAHLDLYRIK 83
                  79***************99999844......45555666666666666434444445666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       393  (0.0219198); expected 358.6 (0.02)
Passed bias filter:                      382  (0.0213063); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1184.93
//
Query:       AHX11598.1  [L=191]
Description: ribonuclease HII family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.1e-29  101.1   0.1    8.9e-29  100.7   0.1    1.1  1  RNase_HII       Ribonuclease HII
  ------ inclusion threshold ------
      0.091   12.4   0.2       0.27   10.9   0.2    1.9  1  Endonuclease_5  Endonuclease V


Domain annotation for each model (and alignments):
>> RNase_HII  Ribonuclease HII
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.1     1e-32   8.9e-29       1     197 [.       9     185 ..       9     186 .. 0.86

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 1e-32
                 EEEEEE-TT-SBS-EEEEEEEECGHHHHHHHCTTGTTGTTS-HHHHHHHHHHHHSEEEEEEE-HHHHH.HHTTTS-HHHHHHHHHHHHHHHHHHTCEEC CS
   RNase_HII   1 iGiDEaGrGpvlGplvvaavavekereeelkklgvkDSKkLskqkreeLaklikkkiekrklvaeeikyaseneinlneikaaltlaviklleklgvkv 99 
                 +G+DEaGrG+++Gp+v+ av+++++           DSK Ls+ +r+   + i      ++++ + i  a ++ei+  +i +a++la++++l++l++ +
  AHX11598.1   9 AGVDEAGRGSIAGPVVAGAVILKETLT------IPGDSKSLSSTARSLWYSRIA-----SAAHWG-IGVATVREIENMNILEATLLAMERALNNLQITP 95 
                 6*************9988888877665......458*****************9.....555555.88899**************************** PP

                 CECCCE--SSHHHHHHHHHHHHCCEEEEETTGGGT-HHHHHHHHHHHHHHHHHHHHHH.HHCS.H.--TTSSTTSHHHHHHHHHHHHHS--TTB-TTSH CS
   RNase_HII 100 deilvdgvttpeslkkkleqiikikvtvekkadekyllvaaASiiAkverdeelellk.rkpg.tldkgsGyasdektrallkkgatsklpdivrlsfk 196
                 d +l+dg +  + +  k +++i+       k+d+++  + aASi+Akv rd+ +e l    p+  +++++Gy+++ + +a+  +g+ +     +r+ f+
  AHX11598.1  96 DVVLIDGQQVIH-NVGKYKKVIS-----IIKGDTIHEEIKAASIVAKVARDVFMEELDlLYPQyLWKINKGYGTKSHVQAIFDHGVSQ----YHRRTFA 184
                 ******888766.5556666777.....258********************66666651556689*********************99....9999998 PP

                 H CS
   RNase_HII 197 t 197
                  
  AHX11598.1 185 P 185
                 6 PP

>> Endonuclease_5  Endonuclease V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2     3e-05      0.27      76     100 ..      84     108 ..       1     111 [. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3e-05
                     HHHHHCC-SS--SEEEEEC-SSSST CS
  Endonuclease_5  76 llkaleklkqkpdvllvDGnGiaHp 100
                     + +al++l+ +pdv+l+DG+ ++H 
      AHX11598.1  84 MERALNNLQITPDVVLIDGQQVIHN 108
                     45678888889**********9996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (191 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       483  (0.0269396); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.22s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1565.61
//
Query:       AHX11599.1  [L=159]
Description: hypothetical protein NHE_0666 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (159 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       941  (0.0524848); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1300.20
//
Query:       AHX11600.1  [L=52]
Description: hypothetical protein NHE_0667 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (52 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      142  (0.00792013); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 442.95
//
Query:       AHX11601.1  [L=284]
Description: D-alanyl-D-alanine carboxypeptidase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.5e-67  226.0   1.4    5.6e-67  225.7   1.4    1.0  1  Peptidase_S11    D-alanyl-D-alanine carboxypeptidase
    2.5e-10   40.3   0.0    3.1e-10   40.0   0.0    1.2  1  Beta-lactamase2  Beta-lactamase enzyme family
     0.0006   18.7   1.2      0.032   13.0   0.1    2.1  2  Peptidase_S13    D-Ala-D-Ala carboxypeptidase 3 (S13) family


Domain annotation for each model (and alignments):
>> Peptidase_S11  D-alanyl-D-alanine carboxypeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  225.7   1.4   9.4e-71   5.6e-67      12     240 ..      22     242 ..      15     243 .. 0.97

  Alignments for each domain:
  == domain 1  score: 225.7 bits;  conditional E-value: 9.4e-71
                    SSSEEEEEETTTTEEEEEESTTS-BE-GGGHHHHHHHHHHHHHHTTSS-TTSEEE--GGGHGCCSGTTSSTTS-TTT-EEEHHHHHHHHHCC--HH CS
  Peptidase_S11  12 aaksailvdantGkvLyeknadevveiASltKlmTaylvlealkkgklkeddkvtisedayalgnnkevsniflkkgskvsvkdLlegllvssgNd 107
                    +  sai++d++tG vL ++ adev+ +ASltK+mTay+v + lkk++lk+++k+ +se+a+++      s++ lk+g+ vs+kd l  ++++s+Nd
     AHX11601.1  22 HCTSAIAIDQKTGGVLVKEKADEVLYPASLTKMMTAYIVFDHLKKKSLKWNQKLYVSESAASKA----PSKLGLKPGEYVSLKDALLTMVMKSAND 113
                    6789**********************************************************99....8*************************** PP

                    HHHHHHHHHHSSHHHHHHHHHHHHHHTT-TT-B-SSSSSTSHTTCBB-HHHHHHHHHHHHHHHHHHHHGGGESEEEETTECTEEEESSTGGGGTTT CS
  Peptidase_S11 108 AavalAekiaGsekaFvkmMnkkakelGlkntkfvnptGLdnenqvssArdlailakallkdlpeelkitkeksltfngikklnyknknkllyrkt 203
                     a  lAeki+Gse++F kmM kka+++G++nt+f n tGL + ++vs+A d+aila+++++d+pe  +i   ks++++   + +  n+nkll ++ 
     AHX11601.1 114 SATVLAEKIGGSEENFAKMMTKKARSFGMRNTRFRNCTGLHAIDHVSTASDMAILARRVINDFPEYTHIFGLKSFKYK---DEWIHNTNKLLHSSP 206
                    *****************************************************************************7...88899*******999 PP

                    SEEEEEEEEEETTTEEEEEEEEEETTEEEEEEEEEES CS
  Peptidase_S11 204 lnvdglktGytkkAgeclvatavenqmrlisVvlnak 240
                     ++ g+ktGyt+ Ag++l + a ++++r+i++v+ a+
     AHX11601.1 207 -EIAGIKTGYTNYAGYNLASLAYRKGKRVITIVMHAP 242
                    .*********************************997 PP

>> Beta-lactamase2  Beta-lactamase enzyme family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.0   0.0   5.2e-14   3.1e-10       7     143 ..      38     175 ..      32     236 .. 0.88

  Alignments for each domain:
  == domain 1  score: 40.0 bits;  conditional E-value: 5.2e-14
                      EEESTTS-EE-GGGGHHHHHHHHHHHHHCTSTGTT-EEEGGHHHHTSSSTSGGGSTTSEEEHHHHHHHHHHTT-HHHHHHHHHHHT..HHHHHH CS
  Beta-lactamase2   7 lgvnadeefpaaStiKvpillalleavlegklslderltltaedivggsgilqklpgktlslrdlltlmiavSDNtAtnlLidrlg..leavna 98 
                      ++ +ade+++ aS+ K + ++ +++ ++++ l+++++l +++++  +   +l  +pg  +sl+d l  m+  S N  + +L +++g   e++ +
       AHX11601.1  38 VKEKADEVLYPASLTKMMTAYIVFDHLKKKSLKWNQKLYVSESAASKAPSKLGLKPGEYVSLKDALLTMVMKSANDSATVLAEKIGgsEENFAK 131
                      47789******************************************9999*999999***************************767788877 PP

                      HHHHC....THTTSB--SHTTCCHHHTTSSTTEE-HHHHHHHHHHHHHT CS
  Beta-lactamase2  99 wlkel....glretrlrrklpdleaadkdkrntttardlarllealarg 143
                      ++ ++    g+r+tr+r+ + +l a     + ++ta d+a l ++++++
       AHX11601.1 132 MMTKKarsfGMRNTRFRN-CTGLHA----IDHVSTASDMAILARRVIND 175
                      775532233889998885.555554....899********999999875 PP

>> Peptidase_S13  D-Ala-D-Ala carboxypeptidase 3 (S13) family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.0   0.1   5.3e-06     0.032      18      61 ..      24      66 ..      14      91 .. 0.82
   2 !    4.5   0.2     0.002        12     274     348 ..      99     165 ..      95     180 .. 0.75

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 5.3e-06
                   EEEEEEEETTTTEEEEEESTTSEB--GGGHHHHHHHHHHHHT-T CS
  Peptidase_S13 18 vagvvvqdaetgkelydhqgdtpllPAStqKllTAaaAlltLga 61
                    +++   d +tg +l++ ++d+ l PAS  K++TA   +  L +
     AHX11601.1 24 TSAI-AIDQKTGGVLVKEKADEVLYPASLTKMMTAYIVFDHLKK 66
                   4555.568899************************999888865 PP

  == domain 2  score: 4.5 bits;  conditional E-value: 0.002
                    HHHHHHHHHHHT-HHHHHHHHHHHHHHHCS-BSHHHHHHHHHHHHHHTT--CTTSB-S-SSS-STT-BBEHHHHH CS
  Peptidase_S13 274 LsellkkmmkkSdNliAesllrevakeikrpgsfeagldavrerLskagidtanlvLeDgSGLSrknlvtaktla 348
                    L++ l +m+ kS N  A +l  +++      gs e+ ++ ++++  ++g+   n++ ++  GL   + v+ +  +
     AHX11601.1  99 LKDALLTMVMKSANDSATVLAEKIG------GSEENFAKMMTKKARSFGM--RNTRFRNCTGLHAIDHVSTASDM 165
                    89999********************......6666666666666666665..46667777777777777665544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (284 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2075.41
//
Query:       AHX11602.1  [L=660]
Description: transketolase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   1.7e-118  395.4   0.0   2.4e-118  394.9   0.0    1.1  1  Transketolase_N  Transketolase, thiamine diphosphate binding 
    3.8e-37  127.7   0.0    7.8e-37  126.7   0.0    1.4  1  Transket_pyr     Transketolase, pyrimidine binding domain
    1.5e-07   30.9   0.0    7.7e-05   22.0   0.0    2.6  2  DXP_synthase_N   1-deoxy-D-xylulose-5-phosphate synthase
    1.9e-06   27.0   0.0    5.2e-06   25.6   0.0    1.6  2  E1_dh            Dehydrogenase E1 component
     0.0013   18.6   0.1       0.01   15.7   0.0    2.4  2  Transketolase_C  Transketolase, C-terminal domain
     0.0014   18.4   0.1     0.0069   16.2   0.1    2.0  1  TPP_enzyme_C     Thiamine pyrophosphate enzyme, C-terminal TP
  ------ inclusion threshold ------
       0.14   12.0   0.0       0.32   10.9   0.0    1.5  1  SIS              SIS domain


Domain annotation for each model (and alignments):
>> Transketolase_N  Transketolase, thiamine diphosphate binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  394.9   0.0  9.3e-122  2.4e-118       4     323 ..       6     317 ..       3     326 .. 0.96

  Alignments for each domain:
  == domain 1  score: 394.9 bits;  conditional E-value: 9.3e-122
                      HHHHHHHHHHHHHHHHHT-S--HHHHHHHHHHHHHHHHT--B-TTBTT-TTS-EEEESSGGGHHHHHHHHHHTTS.S--HHHHTTTTSTT-SS- CS
  Transketolase_N   4 kavnaiRvLavDavekaksGhPGaplgladiaevlfkkllkhnPndpkwidRDRfvLsnGhaslllYsllhLtGy.dlsledlksfrqlgsktp 96 
                      ++  aiR+L++Dav++a+sGhPG+plg+ad+a+vlf+k+lk nP+dp+w dRDRf+Ls+Gh+s+llYsll+LtGy d++le++k+frql+sktp
       AHX11602.1   6 RMSAAIRILTIDAVSRANSGHPGMPLGMADVATVLFTKFLKFNPSDPDWPDRDRFILSAGHGSMLLYSLLYLTGYpDYTLEEIKNFRQLHSKTP 99 
                      67789***************************************************************************************** PP

                      SS--TTTSTT--S---STTHHHHHHHHHHHHHHHHHHHH-BTTB-S----EEEEEEHHHHHSHHHHHHHHHHHHTT-TTEEEEEEESSEETTEE CS
  Transketolase_N  97 GhPelghtagvevttGPLGqGianavglalaektlaatynkpgfdivdhytyvilgDgclmeGvsseasslagtlkLgkLivlyDdnkisidGe 190
                      GhPe+g ++g+e t+GPLGqG+   +g+alae+ l a++     ++vdh+ty+i+gDgclmeG+s+ea+s+ag++kL k+i l+DdnkisidG+
       AHX11602.1 100 GHPEYGVAKGIENTSGPLGQGLGIGIGMALAEAILSARFG---RELVDHHTYIIAGDGCLMEGISHEAASFAGHMKLRKVILLFDDNKISIDGS 190
                      **************************************97...68************************************************* PP

                      GGGT--S-HHHHHHHTT-EEEEETTTT-HHHHHHHHHHHHH-TTS-EEEEEE--TTTTSTTTTTSGGGTSS---HHHHHHHHHHTTS-TT-TS- CS
  Transketolase_N 191 teisftedvakrfeaygWhvievedgedveaikaaieeakaekdkPsliklrtviGygspakagtedvhGapLgedevaalkkklGfdpeksfe 284
                      t+  ++++ ++rfe+ygWh++e  dg+d  ai++aie+ak + dkPs+i+ rt+iG   p k+gte++h   L e e  + k+ l +  ++ f+
       AHX11602.1 191 TSLCTSDEHMRRFESYGWHTQE-IDGHDFLAIEKAIENAKLS-DKPSIIAARTIIGRFMP-KEGTEKTHSGGLSETERIEFKRILNYP-TEDFQ 280
                      *******************998.9*****************9.**************995.89**********************996.***** PP

                      --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHH CS
  Transketolase_N 285 vpeevydaykekvaegakaeeeWeekfaaykkkapeeaa 323
                      +pe+v +++++      +  ++W++ f+   ++ +ee +
       AHX11602.1 281 IPEDVLNKWRTLHS--IEEYQNWRQYFSGLPHEVAEEFN 317
                      *********99877..89999****99998887776654 PP

>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.7   0.0     3e-40   7.8e-37       4     175 ..     346     514 ..     344     515 .. 0.95

  Alignments for each domain:
  == domain 1  score: 126.7 bits;  conditional E-value: 3e-40
                   EHHHHHHHHHHHHHCTTTTEEEEESSTHHHHTTCHCCHHEGGT...TEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGGHHGGHHHHH CS
  Transket_pyr   4 awrkaeaealaellkedpevvligaDvaggtfsvrkgllhdqg...egrvidsgisEqavlgfavGaalagpllviveaqFgdFangAqiyadqair 97 
                   a+r+ ++  ++ l  + pe+++++ D++g+++ + +  +   +   +g++i +g++E+ +++ ++G+al+++  ++++++F+ F++    y ++air
    AHX11602.1 346 ATRQSSGRIIKFLTSRIPEMIGGSCDLTGSNNVTPEPFRAITKeryNGNYIYYGVREHFMAACMNGMALHKG-VIPYGGTFFIFSD----YLRPAIR 437
                   6899999************************9998877777777789************************6.*************....******* PP

                   CHHHHHT--EE.EEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEE CS
  Transket_pyr  98 sgeakgklkvg.vvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkPvvlrlpksll 175
                    ++a+++++v+ v+t+++igvgedGp+hq++e++ +l lip+l+ +rP+d  e+ ++++ a++   + P++++l+++++
    AHX11602.1 438 -MSALMGIQVIyVMTHDSIGVGEDGPTHQPIEHLDSLNLIPNLYLFRPCDYIEVLECWQNALKIT-NAPSMIVLSRQKI 514
                   .**************************************************************75.79********975 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.0   0.0     3e-08   7.7e-05      20     176 ..       6     188 ..       2     196 .. 0.72
   2 !    5.8   0.0    0.0026       6.8     243     271 ..     211     239 ..     191     241 .. 0.82

  Alignments for each domain:
  == domain 1  score: 22.0 bits;  conditional E-value: 3e-08
  DXP_synthase_N  20 elaeelrefliesvsk.tggHlasnLgvveLtlalhyvf...dt......pkDklvwDvgHqa...YvhKiltgRkd.kfktlrqkgGls....g 96 
                     ++++ +r  +i++vs+ ++gH +  Lg+ +++  l++ f   +       ++D+++   gH +   Y    ltg  d +++++++   l+    g
      AHX11602.1   6 RMSAAIRILTIDAVSRaNSGHPGMPLGMADVATVLFTKFlkfNPsdpdwpDRDRFILSAGHGSmllYSLLYLTGYPDyTLEEIKNFRQLHsktpG 100
                     57888999999999863789999999999999999887633332222222479999999998755577778899764234444444444311125 PP

  DXP_synthase_N  97 fpkrsEseyDafeagHsstsisaalGlavardlkge.......kkkvvaviGDgaltgGmafealnnigelk.kkllvilNdNemsis 176
                     +p+   ++    ++g  +  + ++ G+a a+ + +        ++++  + GDg l  G+++ea   +g++k +k+++++ dN+ si+
      AHX11602.1 101 HPEYGVAKGIENTSGPLGQGLGIGIGMALAEAILSArfgrelvDHHTYIIAGDGCLMEGISHEAASFAGHMKlRKVILLFDDNKISID 188
                     666555555566667777888889999999777665455566668888999*******************98467888899****997 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.0026
  DXP_synthase_N 243 GpidGhdleelikvleevkklkgpvllhv 271
                       idGhd+ +++k++e++k  ++p ++  
      AHX11602.1 211 QEIDGHDFLAIEKAIENAKLSDKPSIIAA 239
                     579*********************99865 PP

>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   0.0     2e-09   5.2e-06      91     208 ..     107     229 ..      77     241 .. 0.82
   2 ?   -2.4   0.0      0.72   1.8e+03     143     166 ..     435     458 ..     434     460 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 2e-09
                 BTT..BEEE-SSTTTHHHHHHHHHHHHH.......HHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--.EEEEEEEESEETTEEHHHH-S---GGG. CS
       E1_dh  91 ekesrilggngivgaqvplvaGialaak.......iegkkevailliGDgAanqGdvyealnlaalwklp.vifvveNNkygisTeaekasaskeladr 181
                 +k+  i +++g++g    ++ G+ala          e  ++ + ++ GDg   +G+ +ea+ +a  +kl  vi+    Nk+ i  +++  + s+e + r
  AHX11602.1 107 AKG--IENTSGPLGQGLGIGIGMALAEAilsarfgRELVDHHTYIIAGDGCLMEGISHEAASFAGHMKLRkVILLFDDNKISIDGSTSLCT-SDEHMRR 202
                 444..8889999999988888999999999999988889999***********************9999527***********98887765.5666677 PP

                 .TTTTS-EEEEETTSHHHHHHHHHHHH CS
       E1_dh 182 argvgipglrVdgnDplavyeAvkfAa 208
                    +g    ++dg D+la+ +A   A+
  AHX11602.1 203 FESYGWHTQEIDGHDFLAIEKAIENAK 229
                 99*****************99877665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.72
                 HHHHHHHTT--EEEEEEEESEETT CS
       E1_dh 143 alnlaalwklpvifvveNNkygis 166
                 a+ ++al++++vi+v     +g++
  AHX11602.1 435 AIRMSALMGIQVIYVMTHDSIGVG 458
                 678************988888765 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.0   0.0       2.5   6.3e+03      60      84 ..     144     168 ..     124     174 .. 0.74
   2 !   15.7   0.0     4e-06      0.01       7      52 ..     538     583 ..     532     646 .. 0.78

  Alignments for each domain:
  == domain 1  score: -3.0 bits;  conditional E-value: 2.5
                      HHSEEEEEEEEESTTSHHHHHHHHH CS
  Transketolase_C  60 ktgrlvvveeavkrgGigsevaaal 84 
                       ++ +++  +++ + Gi+ e a++ 
       AHX11602.1 144 DHHTYIIAGDGCLMEGISHEAASFA 168
                      3888888888888888888888775 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 4e-06
                      ETTSSEEEEEETTHHHHHHHHHHHHHTTTTCEEEEE-SEEESHHHH CS
  Transketolase_C   7 regkdvtlvayGsmveealeAaeeLekegisaeVvdlrtvkplDke 52 
                      ++  ++ l+a Gs+v  + eA   Le+ g+ + +++++++  l k+
       AHX11602.1 538 SKSARISLIASGSEVAICAEAQRILEELGYPTALISVPCMALLKKN 583
                      567889*********************************9998775 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.1   2.7e-06    0.0069      24      90 ..     111     189 ..      99     239 .. 0.66

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2.7e-06
                   ETTTS-TTTHHHHHHHHHHH.........ST..TSEEEEEEEHHHHHHT.GGGHHHHHHT.T-SEEEEEEE-SBCCCHHH CS
  TPP_enzyme_C  24 sgglgtmGyglpaAiGakla.........kp..drevvaivGDGgflmi.lqelatavrr.nlpitvvvlnNegygmtgg 90 
                   +++ g +G gl+++iG++la         ++  d++ + i+GDG+++    +e a ++ + +l  ++++++++    + g
    AHX11602.1 111 ENTSGPLGQGLGIGIGMALAeailsarfgRElvDHHTYIIAGDGCLMEGiSHEAASFAGHmKLRKVILLFDDNKIS-IDG 189
                   567899*************4445566776334589************99667777766662667788888877663.333 PP

>> SIS  SIS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00012      0.32       4      37 ..     539     572 ..     537     575 .. 0.91

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00012
                 TSSEEEEEESHHHHHHHHHHHHHHHHHHTSEEEE CS
         SIS   4 kakriyvlGaGtsyaiakelalkleeiggivvev 37 
                 k+ ri ++++G+  ai++e+++ lee+g++++ +
  AHX11602.1 539 KSARISLIASGSEVAICAEAQRILEELGYPTALI 572
                 678**************************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (660 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.63u 0.29s 00:00:00.92 Elapsed: 00:00:00.45
# Mc/sec: 4377.06
//
Query:       AHX11603.1  [L=457]
Description: NADH-Ubiquinone/plastoquinone (complex I), various chains family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.9e-47  160.9  29.5    3.9e-47  160.9  29.5    2.8  2  Proton_antipo_M  Proton-conducting membrane transporter
    1.8e-07   30.8   5.8    5.9e-07   29.1   5.8    2.0  1  NADHdeh_related  NADH dehydrogenase I, subunit N related prot
  ------ inclusion threshold ------
      0.064   13.3   0.0      0.064   13.3   0.0    2.9  2  Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), 


Domain annotation for each model (and alignments):
>> Proton_antipo_M  Proton-conducting membrane transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   1.9      0.15   8.8e+02     131     163 ..      12      44 ..       3      96 .. 0.73
   2 !  160.9  29.5   6.6e-51   3.9e-47       1     292 [.     122     408 ..     122     409 .. 0.93

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.15
  Proton_antipo_M 131 llirllllla.vssneisqlllilaiismllgsl 163
                      + +++  l+  +s+n+i++l+l+l + s  + s 
       AHX11603.1  12 IPMMV-ALFLvFSNNKIYKLVLLLTAQSFGIISA 44 
                      22333.3333477888888888887776544444 PP

  == domain 2  score: 160.9 bits;  conditional E-value: 6.6e-51
  Proton_antipo_M   1 andLlllylglElvllplylLiglwkkkpksleAslklflltllgsliLLlgilllynltgtlefeelskalelglnslelllllllllvgllv 94 
                      +ndL+ +y++lEl +l++y Li+ + ++ +s++A++ +++++ ++  + L+g+ lly+ tg+l++++++ a el ++s    +++ll ++gl +
       AHX11603.1 122 SNDLFNIYVFLELSSLATYALIATKHTH-SSYKAAFEYLVIGTIAATFYLIGVGLLYATTGNLNITAIAAAPELLFSSRIGRAGILLTILGLSA 214
                      79*********************99777.******************************************999999999999999******** PP

  Proton_antipo_M  95 KsaqvplhlWlpdayveaPtpvsallAatlvkagvlllirllllla......vssneisqlllilaiismllgslvalaqtdiKrllAySsish 182
                      K a +plh+Wl+  y + +t v ++l++t +k+g++ll++++  ++      +    + +++li +++++++ ++ a+   +iK+ l ySs+s+
       AHX11603.1 215 KCAIFPLHFWLVRCYSATSTTVATFLSGTSSKVGLYLLAKFIYTIFgervfiFPVVGLDKIILISSALAIIFCGIQAILSKEIKQALSYSSVSQ 308
                      *****************************************9988866553334455789********************************** PP

  Proton_antipo_M 183 lGymlialavatqygveaaiihllthalfkallFllagsviyerektrdirayggLakkmPilalvllvlllslaGlPptagFlskfliLeaav 276
                      +Gy+++ l+++++y++  a++++++ha+ k++lF+l+g+v +e++k +++ +              ll+ +lslaG+P tagFl+k+ +L+ ++
       AHX11603.1 309 IGYIILTLSLDSVYSIPIAMLQMFAHAFAKSALFILSGGVQSEKNKKHSFVQ-----------DCYLLISTLSLAGIPITAGFLGKVQLLMLVI 391
                      ****************************************777777666655...........5667899************************ PP

  Proton_antipo_M 277 avslillvla.vvasvl 292
                      + ++++ +++ +++s++
       AHX11603.1 392 QTGHYVTLATlIIGSII 408
                      *****999886777766 PP

>> NADHdeh_related  NADH dehydrogenase I, subunit N related protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   5.8     1e-10   5.9e-07      70     159 ..     104     193 ..      70     232 .. 0.84

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 1e-10
  NADHdeh_related  70 irrllaivcglatlgavvtgdvfnftlflaliGianiGivaavkkefvleaafnyGlvaliatlplfggaalilastGtlsifelaklag 159
                      +   + i+c     g +++ d+fn  +fl l  +a   ++a+ + +   +aaf+y ++  ia+++ + g +l+ a+tG l i  +a+   
       AHX11603.1 104 FFYSILILCHTGLSGMIISNDLFNIYVFLELSSLATYALIATKHTHSSYKAAFEYLVIGTIAATFYLIGVGLLYATTGNLNITAIAAAPE 193
                      44556789999999********************************************************************99887754 PP

>> Proton_antipo_N  NADH-Ubiquinone oxidoreductase (complex I), chain 5 N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -4.5   1.3         3   1.8e+04      25      39 ..       5      19 ..       4      19 .. 0.76
   2 ?   13.3   0.0   1.1e-05     0.064      14      41 ..      70      97 ..      61     109 .. 0.89

  Alignments for each domain:
  == domain 1  score: -4.5 bits;  conditional E-value: 3
  Proton_antipo_N 25 mllvvtfvsllvhlY 39
                      l+++ ++ ++v l+
       AHX11603.1  5 LLALIVIIPMMVALF 19
                     577888888898876 PP

  == domain 2  score: 13.3 bits;  conditional E-value: 1.1e-05
  Proton_antipo_N 14 igfllDklsalmllvvtfvsllvhlYSi 41
                     i++  Dk++almll++ ++sl   l S+
       AHX11603.1 70 IQITADKYTALMLLLINVISLTATLHSF 97
                     67899****************9999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (457 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       864  (0.0481901); expected 358.6 (0.02)
Passed bias filter:                      259  (0.0144459); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.53u 0.24s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3244.20
//
Query:       AHX11604.1  [L=611]
Description: tRNA uridine 5-carboxymethylaminomethyl modification enzyme GidA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   2.3e-153  510.9   0.6   3.4e-153  510.4   0.6    1.2  1  GIDA           Glucose inhibited division protein A
    1.7e-69  234.2   1.3    2.6e-69  233.6   0.3    1.7  2  GIDA_assoc     GidA associated domain
    6.5e-09   35.6   0.9      1e-08   35.0   0.9    1.3  1  FAD_oxidored   FAD dependent oxidoreductase
    2.1e-08   33.7   0.8    6.9e-08   32.1   1.1    1.6  2  Pyr_redox_2    Pyridine nucleotide-disulphide oxidoreductase
    4.1e-05   23.0   2.1     0.0068   15.7   1.4    2.3  2  AlaDh_PNT_C    Alanine dehydrogenase/PNT, C-terminal domain
    0.00044   19.6   0.7       0.13   11.5   0.5    2.5  2  Pyr_redox_3    Pyridine nucleotide-disulphide oxidoreductase
    0.00072   18.4   3.9      0.062   12.0   1.5    3.1  3  HI0933_like    HI0933-like protein
     0.0028   17.3   3.5        0.2   11.2   0.0    2.3  2  DAO            FAD dependent oxidoreductase
     0.0073   16.8   0.9      0.018   15.6   0.9    1.7  1  Pyr_redox      Pyridine nucleotide-disulphide oxidoreductase
     0.0087   15.2   4.2     0.0087   15.2   4.2    2.4  3  FAD_binding_2  FAD binding domain
  ------ inclusion threshold ------
      0.026   14.5   0.0      0.026   14.5   0.0    1.9  2  NAD_binding_9  FAD-NAD(P)-binding
       0.61    9.1   3.3        2.1    7.3   1.2    2.1  2  Lycopene_cycl  Lycopene cyclase protein


Domain annotation for each model (and alignments):
>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  510.4   0.6  2.3e-156  3.4e-153       1     387 [.       5     388 ..       5     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 510.4 bits;  conditional E-value: 2.3e-156
                 CEEEE-SSHHHHHHHHHHHHTT--EEEEES-GGGTT--SSSSEEE-TTHHHHHHHHHHHT-SHHHHHHHHEEEEEEESTTS-CCC-EEEEEE-HHHHHH CS
        GIDA   1 dviViGgGhAGceAAlaaarlGakvlLithkldtiaelsCnpsiggiakgllvrEidalggliikaadkagiqfrilNrskGpavralraqvdrelysk 99 
                 dv+ViGgGhAG+eAA+aa+r Ga  +L+t+++d+i+e+sCnp+iggi+kg++vrE+da+gg+++ a+d ++i+ r+lNrskG av+++raq+dr+ly++
  AHX11604.1   5 DVVVIGGGHAGVEAAAAASRVGATAALVTNSTDNIGEMSCNPAIGGIGKGTVVREVDAMGGIMGLAIDMSSIHSRMLNRSKGAAVWGPRAQADRKLYKR 103
                 79************************************************************************************************* PP

                 HHHHHHHTSTTEEEEES-EEEEEECTTEEEEEEETTS-EEEECEEEE--TT-BT-EEEETTEEEESSCTTC--B-THHHHHHHTT--EEEEEEEE--EE CS
        GIDA 100 evteklenepnleiieeeveeliveekkvkgvvtedgetikakavviatGtflkgkihigekelsaGrlgeltseglseslkelgfellrlktgtppri 198
                 +v   l++++nl+iie+ v +l+++++ v++v+te++ ti++ avv+atGtfl+g i+ig++++++Gr ge++s+gl ++++   f++ rlktgtp+ri
  AHX11604.1 104 AVFSLLKESKNLTIIEDHVIDLMIKDGCVSAVCTERNGTIECAAVVLATGTFLNGVIQIGKERIESGRFGEKASQGLGATIR-NFFRVSRLKTGTPARI 201
                 **********************************************************************************.7799************ PP

                 EGGGS-TTTSEEE---SS-B-SSSSSSSTCG----EEEEE--HHHHHHHHCTCCC-T.T----B--S-CCC-SSTCCCCCCSTT-S--EEEEEESSTT- CS
        GIDA 199 dkesidfskleeqsgdkegeefsylnkplnkeqvecfltatneathkiikenlkksaklfegcieelgprycpsiedkivrladkeshqvfLepeglet 297
                  ++s+++s l+eq gd+++ +fsy+++ ++ +q++c++++tn++thkii + l+ sa   +  i + gprycpsiedk+vr+a+k+shq+f+epegl++
  AHX11604.1 202 YRDSVNYSALTEQVGDTPPVPFSYMSTAITVPQISCYIAHTNQRTHKIITDSLQFSA--TRNGISSRGPRYCPSIEDKVVRFAEKSSHQIFIEPEGLDS 298
                 ******************************************************988..444579********************************** PP

                 -EEEEET----S-HHHHHHHHTTSTT-TT--EEE--EEEEEEEE-GGGB-TTSBBSSSBTEEE-CGGGTB-SHHHHHHHHHHHHHHHHHH CS
        GIDA 298 eliylvgfstslpeevqkevlrsipGLenaeivrpGyaieydyvdprqllntLetkkvkgLflAGqinGteGYeEaaaqGllAGinaark 387
                 +l+y++g+s+slp e+q++++rsi+GLena+i+r++yaieydyvdpr+l++tLetk++k+L+lAGqinGt+GYeEaa+qG++AG naa +
  AHX11604.1 299 DLVYPNGISNSLPREIQEAFIRSIEGLENAKIARYAYAIEYDYVDPRELKSTLETKRIKNLYLAGQINGTTGYEEAAGQGIVAGSNAAGS 388
                 ***************************************************************************************975 PP

>> GIDA_assoc  GidA associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0       2.1   3.1e+03     153     201 ..     319     368 ..     311     371 .. 0.60
   2 !  233.6   0.3   1.7e-72   2.6e-69       1     209 [.     390     601 ..     390     602 .. 0.97

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 2.1
                 CHHHHHHHTSB--T...TS-CCCSTT--CHHHHHHHHH--SCHHHHTTSTTS CS
  GIDA_assoc 153 ieklkkeenlkipe...dldYskikgLskearekLkkvrPetlgqAsrisGv 201
                 i++++ +en ki +    ++Y+ ++   +e ++ L++ r ++l+ A +i+G 
  AHX11604.1 319 IRSIEGLENAKIARyayAIEYDYVD--PRELKSTLETKRIKNLYLAGQINGT 368
                 5555556666664311133344332..5777888888888888888888886 PP

  == domain 2  score: 233.6 bits;  conditional E-value: 1.7e-72
                 ----TTT-HHHHHHHHHHHH--S.S-B-CCCB--TTTCCC-CCCHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHH...HH CS
  GIDA_assoc   1 lilkRseaYiGVLiDDLvtkgvk.EPYRmfTSRaEyRlllRaDnAdlRLtekgrelGlvseeryekfeekkeeieelkellkstklkseewkkl..lek 96 
                 l+++R+e+YiGV+iDDL t g++ EPYR+fTSRaEyRl lR+DnAd+RLtek++++Glv+ ery+++++k e ++e ke+lk++ +++ + ++   +++
  AHX11604.1 390 LVINRAEGYIGVMIDDLSTLGTNdEPYRLFTSRAEYRLNLRSDNADFRLTEKAYRAGLVNAERYATYKKKYEILAEYKERLKQLIITPYTLNNFgiSIS 488
                 689******************9659*************************************************************9999999888999 PP

                 HT....EHHHHCTTST--HHHHHCCHHHHHHHSCHHHHHHHHHHHCHHHHHHHHHHCHHHHHHHTSB--TTS-CCCSTT--CHHHHHHHHH--SCHHHH CS
  GIDA_assoc  97 keskklslaellkrpevkledlleelpeeeeeseeeleqveieakYegyiekqeeeieklkkeenlkipedldYskikgLskearekLkkvrPetlgqA 195
                 +++ k+s+++l+++p++++e+l++ +pe +e s+e ++ +e++akYe+y+++q+++i+ lk +e+++ip+++d+s++k+Ls+e+ ekL++v+Petl+q 
  AHX11604.1 489 QDGVKKSAWDLIAYPSITFEHLVRVWPELSEISSEYIQMIETDAKYEPYLSRQDQDIKILKDDEEIEIPSHFDFSEVKTLSSEVLEKLSAVKPETLAQT 587
                 999999***********************9999999*************************************************************** PP

                 TTSTTS-HHHHHHH CS
  GIDA_assoc 196 srisGvtpaaisvL 209
                 +ri+G+tpaa+  +
  AHX11604.1 588 KRIPGITPAAVISI 601
                 **********9765 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.0   0.9   6.9e-12     1e-08       1     181 [.       5     193 ..       5     259 .. 0.70

  Alignments for each domain:
  == domain 1  score: 35.0 bits;  conditional E-value: 6.9e-12
  FAD_oxidored   1 DvvVvGGgpaGvaAAiaAaraGakvlLve.ergvlGGlltsglvatdig.nkaee.qvvtgiareflerlrqrgga..rlkkrskw...ntfepeva 89 
                   DvvV+GGg aGv AA aA r Ga+ +Lv   ++ +G ++ + + + + + +  +e  + +gi++  ++    +     r k ++ w   +  + + +
    AHX11604.1   5 DVVVIGGGHAGVEAAAAASRVGATAALVTnSTDNIGEMSCNPAIGGIGKgTVVREvDAMGGIMGLAIDMSSIHSRMlnRSKGAAVWgprAQADRKLY 101
                   9************************9998467788888877666555441333337778888777666553322222222233334434389***** PP

  FAD_oxidored  90 kavleemlae.agvtvllntrlvevekegkriesvtveskegrktirAkvfiDATgdGdlaalaGvpyrvGresreetgep..aagtlmfrlegv 181
                   k+++  +l+e +++t++ +++++ ++k+g  + +v++e ++g+++ +A v   +T    ++      ++ Gr +++   +   a  + +fr++ +
    AHX11604.1 102 KRAVFSLLKEsKNLTIIEDHVIDLMIKDG-CVSAVCTE-RNGTIECAAVVLATGTFLNGVIQIGKERIESGRFGEK-ASQGlgATIRNFFRVSRL 193
                   ********55499***9999999999997.89999996.4567777776666666666666666666666666666.444434444446666666 PP

>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.1   1.1   4.6e-11   6.9e-08       1     109 [.       4     154 ..       4     180 .. 0.80
   2 ?   -2.9   0.0       2.1   3.1e+03     261     285 ..     348     372 ..     343     378 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.1 bits;  conditional E-value: 4.6e-11
                  CSEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHHHCHHHHHHHHHHHHH......................................... CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......................................... RF
  Pyr_redox_2   1 kdvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcllskallgvaedaeias......................................... 57 
                  +dvvviGgG+AG++aa  +++ ga  +lv  + t   g ++  +a+ g+++ + +++                                         
   AHX11604.1   4 YDVVVIGGGHAGVEAAAAASRVGATAALV-TNSTDNIGEMSCNPAIGGIGKGTVVREvdamggimglaidmssihsrmlnrskgaavwgpraqadrkl 100
                  69***************************.777777777888888888888887777889999999*******************9999998888777 PP

                  .........HHHHCHHHHCCCCHCCTCEEEEESCEEEEETEEECTCEEEEEESEEEE---E CS
                  .........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  58 .........evvkklnqgielllgeevvkidpgkkkvklekkkegdeekiaydklvlAtGs 109
                           +     +++++ + + +v+++  + ++v    ++   + +i++ ++vlAtG 
   AHX11604.1 101 ykravfsllK----ESKNLTIIED-HVIDLMIKDGCVSAVCTE--RNGTIECAAVVLATGT 154
                  7765543221....2334454444.788888777888875554..5569***********4 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.1
                  -TTSBES.STTEEE-GGGCTECCSS- CS
                  xxxxxxx.xxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2 261 deflrtn.vpgiyaiGDvaggkggpe 285
                  +++l+t+ ++++y++G +  g++g+e
   AHX11604.1 348 KSTLETKrIKNLYLAGQIN-GTTGYE 372
                  678999889*******987.444444 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   1.4   4.6e-06    0.0068      30      56 ..       5      31 ..       1      44 [. 0.85
   2 !    5.5   0.0    0.0061       9.1     108     183 ..     116     190 ..     108     214 .. 0.82

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 4.6e-06
                 EEEEESTSHHHHHHHHHHHHTT-EEEE CS
  AlaDh_PNT_C 30 kvlviGgGvaGlqAiatakglgakVtv 56
                  v+viGgG aG++A+a+a+++ga+  +
   AHX11604.1  5 DVVVIGGGHAGVEAAAAASRVGATAAL 31
                 69********************98665 PP

  == domain 2  score: 5.5 bits;  conditional E-value: 0.0061
                  -SC-HHHHHTS-TTEEEEETTGGGT-SBTT--TBBTTSEEEEETTEEEEEBSTGG.GGSHHHHHHHHHHHHHHHHHH CS
  AlaDh_PNT_C 108 kLvteemvksMkpgsVivDvAidqGGnvetsrltthgepvveekgvvhygvanlp.gavprtasalltnntlpylee 183
                  +++++++++ M +   +  v +++ G++e ++    +  ++  +gv+++g + ++ g+  ++as+ l  ++ ++ + 
   AHX11604.1 116 TIIEDHVIDLMIKDGCVSAVCTERNGTIE-CAAVVLATGTFL-NGVIQIGKERIEsGRFGEKASQGLGATIRNFFRV 190
                  689999999**9999999***********.656666666666.8**********74699********9999999765 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.5   8.9e-05      0.13     166     197 ..       5      36 ..       1      47 [. 0.72
   2 !    5.6   0.0    0.0054       8.1      91     135 ..     110     155 ..      89     162 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 8.9e-05
  Pyr_redox_3 166 kvvViGgknSavDaAlelvrkgaeVtvvtrgs 197
                  +vvViGg+  +v+aA    r ga+  +vt+++
   AHX11604.1   5 DVVVIGGGHAGVEAAAAASRVGATAALVTNST 36 
                  67888888888888888888887777777654 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0054
  Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGef 135
                   +s++l i +++ +  + k++    v t+++ t+e+  v++AtG f
   AHX11604.1 110 KESKNLTIIEDHVIDLMIKDGCVSAVCTERNgTIECAAVVLATGTF 155
                  57899999999999999898888888887755************99 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.0   1.5   4.1e-05     0.062       1      31 [.       4      34 ..       4      43 .. 0.85
   2 ?    2.7   0.0     0.027        40     129     164 ..     119     154 ..     103     163 .. 0.75
   3 ?    1.6   0.0     0.058        87     367     384 ..     348     365 ..     342     376 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 4.1e-05
                 -SEEEE--SHHHHHHHHHHHHTT--EEEE-S CS
  HI0933_like  1 kdviviGgGaAGlmaAisaakrgkrVlllek 31
                 +dv+viGgG AG+ aA++a++ g+  +l+ +
   AHX11604.1  4 YDVVVIGGGHAGVEAAAAASRVGATAALVTN 34
                 59*******************9999888755 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.027
                  S--EEEEECETTE.EEEEE.TTEEEEESEEEE---- CS
  HI0933_like 129 etevksvekeedgkfrvktkseeeleadklvlAtGG 164
                  e +v ++  +++ +  v t+ ++++e++++vlAtG 
   AHX11604.1 119 EDHVIDLMIKDGCVSAVCTERNGTIECAAVVLATGT 154
                  344445556666667888899*************95 PP

  == domain 3  score: 1.6 bits;  conditional E-value: 0.058
                  TTT-BBTTSTTEEE-GGG CS
  HI0933_like 367 sktmeskkvpgLffaGEv 384
                  ++t+e+k++++L++aG +
   AHX11604.1 348 KSTLETKRIKNLYLAGQI 365
                  469*************76 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.6   1.6    0.0067        10       1      25 [.       5      31 ..       5      43 .. 0.83
   2 !   11.2   0.0   0.00013       0.2     131     206 ..      84     159 ..      68     186 .. 0.77

  Alignments for each domain:
  == domain 1  score: 5.6 bits;  conditional E-value: 0.0067
                EEEEECTSHHHHHHHHHHHHTT..EEE CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtl 25
                dvv+iGGG +G+ +A +++r g   +l
  AHX11604.1  5 DVVVIGGGHAGVEAAAAASRVGatAAL 31
                9***************99887776433 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00013
                 TSEE.EEETTEEEEEHHHHHHHHHHHH.HHTT-EEEESECEEEEEEEETCEEEEEEECT.EEEEEEEEEEE--GGGHH.H CS
         DAO 131 llga.lfypdtgqvdpakltaalaraa.ealGveilegtevtgleeedgkvwgverttp.gendaadavVnaaGawsd.l 206
                  +ga ++ p  +q+d   + +a+ + + e++  +i+e   v +l  +dg v+ v  t++ g++ ++ avV+a+G + +  
  AHX11604.1  84 SKGAaVWGPR-AQADRKLYKRAVFSLLkESKNLTIIED-HVIDLMIKDGCVSAVC-TERnGTI-ECAAVVLATGTFLNgV 159
                 4544277777.9999999999999998355569****9.999*9999*******4.4444664.4588******996643 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.9   1.2e-05     0.018       2      31 ..       6      35 ..       5      50 .. 0.87

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.2e-05
                EEEECSSHHHHHHHHHHHHTTSEEEEEESS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvvers 31
                vvv+GgG  g+E+A+a+++ g+   +v +s
  AHX11604.1  6 VVVIGGGHAGVEAAAAASRVGATAALVTNS 35
                8********************998888776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   4.2   5.8e-06    0.0087       1      32 [.       5      36 ..       5      50 .. 0.92
   2 ?    3.2   0.0     0.026        39     156     210 ..     115     166 ..      81     186 .. 0.65
   3 ?   -3.3   0.1       2.5   3.7e+03     390     416 ..     354     378 ..     351     379 .. 0.84

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 5.8e-06
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSS CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeq 32
                   Dv+ViG+G AG  AA++a++ G++ a+v++  
     AHX11604.1  5 DVVVIGGGHAGVEAAAAASRVGATAALVTNST 36
                   9*************************999865 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.026
                    EEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE-----GG......... CS
  FAD_binding_2 156 vdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgGfgr...allkel 210
                    +++ e + +d L+++ ++++ av++ +++g+   i+  avvlatg f +   +  ke+
     AHX11604.1 115 LTIIEDHVID-LMIK-DGCVSAVCT-ERNGT---IECAAVVLATGTFLNgviQIGKER 166
                    6666666555.5553.566666666.25555...44589*******987555444444 PP

  == domain 3  score: -3.3 bits;  conditional E-value: 2.5
                    ESSBTEEE-STCEESSSSTTS--TTHH CS
  FAD_binding_2 390 qpipGLYAaGevaaggvhganrlgGns 416
                    + i++LY aG     g  g+++ +G +
     AHX11604.1 354 KRIKNLYLAGQIN--GTTGYEEAAGQG 378
                    689*******998..899999988876 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   1.5       3.8   5.7e+03       1      15 [.       7      21 ..       7      28 .. 0.85
   2 ?   14.5   0.0   1.7e-05     0.026     106     155 ..     103     154 ..      85     155 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 3.8
  NAD_binding_9  1 aivGaGprGlavler 15
                   +++G+G +G+ ++++
     AHX11604.1  7 VVIGGGHAGVEAAAA 21
                   69*******988865 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 1.7e-05
  NAD_binding_9 106 ellarl.pegvtvevhraevvdleeradgq.avlladgaslaadaVvLAlGh 155
                    +++ +l +e+ ++++++++v+dl  +++ + av+++++ ++++ aVvLA+G 
     AHX11604.1 103 RAVFSLlKESKNLTIIEDHVIDLMIKDGCVsAVCTERNGTIECAAVVLATGT 154
                    3333333667789***********99999879*******************7 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.3   1.2    0.0014       2.1       1      32 [.       5      34 ..       5      41 .. 0.81
   2 ?    1.4   0.0      0.09   1.4e+02     106     142 ..     119     155 ..      94     167 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.3 bits;  conditional E-value: 0.0014
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvliea 32
                   DvvviG+G Ag+  Aa    ++ g    l+  
     AHX11604.1  5 DVVVIGGGHAGVEAAAAA--SRVGATAALVTN 34
                   9************99988..777777776655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.09
  Lycopene_cycl 106 eakvesveeeeageslvvleggrkirarlvvdargla 142
                    e  v   + ++   s v++e + +i++ +vv a+g +
     AHX11604.1 119 EDHVIDLMIKDGCVSAVCTERNGTIECAAVVLATGTF 155
                    55666666666667788888899***********965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (611 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      483  (0.0269396); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.46
# Mc/sec: 4023.57
//
Query:       AHX11605.1  [L=174]
Description: hypothetical protein NHE_0672 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (174 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       283  (0.0157845); expected 358.6 (0.02)
Passed bias filter:                      248  (0.0138323); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.39
# Mc/sec: 1337.08
//
Query:       AHX11606.1  [L=114]
Description: hypothetical protein NHE_0673 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0016   18.3   1.1      0.015   15.1   0.4    2.3  2  Matrilin_ccoil   Trimeric coiled-coil oligomerisation domain 
     0.0049   17.3   0.3     0.0078   16.7   0.3    1.4  1  DUF16            Protein of unknown function DUF16
     0.0076   15.2   2.5     0.0088   15.0   2.5    1.1  1  Spc7             Spc7 kinetochore protein
  ------ inclusion threshold ------
      0.011   15.5   0.2      0.013   15.2   0.2    1.1  1  Leptin           Leptin
      0.022   14.4   2.0       0.81    9.4   0.4    2.2  2  Nbl1_Borealin_N  Nbl1 / Borealin N terminal
      0.034   13.9   0.8        7.2    6.4   0.1    2.2  2  Viral_P18        ssRNA positive strand viral 18kD cysteine ri
      0.039   14.5   2.2       0.73   10.4   0.6    2.1  2  MerR-DNA-bind    MerR, DNA binding
      0.041   12.5   1.7        1.7    7.2   0.1    2.0  2  DUF4455          Domain of unknown function (DUF4455)
      0.071   13.1   1.2       0.58   10.2   0.2    2.0  2  DUF1664          Protein of unknown function (DUF1664)
      0.071   13.6   0.8       0.82   10.2   0.8    2.2  1  NPV_P10          Nucleopolyhedrovirus P10 protein
      0.078   12.7   2.3       0.39   10.4   0.2    2.0  2  LXG              LXG domain of WXG superfamily
      0.085   11.5   2.7       0.28    9.8   2.7    1.7  1  FapA             Flagellar Assembly Protein A
       0.13   12.7   1.2         16    6.0   0.1    2.3  2  FlaC_arch        Flagella accessory protein C (FlaC)
       0.19   11.9   0.1       0.19   11.9   0.1    1.9  2  GBR2_CC          Gamma-aminobutyric acid type B receptor subu
        0.2   10.9   0.6       0.24   10.6   0.6    1.0  1  TMPIT            TMPIT-like protein
       0.46   10.7   3.4        8.2    6.7   0.2    2.6  2  XhlA             Haemolysin XhlA


Domain annotation for each model (and alignments):
>> Matrilin_ccoil  Trimeric coiled-coil oligomerisation domain of matrilin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.32   3.6e+02      19      30 ..      26      37 ..      23      45 .. 0.82
   2 !   15.1   0.4   1.3e-05     0.015      16      39 ..      77     100 ..      76     102 .. 0.94

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.32
                    HHHHHHHHHHHH CS
  Matrilin_ccoil 19 kVeseiqaLtqk 30
                    +V+++i+++t++
      AHX11606.1 26 SVQEQIKKFTEN 37
                    699******985 PP

  == domain 2  score: 15.1 bits;  conditional E-value: 1.3e-05
                     HHHHHHHHHHHHHHHHHHHHHHHH CS
  Matrilin_ccoil  16 FQtkVeseiqaLtqkLeavtkRle 39 
                     F+t+V++++++L ++L+ + kRl 
      AHX11606.1  77 FKTEVQESLKRLRARLAKMDKRLD 100
                     9*********************96 PP

>> DUF16  Protein of unknown function DUF16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.7   0.3     7e-06    0.0078      39     102 ..      20     102 ..       3     104 .. 0.76

  Alignments for each domain:
  == domain 1  score: 16.7 bits;  conditional E-value: 7e-06
                 HHHHHH...HHHHHHHHHHHHHHHHH...HHHHHHHHHHHH.......................HHHHHHHHHHHHHHHHHHH CS
       DUF16  39 ieakvdklgeqinkleqkvekqgeki...kelkveqkaqgeeln................kvdetleliletLqkinkRlDsi 102
                 +e+ +++ +eqi+k +++ e +++ +   ++l+ e  +  e+l                 +v+e+l+ +   L+k++kRlD+i
  AHX11606.1  20 SEEYMASVQEQIKKFTENPEMLQKALgpfMKLQSEYMKDPEKLGslmsgleggteesfktEVQESLKRLRARLAKMDKRLDEI 102
                 4666677788888888887777766422267777777777766689999999999999999********************98 PP

>> Spc7  Spc7 kinetochore protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   2.5   7.9e-06    0.0088     138     228 ..      21     112 ..      15     114 .] 0.84

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 7.9e-06
        Spc7 138 egLkegleenlegleedkelLekqeeeldellpeleeekaeleeeleklqe.aaeelesidkeeLeelreelaelkaeieekkkelaelqeq 228
                 e+ + +++e++++++e  e+L+k    +++l  e+ +  ++l + +  l+   +e++++  +e+L+ lr +la+ ++ ++e ++ l++l ++
  AHX11606.1  21 EEYMASVQEQIKKFTENPEMLQKALGPFMKLQSEYMKDPEKLGSLMSGLEGgTEESFKTEVQESLKRLRARLAKMDKRLDEIMALLSDLSSK 112
                 5667788999999999999999999999999999999999999999988884444555566**************************99887 PP

>> Leptin  Leptin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.2   1.2e-05     0.013      72     142 ..      28     102 ..       7     105 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.2e-05
                 HHHHHHHHHHHHHHHHHHHHHTT---------S-GGGGHHHH....-BTTB-HHHHHHHHHHHHHHHHHHHGGG- CS
      Leptin  72 vvqisnDlenLrallkllatsksCelekaseletleslekvl....easlystevvaLeRlqksLlellkqLdli 142
                   qi +  en  +l k l+  +  + e  +++e+l sl + l    e+s  +  + +L+Rl+  L ++ k+Ld+i
  AHX11606.1  28 QEQIKKFTENPEMLQKALGPFMKLQSEYMKDPEKLGSLMSGLeggtEESFKTEVQESLKRLRARLAKMDKRLDEI 102
                 46899999999*********9999999999999998876544111056655555679****************87 PP

>> Nbl1_Borealin_N  Nbl1 / Borealin N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   0.1     0.024        27       8      30 ..      13      44 ..      12      56 .. 0.86
   2 ?    9.4   0.4   0.00072      0.81       8      32 ..      76     100 ..      75     106 .. 0.83

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.024
  Nbl1_Borealin_N  8 nfdlE.........veeRirrlraelelllkt 30
                     ++dlE         v+e+i+++ ++ e+l k 
       AHX11606.1 13 DLDLEslseeymasVQEQIKKFTENPEMLQKA 44
                     78999999999999********9999998776 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00072
  Nbl1_Borealin_N   8 nfdlEveeRirrlraelelllktlr 32 
                       f +Ev+e  +rlra l+++ k l+
       AHX11606.1  76 SFKTEVQESLKRLRARLAKMDKRLD 100
                      6999************998866665 PP

>> Viral_P18  ssRNA positive strand viral 18kD cysteine rich protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.1    0.0065       7.2      79     114 ..       9      43 ..       2      54 .. 0.81
   2 ?    6.4   0.1    0.0064       7.2      91     115 ..      85     109 ..      59     113 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0065
   Viral_P18  79 ddelkldrlearresllasiqkklkaydekiallae 114
                 d +l+ld le   e  +as+q+++k++ e + +l +
  AHX11606.1   9 DSDLDLD-LESLSEEYMASVQEQIKKFTENPEMLQK 43 
                 5566665.89999****************9999976 PP

  == domain 2  score: 6.4 bits;  conditional E-value: 0.0064
   Viral_P18  91 resllasiqkklkaydekiallaek 115
                  + l+a++ k  k+ de +all++ 
  AHX11606.1  85 LKRLRARLAKMDKRLDEIMALLSDL 109
                 3469999999999********9975 PP

>> MerR-DNA-bind  MerR, DNA binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.7   0.0     0.081        91      36      63 ..      15      42 ..       3      44 .. 0.82
   2 ?   10.4   0.6   0.00065      0.73      34      63 ..      81     110 ..      74     111 .. 0.88

  Alignments for each domain:
  == domain 1  score: 3.7 bits;  conditional E-value: 0.081
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  MerR-DNA-bind 36 dvrallarklaeleeriaeLqalraeLa 63
                   d++ l+++ +a+++e+i++ ++  + L+
     AHX11606.1 15 DLESLSEEYMASVQEQIKKFTENPEMLQ 42
                   5568899999********9999887776 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00065
                    HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  MerR-DNA-bind  34 cqdvrallarklaeleeriaeLqalraeLa 63 
                     q+ ++ l+++la+ ++r++e+ al  +L 
     AHX11606.1  81 VQESLKRLRARLAKMDKRLDEIMALLSDLS 110
                    5788899******************99986 PP

>> DUF4455  Domain of unknown function (DUF4455)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.1    0.0015       1.7     418     450 ..      15      47 ..       3      57 .. 0.86
   2 ?    5.1   0.2    0.0065       7.3      26      57 ..      77     108 ..      71     114 .] 0.63

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.0015
     DUF4455 418 lLddikkeYeefhkdqvaiveeyPemvleeles 450
                  L+ + +eY+   ++q+++ +e+Pem +++l  
  AHX11606.1  15 DLESLSEEYMASVQEQIKKFTENPEMLQKALGP 47 
                 589999**********************99865 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0065
     DUF4455  26 veplileageellkklsesdeeieklfkkled 57 
                 +++ + e  ++l+ +l++ d++++++++ l d
  AHX11606.1  77 FKTEVQESLKRLRARLAKMDKRLDEIMALLSD 108
                 55666666777777777777777777666643 PP

>> DUF1664  Protein of unknown function (DUF1664)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0      0.17     2e+02      55      71 ..      25      41 ..       2      71 .. 0.53
   2 ?   10.2   0.2   0.00052      0.58      52      84 ..      76     108 ..      71     112 .. 0.85

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.17
     DUF1664 55 eslaatkrhLssridrv 71
                +s++++ ++++++ + +
  AHX11606.1 25 ASVQEQIKKFTENPEML 41
                22222222222222222 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00052
     DUF1664  52 qvseslaatkrhLssridrvdkkldeqkeiske 84 
                 ++++++++  ++L +r++++dk+lde +++ ++
  AHX11606.1  76 SFKTEVQESLKRLRARLAKMDKRLDEIMALLSD 108
                 6778999999****************9998765 PP

>> NPV_P10  Nucleopolyhedrovirus P10 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.8   0.00073      0.82      38      66 ..      79     107 ..       2     112 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 0.00073
     NPV_P10  38 telnekLdaqsaqLaeletkvenIqdiLn 66 
                 te++e L ++ a La++++ +++I  +L+
  AHX11606.1  79 TEVQESLKRLRARLAKMDKRLDEIMALLS 107
                 48888888888888888888888888887 PP

>> LXG  LXG domain of WXG superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.1   0.5     0.059        66      79     121 ..       4      44 ..       1      60 [. 0.72
   2 ?   10.4   0.2   0.00035      0.39      83     132 ..      61     109 ..      31     113 .. 0.80

  Alignments for each domain:
  == domain 1  score: 3.1 bits;  conditional E-value: 0.059
         LXG  79 kikealesvepssngfidedfLeqelenglkkakevteelkde 121
                 +ik+++++++++  + ++e+++  +++ ++kk+ e  e l+++
  AHX11606.1   4 DIKNNDSDLDLD-LESLSEEYMA-SVQEQIKKFTENPEMLQKA 44 
                 677777777777.5667777777.7888888877776666655 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
         LXG  83 alesvepssngfidedfLeqelenglkkakevteelkdeinkilasvsdi 132
                 +l s+ +  +g  +e+f   e++  lk++++ ++ +++++++i+a  sd+
  AHX11606.1  61 KLGSLMSGLEGGTEESFKT-EVQESLKRLRARLAKMDKRLDEIMALLSDL 109
                 5555556666777888887.*************************99997 PP

>> FapA  Flagellar Assembly Protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   2.7   0.00025      0.28     332     409 ..      16     100 ..       5     114 .] 0.67

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00025
        FapA 332 epelkekl.keleeeleeleeeleklkkkikklpklkaekqlesekkeqlkklletk......eklkeeleeleeelkelkeele 409
                   +l e++ + ++e+++++ e+ e+l+k++  + kl+ e++ ++ek+ +l + le         + +e+l+ l+++l++++++l+
  AHX11606.1  16 LESLSEEYmASVQEQIKKFTENPEMLQKALGPFMKLQSEYMKDPEKLGSLMSGLEGGteesfkTEVQESLKRLRARLAKMDKRLD 100
                 4566677779999999999999999999977777777788878887777777666664544444444444444444444444443 PP

>> FlaC_arch  Flagella accessory protein C (FlaC)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1     0.017        19       5      38 ..      12      46 ..      10      52 .. 0.80
   2 ?    6.0   0.1     0.014        16      18      43 ..      80     105 ..      60     112 .. 0.82

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.017
   FlaC_arch  5 lEnklsklst.eletvkkeneelsksveelkenVk 38
                l+ +l++ls   +++v++++++  ++ e+l++   
  AHX11606.1 12 LDLDLESLSEeYMASVQEQIKKFTENPEMLQKALG 46
                5667888888679***************9998765 PP

  == domain 2  score: 6.0 bits;  conditional E-value: 0.014
   FlaC_arch  18 tvkkeneelsksveelkenVkdllsL 43 
                  v+++++ l+  + +++++  ++++L
  AHX11606.1  80 EVQESLKRLRARLAKMDKRLDEIMAL 105
                 47788888888888888888888876 PP

>> GBR2_CC  Gamma-aminobutyric acid type B receptor subunit 2 coiled-coil domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.4       5.3     6e+03      27      32 ..      12      17 ..      10      19 .. 0.81
   2 ?   11.9   0.1   0.00017      0.19      13      34 ..      81     102 ..      76     106 .. 0.90

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.3
     GBR2_CC 27 lDKdLE 32
                lD dLE
  AHX11606.1 12 LDLDLE 17
                899999 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 0.00017
     GBR2_CC  13 lQaenHslRmkitelDKdLEEV 34 
                  Q  + +lR ++  +DK L+E+
  AHX11606.1  81 VQESLKRLRARLAKMDKRLDEI 102
                 688999**************97 PP

>> TMPIT  TMPIT-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.6   0.6   0.00022      0.24       8      90 ..      20     107 ..      14     112 .. 0.60

  Alignments for each domain:
  == domain 1  score: 10.6 bits;  conditional E-value: 0.00022
       TMPIT   8 ekef.keleetakeykqkleelsklqskcskeikkqkkrlkelksslkklkksvk....eeeeeeveelkeelkerkkvlkevesllp 90 
                 ++e+  +++e+ k+++++ e l+k    ++k  ++  k+ ++l s ++ l+  ++    +e +e +++l+++l++++k l+e+ +ll 
  AHX11606.1  20 SEEYmASVQEQIKKFTENPEMLQKALGPFMKLQSEYMKDPEKLGSLMSGLEGGTEesfkTEVQESLKRLRARLAKMDKRLDEIMALLS 107
                 5554145666666666666666666665555555555555555555444444322222277888888888888888888888887765 PP

>> XhlA  Haemolysin XhlA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.4   0.4      0.04        45      29      47 ..      19      37 ..       1      39 [. 0.68
   2 ?    6.7   0.2    0.0074       8.2       2      23 ..      81     102 ..      80     113 .. 0.70

  Alignments for each domain:
  == domain 1  score: 4.4 bits;  conditional E-value: 0.04
        XhlA 29 eaeekiknleedlkklesn 47
                  ee   +++e++kk+++n
  AHX11606.1 19 LSEEYMASVQEQIKKFTEN 37
                3466777899999999988 PP

  == domain 2  score: 6.7 bits;  conditional E-value: 0.0074
        XhlA   2 ikerlerietkldnleervdkl 23 
                 ++e l+r+ ++l ++++r+d++
  AHX11606.1  81 VQESLKRLRARLAKMDKRLDEI 102
                 6777777777777777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (114 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1422  (0.0793128); expected 358.6 (0.02)
Passed bias filter:                      861  (0.0480228); expected 358.6 (0.02)
Passed Vit filter:                       104  (0.00580066); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.43u 0.29s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 842.66
//
Query:       AHX11607.1  [L=177]
Description: outer membrane lipocarrier LolA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.6e-08   33.7   0.0    3.7e-08   33.2   0.0    1.2  1  LolA      Outer membrane lipoprotein carrier protein LolA
  ------ inclusion threshold ------
       0.21   12.1   0.2        1.2    9.7   0.0    2.3  3  CX        CX module


Domain annotation for each model (and alignments):
>> LolA  Outer membrane lipoprotein carrier protein LolA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.2   0.0   4.2e-12   3.7e-08       2     163 ..      30     175 ..      29     177 .] 0.88

  Alignments for each domain:
  == domain 1  score: 33.2 bits;  conditional E-value: 4.2e-12
                 T-SEEEEEEEEEEE-TTS--EEEEEEEEEEETTTEEEEEE-TTS-EEEEEETTEEEEEETTTTEEEEEEHHHHTTT-GGGGGGS-HHHHTTTEEEEEEE CS
        LolA   2 kvktlsadFvQtvtsgegkkiqetsGklaikrPgkfrweytsPdeqlivsdgktvwlydpdleqvtieslkqalsktplvlLledkaklskdynvsvkk 100
                 ++ktl adFvQ  ++g+     +++G + ++ P +f++ y+  + ++i +++  + + d++l+++   +     +  p+  +l++  kls+  +++   
  AHX11607.1  30 SFKTLRADFVQRNPDGT-----KSTGVVFLSLPHRFKIVYQD-SGISISGNKGMITYHDSELQET---RKFFMSRGDPFLKMLSNVGKLSQYHRIK--- 116
                 689**************.....****************9988.9999999999999999999999...4444556789999999******999988... PP

                 ETTEEEEEEEESSS-SSECEEEEEE.ETTE.EEEEEEEETT--EEEEEEEEEEES----GGGG- CS
        LolA 101 eqdldtltlkpkakdanlsritigfdkkgl.lkqlkvvdaqGqrttitfsnvkenakladdlFk 163
                 + +l  l     ++++n ++ +i +++k   +k++   ++ G+ t +tfs+ + n +l++d+F 
  AHX11607.1 117 KAGLSYL-----ETSSNGRKCSIVVQEKPFqIKEIIFENESGEVTHMTFSKAHYNLTLSNDAFA 175
                 4554444.....45778999*********99********************************7 PP

>> CX  CX module
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0      0.42   3.8e+03      33      44 ..      42      53 ..      39      54 .. 0.87
   2 ?   -2.8   0.0       1.1   9.5e+03      21      31 ..      78      88 ..      77      90 .. 0.78
   3 ?    9.7   0.0   0.00014       1.2       6      44 ..     121     160 ..     119     165 .. 0.88

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 0.42
          CX 33 fpngtrpksivF 44
                 p+gt+ + +vF
  AHX11607.1 42 NPDGTKSTGVVF 53
                589*****9999 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 1.1
          CX 21 iseddgelekv 31
                i+ +d+el+++
  AHX11607.1 78 ITYHDSELQET 88
                67789999987 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.00014
          CX   6 syaeskerpkvCeykiseddgelekvtfpngtr.pksivF 44 
                 sy e++++ ++C++ ++e+  ++++++f+n +  ++ ++F
  AHX11607.1 121 SYLETSSNGRKCSIVVQEKPFQIKEIIFENESGeVTHMTF 160
                 68899999**********************9854777777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       347  (0.0193541); expected 358.6 (0.02)
Passed bias filter:                      301  (0.0167884); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.21s 00:00:00.62 Elapsed: 00:00:00.40
# Mc/sec: 1335.73
//
Query:       AHX11608.1  [L=264]
Description: cytidylyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-16   59.3   0.0    6.2e-16   58.9   0.0    1.2  1  CTP_transf_like  Cytidylyltransferase-like


Domain annotation for each model (and alignments):
>> CTP_transf_like  Cytidylyltransferase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   3.5e-20   6.2e-16       1     141 [.      92     250 ..      92     252 .. 0.74

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 3.5e-20
                      EEEE--TT--HHHHHHHHHHHHHSSES.EEEEEESSTHCSST-.SCSSTHHHHHHHHHHHTTCTTEEEEEEESEHHHHHHHTTTT....EEEEE CS
  CTP_transf_like   1 lagGtFDpiHlGHlrlleqakklleed.livgvpsdeppkkkk.kplasaeeRlemlelakevdevisvdpweltrevlkklkpd....klylv 88 
                      l+gG+F+p+H+GHl l  +a+k l++  ++++ + ++p k+   +++   e R + +  + ++ +++  ++ ++  ++lk+lk+      + ++
       AHX11608.1  92 LLGGSFNPPHHGHLYLSLEALKRLNLHqVWWLFCKNNPLKQIRyESFKVREKRARAIVGMNRKIRLVNSNDLYTY-KTLKQLKSRypqcVFTWI 184
                      689************************888888888888877545555556666666666444443333444433.466666665555999*** PP

                      EEHHHHHHHHCHHHHHHHHHHHHHEEEEEE...............HTTCEEEEEEECCTTTCSHHHHH CS
  CTP_transf_like  89 igadvledfsewkeleeilgnvklvvvsrp...............ekqanvllkaekrtngiSstkir 141
                      +g d+ ++++ w+++eei+++v+++v++r                ek++   ++   r n+ Sst +r
       AHX11608.1 185 MGMDSATTIHLWERWEEIIRSVRFAVFNRGdylhkcmrskfisrtEKSRISNII--IRKNNLSSTLLR 250
                      ******************************999888888888765333333333..367778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (264 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       560  (0.0312343); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 2073.46
//
Query:       AHX11609.1  [L=585]
Description: single-stranded-DNA-specific exonuclease RecJ [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-20   73.9   2.7    1.8e-20   73.7   1.0    2.0  2  DHHA1     DHHA1 domain
    9.4e-19   67.7   0.0    1.8e-18   66.8   0.0    1.5  1  RecJ_OB   RecJ OB domain
    6.6e-10   39.1   0.1    1.4e-09   38.1   0.1    1.5  1  DHH       DHH family
  ------ inclusion threshold ------
       0.11   12.7   0.0       0.43   10.8   0.0    2.0  1  Toprim    Toprim domain


Domain annotation for each model (and alignments):
>> DHHA1  DHHA1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       2.4   1.1e+04      57      76 ..      79      98 ..      78     120 .. 0.65
   2 !   73.7   1.0   4.1e-24   1.8e-20       1     137 [.     341     462 ..     341     463 .. 0.86

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 2.4
                HHHHHHHHTHGBTTCEEEEE CS
       DHHA1 57 giaadklksklkkpvivfva 76
                ++a++++++ +kk + ++++
  AHX11609.1 79 AQAVERILEAIKKNEKIVIY 98
                56666777766664444444 PP

  == domain 2  score: 73.7 bits;  conditional E-value: 4.1e-24
                 HHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHHTCEEECTCEEEEEECHCCHHHHHHHHHHHHHHTHGBTTCEEEEEEEECTEEEEEEEESSHSS-HHHH CS
       DHHA1   1 leslneerkelekeleelkealaklkaeellekaeevkgvkvlvaevgeewdagalgiaadklksklkkpvivfvakeegdkvkvsarskkdgvdagel 99 
                 l++ln +rke+ek    l+ea++++++           + kv+ +++ ++w++g++gi+a+++k++++ p+i++ + ++    k sars+k + ++g++
  AHX11609.1 341 LRALNLRRKEIEKTA--LQEAITQIENT----------NRKVIMVAS-KNWHQGIIGIVASRIKDRYHLPTIIVSIDNN--IGKASARSIK-NANIGTA 423
                 688999999999999..99999887653..........888888888.9****************99999999998765..**********.7777744 PP

                 HHH.HHHHTTCCEEEETCEEEEEEEHCHHHHHHHHHHHH CS
       DHHA1 100 ake.aaaklgggGGGHdlAaGagipaekleealealeea 137
                 + +   + l+  GGGH++AaG++ +++k++e+++++ee+
  AHX11609.1 424 VIAaKEKGLIIEGGGHRMAAGFSCEIGKIPEIQQFFEEH 462
                 44414899****************************997 PP

>> RecJ_OB  RecJ OB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.8   0.0     4e-22   1.8e-18       1     108 []     474     582 ..     474     582 .. 0.97

  Alignments for each domain:
  == domain 1  score: 66.8 bits;  conditional E-value: 4e-22
     RecJ_OB   1 iDaeldlseiteelleelerlePfGkgnpePvfllknvkvesarivgkeknhlklkledes.gksleaiaFnlaeklee.lekgdkvdiaytleinefn 97 
                 +D+el ++ it +l+eel+ l+P+G+gnpeP f+l  v+v   +i+g+   h+ ++l+d    k++++iaF+ ++kl e + + ++ ++++++++++++
  AHX11609.1 474 VDGELYVDTITYDLYEELKVLAPCGPGNPEPRFVLTSVRVVTSKIIGE-DGHIACTLRDIRtYKTIRGIAFHPNSKLTEaILNCEATRFLVKVKLENWQ 571
                 79**********************************************.99******9987799************999999999************** PP

     RecJ_OB  98 gretlqlrikd 108
                   ++ q++i+d
  AHX11609.1 572 SVSKPQVIIED 582
                 *********98 PP

>> DHH  DHH family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.1   0.1     3e-13   1.4e-09       1      57 [.      94     196 ..      94     232 .. 0.80

  Alignments for each domain:
  == domain 1  score: 38.1 bits;  conditional E-value: 3e-13
                 EEEEE-ECSSSHHHHHHHHHHHH.......................................CECS--TCGGCGCCHHCCCSEEEEEEE-S---S.... CS
                 xxxxxxxxxxxxxxxxxxxxxxx.......................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.... RF
         DHH   1 kilivghknpDtDsigSaialan.......................................llvDhneksqavegeakeeaedviiiDHHrlge.... 56 
                 ki+i  ++++D+D+++S+ +++n                                       ++vD+++ ++++++ a++ + d+i++DHH + +    
  AHX11609.1  94 KIVI--YGDYDVDGATSSALIKNylrnigkevsiyipdritegygpnstaftklreegytlcITVDCGILAHKEIESANSIGLDIIVVDHHISTDvipp 190
                 5777..***********8888887888888888888888888888888888888888888888****************************99876666 PP

                 .....S CS
                 .....x RF
         DHH  57 .....e 57 
                      +
  AHX11609.1 191 avaviN 196
                 666552 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.5e-05      0.43      47      91 ..      76     120 ..       8     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.5e-05
                 TTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHHH CS
      Toprim  47 edkkkvlkalkelakradeiilatDpDreGeaiawellevlkell 91 
                  +  ++++ + e  k+ ++i++  D D++G + + ++ ++l+++ 
  AHX11609.1  76 LGVAQAVERILEAIKKNEKIVIYGDYDVDGATSSALIKNYLRNIG 120
                 455667777889999***********************8887554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (585 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       649  (0.0361983); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.57u 0.26s 00:00:00.83 Elapsed: 00:00:00.41
# Mc/sec: 4253.78
//
Query:       AHX11610.1  [L=413]
Description: NADH oxidoreductase (quinone), F subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    2.4e-50  170.4   0.0    4.9e-50  169.4   0.0    1.5  2  Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subu
    1.4e-29  102.0   0.0    2.4e-29  101.2   0.0    1.4  1  NADH_4Fe-4S   NADH-ubiquinone oxidoreductase-F iron-sulfur bi
    8.1e-07   28.8   0.1    1.6e-06   27.8   0.1    1.5  1  SLBB          SLBB domain


Domain annotation for each model (and alignments):
>> Complex1_51K  Respiratory-chain NADH dehydrogenase 51 Kd subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.4   0.0   8.1e-54   4.9e-50       1     151 [.      47     213 ..      47     214 .. 0.98
   2 ?   -3.5   0.0       1.4   8.3e+03     137     146 ..     313     322 ..     300     332 .. 0.56

  Alignments for each domain:
  == domain 1  score: 169.4 bits;  conditional E-value: 8.1e-54
  Complex1_51K   1 vkeagivGrGGagfPthvKlkakakkkk....kylivNaaEcEPgltkDrllmreepheileGlkiaaealgaekgvigvrdekpeaiealekalae 93 
                   +k++g++GrGGagfPt++K++++++kk+     ylivNa+E+EPg++kDr+++r eph+++eG+ +a +a++++ ++i+vr+e +++   leka+++
    AHX11610.1  47 IKKSGLRGRGGAGFPTGMKWSFMPQKKNpgqsSYLIVNADESEPGTCKDRDILRFEPHKLIEGIVLASHAMRIDVTYIYVRGEFHNESLILEKAIEQ 143
                   79**********************98889******************************************************************** PP

  Complex1_51K  94 akaagl....ldievvklagkYpaGeekaLiesltgr.evprgkppadvgv.......vvnNveTlaavy 151
                   a++a+l    l+i v+++ag+Y++Gee+aL+esl+g+ ++pr kpp+ +g+       ++nNveT+a+v 
    AHX11610.1 144 ATDAQLipdnLKIVVHRGAGAYICGEETALLESLEGKkGMPRLKPPFPAGCglygkptTINNVETVASVS 213
                   ***999****************************************9999999**************996 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 1.4
  Complex1_51K 137 vgvvvnNveT 146
                   +g++v+N eT
    AHX11610.1 313 AGIIVMNKET 322
                   3344444443 PP

>> NADH_4Fe-4S  NADH-ubiquinone oxidoreductase-F iron-sulfur binding region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.2   0.0     4e-33   2.4e-29       2      84 ..     327     409 ..     326     410 .. 0.97

  Alignments for each domain:
  == domain 1  score: 101.2 bits;  conditional E-value: 4e-33
                  HHHHHHHHHHHH--S--HHHHIIIIHHHHHHHHHTBT---HHHHHHHHHHHHHHSS--SSTHHHHHHHHHHHHHHHHHHHHHH CS
  NADH_4Fe-4S   2 varrllefyaaesCGkCtpCreGtkrllelleriaagegteedldlleelaetikgtslCalgdsaanpvlsalrkFreefea 84 
                  +++rl +fy +esCG+CtpCreGt +l ++++r+a+g+g+++d+d+l +l+++i+g+++Calgd+a +p++ ++++Fr e+e+
   AHX11610.1 327 AIERLSHFYMHESCGQCTPCREGTGWLWNIMKRLAEGTGKKSDIDTLLKLTKQIEGHTICALGDAASWPIQGLIKNFRREIED 409
                  578999**************************************************************************985 PP

>> SLBB  SLBB domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.8   0.1   2.7e-10   1.6e-06       2      56 ..     237     286 ..     236     288 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.8 bits;  conditional E-value: 2.7e-10
                 EEEESSBSS-EEEEEETT-BHHHHHHT.TT-SBSS.........-E.EEE-SSSSS- CS
        SLBB   2 VtVtGeVkrPgnyevpigttlsdlieq.aGGltddadlksvnLarl.avipgGpmmg 56 
                 ++++G+V+rP+n+e  +g +l+ lie+ aGG+    d        l avipgG++ +
  AHX11610.1 237 FCISGHVNRPCNVEEVLGVPLKLLIEEyAGGVIGGWD-------NLlAVIPGGSSVP 286
                 89*************************6777777766.......7999*****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       459  (0.025601); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.41
# Mc/sec: 3008.77
//
Query:       AHX11611.1  [L=432]
Description: bifunctional FolC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.4e-10   41.5   0.0    2.6e-10   40.6   0.0    1.4  1  Mur_ligase_M  Mur ligase middle domain
    0.00049   20.3   0.0      0.001   19.3   0.0    1.5  1  Mur_ligase_C  Mur ligase family, glutamate ligase domain


Domain annotation for each model (and alignments):
>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.6   0.0   2.9e-14   2.6e-10       1     190 [.      46     261 ..      46     264 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.6 bits;  conditional E-value: 2.9e-14
                   EESSS-HHHHHHHHHHHHHCTEEEEETTC.......................................SS-THHHHHHHHHHHHHTT-SEEEEE--H CS
  Mur_ligase_M   1 vTGtnGKTTtteliaailekagkvigtvg.......................................ttnneiglpktlaemekkeaeyavlEvss 58 
                   v+GtnGK +t  ++++il++ag  + +                                         t+ + ++l + la  +  +a++  +E+++
    AHX11611.1  46 VAGTNGKGSTIAFLRSILKSAGYSLNIYTsphlryfnerivicneeisdralydvledvrvaskgeklTFFEGTTLAAILAFSRT-NADFSLIETGM 141
                   89*******************54444444457************************************99999999999987777.*********** PP

                   CHHHCTTTCCHCBESEEEE---TSTTHHHH.SSHHHHHHHHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEE CS
  Mur_ligase_M  59 hglgekrlegllkpdvavitnispdHldfh.gtlenyaeaKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieek 154
                    g  ++      kp + +it+i+ dH +++  +  ++a++K+ ++++    +++v    d+++k + k ++ +++ v++ g e +         ++ 
    AHX11611.1 142 GGRLDATNVF-PKPLITIITSIDLDHTEYLgRSTPEIAYEKSGIMKNGV--SCVVAGQTDEVMKVIEKVAAMRRAPVFRQGYEWNV--------SK- 226
                   *655544444.8******************77899**********9877..4999999***9999888888888888888877765........23. PP

                   TTEEEEEEEEE.TTEEEEEEESSCSCHHHHHHHHHHH CS
  Mur_ligase_M 155 segteiellev.kggeleieipllGkhnvyNalaaia 190
                   s+g  +  +e+  ++el    +l G+h++ Na   +a
    AHX11611.1 227 SQGCLL--FETgGYQELYSLPNLRGDHQIVNAGNTVA 261
                   333332..44423333334457888888888765555 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   1.2e-07     0.001       1      85 [.     289     374 ..     289     379 .. 0.78

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 1.2e-07
                   CTTSSEEEEE.........TTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSE.EEEEESS-TTS CS
  Mur_ligase_C   1 vkgRlevvge.........adgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasalads.lvvlgdyprae 85 
                   ++ Rl++v++          +g  +++D ahnp++++   + l     +++ ++++g    +g++ ++f+ +++   +    + +v ++++pr++
    AHX11611.1 289 WPARLQRVSRntnelvrilPQGWELYIDGAHNPAGAKTISEWL----GESKAHIILGM--TRGKDVKEFLSRIKSNIET---IaVVCVQGEPRSQ 374
                   688999999999999999999************9988777777....8899******8..7577777766666666665...4355557778765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (432 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       335  (0.0186848); expected 358.6 (0.02)
Passed bias filter:                      325  (0.0181271); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.43
# Mc/sec: 3050.60
//
Query:       AHX11612.1  [L=447]
Description: tRNA modification GTPase TrmE [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.9e-45  155.6   2.3    2.6e-45  155.1   2.3    1.2  1  MnmE_helical  MnmE helical domain
    3.9e-34  117.4   0.0      1e-33  116.0   0.0    1.8  1  TrmE_N        GTP-binding protein TrmE N-terminus
    1.2e-23   83.3   0.1    3.4e-23   81.9   0.0    1.8  2  MMR_HSR1      50S ribosome-binding GTPase
    2.3e-10   40.2   0.0    5.2e-10   39.1   0.0    1.6  1  FeoB_N        Ferrous iron transport protein B
    3.3e-06   27.3   0.1     0.0013   18.9   0.0    2.5  2  Dynamin_N     Dynamin family
    0.00044   19.8   0.1       0.84    9.1   0.0    3.4  2  GTP_EFTU      Elongation factor Tu GTP binding domain
    0.00089   19.2   0.2       0.11   12.5   0.0    3.2  3  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
     0.0016   17.9   0.7      0.014   14.9   0.1    2.5  2  Arf           ADP-ribosylation factor family
     0.0026   18.3   0.1      0.009   16.6   0.0    2.2  2  AAA_18        AAA domain
     0.0039   17.7   0.0      0.011   16.3   0.0    1.8  2  ABC_tran      ABC transporter
     0.0098   16.1   0.0      0.016   15.4   0.0    1.4  1  AAA_28        AAA domain
  ------ inclusion threshold ------
      0.013   15.5   0.5       0.45   10.4   0.0    3.0  3  RsgA_GTPase   RsgA GTPase
      0.027   14.6   0.2       0.33   11.1   0.0    2.7  3  DUF4581       Domain of unknown function (DUF4581)
       0.11   12.3   0.1        3.2    7.6   0.0    2.9  2  NOG1          Nucleolar GTP-binding protein 1 (NOG1)


Domain annotation for each model (and alignments):
>> MnmE_helical  MnmE helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.1   2.3   2.1e-48   2.6e-45       1     206 []     119     444 ..     119     444 .. 0.94

  Alignments for each domain:
  == domain 1  score: 155.1 bits;  conditional E-value: 2.1e-48
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx. RF
  MnmE_helical   1 LtqaEavadlIdAeteaaakaalrqleGelskkikelrekllellaeleaaiDFpeedleelseeelaekleelkeelekllatakrgellreGik. 96 
                   Lt+aE+++dlI+Aet+a++k+a r+++G+l+++++++r k ++ l++lea+iDFp+e+++    +++ +++eel+  ++++l++ + ge +r+G+  
    AHX11612.1 119 LTKAEGIIDLINAETSAQLKQASRHISGHLEEEYDSIRMKAIRSLSHLEAYIDFPDEEIPVSVVDSVTRSVEELIGLISNHLDDGRVGEKIRKGFLi 215
                   9************************************************************************************************ PP

                   ................................................................................................. RF
  MnmE_helical  97 ................................................................................................. 96 
                                                                                                                    
    AHX11612.1 216 tiigkpnagkstlfnylakrelaivtdipgttrdvlevkldcngypivlldtagiqdtddkiekegiakainsasdsdiviflrdiselhapcsdad 312
                   ************************************************************************************************9 PP

                   ..........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  MnmE_helical  97 ..........................DllkekeekeeeevlkiSaktgegieeLeeaike.leleei.eeeplltnaRhkealekalealeeakeal 165
                                             D +++++ + ++e + +S+++++g+e L+++i + ++  ++  e+ ++t++Rh+ ale al +l+     +
    AHX11612.1 313 tskltellehiearelpiirvatkadDFSESSRYDVTNEYILLSVHKEKGVELLLDKIFSiIS--TVdRESYVITHQRHRVALEGALMHLR----RF 403
                   9999999999999999999999999876666665666666679***************66333..3345789******************9....44 PP

                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  MnmE_helical 166 eaglpldlvaedLrealeaLgeItGevvtedlLdeIFskFC 206
                   + +l+ +l+ae+L+ a++++g++tG+++ +++LdeIFs+FC
    AHX11612.1 404 SFDLSIELAAEELKLAADYIGSVTGKIKLDEILDEIFSTFC 444
                   5556789********************************** PP

>> TrmE_N  GTP-binding protein TrmE N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.0   0.0   8.2e-37     1e-33       1     115 []       3     116 ..       3     116 .. 0.93

  Alignments for each domain:
  == domain 1  score: 116.0 bits;  conditional E-value: 8.2e-37
                 -EEEE-S-SSS-SEEEEEEESTTHHHHHHTTEEE..T--CTEEEEEEEECT..TCEEEEEEEEEEBTTCSTTSSEEEEEEEESSHHHHHHHHHHHHCTT CS
      TrmE_N   1 TIaAlatpagkgaiaiiRvsGpkaleiakklfkk..elkprkallgklvdeeekevlDevlvlvfkaprsyTgedvvElhlhGgpavvkavleallkag 97 
                 TI+Al+t  gk+++a+ RvsGp+al +++ l     ++kpr++++ kl+++  + +lDe l+++f+ap s+TgedvvE+h hG+ a+++ + e+l +++
  AHX11612.1   3 TIYALSTVFGKSGVAVFRVSGPDALGVLEVLNLGvaSVKPRSVHFAKLYEK--DLLLDELLIIYFSAPASFTGEDVVEIHSHGSIAILRYITERL-SQR 98 
                 9************************99975533355899*********965..889***************************************.899 PP

                 -EE--CTHHHHHHHHTTS CS
      TrmE_N  98 arlAepGEFtkRaflngk 115
                 + lAepGEFt+Ra ln+k
  AHX11612.1  99 FVLAEPGEFTRRAVLNNK 116
                 ****************98 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       3.4   4.4e+03      69     101 ..     115     148 ..     104     161 .. 0.61
   2 !   81.9   0.0   2.7e-26   3.4e-23       2     114 .]     215     336 ..     214     336 .. 0.80

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 3.4
                 HHHHHHCTSEEEEEEETT.TTCSHHHHHHHHHHH CS
    MMR_HSR1  69 aflaleeadlillvvdas.eeklkpldeeleell 101
                 +  +l +a+ i+ +++a+ +++lk+  +++   l
  AHX11612.1 115 NKMDLTKAEGIIDLINAEtSAQLKQASRHISGHL 148
                 4445667888888888664335555555555555 PP

  == domain 2  score: 81.9 bits;  conditional E-value: 2.7e-26
                 EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCSS...HHHHHHHHHHHHHHHHCTSEEEEEEETT.......... CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGlie...gaseekglgkaflaleeadlillvvdas.......... 86 
                 + i+G+pN+GKStL+n l ++  aiv+d+pgtTrd+ e +++ +g +i+l+Dt+G i+   ++ e++g++ka+ +  ++d+++++ d+s          
  AHX11612.1 215 ITIIGKPNAGKSTLFNYLAKReLAIVTDIPGTTRDVLEVKLDCNGYPIVLLDTAG-IQdtdDKIEKEGIAKAINSASDSDIVIFLRDISelhapcsdad 312
                 789*****************978********************************.64453444455********************997766654322 PP

                 TTCSHHHHHHHHHHHHHTTSEEEEEEES CS
    MMR_HSR1  87 eeklkpldeeleelleeakkplilvlnk 114
                 +     +  el e +e ++ p+i v++k
  AHX11612.1 313 T----SKLTELLEHIEARELPIIRVATK 336
                 1....22244555545577888888876 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.0   4.1e-13   5.2e-10       3      91 ..     215     304 ..     213     308 .. 0.93

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 4.1e-13
                 EEEEESTTSSHHHHHHHHHTTSEE.EEESTTSSSEEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHHCTSSSEEEEEEEGGGH CS
      FeoB_N   3 valvGnpnvGkttlfnaltgakqk.vgNwpGvtvekkegklklkgkeveivDlPGiYslsayseeekvardflleeepdvvvnvvdatnl 91 
                 ++++G+pn+Gk+tlfn l++ +   v   pG+t +  e+kl+++g+ + ++D  Gi + ++  e e +a+ +   ++ d+v+ + d ++l
  AHX11612.1 215 ITIIGKPNAGKSTLFNYLAKRELAiVTDIPGTTRDVLEVKLDCNGYPIVLLDTAGIQDTDDKIEKEGIAKAINSASDSDIVIFLRDISEL 304
                 789****************99965389*******************************************************99988776 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   9.8e-07    0.0013       1      41 [.     215     256 ..     215     261 .. 0.88
   2 !    6.2   0.0    0.0079        10     102     167 ..     261     336 ..     255     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 9.8e-07
                 EEEEEBTTTTHHHHHHHHHTS--S---SSS.---S-EEEEEC CS
   Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnp.tTrrplelqlg 41 
                 i+++G+ ++GKS++ n L ++++  +  +p tTr +le++l+
  AHX11612.1 215 ITIIGKPNAGKSTLFNYLAKRELAIVTDIPgTTRDVLEVKLD 256
                 789*******************99988885388999999885 PP

  == domain 2  score: 6.2 bits;  conditional E-value: 0.0079
                 SEEEEE---B-SSSGTTS.HHHHHHH...STTEEEEEEEETTS...-CCC-CHHHHHHHHSTTBTT...EEEEEE- CS
   Dynamin_N 102 gltlvDlPGldsvnkrdq.elvkeyi...kkadiilavtsanh...dlsnsealflarevdpkgkr...tivvltk 167
                  ++l+D+ G+++++++ + e + ++i    ++di++++ + +     +s+++ ++l ++++  + r   +i v tk
  AHX11612.1 261 PIVLLDTAGIQDTDDKIEkEGIAKAInsaSDSDIVIFLRDISElhaPCSDADTSKLTELLEHIEARelpIIRVATK 336
                 589*********988877744444442226789****987766555899999999999998888886666777666 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.0   0.0     0.099   1.3e+02     125     154 ..     110     157 ..      99     201 .. 0.56
   2 !    9.1   0.0   0.00065      0.84       7     150 ..     216     355 ..     210     439 .. 0.65

  Alignments for each domain:
  == domain 1  score: 2.0 bits;  conditional E-value: 0.099
                 EEEEEESCGST.........HHHHHHHHHHHHHHHHHH................H CS
    GTP_EFTU 125 iivfiNKmDrl.........kaelkeiveevkqklsrk................e 154
                 + v+ NKmD +         +        e + +l++                 +
  AHX11612.1 110 RAVLNNKMDLTkaegiidliN-------AETSAQLKQAsrhisghleeeydsirM 157
                 567889****96655444442.......444444433322222223233333330 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00065
                 EEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEETTCSSEEEEEEEESSSGGG........HHHHHHHHHT-SEE CS
    GTP_EFTU   7 giighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisleketkkylinliDtPGHvdF........skevirglrvlDga 97 
                 +iig  ++GK+TL   L ++  ai             D        g T ++  ++l+   + y i l+Dt G +d         + + i++++  D++
  AHX11612.1 216 TIIGKPNAGKSTLFNYLAKRELAIVT-----------D------IPGTTRDVLEVKLD--CNGYPIVLLDTAGIQDTddkiekegIAKAINSASDSDIV 295
                 56666666666666666543333322...........1......23555566666666..777777777777766641111111122334557777777 PP

                 EEEEETTTB.......STHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHH CS
    GTP_EFTU  98 vlvvdaveG.......vepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqkl 150
                 +++ d++e         +++  e+l+++ ++++pii + +K+D   ++ +  v++ +  l
  AHX11612.1 296 IFLRDISELhapcsdaDTSKLTELLEHIEARELPIIRVATKADDFSESSRYDVTNEYILL 355
                 777777743333333355666677777777778888888888887666666665555555 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.34   4.4e+02      57      96 ..     109     155 ..      96     164 .. 0.59
   2 !   12.5   0.0   8.5e-05      0.11      41     102 ..     312     372 ..     297     375 .. 0.83
   3 ?    1.3   0.0      0.26   3.3e+02      83     103 ..     422     442 ..     406     444 .. 0.77

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.34
  MMR_HSR1_Xtn  57 pclyvlNKiDlisleeldelare.......pnsvviSaekelnldeL 96 
                   +  ++ NK+Dl + e + +l +        + s  iS + e + d++
    AHX11612.1 109 RRAVLNNKMDLTKAEGIIDLINAetsaqlkQASRHISGHLEEEYDSI 155
                   55667788888666655444432122223234555666666666655 PP

  == domain 2  score: 12.5 bits;  conditional E-value: 8.5e-05
  MMR_HSR1_Xtn  41 tvDdlidvieg.nrvYipclyvlNKiDlisleeldelarepnsvviSaekelnldeLkekiwe 102
                   ++ +l + +e+ +   +p + v  K+D  s+++  ++++  +++ +S++ke++++ L++ki++
    AHX11612.1 312 DTSKLTELLEHiEARELPIIRVATKADDFSESSRYDVTN--EYILLSVHKEKGVELLLDKIFS 372
                   55566666666555668999********99988888777..69******************97 PP

  == domain 3  score: 1.3 bits;  conditional E-value: 0.26
  MMR_HSR1_Xtn  83 vviSaekelnldeLkekiwee 103
                    + S+  +++lde++++i+++
    AHX11612.1 422 YIGSVTGKIKLDEILDEIFST 442
                   56799999**********975 PP

>> Arf  ADP-ribosylation factor family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       1.2   1.5e+03     120     143 ..     112     135 ..     108     151 .. 0.66
   2 !   14.9   0.1   1.1e-05     0.014      12     149 ..     210     361 ..     204     372 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.2
                 EEEE-TTSTTSS-HHHHHHHTTGG CS
         Arf 120 vlaNKqDlpealseeelrellgle 143
                 vl NK+Dl++a    +l ++ +  
  AHX11612.1 112 VLNNKMDLTKAEGIIDLINAETSA 135
                 788999988886555554444444 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 1.1e-05
                 TTEEEEEEEESTTSSHHHHHHHHHHSSC..EECSSSSSEEEEEEEE..TTEEEEEEEE-SSGGG.GGGGG.......GGCTTESEEEEEEETT-CT..T CS
         Arf  12 kkelrilllGLDnaGKtTilkklkleel..vttvPTigfnveelei..knlkftvwDvGGqekl.RplWk.......nYfektdavifvvDsadre..R 96 
                 +k + i ++G  naGK+T+ + l + el  vt +P +  +v e++   +++ + + D  G +    ++ k       n  ++ d vif+ D ++ +   
  AHX11612.1 210 RKGFLITIIGKPNAGKSTLFNYLAKRELaiVTDIPGTTRDVLEVKLdcNGYPIVLLDTAGIQDTdDKIEKegiakaiNSASDSDIVIFLRDISELHapC 308
                 56677999***************9998622678898888887776554899******9985543133333111111134566799******88765323 PP

                 HHHHHHHHHHHCTSGCCTTSEEEEEEE-TTSTTSS-HHHHHHHTTGGGSSSSS CS
         Arf  97 leeakeeLkalleeeelkevallvlaNKqDlpealseeelrellgleelkgkr 149
                  +   ++L++lle+ e +e +++ +a K D  +  s+ +++++  l ++++++
  AHX11612.1 309 SDADTSKLTELLEHIEARELPIIRVATKADDFSESSRYDVTNEYILLSVHKEK 361
                 4555689***********************99999999999988888877555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0       4.1   5.3e+03      24      74 ..     101     152 ..      89     176 .. 0.55
   2 !   16.6   0.0   7.1e-06     0.009       1      25 [.     215     248 ..     215     401 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 4.1
      AAA_18  24 f...gvnlrdvakenglllevdpealdeskrldedkldklldaleenssaleeg 74 
                 +   g+  r  + +n + l+  +  +d  + +   +l+++++ + ++ +  ee 
  AHX11612.1 101 LaepGEFTRRAVLNNKMDLTKAEGIIDLINAETSAQLKQASRHISGHLE--EEY 152
                 1555555566666666666666654455555555555555555555432..444 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 7.1e-06
      AAA_18   1 IlltGtpGvGKttlakeLskrl.gf........g 25 
                 I + G+p +GK+tl ++L+kr+ ++         
  AHX11612.1 215 ITIIGKPNAGKSTLFNYLAKRElAIvtdipgttR 248
                 89*******************7555666654440 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.4   6.9e+03      38      67 ..     122     151 ..     113     181 .. 0.66
   2 !   16.3   0.0   8.5e-06     0.011       7      50 ..     208     271 ..     203     349 .. 0.63

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.4
                 SEEEEEETTCEGGGB-HHHCCHCEEEE-SS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  38 teGeilldgkdlkeqeleslrkeigvlpqe 67 
                 +eG i l +++++ q ++ +r+ +g l++e
  AHX11612.1 122 AEGIIDLINAETSAQLKQASRHISGHLEEE 151
                 567776666666665555555555555555 PP

  == domain 2  score: 16.3 bits;  conditional E-value: 8.5e-06
                 EEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEE....................EETTCEGG CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....................xxxxxxxx RF
    ABC_tran   7 klkegekvaivGenGaGKStLlkllagllkpteGei....................lldgkdlk 50 
                 k+++g ++ i+G+  aGKStL++ la+ +     +i                    lld + ++
  AHX11612.1 208 KIRKGFLITIIGKPNAGKSTLFNYLAKRELAIVTDIpgttrdvlevkldcngypivLLDTAGIQ 271
                 79999*********************99877666664444555555555555555544444444 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   1.3e-05     0.016       2      87 ..     215     306 ..     214     340 .. 0.71

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 1.3e-05
      AAA_28   2 ivitGgestGKTtlleaLaargypvv...pEaareileeklakgedalpwv.edllafaervleeqleeeaaa....aankvlfcDrglldtla 87 
                 i i+G + +GK+tl + La+r+  +v   p + r++le kl++++   p v  d   +++   + ++e  a+a    ++++++++ r++ +  a
  AHX11612.1 215 ITIIGKPNAGKSTLFNYLAKRELAIVtdiPGTTRDVLEVKLDCNGY--PIVlLDTAGIQDTDDKIEKEGIAKAinsaSDSDIVIFLRDISELHA 306
                 88*******************77766556999********999984..5555566666655444444444444444477888887777665555 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.68   8.6e+02      35      68 ..      95     129 ..      86     163 .. 0.60
   2 ?   10.4   0.0   0.00035      0.45     100     153 ..     213     259 ..     181     275 .. 0.74
   3 ?    0.9   0.0       0.3   3.8e+02      30      66 ..     311     347 ..     304     375 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.68
                  HHHHHHHHHHTT-.EEEEEEE-GGG--HHHHHHHH CS
  RsgA_GTPase  35 ldrfLvlaeekgi.epvivlnKiDlleeeeeleel 68 
                  l++  vlae  +  +  ++ nK+Dl++ e  ++ +
   AHX11612.1  95 LSQRFVLAEPGEFtRRAVLNNKMDLTKAEGIIDLI 129
                  44444555555541555666899999988833222 PP

  == domain 2  score: 10.4 bits;  conditional E-value: 0.00035
                  SEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTE CS
  RsgA_GTPase 100 ktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegg 153
                   +++++G+  +GKStL n l+ ++ + + ++         TT+ v  ++l+ +g
   AHX11612.1 213 FLITIIGKPNAGKSTLFNYLAKRELAIVTDIPG-------TTRDVLEVKLDCNG 259
                  67889****************997777777765.......56666666665555 PP

  == domain 3  score: 0.9 bits;  conditional E-value: 0.3
                  --HHHHHHHHHHHHHTT-EEEEEEE-GGG--HHHHHH CS
  RsgA_GTPase  30 lslnlldrfLvlaeekgiepvivlnKiDlleeeeele 66 
                   +++ l+ +L ++e+++++++ v +K+D  +e+++++
   AHX11612.1 311 ADTSKLTELLEHIEARELPIIRVATKADDFSESSRYD 347
                  6778899999999*****9999*****9999988333 PP

>> DUF4581  Domain of unknown function (DUF4581)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0       2.3   2.9e+03      74     100 ..     170     196 ..     158     207 .. 0.73
   2 ?   -1.0   0.0       1.4   1.8e+03      63     117 ..     294     351 ..     281     365 .. 0.69
   3 ?   11.1   0.0   0.00026      0.33      67      93 ..     416     443 ..     401     445 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 2.3
     DUF4581  74 isscgkktllevlekvfksfrpllglp 100
                 i          v++ v +s+  l+gl 
  AHX11612.1 170 IDFPDEEIPVSVVDSVTRSVEELIGLI 196
                 555555566789999*******99985 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 1.4
     DUF4581  63 clpflqlaqdyisscg...kktllevlekvfksfrpllglpdvdddtfeeynadveee 117
                  + fl+   +  + c       l e+le++     p++ +    dd  e  + dv +e
  AHX11612.1 294 IVIFLRDISELHAPCSdadTSKLTELLEHIEARELPIIRVATKADDFSESSRYDVTNE 351
                 5555555555555454111456899999999999999999999999888888888655 PP

  == domain 3  score: 11.1 bits;  conditional E-value: 0.00026
     DUF4581  67 lqlaqdyiss.cgkktllevlekvfksf 93 
                 l+la dyi s  gk  l e+l+ +f +f
  AHX11612.1 416 LKLAADYIGSvTGKIKLDEILDEIFSTF 443
                 89******87358999*********998 PP

>> NOG1  Nucleolar GTP-binding protein 1 (NOG1)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0      0.26   3.4e+02       3      17 ..     156     170 ..     154     172 .. 0.85
   2 ?    7.6   0.0    0.0025       3.2      15      58 .]     293     338 ..     277     338 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.26
        NOG1   3 EkqAiaALkhladav 17 
                  ++Ai +L hl++ +
  AHX11612.1 156 RMKAIRSLSHLEAYI 170
                 59*********9988 PP

  == domain 2  score: 7.6 bits;  conditional E-value: 0.0025
        NOG1  15 davlFllDpseecg....ysleeQlsLleeikelfankpvivvlnKiD 58 
                 d+v+Fl D+se        ++ +  +Lle+i+++  + p+i v++K+D
  AHX11612.1 293 DIVIFLRDISELHApcsdADTSKLTELLEHIEAR--ELPIIRVATKAD 338
                 89********976655558888888899999988..68********99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (447 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       446  (0.0248759); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        60  (0.00334653); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.56u 0.27s 00:00:00.83 Elapsed: 00:00:00.43
# Mc/sec: 3090.46
//
Query:       AHX11613.1  [L=744]
Description: outer membrane assembly complex, YaeT protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-47  160.3   2.3    1.5e-46  159.4   2.3    1.5  1  Bac_surface_Ag  Surface antigen
    1.8e-44  150.2  21.3      1e-12   48.4   1.2    5.5  5  POTRA           Surface antigen variable number repeat
    6.8e-08   32.7   2.9      0.079   13.3   0.0    4.1  4  POTRA_1         POTRA domain, FtsQ-type
     0.0021   17.9   0.9          2    8.3   0.0    4.1  5  POTRA_2         POTRA domain, ShlB-type


Domain annotation for each model (and alignments):
>> Bac_surface_Ag  Surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  159.4   2.3   3.4e-50   1.5e-46       1     320 [.     437     740 ..     437     744 .] 0.95

  Alignments for each domain:
  == domain 1  score: 159.4 bits;  conditional E-value: 3.4e-50
                     STSSSS-EEEEEEEESSSEEEEEEEEEESTSSTTS-EEEEEEEEEEGGGTBS.S-EEEEEEEEEEEEEEESSSEEEEEEEEEEEEEEES---BHH CS
  Bac_surface_Ag   1 NllGtGqslslsaslgsyeqslnlsftePyflgdrvslglslfaresdsdesdsyrtksvgfsvslgrpltenyslslglsvqknkilkdsssen 95 
                     N+lGt++ +++ + +++  +  +  f + +++++ ++  +s+f+++++ +e + y++ s g+++slg++++ +  l+l +s++++ + + + +++
      AHX11613.1 437 NFLGTADAVGMALRKSTSGFDCSADFQKKRIFNTLITGDVSVFFKKQNMQEGSLYKIASKGINSSLGYHIRDDLYLNLSYSLNSDNVFDVDDEAP 531
                     9*************************************************************************************999988886 PP

                     HHHHHHSCS--EEEEEEEEEEEEEEEEEESSSSS-SSEEEEEEEEEEE-..TTSSS-EEEEEEEEEEEEESSTTSSSEEEEEEEEEEEEESSSS- CS
  Bac_surface_Ag  96 nrnvssasklqtgksltsslslslsydtrddalfPtrGvllklrleftgpllggdvsylkldakasyyvpltkekdlvlaarvalgyisgygtkd 190
                     +       k+ +g +  s++++ l  d++d+++fP+rG+ ++++ +f+g  +ggdv++++ d k+  +++l+ +++ v+++ +a+  i gy ++ 
      AHX11613.1 532 DS-----VKKTAGSKVLSAIGYILFLDKLDNYFFPSRGYAVRFGHKFAG--VGGDVKFVRQDLKIGGFQSLF-NQNAVVSLILAGRAIYGYDGQA 618
                     66.....3899**************************************..*********************.6788888888888888999999 PP

                     .--GGG-B-BSSTTSSTEE-TT-BS-EEE.EEEE--BSEEEEEEEEEEEE-SSS-GGTTEEEEEEEEEEEEE-TT--TTTTTTS--TTTS-EEEE CS
  Bac_surface_Ag 191 elpfyerFyaGGsnsvRGfesgglgprde.sgdalGGdsyavaslElrfplpflkkqnsvrlalFfDaGnvwdkegqspsssrsasstaeirasv 284
                      + +++rF+    n +RGf+  g+gprd  +++alGG+ ++ +++E+r+pl +l+ +  ++ alF+ +G+v+  +g +++  +s      +r+sv
      AHX11613.1 619 -VDINHRFF---GNEMRGFAIEGIGPRDVdTNNALGGQLFLLGTTEVRTPL-KLPAELDLKAALFYEVGSVTWINGAANDVYDS----GALRSSV 704
                     .*******9...3589*************999******************8.9998888********************98874....578**** PP

                     EEEEEEEETTEEEEEEEEEEEE-STT--EESEEEEE CS
  Bac_surface_Ag 285 GvgLrwqsPlGPlrfdyAiplkkedgdktqrFqFgi 320
                     G+g+ w  PlG lr+d+A +l k + dk ++++Fg+
      AHX11613.1 705 GAGIIWSGPLGVLRVDVARALVKDKMDKVSTIKFGV 740
                     **********************************96 PP

>> POTRA  Surface antigen variable number repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.8   0.1   6.9e-06     0.031       3      48 ..      22      63 ..      20      87 .. 0.81
   2 !   25.2   0.1   4.2e-09   1.9e-05       3      79 ..      90     164 ..      88     165 .. 0.88
   3 !   42.4   1.1   1.7e-14   7.8e-11       3      80 .]     170     254 ..     168     254 .. 0.88
   4 !   31.3   0.2   5.1e-11   2.3e-07       1      78 [.     257     333 ..     257     335 .. 0.88
   5 !   48.4   1.2   2.3e-16     1e-12       2      80 .]     339     410 ..     338     410 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 6.9e-06
                EEEEEEES.SSS-HHHHHTTTSSSTTSBHCHHHHHHHHHHHHHHHH CS
       POTRA  3 ikkinfeGnkktkdeelrrelelkegdvynpekleadkealksrya 48
                +++i+++Gn++++++ +r++l++k g+ + p+ l+a  +    ++ 
  AHX11613.1 22 VNEISISGNRRVEQSIIRELLGVKLGQDLQPDSLNALFK----KLD 63
                899************************999999999988....444 PP

  == domain 2  score: 25.2 bits;  conditional E-value: 4.2e-09
                 EEEEEEES.SSS-HHHHHTTTSSSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EEEEEEHSSTTSEEEEEEEEEEEE CS
       POTRA   3 ikkinfeGnkktkdeelrrelelkegdvynpekleadkealksryanlGyfdasVqvelpeddedknrvdltinvdE 79 
                  +++ ++Gnk ++++ ++++l+ +e+ +++p+ +e+ + alk++y++      ++++++  ++ d+nr+dl+++++E
  AHX11613.1  90 LRDVIVSGNKLLSTSAVLKILGCRENTLFDPQAFENNLFALKNYYRSSIKEGTKIEYQK--IPIDENRIDLEVKIRE 164
                 689******************************************99888776776644..6778888889999998 PP

  == domain 3  score: 42.4 bits;  conditional E-value: 1.7e-14
                 EEEEEEES.SSS-HHHHHTTTSSSTT.........SBHCHHHHHHHHHHHHHHHHCTT-EE.EE....EEEEHSSTTSEEEEEEEEEEEE- CS
       POTRA   3 ikkinfeGnkktkdeelrrelelkeg.........dvynpekleadkealksryanlGyfdasV....qvelpeddedknrvdltinvdEg 80 
                 i++i+f+Gn+k++d  l+r+++ ke           +y+++kle d+e l+ +y+ +Gyfd  V    +v      ++ n v+l +++ Eg
  AHX11613.1 170 IRSIQFVGNEKYSDVSLKRVIRSKEIsvfrlfgtsHYYSRDKLELDEEILRTFYRTQGYFD-YVlkgaKV-----VKQDNGVSLQFKISEG 254
                 99*******************98777788888888**************************.78787744.....45566677*******8 PP

  == domain 4  score: 31.3 bits;  conditional E-value: 5.1e-11
                 EEEEEEEEES..SSS-HHHHHTTTSSSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EEEEEE.HSSTTSEEEEEEEEEEE CS
       POTRA   1 vkikkinfeG.nkktkdeelrrelelkegdvynpekleadkealksryanlGyfdasVqvel.peddedknrvdltinvd 78 
                 ++++ki++      ++ ++l +e+++ egd++n + ++++  ++ +++++ Gy + +V++e  +++d+ +n   +t++v+
  AHX11613.1 257 YRFGKIEIAAsQADLDAKKLYKEISMAEGDIFNIDAVSRTSAKILNALNKDGYTFMDVVPEYsQSKDGSVN---VTYRVV 333
                 6778888875344889999**********************************999**8888778888888...***996 PP

  == domain 5  score: 48.4 bits;  conditional E-value: 2.3e-16
                 EEEEEEEES.SSS-HHHHHTTTSSSTTSBHCHHHHHHHHHHHHHHHHCTT-EE.EEEEEE.HSSTTSEEEEEEEEEEEE- CS
       POTRA   2 kikkinfeGnkktkdeelrrelelkegdvynpekleadkealksryanlGyfdasVqvel.peddedknrvdltinvdEg 80 
                 ki+kin+ Gn kt+d+++rre  l e+d+y p+k+ ++++    r++nlG+fd +V++e+ +    d+    l+i+v+E+
  AHX11613.1 339 KIRKINILGNVKTRDYVIRRETLLSENDIYYPAKIAESRR----RILNLGFFD-EVSIEErQ---LDNQSLELNIRVKER 410
                 79**************************************....*********.**998854...4555555*****996 PP

>> POTRA_1  POTRA domain, FtsQ-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.0   1.8e-05     0.079       2      30 ..      21      49 ..      20      68 .. 0.90
   2 !   10.2   0.0   0.00016      0.71       3      31 ..      90     118 ..      90     131 .. 0.81
   3 ?   -2.4   0.0       1.4   6.1e+03       3      24 ..     170     191 ..     169     204 .. 0.81
   4 !    6.5   0.4    0.0023        10       2      69 .]     339     410 ..     338     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.8e-05
                XX-EEEEES-SS--HHHHHHHHHTTSTT- CS
     POTRA_1  2 pikqvevsGnkhlsseeiikalgiekgts 30
                +++++++sGn+++ +  i++ lg++ g+ 
  AHX11613.1 21 NVNEISISGNRRVEQSIIRELLGVKLGQD 49
                689*********************99875 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00016
                 X-EEEEES-SS--HHHHHHHHHTTSTT-G CS
     POTRA_1   3 ikqvevsGnkhlsseeiikalgiekgtsl 31 
                 +++v vsGnk ls+ +++k+lg  ++t +
  AHX11613.1  90 LRDVIVSGNKLLSTSAVLKILGCRENTLF 118
                 589******************99887643 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 1.4
                 X-EEEEES-SS--HHHHHHHHH CS
     POTRA_1   3 ikqvevsGnkhlsseeiikalg 24 
                 i++++++Gn+  s+  ++++++
  AHX11613.1 170 IRSIQFVGNEKYSDVSLKRVIR 191
                 7899999*99999888877765 PP

  == domain 4  score: 6.5 bits;  conditional E-value: 0.0023
                 XX-EEEEES-SS--HHHHHHHHHTTSTT-GGGS-HHHHHHHHHH-TTEEEEEEEEE.TTT...EEEEEEEC- CS
     POTRA_1   2 pikqvevsGnkhlsseeiikalgiekgtslfsldleaieqrleklpwvksasVrrq.wPn...tleitveEr 69 
                 +i+++++ Gn  + +  i+++  +++++ +   ++++ ++r++ l   +++s++ + + n    l+i+v+Er
  AHX11613.1 339 KIRKINILGNVKTRDYVIRRETLLSENDIYYPAKIAESRRRILNLGFFDEVSIEERqLDNqslELNIRVKER 410
                 89***************************************************8553777655588999997 PP

>> POTRA_2  POTRA domain, ShlB-type
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0   0.00044         2       3      43 ..      22      62 ..      21      64 .. 0.95
   2 ?   -3.4   0.0       1.9   8.7e+03      64      75 ..      75      86 ..      73      86 .. 0.87
   3 ?   -3.1   0.0       1.6   7.4e+03       4      23 ..      91     110 ..      90     121 .. 0.83
   4 ?   -1.7   0.0       0.6   2.7e+03       3      24 ..     170     191 ..     169     194 .. 0.85
   5 !    4.6   0.0    0.0063        28      16      71 ..     273     328 ..     261     330 .. 0.83

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.00044
                .SEEEEESGCCSSHCCHHHHHCCCSSSEEEHHHHHHHHHHH CS
     POTRA_2  3 ikkielegntllsleeleallqpylgkclgladlnqlakel 43
                +++i + gn++++++ +++ll   lg++l+   ln+l k+l
  AHX11613.1 22 VNEISISGNRRVEQSIIRELLGVKLGQDLQPDSLNALFKKL 62
                899**********************************9987 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.9
                EETTEEEEEEE- CS
     POTRA_2 64 lesGtlklkVve 75
                + sG+lk+ V+e
  AHX11613.1 75 FTSGVLKVHVTE 86
                689******987 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.6
                 SEEEEESGCCSSHCCHHHHH CS
     POTRA_2   4 kkielegntllsleeleall 23 
                 +++ + gn+lls++++ ++l
  AHX11613.1  91 RDVIVSGNKLLSTSAVLKIL 110
                 6788999**99999887775 PP

  == domain 4  score: -1.7 bits;  conditional E-value: 0.6
                 .SEEEEESGCCSSHCCHHHHHC CS
     POTRA_2   3 ikkielegntllsleeleallq 24 
                 i++i++ gn+ +s+  l+++++
  AHX11613.1 170 IRSIQFVGNEKYSDVSLKRVIR 191
                 899********99988888765 PP

  == domain 5  score: 4.6 bits;  conditional E-value: 0.0063
                 HCCHHHHHCCCSSSEEEHHHHHHHHHHHHHHHHHTT-TT-EEEEEECCEETTEEEE CS
     POTRA_2  16 leeleallqpylgkclgladlnqlakeltnayiekGYvtsrvllppqdlesGtlkl 71 
                  ++l + +  ++g   ++  +++ ++++ na+ ++GY    v+ +  + ++G +++
  AHX11613.1 273 AKKLYKEISMAEGDIFNIDAVSRTSAKILNALNKDGYTFMDVVPEYSQSKDGSVNV 328
                 5566666677788888899999**********************998899999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (744 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       422  (0.0235373); expected 358.6 (0.02)
Passed bias filter:                      328  (0.0182944); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.43
# Mc/sec: 5172.60
//
Query:       AHX11614.1  [L=353]
Description: RIP metalloprotease RseP [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.3e-71  239.1   1.5    4.9e-71  238.9   1.5    1.0  1  Peptidase_M50   Peptidase family M50
    1.1e-12   47.6   0.0    1.9e-12   46.8   0.0    1.5  1  PDZ_6           PDZ domain
    1.5e-08   34.8   0.0    3.8e-08   33.5   0.0    1.7  2  PDZ_2           PDZ domain
    2.4e-07   31.0   0.1    9.5e-07   29.1   0.0    1.9  2  PDZ             PDZ domain
    0.00016   21.4   0.1    0.00016   21.4   0.1    2.7  3  Peptidase_M50B  Peptidase M50B-like
  ------ inclusion threshold ------
      0.027   14.8   0.1      0.027   14.8   0.1    3.0  4  DUF3267         Putative zincin peptidase


Domain annotation for each model (and alignments):
>> Peptidase_M50  Peptidase family M50
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.9   1.5   1.7e-74   4.9e-71       6     249 ..       2     338 ..       1     339 [. 0.95

  Alignments for each domain:
  == domain 1  score: 238.9 bits;  conditional E-value: 1.7e-74
                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..............XXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxx RF
  Peptidase_M50   6 lgilvvvHElGHflvAklcgvkveefsigfGpkllsfk.kgeteYaiallpLGGyVkmageepeeelseeeaka..........flkkspwqrlli 90 
                    ++++v+ HE+GH+++Ak++gvkveefsigfG++ll+f+ + +t+++++++p GGyVkm+g+ +e++ +++e+ +          ++ k++ q++l+
     AHX11614.1   2 VSVIVFAHEFGHYIFAKMFGVKVEEFSIGFGKELLGFNdRSGTRWKFSMIPAGGYVKMFGDADETSAPDNEKIRhmqddvksrtLHCKPLYQKALV 97 
                    789***********************************************************9999888888889********************* PP

                    XXXXXXXXXXXXXXXXXX............................................................................-E CS
                    xxxxxxxxxxxxxxxxxx............................................................................xx RF
  Peptidase_M50  91 vlAGplanfilailvfvv............................................................................pk 110
                    +++Gplanfi+a+l++ +                                                                            p+
     AHX11614.1  98 IFGGPLANFIFAFLLLSFlygylgkvtvdpivtsvvaespaahagfqvgdkilkmngtpvagfdkvkqfvylnrereisfvvlrdgkelfiqatPR 193
                    ****************999**********************************************************9999999999999998854 PP

                    EECE....CTTTSCEE-SEEEC-..XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxx....xxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 111 kske....seeekrgviGvspkp..vkkegllealkegvektlkvvvltvkalgklitgklslktlggpisiaqlaseaaeaglssflqllalisv 200
                     ++     +++e+  ++G++ +   ++k +++ a+k ++ ++ +v++ t+k lg+ i g  s++ +ggpi ia++++++++ g  ++++++a++s+
     AHX11614.1 194 IESGtdifGNQENLPRLGIESSIvhYSKVSPMTAMKLSIIEVGNVIRSTLKILGQTIIGRSSPDSIGGPIKIAKYSGQSFQRGYAMVIWFMAMLSI 289
                    444466888899999999988775588999****************************************************************** PP

                    XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Peptidase_M50 201 nLgilNLlPipvLDGghllfalleairrkplserkeevanlvglallll 249
                    nLg++NL+Pip+LDGghllf+l+e+i++ ++ ++ +e+a++vg+a+ll+
     AHX11614.1 290 NLGLFNLFPIPMLDGGHLLFYLIEWINGDKVAVKYQEWASKVGIAILLA 338
                    ***********************************************97 PP

>> PDZ_6  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.8   0.0   6.5e-16   1.9e-12       1      56 []     128     181 ..     128     181 .. 0.95

  Alignments for each domain:
  == domain 1  score: 46.8 bits;  conditional E-value: 6.5e-16
       PDZ_6   1 vVtaVdpgsPAdrAGlrvGDiilsvNGqpveglsladvaallrgsagesvvlvvrr 56 
                 +Vt+V+++sPA++AG++vGD il+ NG+pv     + v++ +  + ++++++vv r
  AHX11614.1 128 IVTSVVAESPAAHAGFQVGDKILKMNGTPV--AGFDKVKQFVYLNREREISFVVLR 181
                 69****************************..***********9999999999977 PP

>> PDZ_2  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.5   0.0   1.3e-11   3.8e-08      16      76 ..     127     186 ..     118     191 .. 0.87
   2 ?   -4.0   0.0         6   1.8e+04      61      69 ..     316     324 ..     310     326 .. 0.81

  Alignments for each domain:
  == domain 1  score: 33.5 bits;  conditional E-value: 1.3e-11
                 EEEEEE-TTSGGGGT.--TT-EEEEETTB--SSHHHHHHHHHTS-TT-EEEEEEEETTEEE CS
       PDZ_2  16 vlvvsVkeggPaakaglkagDvilkvdgkkvksledlislllkkkpGdtVkltvlRdgkkk 76 
                  +v+sV  ++Paa ag++ gD+ilk +g++v   +++++ ++     +++++ vlRdgk++
  AHX11614.1 127 PIVTSVVAESPAAHAGFQVGDKILKMNGTPVAGFDKVKQFVY-LNREREISFVVLRDGKEL 186
                 5899***************************99999888887.445689*********986 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 6
                 TT-EEEEEE CS
       PDZ_2  61 pGdtVkltv 69 
                 +Gd+V +++
  AHX11614.1 316 NGDKVAVKY 324
                 689999988 PP

>> PDZ  PDZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.0   3.2e-10   9.5e-07      29      66 ..     128     165 ..     122     180 .. 0.79
   2 ?   -1.8   0.0       1.3     4e+03      27      50 ..     216     239 ..     189     241 .. 0.67

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 3.2e-10
                 EEEEECTTSHHHHHTSSTTEEEEEETTEETTTSHHHHH CS
         PDZ  29 fvsevlpggaaeadglkvGDkIlsvNgvdvenvsheea 66 
                 +v++v++ ++a+ +g +vGDkIl++Ng++v+++ + ++
  AHX11614.1 128 IVTSVVAESPAAHAGFQVGDKILKMNGTPVAGFDKVKQ 165
                 79******5555555****************9965544 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.3
                 SEEEEEECTTSHHHHHTSSTTEEE CS
         PDZ  27 gifvsevlpggaaeadglkvGDkI 50 
                  ++ s+v+p+ a + + ++vG +I
  AHX11614.1 216 IVHYSKVSPMTAMKLSIIEVGNVI 239
                 455578888877777778888777 PP

>> Peptidase_M50B  Peptidase M50B-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.4   0.1   5.5e-08   0.00016      23      75 ..       4      57 ..       1      58 [. 0.77
   2 ?   -1.3   0.2      0.48   1.4e+03      65      88 ..      93     115 ..      87     134 .. 0.65
   3 ?   -0.9   1.5      0.37   1.1e+03      97     138 ..     279     320 ..     260     351 .. 0.55

  Alignments for each domain:
  == domain 1  score: 21.4 bits;  conditional E-value: 5.5e-08
  Peptidase_M50B 23 lvvffHElGHalaalLtGgrvkgielhsdes..GvtvtrgpgglgqiltllaGYl 75
                    + vf+HE+GH ++a+++G +v+++++   ++  G+   +g ++++  ++ ++GY+
      AHX11614.1  4 VIVFAHEFGHYIFAKMFGVKVEEFSIGFGKEllGFNDRSG-TRWKFSMIPAGGYV 57
                    689*********************9987754336666666.55556677777775 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.48
  Peptidase_M50B  65 gqiltllaGYlgpallGlllills 88 
                     +++l++++G+l+  ++  +l+l+ 
      AHX11614.1  93 QKALVIFGGPLANFIFA-FLLLSF 115
                     56788888888765444.444433 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.37
  Peptidase_M50B  97 lvllvllllvllllvrnlfglvlllllgallllvlllaedel 138
                     +v+ ++++l++ l   nlf++ +l +  +l++l+ +++ d++
      AHX11614.1 279 MVIWFMAMLSINLGLFNLFPIPMLDGGHLLFYLIEWINGDKV 320
                     444444455555555555555555555666666666655533 PP

>> DUF3267  Putative zincin peptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.1   8.9e-06     0.027       3      53 ..       4      51 ..       2      53 .. 0.80
   2 ?   -1.3   0.2      0.88   2.6e+03      55      72 ..     107     124 ..      91     152 .. 0.48
   3 ?   -0.9   0.2      0.66     2e+03      42      69 ..     270     297 ..     260     317 .. 0.57
   4 ?   -2.0   0.1       1.5   4.5e+03      80      93 ..     334     347 ..     324     352 .. 0.61

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 8.9e-06
     DUF3267  3 vlvilHEllHglffklfgkkpkkkvkfgi.klliayatsseallskkqfiii 53
                v+v+ HE+ H +f k+fg+k+  ++++g+ k l  +  +s+   ++++f +i
  AHX11614.1  4 VIVFAHEFGHYIFAKMFGVKV-EEFSIGFgKELLGFNDRSG---TRWKFSMI 51
                7899*************9975.7888888888777777766...66777665 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.88
     DUF3267  55 laPfvllgilllllalll 72 
                 ++ f+ll++l  +l+ ++
  AHX11614.1 107 IFAFLLLSFLYGYLGKVT 124
                 333444444444444443 PP

  == domain 3  score: -0.9 bits;  conditional E-value: 0.66
     DUF3267  42 eallskkqfiiillaPfvllgillllla 69 
                 ++ +++   ++i ++ ++ +++ l+ l+
  AHX11614.1 270 GQSFQRGYAMVIWFMAMLSINLGLFNLF 297
                 5555666666666666666665555444 PP

  == domain 4  score: -2.0 bits;  conditional E-value: 1.5
     DUF3267  80 llllalnaagsagD 93 
                 ++lla+ ++++++D
  AHX11614.1 334 AILLAILVFAAFND 347
                 45555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (353 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.47u 0.24s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2580.41
//
Query:       AHX11615.1  [L=281]
Description: GHMP kinase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    3.4e-07   30.4   1.0    5.8e-07   29.7   1.0    1.4  1  GHMP_kinases_N  GHMP kinases N terminal domain
    1.9e-05   25.0   0.0    3.7e-05   24.0   0.0    1.4  1  GHMP_kinases_C  GHMP kinases C terminal
  ------ inclusion threshold ------
      0.085   13.0   0.0        2.6    8.1   0.0    2.2  2  BspA_v          Adhesin BspA variable domain


Domain annotation for each model (and alignments):
>> GHMP_kinases_N  GHMP kinases N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   1.0   9.6e-11   5.8e-07       1      65 [.      88     143 ..      88     144 .. 0.89

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 9.6e-11
                     EEEEEESSHTTSSSCHHHHHHHHHHHHHHHHTTEHHHHHHHHHHHHHHHHHHHHHSHHHHHHHHS CS
  GHMP_kinases_N   1 divikseiPvgaGLGSSAAlavalvaAllallglsleeaklaleaerlaqggngsggDvaasvyG 65 
                     d++i+++iPv+aG+G+++A+a+al++ + + +        +++   r++  + + g D  a+++G
      AHX11615.1  88 DVRITKNIPVAAGMGGGSADAAALLRYFSSVY-------SISAPVLREI--ALSIGLDTIACLHG 143
                     689*****************************.......5777777766..58899999999998 PP

>> GHMP_kinases_C  GHMP kinases C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0   6.2e-09   3.7e-05      25      81 ..     215     270 ..     199     273 .. 0.87

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 6.2e-09
  GHMP_kinases_C  25 lkavvgilppeleelleal.selGalgaklsGaGgGptvfalfkdkdeaeqvaralre 81 
                     l++ + ++ p+++++l+ +   +G   akl+G+  Gpt++++f+++++  ++ ++lr+
      AHX11615.1 215 LTDAAICIAPVIRDVLNDIrNCVGNKFAKLCGS--GPTCIGVFDTEENLGNACSKLRR 270
                     566889999************************..***********999999888865 PP

>> BspA_v  Adhesin BspA variable domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0   0.00044       2.6      15      71 ..      32      91 ..      26     100 .. 0.83
   2 ?    2.6   0.0     0.023   1.4e+02      85     108 ..     175     198 ..     169     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00044
      BspA_v 15 dGsfelthdmidGvkiiGtGkltGkvnyvvva...ngdGsvtvkvssidlykyeyrnvak 71
                d  f +thd  d +++i   +    v++   +   ++  s+t ++s i+ y   y +v+ 
  AHX11615.1 32 DSFFCFTHDFCDTIELISSTQSVHSVEFLNAShpiESQNSITKVLSFIESYADSYFDVRI 91
                66799***************9999999988873335889999999999999999987754 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.023
      BspA_v  85 tkdgneiyeklhnGnnsftdtlnk 108
                  +d+ ++y  +h+ + +f+++l++
  AHX11615.1 175 AVDTSMVYRCFHESDAAFSAKLEN 198
                 579999*************99865 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (281 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       303  (0.0169); expected 358.6 (0.02)
Passed bias filter:                      278  (0.0155056); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.45u 0.23s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 2070.96
//
Query:       AHX11616.1  [L=801]
Description: DNA gyrase, B subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-56  189.9   0.0      4e-56  189.2   0.0    1.3  1  DNA_gyraseB    DNA gyrase B
    2.8e-27   94.7   0.0    5.7e-27   93.7   0.0    1.5  1  DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
    1.6e-22   80.1   0.3    6.1e-22   78.2   0.2    2.0  2  HATPase_c      Histidine kinase-, DNA gyrase B-, and HSP90-li
    2.4e-17   63.0   0.0    4.1e-16   59.1   0.0    2.5  2  Toprim         Toprim domain
    0.00013   21.8   0.1    0.00025   20.9   0.1    1.5  1  HATPase_c_3    Histidine kinase-, DNA gyrase B-, and HSP90-li
  ------ inclusion threshold ------
      0.047   14.2   0.0        0.2   12.1   0.0    2.1  1  Toprim_4       Toprim domain


Domain annotation for each model (and alignments):
>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  189.2   0.0   1.3e-59     4e-56       1     173 [.     242     411 ..     242     412 .. 0.99

  Alignments for each domain:
  == domain 1  score: 189.2 bits;  conditional E-value: 1.3e-59
  DNA_gyraseB   1 GlkdfveelnkdkkelikevlsvegekaveevievevalqwtssysenilsFvNniatpeGGtHvdgfksaltktlneyakkkkllkkkeekisgedi 98 
                  G ++fv +l+++k+ ++ +++ ++ge+  ++ + +++a+qw++sy enil+F+Nni +++GGtH++++k+a+t+++n y+ k++l+kk++ ++sg+di
   AHX11616.1 242 GAEEFVAYLDRNKEHIHPDPIRISGET--DS-VMMDIAMQWNTSYYENILCFTNNICQKDGGTHLAALKNAMTRVVNHYITKENLIKKEKIAVSGDDI 336
                  779************************..77.****************************************************************** PP

  DNA_gyraseB  99 regltavvsvkipepqFeGQTKekLgnsevksivekvvseeleafleenkeeakkilekaveaakareaarkare 173
                  reglta++svk+p+p+F +QTKekL +sevk+++ek+v + l+a+leen+  ak i++k+ve+a areaa+kar+
   AHX11616.1 337 REGLTAILSVKLPDPKFSSQTKEKLISSEVKPAIEKMVGDGLAAWLEENPLRAKLIAKKIVESALAREAAKKARD 411
                  *************************************************************************97 PP

>> DNA_gyraseB_C  DNA gyrase B subunit, carboxyl terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.7   0.0   1.9e-30   5.7e-27       2      62 ..     729     789 ..     728     790 .. 0.96

  Alignments for each domain:
  == domain 1  score: 93.7 bits;  conditional E-value: 1.9e-30
  DNA_gyraseB_C   2 kkveiqRfKGLGEmnpeqLweTTmdpetRrLlqvtiedaeeadelfstLmGkkvepRrefi 62 
                    ++v +qRfKGLGEmnpeqLw TT+dp++R++ +vtie+a+ ad++fs+LmG+ v+pRr+fi
     AHX11616.1 729 SGVGLQRFKGLGEMNPEQLWSTTLDPKNRTIFKVTIEEASVADQMFSMLMGDAVAPRRDFI 789
                    56789*******************************************************9 PP

>> HATPase_c  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.2   0.2   2.1e-25   6.1e-22       2      95 ..      50     158 ..      49     192 .. 0.83
   2 ?   -2.1   0.0       1.8   5.3e+03      68     109 ..     723     765 ..     705     767 .. 0.70

  Alignments for each domain:
  == domain 1  score: 78.2 bits;  conditional E-value: 2.1e-25
                 HHHHHHHHHHHHHHHHHHH..HSTTTEEEEEEEEEETEEEEEEEESSSSSTTHHHT.............GTCSTTCHHCSTCHTSTSSSHHHHHHHHHH CS
   HATPase_c   2 dekrLrqiisnlvdNavkf..atkageieveikaseddlvisveDnGiGipkedlk.............klfekfsqddstkrggggtGlGlsivkklv 85 
                 d ++L+q++ +++dNav++  a+++++i+v +   + d ++sveDnG+G+p ++++             + ++kf+q ds+k++gg +G+G+s+v++l+
  AHX11616.1  50 DGSGLHQMVYEVIDNAVDEslAGHCSTIRVVVG--S-DGSVSVEDNGRGMPTDMHEegisaaevimtqlHAGGKFDQ-DSYKISGGLHGVGVSVVNALS 144
                 7789***************66568888888888..6.9*****************************666666****.********************* PP

                 HHTTTEEEE....E CS
   HATPase_c  86 elmgGeiwv....e 95 
                 + ++ +iw+    +
  AHX11616.1 145 DWLKLTIWRngktH 158
                 *9999***933330 PP

  == domain 2  score: -2.1 bits;  conditional E-value: 1.8
                 CHTSTSSSHHHHHHHHHHHHTT.TEEEEEEET.TTEEEEEEEEE CS
   HATPase_c  68 krggggtGlGlsivkklvelmg.Geiwvesep.grGttftftlp 109
                 ++    +G+Gl   k l e m+  ++w ++ + +  t f +t+ 
  AHX11616.1 723 ADAIAKSGVGLQRFKGLGE-MNpEQLWSTTLDpKNRTIFKVTIE 765
                 3445678888988888888.887788884444366777877765 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.9   0.0      0.18   5.4e+02       4      37 ..     396     433 ..     395     438 .. 0.91
   2 !   59.1   0.0   1.4e-19   4.1e-16       1      93 [.     440     541 ..     440     553 .. 0.87

  Alignments for each domain:
  == domain 1  score: 0.9 bits;  conditional E-value: 0.18
                 EESSHHHHHHHHHTHT....STEEEEEEESSSSEEEHS CS
      Toprim   4 ivEgpsdaktiakalg....sgfqavtaslGhildlet 37 
                 ivE+  + ++++ka++    +g++++t + G++ d ++
  AHX11616.1 396 IVESALAREAAKKARDltrrKGGLEITTLPGKLADCQE 433
                 89************99999999*********9999876 PP

  == domain 2  score: 59.1 bits;  conditional E-value: 1.4e-19
                 EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHS.TTEEEEE..ECTTTHHHHHH......HHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHTHH CS
      Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildlet.efkpvye..eiedkkkvlka......lkelakradeiilatDpDreGeaiawellevlkel 90 
                 el ivEg+s+ +++++ +++++qav++++G+il++e+ +f +++   ei + +++l++      ++  + r+++ii++tD+D++G +i+++ll+++ ++
  AHX11616.1 440 ELLIVEGDSAGGSAKQGRDRKTQAVLPLRGKILNVEKtRFHKIIGsaEIGNLITALGTnigkedFNIGKIRYHKIIIMTDADVDGLHIRTLLLTFFFRY 538
                 699**********************************77777777999999999999999889999999*************************99966 PP

                 HTT CS
      Toprim  91 len 93 
                 +++
  AHX11616.1 539 ARE 541
                 665 PP

>> HATPase_c_3  Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.9   0.1   8.4e-08   0.00025       5      88 ..      56     146 ..      52     168 .. 0.68

  Alignments for each domain:
  == domain 1  score: 20.9 bits;  conditional E-value: 8.4e-08
  HATPase_c_3   5 kAlaelvdNsld....AdaenvkievnknrgktgeivieDdGkGmseeelknalrlatsskeakr.......ksts....lGkkGiGlklAslslgkk 87 
                  + + e++dN++d    +++ ++ ++v  +    g++++eD+G Gm+ +  +++++ a+   ++ +       +  s     G +G+G   +++  +++
   AHX11616.1  56 QMVYEVIDNAVDeslaGHCSTIRVVVGSD----GSVSVEDNGRGMPTDMHEEGISAAEVIMTQLHaggkfdqD--SykisGGLHGVG--VSVVNALSD 145
                  6689*******998877888899999886....6************998888888777766655433333221..133335667777..444444444 PP

  HATPase_c_3  88 l 88 
                  +
   AHX11616.1 146 W 146
                  4 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   6.8e-05       0.2      18      69 ..     486     526 ..     480     536 .. 0.90

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 6.8e-05
    Toprim_4  18 agiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGea 69 
                 a+i n++  lg+++  ++  ++ k+++           ++i+++d+D++G  
  AHX11616.1 486 AEIGNLITALGTNI-GKEDFNIGKIRY----------HKIIIMTDADVDGLH 526
                 6899**********.99999999****..........9***********976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.65u 0.27s 00:00:00.92 Elapsed: 00:00:00.43
# Mc/sec: 5561.69
//
Query:       AHX11617.1  [L=38]
Description: hypothetical protein NHE_0684 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       165  (0.00920297); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 293.00
//
Query:       AHX11618.1  [L=140]
Description: putative peroxiredoxin bcp [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-29  102.7   0.0    1.4e-29  102.5   0.0    1.1  1  AhpC-TSA       AhpC/TSA family
    3.3e-15   56.1   0.0    3.4e-15   56.0   0.0    1.0  1  Redoxin        Redoxin
    0.00075   19.1   0.0    0.00089   18.8   0.0    1.0  1  DUF899         Bacterial protein of unknown function (DUF899)
  ------ inclusion threshold ------
      0.022   14.9   0.0      0.033   14.3   0.0    1.3  1  AhpC-TSA_2     AhpC/TSA antioxidant enzyme
      0.077   13.0   0.0       0.15   12.0   0.0    1.4  2  CoA_binding_3  CoA-binding domain


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  102.5   0.0   3.9e-33   1.4e-29      16     122 ..       3     115 ..       1     117 [. 0.97

  Alignments for each domain:
  == domain 1  score: 102.5 bits;  conditional E-value: 3.9e-33
                 EEEECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHHHHHH-H.SSEEEE-TTSHHHHHTT-EETT......TTEC CS
    AhpC-TSA  16 etvslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkkfiekeslnfpllsDeegkvakaygvlkee......kgla 108
                 + v+ +d+ g+ +v++fypkd++p+Ct+e++++++ + +++e++ +v+g+s d+ ++h++f  +++l+f llsDe+ +v+++yg++ e+      + + 
  AHX11618.1   3 GIVDSKDLLGRNLVIYFYPKDDTPGCTQEAKDFKEGISALEELNTTVLGISKDNIKAHRNFSTRYELPFHLLSDESAEVIEKYGAWVEKsmfgkkYHGI 101
                 668899*****************************************************************************************99** PP

                 SCEEEEE-TTSBEE CS
    AhpC-TSA 109 lratfvidkegkir 122
                  r+tf++d++gk++
  AHX11618.1 102 ERSTFFVDSDGKVQ 115
                 *************8 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   0.0   9.6e-19   3.4e-15      21     135 ..       5     122 ..       1     134 [. 0.85

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 9.6e-19
                 EEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHHHHHHHHHTT-TSEEEE-TTSHHHHHTT-TTEEE.GGG.....EE CS
     Redoxin  21 vslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndafvkefwgkeglkfpvlsDgsaaftkalGlrleedaseg.....lr 114
                 v+ +++ g+++v++f+p  ++P C++e+ ++++    l+e + +v++++ dn    ++f ++++l+f++lsD+sa++ +++G+   e +s++       
  AHX11618.1   5 VDSKDLLGRNLVIYFYPKDDTPGCTQEAKDFKEGISALEELNTTVLGISKDNIKAHRNFSTRYELPFHLLSDESAEVIEKYGAW-VE-KSMFgkkyhGI 101
                 7889999**********************888885555********************************************44.44.45556899888 PP

                 E-EEEEEEETTEEEEEEESSS CS
     Redoxin 115 tpryavidedgkvvylevepe 135
                  ++++ +d dgkv  + + + 
  AHX11618.1 102 ERSTFFVDSDGKVQGIWRKVK 122
                 899**********86655554 PP

>> DUF899  Bacterial protein of unknown function (DUF899)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.0   2.5e-07   0.00089      84     176 ..      24     119 ..       9     129 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 2.5e-07
      DUF899  84 gCpgCslladhvdgalahLeardvtlavvsraplekleaykrrmGwtlpwvssaesdfnrdfnvsleeeqaseelpgl..svflrdd.grvfhtYs 176
                   pgC+  a+++ + ++ Le+ ++t+  +s+  ++   ++ +r    +++ s+ ++++ +++++ +e++   ++ +g+  s+f+ d  g+v   + 
  AHX11618.1  24 DTPGCTQEAKDFKEGISALEELNTTVLGISKDNIKAHRNFSTRYELPFHLLSDESAEVIEKYGAWVEKSMFGKKYHGIerSTFFVDSdGKVQGIWR 119
                 469*******************************************************************99999999775555554399987775 PP

>> AhpC-TSA_2  AhpC/TSA antioxidant enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.1e-06     0.033       6      54 ..      39      88 ..      34     131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.1e-06
  AhpC-TSA_2  6 kpeldaagvklvaigigdps.akkFvkltgfpfelyvDpsaklyqalglk 54
                +++l++ ++++ +i++++++  ++F  + + pf l+ D+sa++ ++ g +
  AHX11618.1 39 ISALEELNTTVLGISKDNIKaHRNFSTRYELPFHLLSDESAEVIEKYGAW 88
                5689999************66**********************9999987 PP

>> CoA_binding_3  CoA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.8   0.0       1.6   5.6e+03      88     114 ..      31      57 ..      27      69 .. 0.70
   2 ?   12.0   0.0   4.2e-05      0.15      84     140 ..      81     137 ..      74     139 .. 0.89

  Alignments for each domain:
  == domain 1  score: -2.8 bits;  conditional E-value: 1.6
  CoA_binding_3  88 ggeelakqiranpelgfrvvgvfddrd 114
                      +++++ i a  el+  v+g+ +d+ 
     AHX11618.1  31 EAKDFKEGISALEELNTTVLGISKDNI 57 
                    566677777777778888888877765 PP

  == domain 2  score: 12.0 bits;  conditional E-value: 4.2e-05
  CoA_binding_3  84 vavgggeelakqiranpelgfrvvgvfddrddarseevagvpvlgnladlveyvret 140
                    v+ ++g+ ++k +  ++  g++++ +f d+d + +  +++v+v g +ad++e++r++
     AHX11618.1  81 VIEKYGAWVEKSMFGKKYHGIERSTFFVDSDGKVQGIWRKVKVQGHVADVLEFIRKH 137
                    56677778888888888899***********9999999*****************87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (140 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      348  (0.0194099); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.25s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 999.26
//
Query:       AHX11619.1  [L=474]
Description: solute symporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.5e-48  165.7  31.7    3.1e-48  164.6  31.7    1.5  1  SSF          Sodium:solute symporter family
  ------ inclusion threshold ------
       0.11   12.3   0.1       0.22   11.3   0.1    1.5  1  Prenyltrans  Prenyltransferase and squalene oxidase repeat


Domain annotation for each model (and alignments):
>> SSF  Sodium:solute symporter family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.6  31.7   3.5e-52   3.1e-48       1     394 [.      32     406 ..      32     418 .. 0.92

  Alignments for each domain:
  == domain 1  score: 164.6 bits;  conditional E-value: 3.5e-52
         SSF   1 yflagrsltgfvlglslaasnisaasfvGlaGavaasGlavvllelgalllvlllllllaerlr....nagalTlpdylskRfkgkrilvylsalslll 95 
                 y++a+rs+  +  g+s  + +is + f  +a ++++ Gl+ ++++lg+ +  +l++ +la+rlr     ++a+T+p+yl++Rf++   + ++++ +++ 
  AHX11619.1  32 YIIANRSIHEIIAGISHVSAEISIGTFTVVASMIYTIGLSRLWIDLGFFVFGILSWQFLAKRLRaqteANNAITIPQYLANRFGSDT-IGIIASGIIIF 129
                 99****************************************************************9999*****************.89999999999 PP

         SSF  96 vitlklsvdlvggaklielalGlnyetavlllaaltalYtviGGllAvvytdtiqavlmlvgalilliivllevG..gleslveklkeaapkvvdlltp 192
                 + t+++ ++++g  k i  ++ ++ e+  + +  +t+lYt++GG++++ yt+++q+++m+++al+l++  +l++G   l ++++k  +  p  + ++ +
  AHX11619.1 130 FTTTYIGANMLGLIKVISRIIDIKPEVIGFSVFSTTTLYTIVGGFRSTCYTNVLQGTVMILAALLLPLSLFLQFGtePLTEFFRKSGAGGP--ASINIG 226
                 ***************************************************************************8888999999988888..333333 PP

         SSF 193 dslkllrdpltalslwlglvlGvaglphilvRflaakdakailkgvlkltivlilvligmisiilfaiklagavpkavgtevgvsniaypeLvvkllpn 291
                 ++           +l   +   ++g ph++ +fl++ +  +i +++  ++ + +l++ g+ +  ++aikl          + + s++ +  L +   ++
  AHX11619.1 227 QA-----------LLYFSFASAIFGTPHTITKFLSIRSCGSISTARNTSIALNALIYCGIAVSAIYAIKLLP--------SSTDSEMLLFYLSKMFSNP 306
                 33...........3333444445667*********************************8888888888765........5899*************** PP

         SSF 292 llaGlllavmlAaimstltslllsassaftkDlYkkirrkasakekelvgvsriivlvvislaillavqeeqkgvlklvelafaglasavlavillalf 390
                 l+  +++ +m+Aa+mst++++l+ ++s +++D+Y  +r+++  ++ +l+ v+r++ +++++la+l+ + + ++ v +l  +   gl+s +++vil++l+
  AHX11619.1 307 LVESIIVLAMIAAVMSTIDAQLVLSASCMVNDVYRYFRPNQ--NDIHLISVARLANVIIGMLALLVSLIFSKS-VGTLAIFSLTGLGSSIGPVILFSLY 402
                 ***************************************99..999********************9999999.9************************ PP

         SSF 391 wkrv 394
                  k  
  AHX11619.1 403 TKAR 406
                 9865 PP

>> Prenyltrans  Prenyltransferase and squalene oxidase repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   2.5e-05      0.22      23      44 .]     253     274 ..     252     274 .. 0.96

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.5e-05
                  STTSSBBHHHHHHHHHHHHHCT CS
  Prenyltrans  23 rpgsesdtyytywalaaLallG 44 
                  ++gs s++++t +al+aL+++G
   AHX11619.1 253 SCGSISTARNTSIALNALIYCG 274
                  69******************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       803  (0.0447878); expected 358.6 (0.02)
Passed bias filter:                      319  (0.0177924); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.56u 0.29s 00:00:00.85 Elapsed: 00:00:00.44
# Mc/sec: 3257.74
//
Query:       AHX11620.1  [L=545]
Description: pentapeptide repeats family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.2e-39  131.8  35.9    6.2e-07   29.5   3.8    7.4  7  Pentapeptide_4  Pentapeptide repeats (9 copies)
    2.6e-23   81.3  32.7    2.1e-05   24.0   0.4   12.1 12  Pentapeptide    Pentapeptide repeats (8 copies)
    1.5e-14   53.8  42.3    4.4e-05   23.6   1.5    9.8 10  Pentapeptide_3  Pentapeptide repeats (9 copies)
     0.0006   19.8  26.1       0.21   11.6   0.7    5.4  7  CfAFP           Choristoneura fumiferana antifreeze protein (


Domain annotation for each model (and alignments):
>> Pentapeptide_4  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.3   2.2e-09   9.7e-06       6      75 ..      52     122 ..      47     133 .. 0.77
   2 !   15.5   0.0   3.3e-06     0.015       2      68 ..     118     184 ..     103     204 .. 0.48
   3 !   14.3   0.0   7.4e-06     0.033      12      65 ..     163     216 ..     147     226 .. 0.52
   4 !   29.5   3.8   1.4e-10   6.2e-07       3      69 ..     224     291 ..     222     300 .. 0.93
   5 !   28.8   0.7   2.3e-10     1e-06       3      66 ..     304     367 ..     302     371 .. 0.95
   6 !   21.3   1.4     5e-08   0.00022       2      72 ..     372     443 ..     371     448 .. 0.94
   7 !   28.2   0.7   3.5e-10   1.6e-06       8      59 ..     493     544 ..     490     545 .] 0.81

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 2.2e-09
  Pentapeptide_4   6 csfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.sdklkdi 75 
                     + f + +  n+ F+  ++++++F+++ lsnv+++++++s+++f ++     s+  + ++++ + s  l++i
      AHX11620.1  52 VDFSGFNMRNALFEGMTIENASFNNTVLSNVMLKNTVISNSNFGDAIVYGGSIIDSKIEDISLvSSDLNNI 122
                     44555555555555558888888888889999999999999999999999999999999999866678776 PP

  == domain 2  score: 15.5 bits;  conditional E-value: 3.3e-06
  Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf 68 
                     ++ +   +n++ ++++  +++l+  + +++++    ++++ + d  ++++ ++ a++  +nl+++++
      AHX11620.1 118 DLNNINIENSNIHGITSIKSHLQYLSVKDSKFGKLILKNTEIIDGILEGMTITGANIRDSNLAEIKI 184
                     3334444445555555555555555555555533333333333333333333333333333333333 PP

  == domain 3  score: 14.3 bits;  conditional E-value: 7.4e-06
  Pentapeptide_4  12 klsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlkn 65 
                     +l++++ + a++rd+n+ e+++sn +   +++ ++df+ ++l+++ +    + +
      AHX11620.1 163 ILEGMTITGANIRDSNLAEIKISNSSIMTSVIAKSDFTRAKLFDTKIDDTLFHT 216
                     344555555555555555555555555555555555555555555544444433 PP

  == domain 4  score: 29.5 bits;  conditional E-value: 1.4e-10
  Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnf.s 69 
                     ++++  n++k+ n ++s + l +c  +   ++n nF+  +++ ++f+++d+ ++s++g  ++n++f +
      AHX11620.1 224 IHNSEVNDSKFINSDLSGSILGNCLVNKMTMTNSNFEYMLIDGSNFTNTDFSNTSLEGAHISNSRFcK 291
                     7999*************************************************************955 PP

  == domain 5  score: 28.8 bits;  conditional E-value: 2.3e-10
  Pentapeptide_4   3 ftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknv 66 
                     ++ ++f ++  +n+++++++l d +F+++r+s+ +  ++n+sd+ f +vd  ++ F++++l+n+
      AHX11620.1 304 IEASQFFDSEVNNTELYKSELVDVSFRNTRISDFSIYNSNVSDAIFLDVDGQKIKFEHSELQNS 367
                     6778999999****************************************************98 PP

  == domain 6  score: 21.3 bits;  conditional E-value: 5e-08
  Pentapeptide_4   2 eftrcsfnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFsgcnlknvnfsd.kl 72 
                     +f++   n+++lsn + + ++l   n+t++ ++  n + ++++ ++f +++l+++s++ + ++n+ fs+ +l
      AHX11620.1 372 RFINLDINKSQLSNDQIRDSTLSLLNMTDSSFTISNIHGTSVDRSSFLMNSLRESSIKKSKITNSSFSRnSL 443
                     5889999************************************************************76466 PP

  == domain 7  score: 28.2 bits;  conditional E-value: 3.5e-10
  Pentapeptide_4   8 fnncklsnvnFsearlrdcnFtecrlsnvnFdecnlsdvdfaevdlkrasFs 59 
                     f++++ sn++F++++l +++Ft++ l    F++ + ++v+f +++l +++F+
      AHX11620.1 493 FRGVNYSNIDFRNTELSNADFTGAVLRGSAFSKHTTRNVKFKDANLEKTTFE 544
                     7888888888888888888888888888888888888888888888888886 PP

>> Pentapeptide  Pentapeptide repeats (8 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   1.1   4.3e-07    0.0019       3      36 ..      49      82 ..      48      86 .. 0.79
   2 !   11.6   0.6   3.6e-05      0.16       9      36 ..      70      97 ..      68      99 .. 0.67
   3 ?    1.1   0.0      0.07   3.2e+02      23      39 ..     114     130 ..     110     132 .. 0.58
   4 ?    2.8   0.0     0.021        94      18      33 ..     164     179 ..     154     188 .. 0.61
   5 !    5.6   0.0    0.0027        12       1      38 [.     197     234 ..     197     234 .. 0.90
   6 !   10.1   0.5   0.00011      0.47       2      38 ..     233     269 ..     232     269 .. 0.83
   7 !   18.7   1.1   2.2e-07     0.001      10      37 ..     266     293 ..     264     294 .. 0.65
   8 ?    2.4   0.0     0.028   1.3e+02      15      38 ..     316     334 ..     307     339 .. 0.53
   9 ?    1.7   0.0     0.046   2.1e+02      11      38 ..     391     418 ..     387     418 .. 0.82
  10 !    4.6   0.0    0.0057        26       7      40 .]     407     440 ..     401     440 .. 0.90
  11 !   24.0   0.4   4.7e-09   2.1e-05       7      35 ..     492     520 ..     492     525 .. 0.55
  12 !   20.3   0.5     7e-08   0.00031       3      39 ..     508     544 ..     508     544 .. 0.96

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 4.3e-07
                  -TT-B-CCSCCEECCCESEEECT-B-TT-EECCE CS
  Pentapeptide  3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsga 36
                  L ++++sg n+++a ++g +  +A+++++ Ls++
    AHX11620.1 49 LVDVDFSGFNMRNALFEGMTIENASFNNTVLSNV 82
                  7788888888888888888888888888888876 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 3.6e-05
                  CCSCCEECCCESEEECT-B-TT-EECCE CS
  Pentapeptide  9 sganLsganlsgAnLtgAnlsgAdLsga 36
                  ++a+++++ ls+  L ++ +s++++ +a
    AHX11620.1 70 ENASFNNTVLSNVMLKNTVISNSNFGDA 97
                  4677777777777777777777777555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.07
                   ECT-B-TT-EECCEEEC CS
  Pentapeptide  23 LtgAnlsgAdLsganLs 39 
                   L +++l++ + +++n  
    AHX11620.1 114 LVSSDLNNINIENSNIH 130
                   44556666666666654 PP

  == domain 4  score: 2.8 bits;  conditional E-value: 0.021
                   CESEEECT-B-TT-EE CS
  Pentapeptide  18 lsgAnLtgAnlsgAdL 33 
                   l+g + tgAn+++++L
    AHX11620.1 164 LEGMTITGANIRDSNL 179
                   4444555555555555 PP

  == domain 5  score: 5.6 bits;  conditional E-value: 0.0027
                   -B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   1 AnLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                   +++++A L  ++ +++ +   +L+++ ++++  +++++
    AHX11620.1 197 SDFTRAKLFDTKIDDTLFHTVKLIRSYIHNSEVNDSKF 234
                   699*********************99999988887776 PP

  == domain 6  score: 10.1 bits;  conditional E-value: 0.00011
                   B-TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide   2 nLsgAnLsganLsganlsgAnLtgAnlsgAdLsganL 38 
                    + + +Lsg++L ++  +  ++t++n++     g+n+
    AHX11620.1 233 KFINSDLSGSILGNCLVNKMTMTNSNFEYMLIDGSNF 269
                   6889999999999999999999999998877777766 PP

  == domain 7  score: 18.7 bits;  conditional E-value: 2.2e-07
                   CSCCEECCCESEEECT-B-TT-EECCEE CS
  Pentapeptide  10 ganLsganlsgAnLtgAnlsgAdLsgan 37 
                   g+n++++++s+++L gA +s+++++ ++
    AHX11620.1 266 GSNFTNTDFSNTSLEGAHISNSRFCKSC 293
                   5677777777777777777777766665 PP

  == domain 8  score: 2.4 bits;  conditional E-value: 0.028
                   ECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide  15 ganlsgAnLtgAnlsgAdLsganL 38 
                   +     + L++++l +  +++++ 
    AHX11620.1 316 N-----TELYKSELVDVSFRNTRI 334
                   3.....444444444444444443 PP

  == domain 9  score: 1.7 bits;  conditional E-value: 0.046
                   SCCEECCCESEEECT-B-TT-EECCEEE CS
  Pentapeptide  11 anLsganlsgAnLtgAnlsgAdLsganL 38 
                   + Ls  n++++++t +n++g+   ++ +
    AHX11620.1 391 STLSLLNMTDSSFTISNIHGTSVDRSSF 418
                   56777899***********999888766 PP

  == domain 10  score: 4.6 bits;  conditional E-value: 0.0057
                   B-CCSCCEECCCESEEECT-B-TT-EECCEEECT CS
  Pentapeptide   7 nLsganLsganlsgAnLtgAnlsgAdLsganLsg 40 
                   n +g++ +++++   +L+++++ +++ +++ +s+
    AHX11620.1 407 NIHGTSVDRSSFLMNSLRESSIKKSKITNSSFSR 440
                   6789999999**********************85 PP

  == domain 11  score: 24.0 bits;  conditional E-value: 4.7e-09
                   B-CCSCCEECCCESEEECT-B-TT-EECC CS
  Pentapeptide   7 nLsganLsganlsgAnLtgAnlsgAdLsg 35 
                   +++g n s+ +++++ L++A+++gA L+g
    AHX11620.1 492 DFRGVNYSNIDFRNTELSNADFTGAVLRG 520
                   45555555555555555555555555555 PP

  == domain 12  score: 20.3 bits;  conditional E-value: 7e-08
                   -TT-B-CCSCCEECCCESEEECT-B-TT-EECCEEEC CS
  Pentapeptide   3 LsgAnLsganLsganlsgAnLtgAnlsgAdLsganLs 39 
                   Ls+A+++ga L+g+ +s  + +++ + +A+L+ + ++
    AHX11620.1 508 LSNADFTGAVLRGSAFSKHTTRNVKFKDANLEKTTFE 544
                   89*******************************9995 PP

>> Pentapeptide_3  Pentapeptide repeats (9 copies)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.6   1.5   9.8e-09   4.4e-05       1      48 []      54      98 ..      51      98 .. 0.92
   2 ?   -0.1   0.0      0.24   1.1e+03      21      42 ..     112     133 ..     104     136 .. 0.82
   3 ?   -0.7   0.0      0.36   1.6e+03      19      19 ..     181     181 ..     145     219 .. 0.61
   4 ?    3.9   0.0     0.013        60      11      37 ..     223     248 ..     214     253 .. 0.82
   5 !   17.1   2.8     1e-06    0.0045       5      44 ..     253     289 ..     250     293 .. 0.79
   6 !    7.1   0.9    0.0013       5.9      15      45 ..     322     350 ..     309     353 .. 0.73
   7 ?    1.1   0.5       0.1   4.5e+02      13      43 ..     389     417 ..     378     440 .. 0.57
   8 ?    0.9   0.9      0.12   5.2e+02      17      42 ..     433     456 ..     414     467 .. 0.52
   9 !   15.2   2.0   4.1e-06     0.018       8      43 ..     489     522 ..     488     528 .. 0.79
  10 !   15.2   2.0   4.1e-06     0.018       1      39 [.     503     544 ..     503     545 .] 0.70

  Alignments for each domain:
  == domain 1  score: 23.6 bits;  conditional E-value: 9.8e-09
  Pentapeptide_3  1 FsganFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdFsgat 48
                    Fsg n+++a  F+g t ++a sF+n++++++++ ++ ++ +++F++a+
      AHX11620.1 54 FSGFNMRNA-LFEGMTIENA-SFNNTVLSNVMLKNTVIS-NSNFGDAI 98
                    888888888.9999999999.9****************9.*****985 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.24
  Pentapeptide_3  21 asFsnadFgsadFsgarFtgdv 42 
                     +s  ++d+++++ ++++++g +
      AHX11620.1 112 ISLVSSDLNNINIENSNIHGIT 133
                     46778999999*****999765 PP

  == domain 3  score: -0.7 bits;  conditional E-value: 0.36
  Pentapeptide_3  19 g 19 
                      
      AHX11620.1 181 E 181
                     2 PP

  == domain 4  score: 3.9 bits;  conditional E-value: 0.013
  Pentapeptide_3  11 dFrgatFsgaasFsnadFgsadFsgar 37 
                     + +++  +++  F n+d++++ + ++ 
      AHX11620.1 223 YIHNSEVNDS-KFINSDLSGSILGNCL 248
                     5688888999.7999999999999986 PP

  == domain 5  score: 17.1 bits;  conditional E-value: 1e-06
  Pentapeptide_3   5 nFsgaadFrgatFsgaasFsnadFgsadFsgarFtgdvdF 44 
                     +++++ +F+    +g+ +F+n+dF++ +++ga+++ +++F
      AHX11620.1 253 TMTNS-NFEYMLIDGS-NFTNTDFSNTSLEGAHIS-NSRF 289
                     67888.8888888888.888888888888888887.7776 PP

  == domain 6  score: 7.1 bits;  conditional E-value: 0.0013
  Pentapeptide_3  15 atFsgaasFsnadFgsadFsgarFtgdvdFs 45 
                     +   +  sF+n+++++ +  +++ + d+ F 
      AHX11620.1 322 SELVDV-SFRNTRISDFSIYNSNVS-DAIFL 350
                     555555.9***********999999.99885 PP

  == domain 7  score: 1.1 bits;  conditional E-value: 0.1
  Pentapeptide_3  13 rgatFsgaasFsnadFgsadFsgarFtgdvd 43 
                     r++t s   +++++ F+ ++  g+  + +++
      AHX11620.1 389 RDSTLSLL-NMTDSSFTISNIHGTSVD-RSS 417
                     55555555.555555555555554444.333 PP

  == domain 8  score: 0.9 bits;  conditional E-value: 0.12
  Pentapeptide_3  17 FsgaasFsnadFgsadFsgarFtgdv 42 
                      +++ sFs+  +g  d+ ++ F  ++
      AHX11620.1 433 ITNS-SFSRNSLGLFDLKDTSFG-RS 456
                     3333.444444444444444442.33 PP

  == domain 9  score: 15.2 bits;  conditional E-value: 4.1e-06
  Pentapeptide_3   8 gaadFrgatFsgaasFsnadFgsadFsgarFtgdvd 43 
                     g+ dFrg++ s+  +F+n+ +++adF ga    ++ 
      AHX11620.1 489 GDRDFRGVNYSNI-DFRNTELSNADFTGAVLR-GSA 522
                     6778999999999.999999999999999877.444 PP

  == domain 10  score: 15.2 bits;  conditional E-value: 4.1e-06
  Pentapeptide_3   1 FsganFsgaadFrgatFsgaa.s...FsnadFgsadFsgarFt 39 
                     F+++++s+a dF+ga+ +g+a s    +n  F +a++++++F+
      AHX11620.1 503 FRNTELSNA-DFTGAVLRGSAfSkhtTRNVKFKDANLEKTTFE 544
                     778888888.888888888885134467777777777777775 PP

>> CfAFP  Choristoneura fumiferana antifreeze protein (CfAFP)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.7   4.6e-05      0.21      25      97 ..      75     147 ..      61     153 .. 0.80
   2 ?    2.7   0.1     0.026   1.2e+02      35      63 ..     175     203 ..     143     214 .. 0.60
   3 ?    3.1   0.1      0.02        88      35      71 ..     175     211 ..     165     229 .. 0.65
   4 !    9.8   1.3   0.00016      0.73      29     105 ..     194     275 ..     185     281 .. 0.75
   5 !    7.3   1.5   0.00095       4.3      28      87 ..     284     342 ..     276     352 .. 0.87
   6 !    4.7   0.4    0.0061        27      73     113 ..     377     417 ..     352     443 .. 0.46
   7 ?   -3.3   0.0       1.9   8.5e+03      47      77 ..     506     536 ..     496     542 .. 0.43

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
       CfAFP  25 nsqisanskcvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgsrydGvyitss 97 
                 n  + +n    +++++n +  ++ +    +  s+ +d  +++s   ++ni++s+++g t   s+ + + ++ s
  AHX11620.1  75 NNTVLSNVMLKNTVISNSNFGDAIVYGGSIIDSKIEDISLVSSDLNNINIENSNIHGITSIKSHLQYLSVKDS 147
                 4445557777777777777777777777788999**************************9998887776655 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.026
       CfAFP  35 vkstltncyidnselessictrsqysday 63 
                   s l+   i ns + +s++++s+++ a+
  AHX11620.1 175 RDSNLAEIKISNSSIMTSVIAKSDFTRAK 203
                 33444445555555555555555555554 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.02
       CfAFP  35 vkstltncyidnselessictrsqysdayvkksvttd 71 
                   s l+   i ns + +s++++s+++ a++ +++  d
  AHX11620.1 175 RDSNLAEIKISNSSIMTSVIAKSDFTRAKLFDTKIDD 211
                 4566667777777777777777777777766655544 PP

  == domain 4  score: 9.8 bits;  conditional E-value: 0.00016
       CfAFP  29 sanskcvkstltncyidnselessictrsqysdayvkksvttdcnid.....ksqlygttctgsrydGvyitsstttgtris 105
                  a s   ++ l    id++  ++    rs   +++v++s+  + +++     ++ +   t t+s+++ + i  s  t+t  s
  AHX11620.1 194 IAKSDFTRAKLFDTKIDDTLFHTVKLIRSYIHNSEVNDSKFINSDLSgsilgNCLVNKMTMTNSNFEYMLIDGSNFTNTDFS 275
                 45667777777778888888888888898888888888888877765111115567899******************99876 PP

  == domain 5  score: 7.3 bits;  conditional E-value: 0.00095
       CfAFP  28 isanskcvkstltncyidnselessictrsqysdayvkksvttdcnidksqlygttctgs 87 
                 is ns+  ks l n +i+n  +e+s    s+ +++++ ks  +d+  +++++   +  +s
  AHX11620.1 284 IS-NSRFCKSCLCNLHIQNLTIEASQFFDSEVNNTELYKSELVDVSFRNTRISDFSIYNS 342
                 55.99999*************************************999998876655555 PP

  == domain 6  score: 4.7 bits;  conditional E-value: 0.0061
       CfAFP  73 nidksqlygttctgsrydGvyitsstttgtrisGpgcsiss 113
                 +i+ksql      +s    + +t s+ t ++i G +   ss
  AHX11620.1 377 DINKSQLSNDQIRDSTLSLLNMTDSSFTISNIHGTSVDRSS 417
                 33333333333333333333333333333333333333332 PP

  == domain 7  score: -3.3 bits;  conditional E-value: 1.9
       CfAFP  47 selessictrsqysdayvkksvttdcnidks 77 
                 +el ++  t +   ++   k +t +++ +++
  AHX11620.1 506 TELSNADFTGAVLRGSAFSKHTTRNVKFKDA 536
                 3333333333334444444444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (545 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       540  (0.0301188); expected 358.6 (0.02)
Passed bias filter:                      244  (0.0136092); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.41
# Mc/sec: 4006.42
//
Query:       AHX11621.1  [L=204]
Description: guanylate kinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      2e-41  141.7   0.1    2.4e-41  141.4   0.1    1.1  1  Guanylate_kin  Guanylate kinase
    4.1e-05   24.1   0.0    8.3e-05   23.1   0.0    1.5  1  AAA_18         AAA domain
    0.00028   20.9   0.2     0.0013   18.8   0.2    2.1  1  MMR_HSR1       50S ribosome-binding GTPase
    0.00052   20.2   0.1     0.0093   16.1   0.1    2.6  1  AAA_33         AAA domain
     0.0014   18.9   0.5       0.11   12.8   0.0    2.9  3  AAA_22         AAA domain
  ------ inclusion threshold ------
      0.011   15.7   0.1      0.033   14.1   0.0    1.9  2  NTPase_1       NTPase
      0.046   14.1   0.0      0.096   13.1   0.0    1.5  1  AAA_16         AAA ATPase domain
      0.071   12.8   0.0      0.098   12.4   0.0    1.3  1  AAA_30         AAA domain
      0.082   12.9   2.8       0.14   12.2   2.8    1.3  1  Stathmin       Stathmin family
      0.083   13.3   0.1       0.16   12.4   0.1    1.9  1  AAA            ATPase family associated with various cellular
      0.085   13.4   0.0       0.12   12.9   0.0    1.6  1  ABC_tran       ABC transporter
        0.1   13.0   0.0        0.2   12.0   0.0    1.5  1  AAA_19         AAA domain
       0.12   12.2   0.9       0.26   11.2   0.9    1.8  1  AAA_31         AAA domain
       0.13   12.1   0.5       0.37   10.7   0.0    1.9  3  RsgA_GTPase    RsgA GTPase
        7.3    7.0  12.7    2.9e+02    1.8  12.7    2.2  1  AAA_23         AAA domain


Domain annotation for each model (and alignments):
>> Guanylate_kin  Guanylate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  141.4   0.1     2e-44   2.4e-41       5     180 ..       8     182 ..       4     184 .. 0.94

  Alignments for each domain:
  == domain 1  score: 141.4 bits;  conditional E-value: 2e-44
                    EEEESTTTSSHHHHHHHHHHHSTTTEEE--EEESS---TTS-TTTSEEE--HHHHHHHHHTTTEEEEEEETTEEEEEEHHHHHHHHHTTSEEEEE- CS
  Guanylate_kin   5 vvlvgpsgaGksslkkaLlselpekfgvsvshtTrdprkgevdGkdYyFvskeemekdiskneflEaaefsgnlygtsveaieevlekgkiviLDv 100
                     +++ psg+Gk ++ + L++++++  + svs tTr+pr +e  G dYyFv ++e++k  ++ ++lE+a++ +n+ygts+e ie+ le g +v+  +
     AHX11621.1   8 FIISSPSGTGKTTIANFLVTQDENI-QRSVSFTTRQPRGNERYGMDYYFVDTDEFHKLLAEGKMLEHARVLQNYYGTSKEYIENTLEAGVDVLCCI 102
                    79**************999887766.579******************************************************************* PP

                    -CHHHHHHHHTTTTEEEEEEEESSHHHHHHHHTTSSSSHHHHHHHHHHHHHHHHGGG.CSSEEEEESSHHHHHHHHHHHHH CS
  Guanylate_kin 101 diqavkqlrkaelspiivFikppslkelqrrlksrgkeqeeklakrlaaaekelqey.efdvvivnddleealkklkelle 180
                    d+q++ q+r++ +s +++F+ ppsl+el+rrl srg++++e+++ rl++a +e+++   +d+vi nddl+e+ +k   +++
     AHX11621.1 103 DWQGADQVRQK-VSSVSIFLLPPSLEELRRRLMSRGTDTKEVIEYRLKEALEEVKHFsKYDYVIINDDLQETKQKALAIIR 182
                    *********86.67899****************************************77************9888766666 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   0.0     7e-08   8.3e-05       3     127 ..      10     150 ..       9     153 .. 0.67

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 7e-08
      AAA_18   3 ltGtpGvGKttlakeLskrl.gf.....gvnlrdvakenglllevdpe....aldeskrldedkldklldaleenss.........aleegknl..vid 80 
                 ++ ++G+GKtt+a+ L     ++           + ++ +  + +  +    ++de+++l  +  +  +  + +n+          +le g ++   id
  AHX11621.1  10 ISSPSGTGKTTIANFLVTQDeNIqrsvsF-----TTRQPRGNERYGMDyyfvDTDEFHKLLAEGKMLEHARVLQNYYgtskeyienTLEAGVDVlcCID 103
                 66789***********7777455554442.....33332222222222335557888888877777777777777777999999987777777556778 PP

      AAA_18  81 ghlaeleseaakdikkvvLtaspeelleRlekRgyeeakikeneeae 127
                 ++ a+ +  +      + L  s eel++Rl  Rg+ +++  e +  e
  AHX11621.1 104 WQGADQVRQKVSSVSIFLLPPSLEELRRRLMSRGTDTKEVIEYRLKE 150
                 88887777777766635566666***********9988766666555 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.8   0.2   1.1e-06    0.0013       9      56 ..      15      61 ..       9     201 .. 0.78

  Alignments for each domain:
  == domain 1  score: 18.8 bits;  conditional E-value: 1.1e-06
                TSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGC CS
    MMR_HSR1  9 NvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGl 56
                 +GK+t+ n l+ + + i  +  +tTr+++  +    g ++++vDt  +
  AHX11621.1 15 GTGKTTIANFLVTQdENIQRSVSFTTRQPRGNERY--GMDYYFVDTDEF 61
                68*********998678999*********999888..899******874 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.1   7.8e-06    0.0093       7     124 ..      13     142 ..       7     160 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 7.8e-06
      AAA_33   7 lpGsGKstlaerllkklg......................avllssdtlrrrlfgtdqqsktdytrvldrlyqilnelarkalsagrnvildatnlsrr 83 
                 ++G+GK+t a  l+ +                        ++++++d++++ l++    +  + +rvl++ y++ +e+++ +l+ag +v+         
  AHX11621.1  13 PSGTGKTTIANFLVTQDEniqrsvsfttrqprgnerygmdYYFVDTDEFHKLLAEG---KMLEHARVLQNYYGTSKEYIENTLEAGVDVLCC------I 102
                 79**********97555555555544444445566666666666666666666632...2347799**********************8763......3 PP

      AAA_33  84 erarflklarrlgvpvrivvvetdeetlkeRlakRaangdd 124
                 +++  +++ ++ +  v+i  + ++ e+l++Rl  R  ++++
  AHX11621.1 103 DWQGADQVRQKVS-SVSIFLLPPSLEELRRRLMSRGTDTKE 142
                 4666677766666.788999999999999999999886544 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.8   0.0   8.8e-05      0.11       8      31 ..       8      31 ..       1      52 [. 0.76
   2 ?    2.7   0.0      0.12   1.4e+02      98     118 ..      59      80 ..      48      91 .. 0.86
   3 ?    0.1   0.1      0.75     9e+02      72     112 ..     137     181 ..     109     195 .. 0.59

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 8.8e-05
      AAA_22  8 lvvtGesGtGKTtllrrlleqlde 31
                 ++  +sGtGKTt ++ l+ q+++
  AHX11621.1  8 FIISSPSGTGKTTIANFLVTQDEN 31
                356679**************9864 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.12
      AAA_22  98 DEaqhlr.seealeeLrsllnl 118
                 DE+++l  + ++le+ r l+n 
  AHX11621.1  59 DEFHKLLaEGKMLEHARVLQNY 80 
                 9****7768**********995 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.75
      AAA_22  72 rlsseell.ealeqalrarav....ielliiDEaqhlrseealeeL 112
                 + +++e++  +l +al++ +       ++i D+ q   +++al  +
  AHX11621.1 137 GTDTKEVIeYRLKEALEEVKHfskyDYVIINDDLQET-KQKALAII 181
                 3344444444444544444444455556777777766.55555555 PP

>> NTPase_1  NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   2.8e-05     0.033       2      72 ..       8      77 ..       7     111 .. 0.69
   2 ?   -1.1   0.0       1.3   1.6e+03      55      61 ..     173     179 ..     130     201 .. 0.58

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 2.8e-05
                EEEE--TTSSHHHHHHHHHHHH...GGGEEEEEEEEE-------EEEEEET.T--EEEEEETT.---SSEET CS
    NTPase_1  2 vfiTGppGvGKtTlvkkvlellkssgvkvgGfyteevreggrrigFkivdlasgeegiLarve.akreprvg 72
                ++i+ p+G+GKtT+ + ++ + ++ + +v    t +  +g++r g ++  ++++e + L  ++   +++rv 
  AHX11621.1  8 FIISSPSGTGKTTIANFLVTQDENIQRSV--SFTTRQPRGNERYGMDYYFVDTDEFHKLLAEGkMLEHARVL 77
                6899*************998775555555..577777889999**999999988866665555344444432 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.3
                 --EEEEE CS
    NTPase_1  55 geegiLa 61 
                  +++ La
  AHX11621.1 173 TKQKALA 179
                 2222222 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   8.1e-05     0.096      27     156 ..       8     182 ..       2     193 .. 0.61

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 8.1e-05
      AAA_16  27 vllsGesGvGKsslvrellr...alekdggiflrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleeala............... 106
                  ++s +sG+GK+++++ l +    ++++ + f++ + + +    +y + +  +  + + + +ll+e +   le++r  l+  ++               
  AHX11621.1   8 FIISSPSGTGKTTIANFLVTqdeNIQRS-VSFTTRQPRGN---ERYGMdYYFVD-T-DEFHKLLAEGKM--LEHARV-LQNYYGtskeyientleagvd 97 
                 57899**********9998755456666.55555555555...56655444444.4.344444444222..222222.333333444555588889999 PP

      AAA_16 107 ..................................avpelagaea.......srllellkrllallsrderp.lvlvlDdlqwadeaslqlla 156
                                                                    + + + lk++l+  ++ ++   v++ Ddlq  ++  l++++
  AHX11621.1  98 vlccidwqgadqvrqkvssvsifllppsleelrrRL-------MsrgtdtkEVIEYRLKEALEEVKHFSKYdYVIINDDLQETKQKALAIIR 182
                 999999988888888777777777666555444433.......1333333366666666666444443443599999999988887777765 PP

>> AAA_30  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   8.2e-05     0.098      19      81 ..       6      69 ..       1     109 [. 0.82

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8.2e-05
      AAA_30 19 rvavltGpAGtGKttalkalreaweaaggrviglAptgkaAkvLaeelgi.eastiakllkrlk 81
                 + ++  p GtGKtt+ + l+   e+ +++v   + + +  ++ + +  + +++  +kll + k
  AHX11621.1  6 ILFIISSPSGTGKTTIANFLVTQDENIQRSVSFTTRQPRGNERYGMDYYFvDTDEFHKLLAEGK 69
                5789999******************999999999999999888887777448888888886655 PP

>> Stathmin  Stathmin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   2.8   0.00011      0.14      66     129 ..     135     198 ..     126     202 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00011
    Stathmin  66 kqlaekrekeeevlqKaaeennnfskaaeeklkqkmeaskenreaqlaalkekLkekekhveev 129
                    ++ +e +e  l++a ee ++fsk     +++ ++++k++  a + a +ekLke + ++e+ 
  AHX11621.1 135 SRGTDTKEVIEYRLKEALEEVKHFSKYDYVIINDDLQETKQKALAIIRAEREKLKENQVQIEKF 198
                 55667788888889999******************************************99986 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1   0.00013      0.16       2      22 ..       9      36 ..       8     195 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.00013
                EEESSTTSSHHHHHHHHHHH.......H CS
         AAA  2 llyGppGtGKTllakavake.......l 22
                +++ p GtGKT++a+ ++++       +
  AHX11621.1  9 IISSPSGTGKTTIANFLVTQdeniqrsV 36
                56789**********9998844433331 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0    0.0001      0.12      16      70 ..      10      60 ..       3     201 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.0001
                EEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S CS
                xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 16 ivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepql 70
                i  ++G+GK+t+++ l  + ++ + ++ +  ++ +       r  + +++ ++  
  AHX11621.1 10 ISSPSGTGKTTIANFLVTQDENIQRSVSFTTRQPRG----NERYGMDYYFVDTDE 60
                5668*****************999999777555444....444444444444333 PP

>> AAA_19  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0   0.00017       0.2      12     124 ..       7     183 ..       2     195 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
      AAA_19  12 vllvtaGpGtGKTrvlkhivallvelggvkpeeillvaftgrAakelrerlaalgaeatTiHrlal................................. 77 
                 ++++  + GtGKT++ +  v+  ++++    +++   +   r  ++    ++ + ++++ +H+l l                                 
  AHX11621.1   7 LFIISSPSGTGKTTIANFLVTQDENIQ----RSVSFTTRQPRGNERYG--MDYYFVDTDEFHKL-Laegkmleharvlqnyygtskeyientleagvdv 98 
                 45667778******9998888777777....55666555555555555..55589999999988.4478888888888888888888888888888888 PP

      AAA_19  78 .......................................ldfddlltealelle.eaeeekklqeee.llivDEfqdvdelqyrLlka 124
                                                         d+++ ++  l   +   ee k++ + + ++i D  q++++ + ++++a
  AHX11621.1  99 lccidwqgadqvrqkvssvsifllppsleelrrrlmsrgTDTKEVIEYRL---KeALEEVKHFSKYDyVIINDDLQETKQKALAIIRA 183
                 88888888888888888888888888888888887665533333332222...23334445554555466668888888777777776 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.9   0.00022      0.26      78     124 ..     116     167 ..       6     180 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00022
      AAA_31  78 venldlipssidLaeaeielvelekk.....eeilkellekvk..deYDyiiiD 124
                 + ++ l+p   +L e+  +l++  +      e++lke+le+vk  ++YDy+ii 
  AHX11621.1 116 SVSIFLLPP--SLEELRRRLMSRGTDtkeviEYRLKEALEEVKhfSKYDYVIIN 167
                 334455554..45566666666555455566777********94458*****94 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00031      0.37     102     131 ..       8      37 ..       2      47 .. 0.79
   2 ?   -2.7   0.0       3.9   4.7e+03      67      99 ..      86     116 ..      78     125 .. 0.64
   3 ?   -2.4   0.1       3.3   3.9e+03      55      70 ..     160     175 ..     140     199 .. 0.55

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00031
                  EEEECSTTSSHHHHHHHHCTT-----S--- CS
  RsgA_GTPase 102 svlvGqSGvGKStLinallpelelktgevs 131
                   ++  +SG GK+t+ n l+ ++e   ++vs
   AHX11621.1   8 FIISSPSGTGKTTIANFLVTQDENIQRSVS 37 
                  577889*************99877766666 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 3.9
                  HHHHHHHHTTSEEEE--TTTHTTHHHHHHHCTT CS
  RsgA_GTPase  67 elkeelealgyevllvsaktkegleelkellkd 99 
                  e+ e++ ++g++vl++     +g++++++++++
   AHX11621.1  86 EYIENTLEAGVDVLCCID--WQGADQVRQKVSS 116
                  556666677777777743..3677777776665 PP

  == domain 3  score: -2.4 bits;  conditional E-value: 3.3
                  -GGG--HHHHHHHHHH CS
  RsgA_GTPase  55 KiDlleeeeeleelke 70 
                  K D +  +++l+e+k+
   AHX11621.1 160 KYDYVIINDDLQETKQ 175
                  3333333332333222 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.8  12.7      0.25   2.9e+02      21      64 ..       7      44 ..       4     199 .. 0.41

  Alignments for each domain:
  == domain 1  score: 1.8 bits;  conditional E-value: 0.25
      AAA_23 21 ltlItGpNGaGKTTildAiklaLygetprlsrksgrgfeksdve 64
                l++I+ p G+GKTTi +++       t++++ +++ +f ++ ++
  AHX11621.1  7 LFIISSPSGTGKTTIANFLV------TQDENIQRSVSFTTRQPR 44
                89**************9973......222333334444555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (204 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1313  (0.0732333); expected 358.6 (0.02)
Passed bias filter:                      705  (0.0393218); expected 358.6 (0.02)
Passed Vit filter:                        99  (0.00552178); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              15  [number of targets reported over threshold]
# CPU time: 0.49u 0.28s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 1485.80
//
Query:       AHX11622.1  [L=99]
Description: hypothetical protein NHE_0689 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 742.67
//
Query:       AHX11623.1  [L=237]
Description: hypothetical protein NHE_0690 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
      0.075   12.8   0.0        8.3    6.1   0.0    2.1  2  SBP_bac_11  Bacterial extracellular solute-binding protein


Domain annotation for each model (and alignments):
>> SBP_bac_11  Bacterial extracellular solute-binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.8   0.0    0.0012        21       1      46 [.      22      67 ..      22      77 .. 0.90
   2 ?    6.1   0.0   0.00046       8.3     163     215 ..     171     221 ..     142     225 .. 0.78

  Alignments for each domain:
  == domain 1  score: 4.8 bits;  conditional E-value: 0.0012
                .EEEE-SSTHHHHHHHHHHHHHHH---EEEEESSHHHHHHHHHHH. CS
  SBP_bac_11  1 ltvaaagslaaalrelaaaFeahtgvkvevsaggsgklarqiadga 46
                l++++ +sl  ++r ++ +++++ ++ ++  +  s +l+++ ++ga
  AHX11623.1 22 LHLVVDSSLSLPVRKIIREYAKEQSIIITADFSASKELLKSSEKGA 67
                67889999*******************************9998886 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.00046
                 EEEHHHHH..HSTTSSEEE.E--TTT--...EEEEEEEE-TT--HHHHHHHHHT CS
  SBP_bac_11 163 ivyeseakaaengdkleav.ylpeglnldpldypaavlkkaakreaAraFlafL 215
                 i + s a  + +g++le + ++p +l+   + y++ ++++    e  r+F++fL
  AHX11623.1 171 ILPGSIAT-QYEGAGLEKLfEIPRNLYP-KIQYTVSIVDSR-GIEQSRDFIRFL 221
                 44445554.34677777777*******5.999999888865.699*******99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (237 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       454  (0.0253221); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1775.67
//
Query:       AHX11624.1  [L=403]
Description: citrate synthase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   1.9e-122  408.8   0.0   2.2e-122  408.6   0.0    1.0  1  Citrate_synt  Citrate synthase, C-terminal domain
  ------ inclusion threshold ------
       0.18   12.0   0.2       0.39   10.9   0.2    1.5  1  DUF5446       Family of unknown function (DUF5446)


Domain annotation for each model (and alignments):
>> Citrate_synt  Citrate synthase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  408.6   0.0  2.4e-126  2.2e-122       2     361 .]      38     385 ..      37     385 .. 0.95

  Alignments for each domain:
  == domain 1  score: 408.6 bits;  conditional E-value: 2.4e-126
                   GTTEEEEEESSEEEETTTTEEEETTEEHHHHHHHHS-HHHHHHHHHHSS---HHHHHHHHHHHHCTTS--HHHHHHHHCSSTTS-HHHHHHHHHHHH CS
  Citrate_synt   2 lrgvaaleteisevdgekgelrYRGydieeLaeekssfeevaylLltgelPtkeelkefkeelaearklpekvlealealpkdahpmavlraavsal 98 
                   + ++a++++ei++vdge+g l+YRGy+++eLa  +++f  v+ylLl+gelP+   +kef+  +++  +lp+ vle++ ++p+dahpm +l++a++al
    AHX11624.1  38 YVSTASCKSEITFVDGEEGVLLYRGYPVDELA-TQCDFLRVVYLLLYGELPDPVRAKEFRTLIQNFPQLPDCVLENICSFPRDAHPMVILISAFAAL 133
                   66799***************************.7*******************************99****************************** PP

                   HHHSTTCTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTS.-----TTSSHHHHHHHHHHSS---HHHHHHHHHHHHHHS--SSSHHHHHHHHHH CS
  Citrate_synt  99 saddeeseakeeseeaalrdalkliAklptiaaaiyrarlgreplepddklsyaenflymlrgkkpdeeeaklldlalvlhaDHelnaSTfaarvva 195
                   +++++    +++ e +       liA++p ++a+iyr+ + ++ + pd  lsy+ nf+ym++g + +++++ +ld++l+lhaDHe+naST +ar+v 
    AHX11624.1 134 ASAHH----DSDFETHKEV----LIANVPRLVAYIYRYITSQDFIPPDACLSYVGNFFYMMFG-EKKPDYESILDKILILHADHEQNASTSTARMVV 221
                   *9985....4443443344....89***************9866699999*************.779****************************** PP

                   TTT--HHHHHHHHHHHHTSTTTTTHHHHHHHHHHHHSSGG.GHHHHHHHHHHTTTS--TTBC-SSSSS--HHHHHHHHHHHHHHTCHTHHHHHHHHH CS
  Citrate_synt 196 StladlysaiaagigalkGplhgganeavlkmleeigsaeveveeylekvlakekerlpGfGHrvykksDpRakilkelaeelaeekgkdpllklae 292
                   S++a +++a++a+ ++l+Gplhggane+vl+ml ei+++   vee++e+v++ke erl+GfGHrvyk++DpRa+ilk+ a+++ +  g++  l +a+
    AHX11624.1 222 SSGASPIAAVSAATATLWGPLHGGANEKVLHMLGEIEKQGGSVEEFIERVKRKE-ERLMGFGHRVYKNYDPRAVILKSTAQDILK--GSSSILSIAS 315
                   ************************************77755***********96.***************************988..9999****** PP

                   HHHHHHHHHHHCHHGCT-EB-THHHHHHHHHHTT--GGGHHHHHHHHHHHHHHHHHHHHH..HT------E CS
  Citrate_synt 293 eleevapevlkekeeknlypNvDfysgvlyralgipeelftvlfaisRvaGwlAhileql..adnkiiRPr 361
                   +le +a++++++ + ++lypNvDfysg++++algip+ +ft++fa++R+ Gw+A+i e l  +++ki RPr
    AHX11624.1 316 KLESIASNDEYFIS-RKLYPNVDFYSGIILNALGIPTYMFTPIFALARTSGWVAQIKEFLsdKEQKIARPR 385
                   **************.*******************************************87556699****8 PP

>> DUF5446  Family of unknown function (DUF5446)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.2   4.3e-05      0.39       8      35 ..     248     274 ..     246     280 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 4.3e-05
     DUF5446   8 dsvLqlLeeiEeeltevEkelseavnet 35 
                 + vL++L eiE++  +vE+ +   v++ 
  AHX11624.1 248 EKVLHMLGEIEKQGGSVEEFIER-VKRK 274
                 78****************98854.4443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      535  (0.0298399); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2855.18
//
Query:       AHX11625.1  [L=439]
Description: phosphoglucosamine mutase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.2e-36  125.4   0.0    3.1e-36  124.1   0.0    1.7  2  PGM_PMM_I    Phosphoglucomutase/phosphomannomutase, alpha/bet
    2.8e-24   85.5   0.0    4.9e-24   84.7   0.0    1.4  1  PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/bet
    1.9e-17   63.8   0.0    4.5e-17   62.5   0.0    1.7  1  PGM_PMM_II   Phosphoglucomutase/phosphomannomutase, alpha/bet
    0.00026   21.1   0.0     0.0008   19.5   0.0    1.8  1  PGM_PMM_IV   Phosphoglucomutase/phosphomannomutase, C-termina
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.27   11.4   0.1    1.6  1  Fibritin_C   Fibritin C-terminal region
       0.12   12.8   0.0       0.32   11.4   0.0    1.7  1  RbsD_FucU    RbsD / FucU transport protein family
       0.27   11.4   1.1       0.85    9.8   0.5    2.2  2  NHL          NHL repeat


Domain annotation for each model (and alignments):
>> PGM_PMM_I  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.1   0.0   1.2e-39   3.1e-36       2     134 ..       3     133 ..       2     137 .. 0.97
   2 ?   -3.5   0.0         3   7.6e+03       3      33 ..     405     434 ..     404     437 .. 0.74

  Alignments for each domain:
  == domain 1  score: 124.1 bits;  conditional E-value: 1.2e-39
                 GGBBTTCEEEECCHCTBSCCHHHHHHHHHHHHCHHCSTS-EEEEEE-S-TTHHHHHHHHHHHHHCCT-CEEEEEEB-HHHHHHHHHHCCECEEEEE--T CS
   PGM_PMM_I   2 qkfgtsGlRgkvgegeltpelveklgqaiaeylkaeakkkkvvvGrDtRvssrelaealaaglaanGvevillgllptPavsfairklkadagimitaS 100
                 ++fgt+G+Rg+++++++ +e v+++++ +a  +++   +++ ++G+DtR s+  +++ ++agl++ G+++i++g++ptP vs+++ +l+++ g+mi+aS
  AHX11625.1   3 KLFGTDGIRGRANAFPMSAESVLQVAKLAALRFRN--YGNTAIIGKDTRLSGYVFESCFVAGLLSLGMNAIIVGPVPTPCVSMLTVSLRCAFGVMISAS 99 
                 68********************************9..5************************************************************* PP

                 TS-TTCCCEEEEETTTCE--CHHHHHHHHHHCCT CS
   PGM_PMM_I 101 HnppeyngiKvylsnGgpispeveekIeaiieke 134
                 Hn  ++ngiK+++++G +is+++e+ Ie++++k+
  AHX11625.1 100 HNEFRDNGIKFFDHRGLKISTDDESFIEENFHKK 133
                 ******************************9987 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3
                 GBBTTCEEEECCHCTBSCCHHHHHHHHHHHH CS
   PGM_PMM_I   3 kfgtsGlRgkvgegeltpelveklgqaiaey 33 
                 k gt+ +  ++geg  + + +e+++q ++e+
  AHX11625.1 405 KSGTENVIRIIGEGS-NISRIEAIVQDLVEI 434
                 567888888888774.888888888877765 PP

>> PGM_PMM_III  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   84.7   0.0   1.9e-27   4.9e-24       1     109 [.     254     362 ..     254     366 .. 0.94

  Alignments for each domain:
  == domain 1  score: 84.7 bits;  conditional E-value: 1.9e-27
                  HHHHHHHHHHHHHHCH.CSTTTCEEEEETTS-THHHHHHHHTT-EEEEESSSCHHHHHHHHHTTECEEEETTCEEEETTTBSS--HHHHHHHHHHHHH CS
  PGM_PMM_III   1 dgdqllallakyllee.klkpgagvvktvmtslalervakklgiklvetkvGdkyvleemkeegavlGgEeSghiifldeattkDGilaallvleila 97 
                  dgdql+a + + +l+  +l+ g+ vv tv +s+ale++++ lg+++v+++vGd+ vl++m e+ga+lGgE Sghii++d+++t DG++aal++l+++ 
   AHX11625.1 254 DGDQLIASIVRLFLRLgRLSSGT-VVLTVASSMALENFLHGLGLRTVRSNVGDREVLKRMIETGANLGGEPSGHIIIRDYVNTSDGLIAALQLLHLMV 350
                  69999999999777777788776.************************************************************************** PP

                  HHTS-HHHHHHH CS
  PGM_PMM_III  98 etgkslsellee 109
                    g s se+ ++
   AHX11625.1 351 IDGASASEITAN 362
                  ********9965 PP

>> PGM_PMM_II  Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.5   0.0   1.8e-20   4.5e-17       2     103 .]     153     250 ..     152     250 .. 0.91

  Alignments for each domain:
  == domain 1  score: 62.5 bits;  conditional E-value: 1.8e-20
                 HHHHHGGGTS-HHHHHHHT-EEEEE-TT-TTHHHHHHHHHHTT-EEEES-----TT-TTSS----T.T-TTTTHHHHGGGGG-SEEEEE-TTS-BEEEE CS
  PGM_PMM_II   2 aYiealkekvdseaikksglkvvidplhGaggeilkellkelgvdvvelnaepdpdfptkapnpee.kealkllielvkkegadlglafDgDaDRlgvv 99 
                 +Y+e +k +++ + ++ +g+k+++d+++G+  +i+++++ elg++vv++n +p+++      n ++   + + ++e vk+e+a++g+afDgD+DRl+v+
  AHX11625.1 153 RYLEFIKRAFP-SDLSLKGIKILLDCANGSMYKIAESVFWELGAEVVTINNAPNGNNI----NLDCgTMHTQGMQERVKREKAHIGIAFDGDGDRLVVA 246
                 69999999998.6788889************************************665....56663468899************************** PP

                 ETTE CS
  PGM_PMM_II 100 derG 103
                 de+G
  AHX11625.1 247 DENG 250
                 **98 PP

>> PGM_PMM_IV  Phosphoglucomutase/phosphomannomutase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   0.0   3.1e-07    0.0008      36      71 ..     399     433 ..     379     435 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 3.1e-07
                 EEEE.EEEETTCCEEEEEEEESSHHHHHHHHHHHHH CS
  PGM_PMM_IV  36 GrrlavRpSGTepllrvyvEaksdeelarlaeevae 71 
                  r++ +R SGTe+++r+  E+++ ++++ ++++++e
  AHX11625.1 399 ERIV-LRKSGTENVIRIIGEGSNISRIEAIVQDLVE 433
                 4555.*****************99999999998876 PP

>> Fibritin_C  Fibritin C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1    0.0001      0.27      22      75 ..     193     248 ..     191     261 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.0001
  Fibritin_C  22 lkgaviklskdiyGtnpsgd..piekrGikktvkeleteiqlqalsesgkiddapk 75 
                 l ++v++++++ +G+n + d  ++  +G+++ vk  +++i++ +  +  ++  a +
  AHX11625.1 193 LGAEVVTINNAPNGNNINLDcgTMHTQGMQERVKREKAHIGIAFDGDGDRLVVADE 248
                 56899**************999*******************555444444433333 PP

>> RbsD_FucU  RbsD / FucU transport protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00012      0.32      19      68 ..     238     290 ..     231     317 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                 -TT-EEEEE-TTS-HHCC....SCEEE.-CBTTBS-HHHHHHHHHCTS-EEEEE CS
   RbsD_FucU  19 GHgDeiviaDaglPipsg....veridlalragvpsfldvleavlselpvekvi 68 
                 G gD++v+aD +  + +g    +++++l lr+g +s  +v+ +v+s + +e+ +
  AHX11625.1 238 GDGDRLVVADENGNVIDGdqliASIVRLFLRLGRLSSGTVVLTVASSMALEN-F 290
                 89*************99999999999*************************4.3 PP

>> NHL  NHL repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.8   0.5   0.00033      0.85       6      22 ..     233     251 ..     232     251 .. 0.88
   2 ?   -2.4   0.0       2.4   6.2e+03      11      20 ..     323     332 ..     323     336 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.8 bits;  conditional E-value: 0.00033
                 EEEEE.TTTEEEEEE.CCC CS
         NHL   6 Gvavd.snGdiyVaD.sen 22 
                 G+a d ++++++VaD ++n
  AHX11625.1 233 GIAFDgDGDRLVVADeNGN 251
                 9**************6665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 2.4
                 TTTEEEEEEC CS
         NHL  11 snGdiyVaDs 20 
                 ++G+i++ D+
  AHX11625.1 323 PSGHIIIRDY 332
                 68***99774 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.49u 0.23s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 3358.39
//
Query:       AHX11626.1  [L=304]
Description: surA N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    6.5e-06   26.0   1.2    1.6e-05   24.7   1.2    1.6  1  SurA_N_3    SurA N-terminal domain
    0.00019   21.3   0.3    0.00049   20.0   0.1    1.8  2  SurA_N_2    SurA N-terminal domain
     0.0012   19.7   0.0     0.0039   18.1   0.0    1.9  1  Rotamase    PPIC-type PPIASE domain
  ------ inclusion threshold ------
      0.026   15.3   0.0      0.062   14.1   0.0    1.7  1  Rotamase_2  PPIC-type PPIASE domain
      0.066   13.4   1.4       0.62   10.3   0.2    2.5  2  DUF3211     Protein of unknown function (DUF3211)


Domain annotation for each model (and alignments):
>> SurA_N_3  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.7   1.2   4.5e-09   1.6e-05      39     159 ..      24     132 ..       4     134 .. 0.77

  Alignments for each domain:
  == domain 1  score: 24.7 bits;  conditional E-value: 4.5e-09
    SurA_N_3  39 nsvakVngekIsraefqqayrrqleqlrqqlggnldaelldelglrqqvldqlidealllqeakklglsvsdeevakeiasipaFqedGkFdkerYkql 137
                 +++a V++  Is +++++ y+++l            +   ++++  +++l+++id +l +q+a+k g++ s+++ +++i + +++ +++    e++++ 
  AHX11626.1  24 KAAALVGNVTISNQDVRD-YQEILG-----------MLGGKTATSYKAALQEMIDLELYNQYAQKVGIRFSQQKYDAAINRLKSLGVKETSLTELFRDC 110
                 457788888888888754.444333...........223345566799**************************************6666668****** PP

    SurA_N_3 138 Laangltpeefeaslredlllq 159
                 L+++ l +e  e+ ++  + ++
  AHX11626.1 111 LKKQVLFAEVVEQVIKPRIQIS 132
                 ****999999999998777666 PP

>> SurA_N_2  SurA N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.1   1.4e-07   0.00049      19     121 ..       8      92 ..       2     108 .. 0.73
   2 ?    1.2   0.1     0.087   3.1e+02      57     102 ..      83     128 ..      83     142 .. 0.79

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 1.4e-07
    SurA_N_2  19 allaFilgdlfgvgsylfssssnevaeVnGekIslqefqqaveearqqlqqqlgenfdeseedeaqlreqvldqlvseklleqeaeklGltvsdeelqd 117
                 +++ F+    f  +++l   + +++a V++ +Is q+    v+ +++ l + lg +        a   +++l+++++ +l++q a+k G+++s+++ ++
  AHX11626.1   8 IIFCFL---CFAPCHSL---EVKAAALVGNVTISNQD----VRDYQEILGM-LGGKT-------ATSYKAALQEMIDLELYNQYAQKVGIRFSQQKYDA 88 
                 555555...55555443...45667777777777665....4555554444.56652.......456899***************************99 PP

    SurA_N_2 118 aiqg 121
                 ai+ 
  AHX11626.1  89 AINR 92 
                 9986 PP

  == domain 2  score: 1.2 bits;  conditional E-value: 0.087
    SurA_N_2  57 qqaveearqqlqqqlgenfdeseedeaqlreqvldqlvseklleqe 102
                 qq+++ a ++l++   ++ + +e     l++qvl + v e++++  
  AHX11626.1  83 QQKYDAAINRLKSLGVKETSLTELFRDCLKKQVLFAEVVEQVIKPR 128
                 6888888888888655556666666799999999999999998765 PP

>> Rotamase  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.0   1.1e-06    0.0039      50      86 ..     159     195 ..     125     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 1.1e-06
                 HCCTTEEECEETTTS-CCCHHHHCCS-CT-B-S-EEE CS
    Rotamase  50 akngGdlgwvekgqlppefekaafslkkGeisepvet 86 
                  +++ dlgw++ ++l+pe++k++++l  G+is+p+e 
  AHX11626.1 159 GSSRKDLGWMKLDELAPEIKKTISKLPVGKISDPIEG 195
                 456679*****************************85 PP

>> Rotamase_2  PPIC-type PPIASE domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   1.7e-05     0.062      59      97 ..     144     196 ..      84     200 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.7e-05
  Rotamase_2  59 skkaadlgifesa..............snlpeelakaafalkpgevsgpvetd 97 
                   ++ ++ +++ +              ++l++e++k +++l++g++s+p+e +
  AHX11626.1 144 LRNKNTVKLTKIDadgssrkdlgwmklDELAPEIKKTISKLPVGKISDPIEGS 196
                 33333333333332333333444444444888******************986 PP

>> DUF3211  Protein of unknown function (DUF3211)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.0       0.1   3.6e+02      88     108 ..     201     221 ..     188     237 .. 0.80
   2 ?   10.3   0.2   0.00017      0.62      81     129 ..     249     301 ..     237     303 .. 0.81

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.1
                 EEETTEEEEEEEES-HHHHHH CS
     DUF3211  88 sveeekikleleyegelekli 108
                   +e+++ l+l+y+ge+ + +
  AHX11626.1 201 ADKENELILDLDYKGEISEKS 221
                 56899**********987654 PP

  == domain 2  score: 10.3 bits;  conditional E-value: 0.00017
                 .EEEEEEEEETTEEEEEEEES-HHHHHHHHH....HHHHHHHHHHHHHHHHHH CS
     DUF3211  81 gsGkieisveeekikleleyegelekliskl....lskrikkfeknldekirl 129
                  +G iei++++  + ++l++     +l++ +    l+k+ikkf+ +l e+ir+
  AHX11626.1 249 STGSIEIKKNNLILLIHLDMSDLHSRLVELIypakLEKEIKKFSADLHENIRV 301
                 5899****9999999999987766665552223359****************7 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (304 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       688  (0.0383736); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.46u 0.22s 00:00:00.68 Elapsed: 00:00:00.36
# Mc/sec: 2515.79
//
Query:       AHX11627.1  [L=414]
Description: phosphopyruvate hydratase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    3.6e-98  328.5   0.6    4.5e-98  328.1   0.6    1.1  1  Enolase_C  Enolase, C-terminal TIM barrel domain
      5e-46  156.1   0.0    8.4e-46  155.4   0.0    1.4  1  Enolase_N  Enolase, N-terminal domain
    5.1e-12   45.8   0.0    6.8e-12   45.4   0.0    1.2  1  MR_MLE_C   Enolase C-terminal domain-like
    7.3e-06   25.3   0.2    1.6e-05   24.2   0.2    1.5  1  MAAL_C     Methylaspartate ammonia-lyase C-terminus


Domain annotation for each model (and alignments):
>> Enolase_C  Enolase, C-terminal TIM barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  328.1   0.6    1e-101   4.5e-98       5     281 ..     150     413 ..     146     414 .] 0.96

  Alignments for each domain:
  == domain 1  score: 328.1 bits;  conditional E-value: 1e-101
                 -EE-EEEEE-GGGSSSS--SSEEEEE-TT-SSHHHHHHHHHHHHHHHHHHHHHCC.GGGG-B-TTS-B----SSHHHHHHHHHHHHHHCT-TCTBEEEE CS
   Enolase_C   5 PvPalnvinGGshagnklalqefmilPvgassfkealrlGaevyhklksvlkkkygksatnvGdeGGfaPnlqsnkealdliveaiekaGykgkvkial 103
                 P P+lnvinGG+ha+n+la+qefmi Pvg ++f+e++   ae++h+lk +l++++  ++ nvGdeGGfaP+l++++e l li eai++    + vkial
  AHX11627.1 150 PTPMLNVINGGMHADNRLAIQEFMICPVGLPTFRESMEKAAEIFHRLKCLLQQHG--KSINVGDEGGFAPDLSNTEEVLVLIREAIAND--AEYVKIAL 244
                 99**************************************************999..899**************************753..4569**** PP

                 E--GGGCEETCTTEEECTTTTTT..GGCEEEHHHHHHHHHHHHHHS-EEEEES-S-TT-HHHHHHHHHHHTTTSEEEESTTTTT-HHHHHHHHHCT--S CS
   Enolase_C 104 dvassefykekdkkydldfkeeesdkskkltseqladlykelvkkyPivsiedpldeddweawkklteelgdkvqivGddltvtnpkrlkeaiekkaan 202
                 d+a+s f+  +++ y++d+k         + ++ +  +y  ++ ky i+siedp+ e+dw+aw+k+t++l +k+ ivGdd++ tn+++l+++i  ++an
  AHX11627.1 245 DAAASTFF--ENGAYNIDGKV--------MDTDGIIAFYSGVAAKYGIISIEDPVSESDWQAWQKVTSKLSEKMNIVGDDVFATNSEILSRGIADGVAN 333
                 ********..778****9988........7788999*************************************************************** PP

                 EEEE-HHHH-SHHHHHHHHHHHHHTT-EEEEE--SC--S--HHHHHHHHCT-SE.EE---S-SHHHHHHHHHHHHHHHHH CS
   Enolase_C 203 alllkvnqiGsltesleavklakeagygvvvshrsGetedttiadlavglsaGq.iktGaparserlakynqllrieeel 281
                 a+l+k+nqiG++te+++++kla+e+gy vv+shrsGeted+ ia+lav+   G  +k+G+++rser+akyn++lriee l
  AHX11627.1 334 AVLIKINQIGTITETVKTIKLAQENGYKVVISHRSGETEDVSIAHLAVACGGGTfLKAGSLSRSERVAKYNEVLRIEEML 413
                 ***************************************************99748**********************87 PP

>> Enolase_N  Enolase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  155.4   0.0   1.9e-49   8.4e-46       1     128 [.       4     131 ..       4     134 .. 0.99

  Alignments for each domain:
  == domain 1  score: 155.4 bits;  conditional E-value: 1.9e-49
                 EEEEEEEEEE-TTS-EEEEEEEEETTC-EEEEE--B-BSSSSSS-B----SSTTSGGGT--HHHHHHHHHTHHHHHTTSBTT-HHHHHHHHHHHH-STT CS
   Enolase_N   1 IkkvkareildSrGnpTvevevttedgalgraavpsGaStgekealelrDgdkkrylgkgvekavenvnekiapaligldvtdqeeiDkllielDgten 99 
                 I+++kare+++SrG p++evev+t+dg +gra++psGaS+g+ ea+el D d+ r  g+g++ka+ n++++iapal g++++dq++iD+l+ielDgt+n
  AHX11627.1   4 IREIKAREVFNSRGCPALEVEVITSDGRIGRAIAPSGASKGSLEACELIDCDEGRLAGRGLLKAIVNIRDVIAPALEGKSIEDQSAIDQLMIELDGTPN 102
                 899************************************************************************************************ PP

                 -TTT-HHHHHHHHHHHHHHHHHHHTS-HH CS
   Enolase_N 100 ksklGaNailavSlAvakaaAkakelply 128
                 ks+lG+Na++avSlAv ka Ak +e+pl 
  AHX11627.1 103 KSRLGGNALTAVSLAVSKAHAKVMEVPLC 131
                 ***************************97 PP

>> MR_MLE_C  Enolase C-terminal domain-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.4   0.0   1.5e-15   6.8e-12      15     175 ..     193     385 ..     181     410 .. 0.80

  Alignments for each domain:
  == domain 1  score: 45.4 bits;  conditional E-value: 1.5e-15
                 -SEEEEETSSS..............HHHHHHHHHHHHHHHHTTTST.SEEEEE-TTTS..............BHHHHHHHHHHHGG.GTESEEESSSST CS
    MR_MLE_C  15 fravKlkvggd..............dvaedvervravreavgpgdd.vdlmvDanqaw..............dlatAirvarelee.ldllwlEEPvpp 83 
                 f ++K  + ++              d+    e++ ++rea+ ++ + v++++Da ++               d++  i +   +++ +++  +E+Pv+ 
  AHX11627.1 193 FHRLKCLLQQHgksinvgdeggfapDLSNTEEVLVLIREAIANDAEyVKIALDAAASTffengaynidgkvmDTDGIIAFYSGVAAkYGIISIEDPVSE 291
                 5555555444455555555677777888888999999***977655379******99667888889999999************877***********9 PP

                 TTHHHHHHHHHH.HH.SSEEEESTTSSS.HHHHHHHHHHTSESEEEEBHHHHTSHHHHHHHHHHHHHTT-EEEEBSCSSHHHHHHHHHHHHTTTT CS
    MR_MLE_C  84 eddleglaelra.ra.sipiaagEslys.radfrelleagavdivqpdvsrvgGitearkvaalaeafgvpvapHsgsgglglaaslhlaaaipn 175
                   d+++ +++++  + ++ i+++   ++  + + + +++g++ +v ++++++g ite++k+++la+++g++v++ + sg  + +  +hla+a  +
  AHX11627.1 292 -SDWQAWQKVTSkLSeKMNIVGDDVFATnSEILSRGIADGVANAVLIKINQIGTITETVKTIKLAQENGYKVVISHRSGETEDVSIAHLAVACGG 385
                 .57********973359*******9998688899*************************************998885565565556666666554 PP

>> MAAL_C  Methylaspartate ammonia-lyase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.2   0.2   3.6e-09   1.6e-05     108     231 ..     283     398 ..     257     413 .. 0.76

  Alignments for each domain:
  == domain 1  score: 24.2 bits;  conditional E-value: 3.6e-09
      MAAL_C 108 lliegPldagskeeqierlaelreklkekgikvelvaDeWcntledi.refvdaeaadlvqiktPDlGginntieavlyckekgvgaylGGscnetdvs 205
                 + ie+P+ + + ++     +++++kl   + k+++v D+   t ++i  + ++++ a++v ik+  +G+i++t++ +  ++e+g ++ +   + et+  
  AHX11627.1 283 ISIEDPVSESDWQAW----QKVTSKL---SEKMNIVGDDVFATNSEIlSRGIADGVANAVLIKINQIGTITETVKTIKLAQENGYKVVISHRSGETEDV 374
                 567777766554443....3333333...456789999988888887356789999****************************************876 PP

      MAAL_C 206 arvsvhvalatrpaqlLakPGlGvDe 231
                 +  ++h+a+a++  ++L    l   e
  AHX11627.1 375 S--IAHLAVACGGGTFLKAGSLSRSE 398
                 5..68999999998888766665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       569  (0.0317363); expected 358.6 (0.02)
Passed bias filter:                      499  (0.027832); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.51u 0.25s 00:00:00.76 Elapsed: 00:00:00.41
# Mc/sec: 3011.98
//
Query:       AHX11628.1  [L=173]
Description: inorganic pyrophosphatase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.4e-46  158.2   0.0    1.7e-46  157.9   0.0    1.1  1  Pyrophosphatase  Inorganic pyrophosphatase


Domain annotation for each model (and alignments):
>> Pyrophosphatase  Inorganic pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  157.9   0.0   9.5e-51   1.7e-46       1     159 [.      19     173 .]      19     173 .] 0.97

  Alignments for each domain:
  == domain 1  score: 157.9 bits;  conditional E-value: 9.5e-51
                      EEEEE-T.TCSEEEEEETTTTEEEEEEE-SSSB-BSSEEEEETT--BTCCBEETSSSEEEEEESSS---TTEEEEEEEEEEEEEEETTEEEEEE CS
  Pyrophosphatase   1 vvvEipr.gsnaKyeidkeegklrldrvlftskgypanYGfipqTledtelkGDgDPlDvlvlgeeplspgevvevkvlGvlamiDegetDdKi 93 
                      v+vEip  +s +Kyei +  g l +dr++  s+ yp+nY fip+Tl       DgDPlDvlv++++pl+pg++++v+++G++ m De+++D+K+
       AHX11628.1  19 VIVEIPSgSSGVKYEIGRG-GILHVDRFIPVSMYYPCNYAFIPNTLGG-----DGDPLDVLVVTRAPLMPGSLIQVRMVGAFVMRDEKGEDEKL 106
                      79*****66779****986.99**************************.....***************************************** PP

                      EEEETT..SGGGTT-SSGGGSTHHHHHHHHHHHHHTTTTSCCT-SEEEEEEEEHHHHHHHHHHHHHHH CS
  Pyrophosphatase  94 iavpvk..dprlkkindiedlpgllleeiehfFetykdlegkkknvkveewkdkeeAekvieeahery 159
                      +avp++  dp +++i+  +d+p+ +l++iehfFe+ykdle ++k v+v +w + ++A+k+++++++++
       AHX11628.1 107 LAVPASkvDPYYSNITAHTDFPEIFLKQIEHFFEHYKDLE-SGKFVEVVGWSGPDAAQKLVTDSVKSW 173
                      *****999**99****************************.66999******************9998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       242  (0.0134977); expected 358.6 (0.02)
Passed bias filter:                      237  (0.0132188); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1353.15
//
Query:       AHX11629.1  [L=566]
Description: penicillin binding transpeptidase domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.3e-53  179.8   0.0    9.9e-53  179.3   0.0    1.1  1  Transpeptidase  Penicillin binding protein transpeptidase dom
      4e-14   53.4   0.1      1e-13   52.1   0.1    1.7  1  PBP_dimer       Penicillin-binding Protein dimerisation domai


Domain annotation for each model (and alignments):
>> Transpeptidase  Penicillin binding protein transpeptidase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  179.3   0.0   1.1e-56   9.9e-53       2     296 ..     243     552 ..     242     559 .. 0.92

  Alignments for each domain:
  == domain 1  score: 179.3 bits;  conditional E-value: 1.1e-56
                     EEEEEETTT-BEEEEEEESE-TTTHHCC..............TCGCCSTHHHH--BB-GGGGHHHHHHHHHHTTSSTTSEEEEETCCEETTSS.E CS
  Transpeptidase   2 aavvldaktgevlamaskpsydpnakvg..............kneplanravqsqyePGStfKvvtaaaaleagvikpdetlddsggkiqggqsi 82 
                     a+ +++  +g++ am+s+psyd+n + +              +n+pl+nr+++ +++P+StfK+++ +aale+++i+++ t+++ g  + g++ +
      AHX11629.1 243 AVCIMEIPSGKIRAMVSSPSYDNNIFSSgiisqkqwadlntdPNKPLLNRTISATFQPASTFKPIVGLAALESKIIDEEYTINCTGSIKIGNRKF 337
                     7899********************9999**********************************************************99999999* PP

                     CTCCCC-SSSSEEEHHHHHHTT-HHHHHHHHHHH-HHHHHHHHHHTTTTS-SSSSSTT-B--.B--SSH.........HHHHHHHHTTT...SBB CS
  Transpeptidase  83 kdweqdnkgsegitlrealekSsntyfvklaqklgadklrkylkkfglGnktgidlpgesaG.vptrkw.........legatisfgiG...ltv 164
                       w++    +++++l++a+++S+n+yf+k+ +k++a+++  ++++fglG++t    ++e+ G +p+ +w           g++i+ +iG   l++
      AHX11629.1 338 HCWKRFG--HGKVNLTRAIAESCNVYFYKIGRKISAEEIIGFAERFGLGTQTFTNMKEERYGiLPDMEWrnkyltqplGRGDIINISIGhgyLSA 430
                     ******5..999**************************************************6666699877766665559************** PP

                     -HHHHHHHHHHHHTTTEEE--BSEEEEEECTTEEEESS-EEEEE-S-HHHHHHHHHHHHHHHHCTTTTGCG.TCTTS--EEEEEEEEECSSSTTS CS
  Transpeptidase 165 tplqlaqayaaiangGklvkPhlvkaivdpdgvrkvkpkelnklpisketaekvkeglkgvvsrgsgtata.avegykvagKTGTAevagkkgng 258
                     tp+qla ++a +a  G    P +           ++ ++   + +i+ e++ +v++g+ +  s++ gt ++ ++e  k++gKTGT+++ g  ++ 
      AHX11629.1 431 TPIQLAVMAARLAT-GRQILPTFD----------DTASEIFPQININHEHLATVRRGMLNTFSNT-GTCRNfTSEMGKISGKTGTGQIRGRMNED 513
                     **************.999999998..........6788899**************9999988888.8999999*****************99888 PP

                     EEEEEEEEEEEEEEST.TS-SEEEEEEECTCSSSSSCCH CS
  Transpeptidase 259 kkegakiswfvgyapa.dnpkyavavlieqpkeaaggka 296
                     +    ++s f+gy++  ++ + a++v+ie++++ + +++
      AHX11629.1 514 HFYRGSNSLFIGYTTNvQDTNHAISVVIEKAEDISASSV 552
                     777667************************993333333 PP

>> PBP_dimer  Penicillin-binding Protein dimerisation domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.1   1.1e-17     1e-13       5     179 ..      56     209 ..      53     210 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 1.1e-17
                 ----EE-TTS-EEEEEEEEEEEEEEESSS-HHHHHHHHHHHHHHCHHHTTS-HHHHHHHHCCCCTSSTTSCECCCCCEECHHHCCCHHHHHCSTT-EEE CS
   PBP_dimer   5 pRGeIyDrngrlLAtnrpsytltitpsklkkkkalekikklaklleseenldderleelalkknsykaykpvviaediseeevarikenakdlpGinie 103
                 pR  ++D +   +A+n++ y++t+tps++ +k     ++ l ++++    l++++        n+ ++ +++ i++ + ++e++ ++ ++++l+Gi+i+
  AHX11629.1  56 PRRIVVDCDRIEIAGNKKIYNITCTPSEIMDKAYI--LEWLTQVFD----LSESETAA---LRNKIHGTETFIIKTPLGWQEISLLEFKSNQLQGIRIN 145
                 666778888889*******************9987..777777776....55544444...5668999******************************* PP

                 EEEEEEETTTSTTHHHH-EEEEC-HHHHHCCCCHTCCTTCEEEESHHHHHTHHHHHECCCEEEEEEECTSSCCEEE CS
   PBP_dimer 104 vepkRyYpkgelaahvlGyvgkiteeelekykekgyssgdliGksGlEkqyEeeLrGkkGkrqvkvdarGrileel 179
                 +e  R Yp g+ +ah++Gy+                ++++  G  GlEk yE+ ++    + + +vd+r r  +el
  AHX11629.1 146 KEYFRTYPLGAAMAHIIGYTVYD------------SKEKKCKGIIGLEKLYESSIQRDAEIIKKEVDSRERYRREL 209
                 *******************9888............788999*****************************998887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (566 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       425  (0.0237046); expected 358.6 (0.02)
Passed bias filter:                      372  (0.0207485); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 4024.85
//
Query:       AHX11630.1  [L=273]
Description: putative 3'-5' exonuclease related to the exonuclease domain of PolB family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-69  231.9   0.6    7.7e-69  231.6   0.6    1.1  1  DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the ex
    6.9e-09   35.9   0.3    2.3e-08   34.2   0.1    2.0  2  RNase_H_2       RNase_H superfamily
      0.007   15.5   0.1      0.011   14.9   0.1    1.3  1  DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
  ------ inclusion threshold ------
      0.026   14.2   0.1      0.052   13.2   0.1    1.5  2  HH_signal       Hedgehog amino-terminal signalling domain


Domain annotation for each model (and alignments):
>> DNA_pol_B_exo2  Predicted 3'-5' exonuclease related to the exonuclease domain of PolB
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  231.6   0.6   1.7e-72   7.7e-69       1     211 [.      48     262 ..      48     264 .. 0.96

  Alignments for each domain:
  == domain 1  score: 231.6 bits;  conditional E-value: 1.7e-72
  DNA_pol_B_exo2   1 sdFlrlalhrvvaisvvkar.....kdekfkvksl...geeessekelikkffegvekkkpqlVsfngrgfDlpvleyralkhgvsapkyfdegd 87 
                     ++Flr+++h+v+++s++ka+      +e +++k++   + e+ +ekel++ ff++v k+ p+lVs+ngr+fDl vl+y+a+++g+ a+ ++ +gd
      AHX11630.1  48 NPFLRQPFHKVIVVSLLKATlavknGYEFLELKKIasgDIESYAEKELVQFFFDHVCKSLPRLVSYNGRAFDLSVLKYKAMRYGIVARDFYYSGD 142
                     58***************999998854455599999887778889*************************************************** PP

  DNA_pol_B_exo2  88 edrekkwnnylsrystr.hlDLmdllseygaranakLdelakllglPGKlgvdGskVaelyqegklkeireYcetDvlnTYlvylrlellrgkls 181
                          kw ny +rys + h+DL+++ls+yg++a++k++el+  +glPGKlg+dG++V+++y++gk++ei+ Yce+DvlnTY++yl + +++g++s
      AHX11630.1 143 -----KWSNYNNRYSADwHTDLIEVLSDYGSSARMKMSELCVAFGLPGKLGIDGANVVSMYDQGKINEIKYYCEIDVLNTYMIYLIMLRHQGRIS 232
                     .....9*********999***************************************************************************** PP

  DNA_pol_B_exo2 182 eeeyaeeiaqvrellekekeekehlkefle 211
                     +++y++++++++ +l+++ ++++ ++efl+
      AHX11630.1 233 SDSYTRNLNELQFYLNENLDKNPSYREFLQ 262
                     ***************999999999****97 PP

>> RNase_H_2  RNase_H superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.6   0.0         1   4.6e+03       2      23 ..       6      25 ..       5      41 .. 0.65
   2 !   34.2   0.1   5.2e-12   2.3e-08      37     162 ..      86     221 ..      68     224 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.6 bits;  conditional E-value: 1
   RNase_H_2  2 ffDiEttGlspkknl.iyliGvl 23
                 fD+Et    p+++l + l G+ 
  AHX11630.1  6 VFDVETI---PDTDLcAALTGCK 25
                6999998...7666635666654 PP

  == domain 2  score: 34.2 bits;  conditional E-value: 5.2e-12
   RNase_H_2  37 laeepeeekailelflellekkkalvtfngksFDvpflkrlfkkyklde.................eefrhiDLlkelrkkkl.esysLksvekelgie 117
                  +e   e++ ++ +f ++ +  + lv++ng++FD+++lk+++ +y +                    +  h DL ++l++ +   +++++++  ++g  
  AHX11630.1  86 DIESYAEKELVQFFFDHVCKSLPRLVSYNGRAFDLSVLKYKAMRYGIVArdfyysgdkwsnynnrySADWHTDLIEVLSDYGSsARMKMSELCVAFGLP 184
                 567778889999999999************************777766667788888888775544555788999999887775666888888888888 PP

   RNase_H_2 118 rreedlsGsqavklyqeylrtgdeellekilaYNedDvralatly 162
                  +  +++G+++v +y+       + ++++i  Y+e Dv++++ +y
  AHX11630.1 185 GK-LGIDGANVVSMYD-------QGKINEIKYYCEIDVLNTYMIY 221
                 88.6**********96.......579***************9998 PP

>> DNA_pol_B_exo1  DNA polymerase family B, exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.1   2.5e-06     0.011     236     283 ..      90     136 ..      45     152 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 2.5e-06
                     SSHHHHHHHHHHHHHHH--SEEEESSTTTTHHHHHHHHHHHCCTCCHC CS
  DNA_pol_B_exo1 236 dsEkelLqaflefikqydPdvitgYNidnFDlpYilnRakelykvkls 283
                       Ekel q f++++ +  P  ++ YN+  FDl +++ +a+ + +v  +
      AHX11630.1  90 YAEKELVQFFFDHVCKSLP-RLVSYNGRAFDLSVLKYKAMRYGIVARD 136
                     46*************8755.5789***************988776554 PP

>> HH_signal  Hedgehog amino-terminal signalling domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.7   0.0       1.8     8e+03     139     151 ..      66      78 ..      64      84 .. 0.78
   2 ?   13.2   0.1   1.2e-05     0.052     115     156 ..     110     151 ..      86     154 .. 0.88

  Alignments for each domain:
  == domain 1  score: -3.7 bits;  conditional E-value: 1.8
                 HHHHHHCT-SEEE CS
   HH_signal 139 arLaveaGfDWvy 151
                 a Lav+ G+++  
  AHX11630.1  66 ATLAVKNGYEFLE 78 
                 7899999998875 PP

  == domain 2  score: 13.2 bits;  conditional E-value: 1.2e-05
                 -GGGGT-EEEEEETT--GGGHHHHHHHHHHCT-SEEEEEESS CS
   HH_signal 115 sLhyeGravdittsDkdrskyglLarLaveaGfDWvyyeska 156
                  + y+Gra d+     +  +yg++ar  + +G  W +y++++
  AHX11630.1 110 LVSYNGRAFDLSVLKYKAMRYGIVARDFYYSGDKWSNYNNRY 151
                 567***********************************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (273 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       453  (0.0252663); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1909.51
//
Query:       AHX11631.1  [L=414]
Description: glutamate--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-80  270.8   0.0    1.2e-43  149.2   0.0    2.1  2  tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic d


Domain annotation for each model (and alignments):
>> tRNA-synt_1c  tRNA synthetases class I (E and Q), catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  120.3   0.0   4.3e-39   7.8e-35       2      97 ..       6     100 ..       5     103 .. 0.97
   2 !  149.2   0.0   6.8e-48   1.2e-43     145     313 ..     103     268 ..      99     269 .. 0.98

  Alignments for each domain:
  == domain 1  score: 120.3 bits;  conditional E-value: 4.3e-39
                   -EEEE---SSSS-BHHHHHHHHHHHHHHHHTT-EEEEEE--SSCCC--HHHHHHHHHHHHHTT---SSEEEEGGGGHHHHHHHHHHHHHTTSEEEE CS
  tRNA-synt_1c   2 VrtRfaPePtGyLHiGhakaallnylfAknnnGkfilRieDTdperekeeaeesiledlkwlgikwdekptyqsdrfdelkkyaeeLikkGkAYvc 97 
                   V tRfaP+PtG LHiG+ ++al+n+l+A++++Gkf+lRieDTd++r+k  + +sil+ l+wl +k+ +++++qs   ++ k++a  L+++GkAY  
    AHX11631.1   6 VITRFAPSPTGNLHIGGLRTALFNFLYARKRGGKFLLRIEDTDAARSKSIYLDSILDGLSWLALKY-DGIVHQSANVERHKAVASALLESGKAYTK 100
                   89****************************************************************.77*************************75 PP

  == domain 2  score: 149.2 bits;  conditional E-value: 6.8e-48
                   EEEESSBTTSSGGGSSTEEEEEEESGGGSBTTTBTSTSEEE-HHHHHHHHHHHTT-SEEEEEGGGGCCHHHHHHHHHHTT-S.-EEEEEE--EEETT CS
  tRNA-synt_1c 145 vvRlkideessvefrDlvrgriklepqeihdlvivksdiyPtYdfavvidDaleeithvlrteefldntpkyiwllealglevppfiheylrlnlek 241
                    +Rl+i + + v+f+Dl+ g+i+ e ++i+d+vi +sd++PtY +avv+dD+++++th++r+ ++++nt  + +++ea+g+  p+++h++l+ n ++
    AHX11631.1 103 AIRLRIMHGAAVQFTDLILGDISTETKNINDVVILRSDGSPTYMLAVVVDDHDMGVTHIIRGSDHITNTFTQKLIYEAMGWSFPNVAHIPLIHNTHG 199
                   69****99999************************************************************************************** PP

                   SB-SHHHHHHHHHTTSSSSTT-TTSCBHHHHHHCTB-HHHHHHHHHHHCCCSSS.EEEEHHHHHHHHHHHHH CS
  tRNA-synt_1c 242 kklSKRklsllvdekqvkewddlreallnflrrlGwtpekerelftreeliksfdlnresksleafdrkkLe 313
                    klSKR++++   + ++ke + l+ea++n+l rlGw  ++++e+f+ ee i  fd+    ks++ fd++kL+
    AHX11631.1 200 AKLSKRDGAVD--VIAYKEAGILPEAMFNYLLRLGWA-HGDKEIFSIEEAIALFDIVGIGKSPARFDNEKLH 268
                   ********987..99*********************9.9*******************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (414 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       427  (0.0238162); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 2989.35
//
Query:       AHX11632.1  [L=186]
Description: glycerol-3-phosphate acyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    7.9e-41  139.8  16.9    8.9e-41  139.7  16.9    1.0  1  G3P_acyltransf  Glycerol-3-phosphate acyltransferase


Domain annotation for each model (and alignments):
>> G3P_acyltransf  Glycerol-3-phosphate acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.7  16.9     5e-45   8.9e-41       2     161 ..      10     179 ..       9     181 .. 0.89

  Alignments for each domain:
  == domain 1  score: 139.7 bits;  conditional E-value: 5e-45
                     HHHHHT--HHHHHHHH.TT--GGGSTTS--SHHHHHHHH-HHHHHHHHHHHHHHHH.HHHHHHHH.......HHHHHHHHHHHS-GGCTT----S CS
  G3P_acyltransf   2 aYllGsipfayligkllkgiDirelgsgNaGatNvlrvlGkkagilvlllDllKgllavllalll.......laglaavlGHifPvflkfkGGKG 89 
                      Y++ +ipfay+i+++  g+Dir +gsgN+GatNv+rv+G kag +v+llD+lK++++v++a  +       ++gl+ v+ H+fPv+l fkGGKG
      AHX11632.1  10 VYIVSAIPFAYCISNY-LGVDIRAEGSGNPGATNVTRVAGLKAGSIVFLLDFLKAAVPVFIAEKYcgevfasVIGLVSVFAHVFPVYLAFKGGKG 103
                     69*************9.8*****************************************9887776777666789******************** PP

                     HHHHHHHHHHHH...HHHHHHHHHHHHHHH--HHHHHHHHHHHHHH.HH......HH..HHHHHHHHHHHTHHHHH CS
  G3P_acyltransf  90 vatalGvllaldllllllallvfllvllltryvslaslvaalllpllllll....llllllllallvilrhrenik 161
                     va ++Gv +al+++++l++  v+l+v++++ry  +asl a+++  ++ +++    ++l +l ++ll+++rh +n+ 
      AHX11632.1 104 VAPMMGVYFALNPVVFLIVSYVWLVVFAIFRYPFIASLSACFVGAIVSYVTfdlyVFLPILTATLLILFRHVSNLT 179
                     ************999999999*****************887766665555568755566677899999******86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (186 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       776  (0.0432818); expected 358.6 (0.02)
Passed bias filter:                      253  (0.0141112); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1405.25
//
Query:       AHX11633.1  [L=358]
Description: cell shape determining, MreB/Mrl family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
   6.2e-139  462.4   6.8   7.2e-139  462.2   6.8    1.0  1  MreB_Mbl  MreB/Mbl protein
    4.4e-14   51.6   1.0      1e-13   50.4   0.4    1.9  2  HSP70     Hsp70 protein
    1.3e-11   44.9   1.1    4.7e-11   43.0   0.8    2.0  2  FtsA      Cell division protein FtsA
      9e-10   38.1   0.1    2.1e-05   23.7   0.0    2.4  2  PilM_2    Type IV pilus assembly protein PilM;
    2.4e-08   33.0   0.0    3.4e-07   29.2   0.0    2.0  2  Actin     Actin
    0.00041   19.3   1.2    0.00085   18.3   1.2    1.6  1  EutA      Ethanolamine utilisation protein EutA
  ------ inclusion threshold ------
      0.026   13.5   1.7      0.056   12.4   1.6    1.6  1  DDR       Diol dehydratase reactivase ATPase-like domain


Domain annotation for each model (and alignments):
>> MreB_Mbl  MreB/Mbl protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  462.2   6.8  2.8e-142  7.2e-139       2     326 ..      23     351 ..      22     352 .. 0.97

  Alignments for each domain:
  == domain 1  score: 462.2 bits;  conditional E-value: 2.8e-142
                 SEEEEEE-SSEEEEEETTTEEEEEEES-EEEETTT--EE..EESHHHHTTTTS-GTTEEEE-SEETTEESSHHHHHHHHHHHHHHHHTSS-SS--EEEE CS
    MreB_Mbl   2 kdlgiDLGtantlvyvkgkgivlnepsvvAikkktkkvl..avGeeAkkmlgktpgnikavrPlkdGviadlevaeellkyfikkvkkkkslskprvvi 98 
                 ++l+iDLGtantlvyv++kgi ln+psvvA+ +++++ +  a G+ Ak mlgktp++ika+rPlkdGviad+++aee++kyfik v++   +++p++vi
  AHX11633.1  23 NNLAIDLGTANTLVYVENKGIKLNQPSVVALVEDKGRFIpyAFGHPAKLMLGKTPDKIKAIRPLKDGVIADFRCAEEMIKYFIKIVNSGALINRPNIVI 121
                 689****************************99988764449********************************************************* PP

                 EE-SS--HHHHHHHHHHHHHTT-SEEEEEEHHHHHHHHTT--TTSSS-EEEEEE-SS-EEEEEEETTEEEEEEEES-SHHHHHHHHHHHHHHHHSEE-- CS
    MreB_Mbl  99 cvPsgiteverrAvkeaakkaGarevllieeplaAAiGaglpveepsgnmvvdiGggttevavislggivtsksvrvaGdeldeaiikyirkkynlliG 197
                 cvPsg+t verrA+++aa++aGarev+lieep+aAAiG glpv+ep+g+m+vdiGggttevavislggiv+s+svrv+Gd +deaii+yirk+ynlliG
  AHX11633.1 122 CVPSGSTPVERRAIQDAAESAGAREVFLIEEPMAAAIGGGLPVTEPKGSMIVDIGGGTTEVAVISLGGIVYSRSVRVGGDVMDEAIISYIRKHYNLLIG 220
                 *************************************************************************************************** PP

                 HHHHHHHHHHH-BSS--HHHH..EEEEEEEETTTTCEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH-EEEESGGGGSBTHHHHHH CS
    MreB_Mbl 198 ertaekikieigsavkeeeee..kmeikGrdlvtglpkevevsseevrealkepvsaiveavkevLektppeLaadivdrgivltGGgallkgldklls 294
                 e+taekik+e+g+++ +++++  +m+++Grd+v+g+pke+ +++++++e+l+ep+s i+ av  +Le++ppeL++di+  gi+++GGga+l++ld +ls
  AHX11633.1 221 ESTAEKIKKELGTVYVRDKAQerSMTLRGRDVVNGIPKEIILTESQIAESLEEPISVIIAAVMVALETIPPELSSDIASSGIMISGGGAMLRNLDYVLS 319
                 **************9877665569*************************************************************************** PP

                 HHHSS-EEE-SSTTTHHHHHHHHTTC-HHHHT CS
    MreB_Mbl 295 eetglpvkvaedpltcvakGtgkvleklkklk 326
                 ++t+l+v+++e+pl+cva Gtgkvle+l++ k
  AHX11633.1 320 NATQLSVSISENPLECVAIGTGKVLESLETFK 351
                 **************************998765 PP

>> HSP70  Hsp70 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0      0.36   9.1e+02       4      18 ..      27      41 ..      25      59 .. 0.78
   2 !   50.4   0.4     4e-17     1e-13     135     241 ..     118     218 ..     112     356 .. 0.71

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 0.36
                EEEXSSEEEEEEEET CS
       HSP70  4 iDLGttnsvvavmeg 18
                iDLGt n++v v ++
  AHX11633.1 27 IDLGTANTLVYVENK 41
                9******99987543 PP

  == domain 2  score: 50.4 bits;  conditional E-value: 4e-17
                 EEEEEEXTTXXHHHHHHHHHHHHHTTXEEEEEEEHHHHHHHHHHTCCSSSCEEEEEEEEXSSXEEEEEEEEETTEEEEEEEEEETTXSHHHHHHHHHHH CS
       HSP70 135 davitvPaYfndaqRqatkdAgkiAGLnvlRivNepTAaalaYGldkkdkernvlvyDlGggtfdvSilelekGvfevkaTagDthlGGedfDealveh 233
                 ++vi vP+  +  +R+a++dA++ AG   + ++ ep Aaa+  Gl  ++ ++  +++D+Gggt++v +++l+  v+     +   ++GG+ +Dea++ +
  AHX11633.1 118 NIVICVPSGSTPVERRAIQDAAESAGAREVFLIEEPMAAAIGGGLPVTE-PKGSMIVDIGGGTTEVAVISLGGIVY-----SRSVRVGGDVMDEAIISY 210
                 68**********************************************9.999999***************86555.....456799************ PP

                 HHHHHHHH CS
       HSP70 234 lveefkkk 241
                 ++++++  
  AHX11633.1 211 IRKHYNLL 218
                 *9998754 PP

>> FtsA  Cell division protein FtsA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0       1.2   3.1e+03       2      18 ..      26      42 ..      25      65 .. 0.78
   2 !   43.0   0.8   1.9e-14   4.7e-11       2      88 ..     172     324 ..     171     343 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 1.2
                EEEE-SSSEEEEEEETT CS
                xxxxxxxxxxxxxxxxx RF
        FtsA  2 lvDiGagktdvavaedg 18
                ++D+G+  t v v ++g
  AHX11633.1 26 AIDLGTANTLVYVENKG 42
                79999999988776665 PP

  == domain 2  score: 43.0 bits;  conditional E-value: 1.9e-14
                 EEEE-SSSEEEEEEETTEEEEEEEES--HHHHHHHHHHHH......T--HHHHHHHHHHH--S--EEEEEHHHHH........................ CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxxxxxxxxxxxxxxxxx........................ RF
        FtsA   2 lvDiGagktdvavaedgalvhlrvigvggngitkdiakal......rtaveeAerikikyGsalaekeigrkels........................ 70 
                 +vDiG+g+t+vav++ g++v++r++ vgg+ +++ i   +       +  ++Ae+ik++ G+++ + + ++++ +                        
  AHX11633.1 172 IVDIGGGTTEVAVISLGGIVYSRSVRVGGDVMDEAIISYIrkhynlLIGESTAEKIKKELGTVYVRDKAQERSMTlrgrdvvngipkeiiltesqiaes 270
                 8**********************************55555222233566899*************5555544444556666667777777778888888 PP

                 ....................................GGGGSTTHHHHHHHHHT- CS
                 ....................................xxxxxxxxxxxxxxxxxx RF
        FtsA  71 ....................................ggsalpnleelaeralsp 88 
                                                     gg++l+nl+ ++++a++ 
  AHX11633.1 271 leepisviiaavmvaletippelssdiassgimisgGGAMLRNLDYVLSNATQL 324
                 88999999999999999999****************************999632 PP

>> PilM_2  Type IV pilus assembly protein PilM;
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.7   0.0   8.3e-09   2.1e-05     180     243 ..     168     235 ..     130     240 .. 0.88
   2 !   11.9   0.0   3.3e-05     0.085     276     314 ..     300     339 ..     292     353 .. 0.82

  Alignments for each domain:
  == domain 1  score: 23.7 bits;  conditional E-value: 8.3e-09
      PilM_2 180 kvvaivdigasrttlsvlrdgkivYtreqafGgeqltqeiv....rrYglsleeaekkkrsgslPedy 243
                 k  +ivdig  +t+++v++ g ivY+r    Gg+ + + i+    ++Y+l   e  ++k++++l+  y
  AHX11633.1 168 KGSMIVDIGGGTTEVAVISLGGIVYSRSVRVGGDVMDEAIIsyirKHYNLLIGESTAEKIKKELGTVY 235
                 5679********************************99987222258*****************9888 PP

  == domain 2  score: 11.9 bits;  conditional E-value: 3.3e-05
      PilM_2 276 dkilLaGGtaslpgleelleeelgisttva.npfaemels 314
                   i+++GG a+l +l+ +l++ +++s+++  np++ ++++
  AHX11633.1 300 SGIMISGGGAMLRNLDYVLSNATQLSVSISeNPLECVAIG 339
                 579*************************964777766665 PP

>> Actin  Actin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2   0.0   1.3e-10   3.4e-07       7     194 ..      25     217 ..      19     249 .. 0.80
   2 ?    1.0   0.0     0.048   1.2e+02     299     341 ..     272     315 ..     255     327 .. 0.77

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 1.3e-10
       Actin   7 vVlDnGssttraGyagedaPkavipslvgkprgrkveaklyvgde.alt..k.rpelevrspvedGvvedwdaveelwehvlkeelkvd.peehplllt 100
                 + +D G+ +t + y +++  k+  ps+v+ ++++     + +g+  +l   k  ++++  +p++dGv+ d   +ee++++ +k   +    +   +++ 
  AHX11633.1  25 LAIDLGTANTLV-YVENKGIKLNQPSVVALVEDKGRFIPYAFGHPaKLMlgKtPDKIKAIRPLKDGVIADFRCAEEMIKYFIKIVNSGAlINRPNIVIC 122
                 668888888866.9999999999******9999988889999999633244437889999**********************99855552566779999 PP

       Actin 101 epplnppkqrekalEivfEkfkvpalylaksavlsafasgks.....tglvvDsGasvtsvvpVldGyvLkkairrsdlgGkaLteqlkellssknvev 194
                  p+ ++p +r  + + + E+ +   ++l ++++ +a   g+       +++vD+G ++t v+ +  G ++    r++ +gG+ ++e + ++++++  ++
  AHX11633.1 123 VPSGSTPVERRAIQD-AAESAGAREVFLIEEPMAAAIGGGLPvtepkGSMIVDIGGGTTEVAVISLGGIVYS--RSVRVGGDVMDEAIISYIRKH-YNL 217
                 999999999987766.56***********************99999999***************99988875..56679************9995.332 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.048
       Actin 299 kskllgiselivaainacdvdlrpeLlan.ivvtGGnsllpglt 341
                 ++ ++ i   ++ a++ ++++l ++++++ i ++GG ++l++l 
  AHX11633.1 272 EEPISVIIAAVMVALETIPPELSSDIASSgIMISGGGAMLRNLD 315
                 3556667889999*************976699*******99885 PP

>> EutA  Ethanolamine utilisation protein EutA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   1.2   3.3e-07   0.00085     147     205 ..     172     226 ..     159     313 .. 0.82

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 3.3e-07
        EutA 147 niDiGGGtsnlalfkeGevidtacldvGGrlikidkdtkkityispklkkiieelglel 205
                  +DiGGGt+ +a+++ G ++ + ++ vGG ++     ++ i+yi+++ + +i e + e 
  AHX11633.1 172 IVDIGGGTTEVAVISLGGIVYSRSVRVGGDVMD----EAIISYIRKHYNLLIGESTAEK 226
                 58***************************9864....4679999999999887766543 PP

>> DDR  Diol dehydratase reactivase ATPase-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   1.6   2.2e-05     0.056     117     189 ..     152     229 ..     123     235 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.2e-05
         DDR 117 EaemAilGalttPGtekplailDlGaGstDaalieeegevkavhlAGAGemvtlliaseLg.....ledrelaEdiKk 189
                 E+ +A++G       +k ++i+D+G+G+t+ a+i+  g v +  +   G+++  +i s +      l   ++aE+iKk
  AHX11633.1 152 EPMAAAIGGGLPVTEPKGSMIVDIGGGTTEVAVISLGGIVYSRSVRVGGDVMDEAIISYIRkhynlLIGESTAEKIKK 229
                 4444444544333456889******************99998777777777665554332211111235567777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (358 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       365  (0.0203581); expected 358.6 (0.02)
Passed bias filter:                      322  (0.0179597); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.54u 0.26s 00:00:00.80 Elapsed: 00:00:00.42
# Mc/sec: 2533.60
//
Query:       AHX11634.1  [L=568]
Description: type IV secretory system Conjugative DNA transfer family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
   3.2e-144  481.2   0.0   4.2e-144  480.8   0.0    1.0  1  T4SS-DNA_transf  Type IV secretory system Conjugative DNA tra
    4.7e-27   94.5   0.0    8.7e-27   93.6   0.0    1.5  1  TraG-D_C         TraM recognition site of TraD and TraG
    1.3e-23   83.6   0.0      2e-23   83.0   0.0    1.3  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
  ------ inclusion threshold ------
      0.064   13.2   0.0       0.24   11.3   0.0    2.0  1  DUF1641          Protein of unknown function (DUF1641)
        1.3    8.1   5.6        1.7    7.7   5.6    1.2  1  Astro_capsid_p   Turkey astrovirus capsid protein
        9.3    7.0  11.6         17    6.2  11.6    1.4  1  FYDLN_acid       Protein of unknown function (FYDLN_acid)


Domain annotation for each model (and alignments):
>> T4SS-DNA_transf  Type IV secretory system Conjugative DNA transfer
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  480.8   0.0  1.4e-147  4.2e-144       1     461 [.      44     484 ..      44     491 .. 0.96

  Alignments for each domain:
  == domain 1  score: 480.8 bits;  conditional E-value: 1.4e-147
  T4SS-DNA_transf   1 rwaadgdlekagllkrektikgevltkdkkalyaggllntdGdfehvlvvAptrsgKgvgvviPnllkwkqsiVvlDpkgElaeltskiRkkqg 94 
                      rwa   +++k gl++r++++ g    kd     ++g+l + G ++h+l++Apt+sgKgvg+viPnll+w++s+Vv+D+k E+++lts+ Rkk g
       AHX11634.1  44 RWATEREIRKIGLRSRKGLLLG----KD-----KRGFLIASG-YQHALLFAPTGSGKGVGFVIPNLLFWEDSVVVHDIKLENFNLTSGYRKKIG 127
                      6888899999999999888888....66.....799888888.78************************************************* PP

  T4SS-DNA_transf  95 rkVfvlePanlkts.drfNpldyidlksevetedilsvaslilkkkgkgkddffsntarqLlvaliaevllkketetegqtlkvvramlsepnl 187
                      +kV+ ++Pa+++++ +++Npld+++ k++++++d++++a+l+++++     df+ n+ar+L+ + ++++ l+ + + ++ + +vvr m+s++  
       AHX11634.1 128 QKVYCWSPADPDGKsHCYNPLDWVSSKPGQMVDDVQKIANLLMPEQ-----DFWVNEARSLFLG-VVLYILAVPEKVKS-FGEVVRVMRSDD-- 212
                      *************99******************************9.....9************.66666666666666.8***********.. PP

  T4SS-DNA_transf 188 edenkeeaklleelkgkeedrvgdnlrvlvektdetrsSvlgtakselalyadplvrnatSksdFdlrdlrrkkvsvyvivnpkdlevvapllr 281
                         ++ +a+ l+++ +k ++ +++n++++ +k+d++rs+v++t++s+l+l+a+pl++  t+ sdF++ +++++ ++vyv+++p++l++++pl++
       AHX11634.1 213 --VTYSLAVALDTMGKKIHPVAYMNIAAFLQKADKERSGVISTMNSSLELWANPLIDTTTATSDFNFMQFKKDLTTVYVGLTPDNLTRLQPLMQ 304
                      ..9******************************************************************************************* PP

  T4SS-DNA_transf 282 lffnmvvellkrklpnkderpkevlflLDEfpslGkleileealatiagYgirltlIiQsisqlketYgkegaksilsnsavvivfaasndeet 375
                      +f+++ +e+l r+lp kde  + vlf++DEfp+lGk+e++++++a+++gY++rl+lIiQ+++qlk++Y+++g++s+lsns+++i+faa+n  et
       AHX11634.1 305 VFYQQATEFLCRSLPSKDEP-YGVLFMMDEFPTLGKMEQFKTGIAYFRGYNVRLFLIIQDTEQLKGIYEEAGMNSFLSNSTYRITFAANN-IET 396
                      ****************9986.*********************************************************************.*** PP

  T4SS-DNA_transf 376 aeyiSkllGktTvekestsk..stdakgksrsrsisekqRaLltPdevlrmdddeeivlikgqkPikakkalYykdedfkaelakpsa 461
                      a+ iS+l+G++Tv +es +k  + d +  srs  +se+qRaLl+P+ev+ +++d++i+li++  Pi++kk++Yy+d++f+++l  p +
       AHX11634.1 397 ANLISQLVGNKTVAQESLNKpkFLDLNPASRSLHVSETQRALLLPQEVIMLPRDQQILLIESTYPIRSKKIKYYEDSFFTKKLMDPIS 484
                      ********************9889*********************************************************9988864 PP

>> TraG-D_C  TraM recognition site of TraD and TraG
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.6   0.0   2.9e-30   8.7e-27       2     126 .]     327     449 ..     326     449 .. 0.93

  Alignments for each domain:
  == domain 1  score: 93.6 bits;  conditional E-value: 2.9e-30
    TraG-D_C   2 vlfllDEfanlgkipdleellstgrsrgislvlilQsiaqleelYgkegaetilgncdvklflgvndeetaeelSkllGektvesestsssssgsggss 100
                 vlf++DEf++lgk++++++ ++ +r+++++l+li+Q+ +ql+ +Y ++g++++l+n++ ++ +++n+ eta  +S+l+G+ktv +es ++ +    + +
  AHX11634.1 327 VLFMMDEFPTLGKMEQFKTGIAYFRGYNVRLFLIIQDTEQLKGIYEEAGMNSFLSNSTYRITFAANNIETANLISQLVGNKTVAQESLNKPKFL--DLN 423
                 89*************************************************************9*******************98776666644..455 PP

    TraG-D_C 101 essssssqseekrpLltpdeirrlpr 126
                   s+s + se++r+Ll p+e+  lpr
  AHX11634.1 424 PASRSLHVSETQRALLLPQEVIMLPR 449
                 78899999*************99985 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.0   0.0   6.7e-27     2e-23      84     380 ..     156     462 ..      74     468 .. 0.80

  Alignments for each domain:
  == domain 1  score: 83.0 bits;  conditional E-value: 6.7e-27
  TrwB_AAD_bind  84 ikeksdfaeiAaalipedggssdpfWaeaartvlaetlrelvrekkksn..aallralltad........leeLkellagteaaalva.....eea 164
                     +   d+++iA+ l+pe     ++fW++ ar ++  ++  +++  +k +   + +r + ++d        l+++ + ++  + +   +     ++a
     AHX11634.1 156 GQMVDDVQKIANLLMPE-----QDFWVNEARSLFLGVVLYILAVPEKVKsfGEVVRVMRSDDvtyslavaLDTMGKKIHPVAYM---NiaaflQKA 243
                    4556799**********.....9***********99877665544433331555554433342111111133333333333333...344477999 PP

  TrwB_AAD_bind 165 ertaasiratlatnlevle.lLaekgerFSireWleeedesgwlfltskaeqrallrpllsawldlaikalls.lpesrerr.lWfflDElpaLgr 257
                    ++  +++ +t+++ le+    L ++ ++ S  ++++ +++  ++++  ++++ + l+pl+++  + a + l + lp+++e   + f++DE+p+Lg+
     AHX11634.1 244 DKERSGVISTMNSSLELWAnPLIDTTTATSDFNFMQFKKDLTTVYVGLTPDNLTRLQPLMQVFYQQATEFLCRsLPSKDEPYgVLFMMDEFPTLGK 339
                    9999*********99987524556666677778888888889***************************99885666666557************* PP

  TrwB_AAD_bind 258 leelksllaegRkfGgavvlglqsiaqlrevYGedaaqsilslvntklilrvsdaetAeelsellGeqeversteslsygannsrdgvslgrqrev 353
                    +e++k+++a  R + +++ l +q+++ql+ +Y e++ +s ls+   ++++++++ etA+ +s+l+G++ v ++  +        + + sl+  +++
     AHX11634.1 340 MEQFKTGIAYFRGYNVRLFLIIQDTEQLKGIYEEAGMNSFLSNSTYRITFAANNIETANLISQLVGNKTVAQESLNKPKFLDLNPASRSLHVSETQ 435
                    ******************************************************************************9999999999******** PP

  TrwB_AAD_bind 354 rpvVlaselqnlpdlegylklpeglpv 380
                    r ++l++e+  lp+ + +l + + +p+
     AHX11634.1 436 RALLLPQEVIMLPRDQQILLIESTYPI 462
                    ****************99999888876 PP

>> DUF1641  Protein of unknown function (DUF1641)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   7.9e-05      0.24       6      32 ..     195     222 ..     185     225 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 7.9e-05
     DUF1641   6 pkpv.GlfgLlraLrDPDVqrGLGflla 32 
                 p++v + ++++r +r  DV ++L+++l 
  AHX11634.1 195 PEKVkSFGEVVRVMRSDDVTYSLAVALD 222
                 89***********************996 PP

>> Astro_capsid_p  Turkey astrovirus capsid protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   5.6   0.00058       1.7     205     279 ..     494     565 ..     398     568 .] 0.79

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.00058
                     EEEEEESS--XXXX....XXXX......XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX..XXXXX CS
  Astro_capsid_p 205 llfemkttvpqeralaegederktgaeeeisdpsdeedeevsdeetdtevesdeDeddevdrfDletsyeSeaeD 279
                       fe k++ ++e++ +e++ +  +++e+++ ++++  d++  +ee  ++ +sdeD ++ vd+ D e+    e e 
      AHX11634.1 494 KKFEEKIRKEKEAKELEENTPLPIEEEQALLEDESLLDDSDYEEEDFEDLDSDEDLSEFVDDLDDEEL---ETEE 565
                     469999999999999999999999*******99999996666666667899****9999999998655...3333 PP

>> FYDLN_acid  Protein of unknown function (FYDLN_acid)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.2  11.6    0.0057        17      28     103 ..     483     564 ..     477     567 .. 0.61

  Alignments for each domain:
  == domain 1  score: 6.2 bits;  conditional E-value: 0.0057
  FYDLN_acid  28 vcpkcgeefepeevlksraaaaeaeeakkkkeeeedeedeeeeedvsdedadeeeee.....dddd.dvdleedddddvfle 103
                 +++ ++e f+p+++ ++ ++++ea+e ++++    +ee++  e++  ++d d eee+     +d+d ++ +++ dd++ ++e
  AHX11634.1 483 ISIPTQEPFDPKKFEEKIRKEKEAKELEENTPLPIEEEQALLEDESLLDDSDYEEEDfedldSDEDlSEFVDDLDDEELETE 564
                 4677999*******55555555555556777777778888877777778888887766665433332222233333344444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (568 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       608  (0.0339115); expected 358.6 (0.02)
Passed bias filter:                      396  (0.0220871); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.59u 0.25s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4069.07
//
Query:       AHX11635.1  [L=331]
Description: P-type DNA transfer ATPase VirB11 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.9e-82  275.8   0.1    3.3e-82  275.6   0.1    1.0  1  T2SSE            Type II/IV secretion system protein
    0.00037   20.8   0.0    0.00058   20.1   0.0    1.3  1  AAA_28           AAA domain
     0.0026   17.3   0.0     0.0051   16.3   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
     0.0038   16.6   0.0      0.011   15.2   0.0    1.7  2  Mg_chelatase     Magnesium chelatase, subunit ChlI
     0.0044   16.4   0.2      0.031   13.6   0.2    2.2  2  FtsK_SpoIIIE     FtsK/SpoIIIE family
  ------ inclusion threshold ------
      0.023   14.8   0.1      0.041   13.9   0.1    1.5  1  Dynamin_N        Dynamin family
      0.035   13.8   0.0      0.059   13.1   0.0    1.4  1  IstB_IS21        IstB-like ATP binding protein
      0.054   12.4   0.1       0.12   11.3   0.0    1.5  1  TrwB_AAD_bind    Type IV secretion-system coupling protein DN
      0.063   13.7   0.0        0.1   12.9   0.0    1.4  1  AAA_16           AAA ATPase domain
      0.072   13.0   0.1       0.13   12.1   0.1    1.5  1  RsgA_GTPase      RsgA GTPase
       0.11   11.3   0.0       0.16   10.7   0.0    1.1  1  PPV_E1_C         Papillomavirus helicase
       0.12   12.8   0.0       0.23   11.8   0.0    1.6  1  RNA_helicase     RNA helicase
       0.14   11.9   0.0       0.28   10.9   0.0    1.5  1  Sigma54_activat  Sigma-54 interaction domain
       0.14   11.4   0.0       0.21   10.8   0.0    1.2  1  Septin           Septin
       0.14   11.4   0.0       0.23   10.7   0.0    1.3  1  Zeta_toxin       Zeta toxin
       0.17   11.9   0.0       0.31   11.0   0.0    1.3  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro


Domain annotation for each model (and alignments):
>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  275.6   0.1   2.9e-85   3.3e-82       3     272 ..      11     310 ..       9     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 275.6 bits;  conditional E-value: 2.9e-85
       T2SSE   3 illeallddekvsdihvekpervkvrervdgielreveelekaalerlisriaalakldiseerplqdarlpekgvrlrvvllPvvag..ealviRkks 99 
                  +l++++ d++v++i v+kp+++++ e+ ++i  +e++ l+ ++l+ l++ +a+++++++s e pl++a+lp ++ r+++vl+P+++     ++iRk+s
  AHX11635.1  11 EPLDEIFSDADVNEISVNKPGEIWI-EKNGEITRSELPVLDFQHLKGLAKLVAQATEQSVSGEYPLLSATLP-NECRIQIVLPPAAESgtVVMSIRKPS 107
                 678999*******************.**********************************************.**************95444889**** PP

       T2SSE 100 akeltlddlgaeealk.....................ekiaevlrkavrerglilvsGgTgsGKttllyallkeinksderivtvEDpvEiql.eganq 176
                 + +l+l+d+  ++a++                      +i+e+l++av  +++i++sGgT++GKtt++++l++ei+++ eri+tvED++E+ l +++n+
  AHX11635.1 108 SVQLSLADYDRMGAFEvlksassstdlddrlkcmldsGEIKEFLATAVVGKKNIIISGGTSTGKTTFANSLMQEIPSH-ERIITVEDAREVVLsKHPNR 205
                 ******************************************************************************.*************9889*** PP

       T2SSE 177 vqlnak.....kakvtfadllraaLRlrPDrimvGEiRdketleilkAvnTGHlgslsTlHansaagalerLeqlgae....veaaelkssilavvdiv 266
                 v+l+++     +a+vt++dl++a+LRlrPDri+vGE+R++e++ +l+A+nTGH+gs++TlHa+++ +a+e+L+ ++++    +++ +++++i++v+d++
  AHX11635.1 206 VHLVSSkggqgRANVTTQDLIEACLRLRPDRIIVGELRGTEAFGFLRAINTGHPGSIATLHADTPNMAIEQLKLMVMQaglgIPPVQVREYIINVIDVI 304
                 *****99******************************************************************************************** PP

       T2SSE 267 vrlvrk 272
                 v+l+r+
  AHX11635.1 305 VQLKRD 310
                 ***996 PP

>> AAA_28  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   5.2e-07   0.00058       1      39 [.     160     202 ..     160     230 .. 0.80

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 5.2e-07
      AAA_28   1 kivitGgestGKTtlleaLaar...gypvv.pEaareileekl 39 
                 +i+i+Gg stGKTt ++ L ++     +++  E are++ +k+
  AHX11635.1 160 NIIISGGTSTGKTTFANSLMQEipsHERIItVEDAREVVLSKH 202
                 59******************77775333444778888876654 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.0   4.6e-06    0.0051      18      61 ..     143     186 ..     130     193 .. 0.87

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.6e-06
       AAA_7  18 dtvrysyllelllknkkpvllvGptGtGKtviikdllkkldkek 61 
                 d+  ++ +l + +  kk++++ G t tGKt+ +++l++++++ +
  AHX11635.1 143 DSGEIKEFLATAVVGKKNIIISGGTSTGKTTFANSLMQEIPSHE 186
                 66677889999999*************************99655 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       2.3   2.6e+03      97     121 ..      28      52 ..       9      61 .. 0.73
   2 !   15.2   0.0   9.6e-06     0.011      10      65 ..     146     201 ..     138     235 .. 0.82

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 2.3
  Mg_chelatase  97 pkpGeislahnGvLfLDElpefkrk 121
                    kpGei   +nG +   Elp ++ +
    AHX11635.1  28 NKPGEIWIEKNGEITRSELPVLDFQ 52 
                   5788888888887777777665555 PP

  == domain 2  score: 15.2 bits;  conditional E-value: 9.6e-06
  Mg_chelatase  10 eakraleiaaaGgHnlllvGppGsGKtmlakrlpsllpplseeealevakiasvag 65 
                   e k+ l  a+ G+ n+++ G   +GKt  a+ l++ +p+ ++  ++e a+   +++
    AHX11635.1 146 EIKEFLATAVVGKKNIIISGGTSTGKTTFANSLMQEIPSHERIITVEDAREVVLSK 201
                   56788999**************************9999988776666666555555 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.76   8.5e+02      67      88 ..     104     126 ..     100     133 .. 0.86
   2 !   13.6   0.2   2.7e-05     0.031      33      61 ..     153     180 ..     129     186 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.76
                   --TTTEEEEEE-TTSS.SCGGGT CS
  FtsK_SpoIIIE  67 htPeeVqliliDykgv.elsale 88 
                    +P  Vql l Dy  + ++++l+
    AHX11635.1 104 RKPSSVQLSLADYDRMgAFEVLK 126
                   689**********9988998876 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 2.7e-05
                   EEGGGS-.SEEEE--TTSSHHHHHHHHHH CS
  FtsK_SpoIIIE  33 ldlkkmashllvaGatgsGKStalntLil 61 
                   +  ++   ++++ G+t +GK+t+ n+L++
    AHX11635.1 153 TAVVGK-KNIIISGGTSTGKTTFANSLMQ 180
                   444444.5*******************97 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.7e-05     0.041       1      33 [.     161     191 ..     161     230 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
                 EEEEEBTTTTHHHHHHHHHTS--S---SSS--- CS
   Dynamin_N   1 iavvGsqSsGKSSvlnaLlgedilprgpnptTr 33 
                 i++ G +S GK++++n+L++e   p+++ ++T 
  AHX11635.1 161 IIISGGTSTGKTTFANSLMQEI--PSHERIITV 191
                 7889***************997..888887774 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.0   5.3e-05     0.059      20      72 ..     132     183 ..     114     232 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.3e-05
   IstB_IS21  20 edidfraarsldkrkvkeLatlsfiekkenivllGpsGvGKshlaialgveav 72 
                  d+d r + +ld  ++ke  +++ +  k+ni++ G++ +GK+ +a +l +e  
  AHX11635.1 132 TDLDDRLKCMLDSGEIKEFLATAVVG-KKNIIISGGTSTGKTTFANSLMQEIP 183
                 56666777788888899888888776.579*****************988754 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0    0.0001      0.12      16      51 ..     159     194 ..     154     209 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.0001
  TrwB_AAD_bind  16 qhilivGttGsGKtqalekllrairargdraivlDl 51 
                    + i+i G+t +GKt+ +++l+++i + +  + v D+
     AHX11635.1 159 KNIIISGGTSTGKTTFANSLMQEIPSHERIITVEDA 194
                    6899********************988776666665 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.3e-05       0.1      22      63 ..     157     197 ..     144     286 .. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.3e-05
      AAA_16  22 grpelvllsGesGvGKsslvrellralekdggiflrgkcdql 63 
                 g   ++++sG   +GK++ +++l++++  ++ i + +++++ 
  AHX11635.1 157 GK-KNIIISGGTSTGKTTFANSLMQEIPSHERIITVEDAREV 197
                 44.7899********************999543333333333 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.1   0.00012      0.13      85     148 ..     143     227 ..      99     230 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00012
                  TTHTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHCTT....................-----S--------------SEEEEE CS
  RsgA_GTPase  85 ktkegleelkellkd.ktsvlvGqSGvGKStLinallpe....................lelktgevseklgrGkhTTtavelle 148
                  +++e  e l++++ + k +++ G +  GK+t+ n+l++e                    +  +++ vs+k g+G+   t++ l+e
   AHX11635.1 143 DSGEIKEFLATAVVGkKNIIISGGTSTGKTTFANSLMQEipsheriitvedarevvlskHPNRVHLVSSKGGQGRANVTTQDLIE 227
                  455555666666655489999*****************99999999999999999999889999999999999998887777765 PP

>> PPV_E1_C  Papillomavirus helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00015      0.16     252     284 ..     147     180 ..     137     191 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00015
    PPV_E1_C 252 lkefLkg..vPkknclvllGppntGkslfamslik 284
                 +kefL    v kkn +++ G + tGk++fa+sl++
  AHX11635.1 147 IKEFLATavVGKKN-IIISGGTSTGKTTFANSLMQ 180
                 78888752134555.788999************97 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00021      0.23       1      26 [.     161     186 ..     161     227 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00021
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkkl 26 
                   i+++G + +GK+t+a++L++++ ++ 
    AHX11635.1 161 IIISGGTSTGKTTFANSLMQEIPSHE 186
                   6899*************999998665 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00025      0.28      14      54 ..     150     189 ..     142     200 .. 0.79

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00025
                      HHHHHCTSSS-EEEECSTTSSHHHHHHHHHHHSTTTTS-EE CS
  Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellaraiheaskrkekpfv 54 
                       +++++  + +++i G + tGK+++a+++ ++ + +e+ ++
       AHX11635.1 150 FLATAVVGKKNIIISGGTSTGKTTFANSLMQEIPSHER-II 189
                      55667777899******************998875544.44 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00019      0.21       6      35 ..     160     189 ..     157     220 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
                 EEEEEEBTTSSCCCCCCTTSSSS------- CS
      Septin   6 tlmvvGesglGkttlintlfetdlieeekl 35 
                 ++++ G  ++Gktt+ n+l+++   +e+ +
  AHX11635.1 160 NIIISGGTSTGKTTFANSLMQEIPSHERII 189
                 899*****************9876666544 PP

>> Zeta_toxin  Zeta toxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.7   0.0   0.00021      0.23      16      50 ..     158     192 ..     147     226 .. 0.88

  Alignments for each domain:
  == domain 1  score: 10.7 bits;  conditional E-value: 0.00021
  Zeta_toxin  16 PklillgGqpGAGKselaellkdelerqgnvvrld 50 
                 +k i+++G++  GK++ a+ l +e+ +++++++++
  AHX11635.1 158 KKNIIISGGTSTGKTTFANSLMQEIPSHERIITVE 192
                 5779**************************99986 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   0.0   0.00028      0.31      12      43 ..     149     182 ..     139     191 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 0.00028
                 HHHHHCH..TEEEEEEESTTSSHHHHHHHHHHHT CS
        TsaE  12 kklakal..gdvilLeGdLGaGKTtlvrglakal 43 
                 + la+a+  ++ i+++G   +GKTt++ +l++++
  AHX11635.1 149 EFLATAVvgKKNIIISGGTSTGKTTFANSLMQEI 182
                 455555566778******************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      531  (0.0296168); expected 358.6 (0.02)
Passed Vit filter:                       100  (0.00557756); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.38
# Mc/sec: 2602.13
//
Query:       AHX11636.1  [L=461]
Description: bacterial conjugation TrbI-like family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.6e-49  168.3   4.0    2.3e-49  167.8   4.0    1.2  1  TrbI      Bacterial conjugation TrbI-like protein


Domain annotation for each model (and alignments):
>> TrbI  Bacterial conjugation TrbI-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  167.8   4.0   1.3e-53   2.3e-49       1     187 []     239     449 ..     239     449 .. 0.95

  Alignments for each domain:
  == domain 1  score: 167.8 bits;  conditional E-value: 1.3e-53
                 EE-TT--EEEEESS-EESSS-EEEEEEE-S-EE-SSSS-EEE-TT-EEEEEEEEEESSSSEEEEEEEEEEE-TT--EEESS----------HHHHHHHH CS
        TrbI   1 ylpaGtvipavLltginsdlpgqvtaqvtedvysatgrallIpkgsrligeydsavakgqeRvlvvwtrlilpdgksielggapgadadGraGlrGrvd 99 
                 +l++G++++avL+t+in+dl+ +v+a+v++dv+s++g+ +lIp+gsrlig+y+s+++++q+Rv +vwtr+ilp+g  i+lg+++g+d++GraG+rG v+
  AHX11636.1 239 VLAEGKMLDAVLETAINTDLQAKVRAVVSRDVFSESGNLILIPRGSRLIGSYSSDISFNQSRVNIVWTRIILPNGIDITLGNFAGVDPLGRAGVRGVVN 337
                 5899*********************************************************************************************** PP

                 HHHHHHHSSS-SEEEEES---EEEE------------........................HHHHHHHHT-TT-BHHHHHHHHHHHHTTS--EEEE-TT CS
        TrbI 100 nhfgkrfgaalllsllsgagellnaassssttsstgt........................qslaaavgegasqalsqvaqrilkraeniqptievpqG 174
                  ++ + +++++ll++++ a+ ++ ++   ++++ ++                          s+ a +g +a q++s++ ++++kr+ n +pti+++qG
  AHX11636.1 338 SKVSNVMSTSILLATARVASGIIVDRIMGADKKLSEVtvstpkrplvkknddvdddgskakGSAGAIIGIQAVQDASKQVTDYVKRMANANPTITINQG 436
                 ******************99999666666666655556777899*****************9************************************* PP

                 -EEEEEESSEEE- CS
        TrbI 175 tkvtvvvnrdldl 187
                 +k++v+v++d+++
  AHX11636.1 437 AKLKVFVDQDIVF 449
                 ***********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (461 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       516  (0.0287802); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 3259.23
//
Query:       AHX11637.1  [L=244]
Description: conjugal transfer family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      7e-52  176.2   1.2      8e-52  176.0   1.2    1.0  1  CagX      Conjugal transfer protein
  ------ inclusion threshold ------
      0.034   14.0   0.0       0.16   11.8   0.0    2.0  2  UvrD_C_2  UvrD-like helicase C-terminal domain


Domain annotation for each model (and alignments):
>> CagX  Conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.0   1.2     9e-56     8e-52       2     211 .]      28     241 ..      27     241 .. 0.96

  Alignments for each domain:
  == domain 1  score: 176.0 bits;  conditional E-value: 9e-56
        CagX   2 riqtvvYspgavvrvraapgyvtdielepgEkivevalGdtvrWeveptkgnhlfvkPteaglktnlvvvTdkRtYsfeLrste.......kekkklmy 93 
                 ri+t+vYs++a++r+++ +gy++ ie++++Ek++++a+G +v+W+++p  gn++f++P e+gl+tn+vvvTd++tY+f+L s++       k++++++y
  AHX11637.1  28 RIKTLVYSRDAIFRIDTGYGYQSFIEFSDKEKVKTIAIGGSVGWNMNP-IGNKIFLRPLEKGLSTNMVVVTDRHTYVFDLFSDSddhleetKKSNQVNY 125
                 99**********************************************.********************************99999****99******* PP

        CagX  94 rvsfrypdeeaaaaaaaaaaaaaekkeaqekapeklnfdYsvsgsaeiaPervfdDgrfTyirfpsankelPavfvvdedgkeelvnyrvegnylvvdr 192
                 +v+f+ypde a+++++++++  + + +  + + + l+ +Ysv+g+ae++  +++++ + T+++f  +  ++P vfvv++d++e+ +++   ++y+v+++
  AHX11637.1 126 VVRFYYPDEVADSNKENPKEGLSLNGKLYDFSYDVLRRNYSVQGKAEFEIAEIMNNTNLTFFKF--KGDKIPRVFVVNPDRSETQAKMWKFKEYVVIEG 222
                 **************77777777777777777*********************************..999******************9999******** PP

        CagX 193 vakklvLrlGkevvriene 211
                 v+kkl+Lr+ ++v++++n+
  AHX11637.1 223 VHKKLHLRYRSSVLEVVNN 241
                 ****************995 PP

>> UvrD_C_2  UvrD-like helicase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.9   0.0      0.16   1.5e+03      11      22 ..      87      98 ..      87     114 .. 0.78
   2 ?   11.8   0.0   1.8e-05      0.16       5      34 ..     184     212 ..     182     220 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.9 bits;  conditional E-value: 0.16
    UvrD_C_2 11 QGsefpaVivfd 22
                +G+  ++V+v+d
  AHX11637.1 87 KGLSTNMVVVTD 98
                799999999965 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1.8e-05
    UvrD_C_2   5 ltihkaQGsefpaVivfdpdlaaarmgelr 34 
                 lt  k++G   p V+v++pd ++ + ++ +
  AHX11637.1 184 LTFFKFKGDKIPRVFVVNPDRSETQAKM-W 212
                 5778****************99998776.5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (244 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       565  (0.0315132); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.29s 00:00:00.71 Elapsed: 00:00:00.43
# Mc/sec: 1695.45
//
Query:       AHX11638.1  [L=225]
Description: virB8 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-49  168.4   0.9    2.1e-49  168.2   0.9    1.0  1  VirB8     VirB8 protein
  ------ inclusion threshold ------
        0.6    9.5   4.2        1.6    8.1   4.2    1.7  1  TraE      TraE protein


Domain annotation for each model (and alignments):
>> VirB8  VirB8 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  168.2   0.9   2.4e-53   2.1e-49       2     214 .]      15     223 ..      14     223 .. 0.96

  Alignments for each domain:
  == domain 1  score: 168.2 bits;  conditional E-value: 2.4e-53
                 .XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXX.XXXXXXXXXXXXXX-HHHHHHHHHHHHHHHHHH-B-TTTH.H CS
       VirB8   2 arqfwderigsarvqarnwrlvafvslliavlavgavvlllplktvePyvvevdkttGeveavapaaekkpsadeavikaflaryvtvReiyddaalvq 100
                  +++++er+g+++ q++ + ++++++ll+ vl+v+ ++++++++t+eP+v+ev k++G v++  pa+ k++sa++a++++f+++yv++Re++++a+  +
  AHX11638.1  15 VEHWYEERVGRVTLQRNFLIVMSLGVLLVLVLSVFTLFAVSTSRTIEPFVIEVSKKSGIVTHLDPATVKEYSANRAITNYFATQYVKAREVFHPATYRY 113
                 689**********************************************************************************************99 PP

                 HHHHHHHHTB-HHHHHHHHHHHSTT-TTSHHHHTTTSEEE.EEEEEEEEEEETTEEEEEEEEEEE.ETTS--EEEEEEEEEEEE...E-S---HHHHTT CS
       VirB8 101 dnydkvyllstgsaakelneyarsnnensPfaqlgketelveveiksvvlaspntaqvrfkettrredgtlaktkrwtatltfryevkqaptteeella 199
                 d+y++v+ +s++++++ +++  +  n++sP++ + +     + ei+s+   +++t q+r++ ++   +g     ++ + ++++ y++++ +++ee+++ 
  AHX11638.1 114 DYYTTVRVFSSPEVYSFFKSSLDLDNPASPLNAYSDVVDS-KYEIRSIRHLDKDTIQIRISISFATSNGRV---RTVDRLISLGYTYMDLELSEEDRQL 208
                 **********************8889**************.*******888888**********9888866...78888888888888*********** PP

                 -TT-EEEEEEEEEE- CS
       VirB8 200 NPlGfyVtsyswske 214
                 NPlGf+V s++++++
  AHX11638.1 209 NPLGFVVVSFQVDDD 223
                 ************975 PP

>> TraE  TraE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   4.2   0.00017       1.6       6     171 ..      19     197 ..      16     202 .. 0.65

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.00017
        TraE   6 sesrlknllaqnnllalllavllaanlllgslilratrkqrvvlvPpeikk...........pftvsaasadaeYleqmtrdvlslalnvtPetvdyqf 93 
                 +e+r  ++  q+n+l ++ + +l++ +l+++++  a+++ r+ + P++i+            p tv+  sa++     ++++ ++ +   +P+t +y  
  AHX11638.1  19 YEERVGRVTLQRNFLIVMSLGVLLVLVLSVFTL-FAVSTSRT-IEPFVIEVskksgivthldPATVKEYSANRAITNYFATQYVKAREVFHPATYRYDY 115
                 6677788999*********99999999999999.56666555.57777765446666666667777777777777777777777777777777777776 PP

        TraE  94 neLlklv.apeaygelkkqla..eeaerik..ksnvssvFypesievdpktltvevrGtlktfvgdkktsserktYrlefsye 171
                  +  +++ +pe y   k++l+  + a  ++   + v s ++++si++  k  t+++r +++  ++++++ +  + + l ++y 
  AHX11638.1 116 YTTVRVFsSPEVYSFFKSSLDldNPASPLNaySDVVDSKYEIRSIRHLDK-DTIQIRISISFATSNGRVRTVDRLISLGYTYM 197
                 55444431567777666654311445555543445666677777665433.66666666777777777777776666666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       695  (0.038764); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1665.12
//
Query:       AHX11639.1  [L=406]
Description: GTP cyclohydrolase II [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      5e-57  192.0   0.0    7.7e-57  191.4   0.0    1.3  1  GTP_cyclohydro2  GTP cyclohydrolase II
  ------ inclusion threshold ------
      0.058   13.2   0.0        1.4    8.9   0.0    2.7  2  DUF2862          Protein of unknown function (DUF2862)


Domain annotation for each model (and alignments):
>> GTP_cyclohydro2  GTP cyclohydrolase II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  191.4   0.0   8.6e-61   7.7e-57       3     163 .]     215     380 ..     213     380 .. 0.94

  Alignments for each domain:
  == domain 1  score: 191.4 bits;  conditional E-value: 8.6e-61
                      EEEEEEEETT.EEEEEEEE--.....EEEEEE-.........EEEEEE--HHHHHS-B--TTTTTHHHHHHHHH.HHH-.EEEEEE--TTTTTH CS
  GTP_cyclohydro2   3 vaeaklptrf.gefrliayedkvdgkehlalvkgdi....pvlvRvHsecltgDvlgslrcdcgeqldealeli.aeegrGvlvylrqegrgig 90 
                      v+ea+++ r   + ++++y++ ++  eh+a+v gd+    ++lvR+Hs+c+tgD+l sl+cdc++ql+++l ++ ++ + G+l+yl qegrgig
       AHX11639.1 215 VSEATIHLRNdIKSKMVCYRSILK--EHYAIVVGDPmeseEPLVRIHSSCYTGDLLASLSCDCRDQLHDSLIRMlDDPQGGILLYLLQEGRGIG 306
                      457888888855699****99987..**************779************************9999888888999************** PP

                      HHHHHHHHHHHH.CT--HHHHHHHHT--S-----HHHHHHHHHTT--EEEEE-S-HHHHHHHCTT....SEEEE CS
  GTP_cyclohydro2  91 llnklkayalqd.eglDTveanlalglpadardygiaaqILkdlgvkkirLlTnnpekveaLegfgievvervp 163
                      l+nk++ay lq  +glDTveanlalg+++d+rd++ia q+L dlgv+k+rL+Tnnp+k+e+L++ gi+++ rvp
       AHX11639.1 307 LVNKIRAYDLQSrKGLDTVEANLALGFKDDERDFSIAKQMLDDLGVQKVRLITNNPRKIEQLTAAGIKITHRVP 380
                      ***********989**********************************************************97 PP

>> DUF2862  Protein of unknown function (DUF2862)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0     0.052   4.7e+02       9      41 ..     165     197 ..     159     197 .. 0.87
   2 ?    8.9   0.0   0.00015       1.4       8      46 ..     273     310 ..     268     314 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.052
                 ---S---TTHHHHBT-..EEEEEEEEE-SSSSE CS
     DUF2862   9 rlrdrvskelveklkkepvgtikdfKmtDGsgi 41 
                 ++ + +++ l++++  e  + i+df +t G +i
  AHX11639.1 165 KMAEILPEILISQICFEDDAGIRDFALTQGLQI 197
                 566778999999*99999**********99776 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00015
                 ----S---TTHHHHBT-..EEEEEEEEE-SSSSEEEEEE CS
     DUF2862   8 erlrdrvskelveklkkepvgtikdfKmtDGsgiGvvvk 46 
                 +  rd++ ++l+  l + p+g i  + +  G+giG+v k
  AHX11639.1 273 CDCRDQLHDSLIRMLDD-PQGGILLYLLQEGRGIGLVNK 310
                 5689***********99.*****************9965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (406 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      444  (0.0247643); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.23s 00:00:00.71 Elapsed: 00:00:00.39
# Mc/sec: 3151.06
//
Query:       AHX11640.1  [L=266]
Description: diaminopimelate epimerase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.5e-26   92.2   0.0    1.8e-14   54.0   0.0    2.1  2  DAP_epimerase  Diaminopimelate epimerase


Domain annotation for each model (and alignments):
>> DAP_epimerase  Diaminopimelate epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.0   0.0     1e-18   1.8e-14       4     108 ..       1     106 [.       1     113 [. 0.94
   2 !   36.4   0.0   2.8e-13   5.1e-09       3     101 ..     145     240 ..     143     250 .. 0.88

  Alignments for each domain:
  == domain 1  score: 54.0 bits;  conditional E-value: 1e-18
                    ECSSEEEEEEECCTTCSSHHH...HHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHHHHHHHHHCTTS-S-SEEEEEET CS
  DAP_epimerase   4 shGnpndvvvvddveaelvle...aelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvrvfaaylreggletkkevtvetl 96 
                    +h+ +nd++++ + e + + e    e++++l +r++g+g d++l+v  +g+ + ++ ++n+dgs a  C nG++++a  l++++  ++ ++ ++++
     AHX11640.1   1 MHACGNDFIIIHNTEFSGIPEldrCETIRRLSSRRTGIGCDQLLIVSNEGPLEAEMIIYNSDGSSAATCLNGAACVALDLMRNN--KEWNFLIKSS 94 
                    7999************9988888889*********************************************************9..79******** PP

                    TEEEEEEEECTT CS
  DAP_epimerase  97 gGeleievkddg 108
                    gG   + +++++
     AHX11640.1  95 GGIFLAHLENEK 106
                    **9999888775 PP

  == domain 2  score: 36.4 bits;  conditional E-value: 2.8e-13
                    EECSSEEEEEEECCTTCSSHHHHHHHHHHHTTTTSTT-SEEEEEEEEETTEEEEEEEETTTEEESTTHCCHHHHHHHHHCTTS-S-SEEEEEETTE CS
  DAP_epimerase   3 kshGnpndvvvvddveaelvleaelvaalcdreagpgadgvlfvkpsgeediklryfnrdgseaemCGnGvrvfaaylreggletkkevtvetlgG 98 
                    +s+Gnp++v++v+  ++ +     ++  + + + +   +++ + +   +     r+ +++ +e+ +CG++++++  ++r+ gl+ ++e+t++++gG
     AHX11640.1 145 VSIGNPHLVFFVETEKEVDEI-HSFADLVRRNNPFTREINLSVSCI-FDGVALSRVIEAGTGETLACGSASAAIYLAARNLGLV-ETELTIRFPGG 237
                    689*********987764444.48******************9994.56667789***************************99.*********** PP

                    EEE CS
  DAP_epimerase  99 ele 101
                    +l 
     AHX11640.1 238 DLI 240
                    985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (266 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       428  (0.0238719); expected 358.6 (0.02)
Passed bias filter:                      415  (0.0231469); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1968.12
//
Query:       AHX11641.1  [L=77]
Description: septum formation initiator family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    3.4e-09   36.3   1.7      4e-09   36.1   1.7    1.1  1  DivIC            Septum formation initiator
  ------ inclusion threshold ------
      0.041   14.2   0.3      0.078   13.3   0.2    1.5  1  Jag_N            Jag N-terminus
      0.056   12.3   0.1      0.062   12.2   0.1    1.0  1  Adenylsucc_synt  Adenylosuccinate synthetase


Domain annotation for each model (and alignments):
>> DivIC  Septum formation initiator
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.1   1.7   6.7e-13     4e-09      14      75 ..       5      70 ..       1      73 [. 0.94

  Alignments for each domain:
  == domain 1  score: 36.1 bits;  conditional E-value: 6.7e-13
                XXXXHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-XX....XXXXXXXXXXXXXXXXXXXXXXX CS
       DivIC 14 kgllaykqlkqeiaalqaelaklkaeneeLeaevkdLks....dedyieerARselglvkpgEtvy 75
                +++++  +lk+ei +  + + +l++++e+Le  +++  +    d d +ee+ R+++gl+k+gE+v+
  AHX11641.1  5 HSIMNAAKLKAEISQARDRIITLQKQKERLELDISLIVDekrlDMDLLEEQSRKKFGLMKKGEKVI 70
                789999*******************************779999********************996 PP

>> Jag_N  Jag N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.3   0.2   1.3e-05     0.078      17      43 ..      40      65 ..      37      70 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 1.3e-05
       Jag_N 17 LgvsrdeveieVleegskGfLGlfgkk 43
                L v++++++ + lee+s++ +Gl  kk
  AHX11641.1 40 LIVDEKRLDMDLLEEQSRKKFGL-MKK 65
                668999*****************.665 PP

>> Adenylsucc_synt  Adenylosuccinate synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1     1e-05     0.062      65     137 ..       2      73 ..       1      75 [. 0.86

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 1e-05
                      E-TTBEE-HHHHHHHHTTSS-TT......TEEEETTSEE--HHHHH.HHHHHHHH----------TTHHHHHHH CS
  Adenylsucc_synt  65 iGngvvvdpealleEieeleakgvelskerllisdrahlvlpyhka.lDkleeaakgkkkiGtTkkGiGpayad 137
                      ++++ +++  +l +Ei++ +++ ++l+k++ +++ ++ l+++  ++ +D lee+++  kk+G  kkG   +y+d
       AHX11641.1   2 LSSHSIMNAAKLKAEISQARDRIITLQKQKERLELDISLIVDEKRLdMDLLEEQSR--KKFGLMKKGEKVIYHD 73 
                      788999*******************9999999999999999987743899999866..69***99997777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (77 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1007  (0.056166); expected 358.6 (0.02)
Passed bias filter:                      479  (0.0267165); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 615.47
//
Query:       AHX11642.1  [L=44]
Description: hypothetical protein NHE_0709 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (44 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       228  (0.0127168); expected 358.6 (0.02)
Passed bias filter:                      203  (0.0113224); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.24s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 352.84
//
Query:       AHX11643.1  [L=332]
Description: transketolase, pyrimidine binding domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.3e-51  172.2   0.1    1.1e-50  171.8   0.1    1.1  1  Transket_pyr     Transketolase, pyrimidine binding domain
      7e-38  129.3   0.0    1.3e-37  128.4   0.0    1.5  1  Transketolase_C  Transketolase, C-terminal domain
  ------ inclusion threshold ------
       0.13   12.0   0.0        3.7    7.2   0.0    2.1  2  Pentaxin         Pentaxin family


Domain annotation for each model (and alignments):
>> Transket_pyr  Transketolase, pyrimidine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  171.8   0.1   1.8e-54   1.1e-50       2     176 ..       3     178 ..       2     180 .. 0.98

  Alignments for each domain:
  == domain 1  score: 171.8 bits;  conditional E-value: 1.8e-54
                   EEEHHHHHHHHHHHHHCTTTTEEEEESSTH..HHHTTCHCCHHEGGTTEGEEE--S-HHHHHHHHHHHHHHCTTEEEEEEEEHHHHGGG..HHGGHH CS
  Transket_pyr   2 kiawrkaeaealaellkedpevvligaDva..ggtfsvrkgllhdqgegrvidsgisEqavlgfavGaalagpllviveaqFgdFangA..qiyadq 94 
                   +i++r+a+++a+ae++++dp+v+++g++++  +g ++v++gll+++ge+rvid++isE++++g+a+Gaa+ag l++i e++ ++F+ +A  qi++++
    AHX11643.1   3 EITVREAIGNAIAEEMRRDPDVFIMGEEIGkyQGAYKVTQGLLQEFGERRVIDTPISEHGFTGIAIGAAFAG-LRPILEFMSFNFSLQAmdQIVNSA 98 
                   799*********************************************************************.9*********************** PP

                   HHHCHHHHHT--EEEEESBSGGGSTTGTTTSBSSHHHHHHTSTTEEEE--SSHHHHHHHHHHHHHSSS.SEEEEEE-SSEEC CS
  Transket_pyr  95 airsgeakgklkvgvvtrlpigvgedGpehqsaeleaflrlipglkvvrPsdpaetkhllrrairredrkPvvlrlpksllr 176
                   a++++++ g+l++++v+r p g+  + ++++s+   a++ +ipglkv++P+ ++++++ll+ air  d++Pv++++++ l+ 
    AHX11643.1  99 AKTHYMSDGQLRCPIVFRGPNGAAAQVAAQHSQCFAAWYSHIPGLKVIAPYFASDYRGLLKSAIR--DNNPVIFLENEILYG 178
                   *****************************************************************..99********99997 PP

>> Transketolase_C  Transketolase, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  128.4   0.0   2.2e-41   1.3e-37       1     124 []     197     320 ..     197     320 .. 0.98

  Alignments for each domain:
  == domain 1  score: 128.4 bits;  conditional E-value: 2.2e-41
                      TEEEEEETTSSEEEEEETTHHHHHHHHHHHHHTT.TTCEEEEE-SEEESHHHHHHHHHHHHHSEEEEEEEEESTTSHHHHHHHHHHHCCCTTCS CS
  Transketolase_C   1 gkaeilregkdvtlvayGsmveealeAaeeLeke.gisaeVvdlrtvkplDketilesvkktgrlvvveeavkrgGigsevaaalaeeafdgld 93 
                      gka++++eg+dvt+v+++  v+ aleAae L++e +i++e++dlrt++plD++t+l+s+ kt++l++vee+ +  ++gse++a+++eeafd +d
       AHX11643.1 197 GKANVIKEGSDVTIVTFSICVKLALEAAEILANEnNIDVEIIDLRTLRPLDFDTVLKSLSKTNKLITVEEGFPVLSFGSEISARIMEEAFDLMD 290
                      89*******************************99*********************************************************** PP

                      SEEEEEEE-SSSSSSGHHHHHHHTT-SHHHH CS
  Transketolase_C  94 apvkrvggpdviepgsaeelekafgldaeki 124
                      ap+ rv+ +d++ p++  +lek++++++ ++
       AHX11643.1 291 APIIRVASKDTPLPYA-RNLEKLVLPQVSDV 320
                      ****************.89*******99875 PP

>> Pentaxin  Pentaxin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   0.0   0.00062       3.7     122     187 ..      21      89 ..       5      96 .. 0.82
   2 ?    2.6   0.0     0.016        94      56      90 ..     183     217 ..     173     229 .. 0.88

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.00062
                 SEE.EEESS-BSCTTCTCSGGGB--EEEEEEEEESS---HHHHHHHHHT-S---..SSEECCGBEEEEE CS
    Pentaxin 122 eas.iilGqeqDsyGGkfdasqslvGelsdlnlWdyvLspeeiktvykgatlsg..nildWralqyevr 187
                 ++   i+G e   y G ++ +q l  e+++  + d+ +s++  + +  ga + g   il++ + ++ ++
  AHX11643.1  21 DPDvFIMGEEIGKYQGAYKVTQGLLQEFGERRVIDTPISEHGFTGIAIGAAFAGlrPILEFMSFNFSLQ 89 
                 4443699*********************************99999999999876335888888888776 PP

  == domain 2  score: 2.6 bits;  conditional E-value: 0.016
                 EEEEECTTEEEEEETTEEEEEE-SS-SSSEEEEEE CS
    Pentaxin  56 LifkekqgeyslyvggaevlvkvseekvepvhvCa 90 
                 L+  +++++y++ +g+a+v+++ s+ ++    +C+
  AHX11643.1 183 LTPEQEENDYTVPIGKANVIKEGSDVTIVTFSICV 217
                 55678999*******************99999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (332 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       475  (0.0264934); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2393.19
//
Query:       AHX11644.1  [L=87]
Description: hypothetical protein NHE_0711 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.01   16.1   8.7      0.014   15.7   8.7    1.3  1  DUF4164   Domain of unknown function (DUF4164)


Domain annotation for each model (and alignments):
>> DUF4164  Domain of unknown function (DUF4164)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.7   8.7   7.6e-07     0.014       5      86 ..       4      83 ..       1      86 [. 0.89

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.6e-07
     DUF4164  5 eleaaltrLeaaldsLEkavdrrleaerkrdeleaeiealgedrsRLaeeLdqaearaarleevnrEvsrrLkaaietirav 86
                ++e  l++L+ al++LEk ++rrl+ e+ +  + +e e+l+ + + L  +     ++ + l+ + +E+  +++ +ie i+++
  AHX11644.1  4 QNEVSLQKLDFALKKLEKVIQRRLQLEEIK--RHQECEKLAIEIAELKRQAKLHMNEIKMLKTIIKEAVANIDEVIEIIEKI 83
                567789******************999865..5688899999999999999999999********************99987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      2130  (0.118802); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 689.02
//
Query:       AHX11645.1  [L=107]
Description: cell division ZapA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.1e-11   42.2   1.6    9.7e-11   42.0   1.6    1.1  1  ZapA      Cell division protein ZapA


Domain annotation for each model (and alignments):
>> ZapA  Cell division protein ZapA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.0   1.6   5.4e-15   9.7e-11       3      81 ..       9      88 ..       8     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 42.0 bits;  conditional E-value: 5.4e-15
        ZapA  3 vtIlgreytlaceegeeeylreaaklvdekikeireagg.nlseerllvmaaLnladellklkkraeeleaeleelaerl 81
                + I++ + ++ac +++e+ l+ +a+++d+++k i ++++ ++++  ll+ aaL l   ll+  +++++    + + +e++
  AHX11645.1  9 IVINNTTHKIACTKEDEKKLEYLAERLDKRMKVIADSSNsKINDITLLLFAALELENLLLDSSQNNDNNARNTTHQQEKI 88
                88*************************************55************999988888777766555555444544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1251  (0.0697752); expected 358.6 (0.02)
Passed bias filter:                      402  (0.0224218); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 821.40
//
Query:       AHX11646.1  [L=439]
Description: trigger factor [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-17   63.7   1.1    2.2e-17   63.7   1.1    2.5  4  Trigger_N  Bacterial trigger factor protein (TF)
    1.3e-12   48.0  12.6    1.8e-09   37.8   4.1    3.7  3  Trigger_C  Bacterial trigger factor protein (TF) C-terminus
    8.3e-12   45.3   0.1    4.8e-11   42.8   0.0    2.3  2  FKBP_C     FKBP-type peptidyl-prolyl cis-trans isomerase


Domain annotation for each model (and alignments):
>> Trigger_N  Bacterial trigger factor protein (TF)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.7   1.1   3.7e-21   2.2e-17       7     136 ..       7     143 ..       1     148 [. 0.83
   2 ?   -2.0   0.1      0.68   4.1e+03      99     107 ..     272     280 ..     230     317 .. 0.54
   3 ?   -1.9   0.0      0.64   3.9e+03      49      87 ..     306     343 ..     303     369 .. 0.59
   4 ?   -2.6   0.1         1   6.3e+03      65      83 ..     408     426 ..     392     436 .. 0.54

  Alignments for each domain:
  == domain 1  score: 63.7 bits;  conditional E-value: 3.7e-21
                 EEETTEEEEEEEE-HHHCHHHHHHHHHHHHTTS-BTTC-TT---CCCHHHHCTCCCHHHHHHHHHHCCCCCCCCCS..-EE..EE.E.E.....EETTC CS
   Trigger_N   7 kleglkvkltvevpaeevekavekalkklakkvkipGFRkGkvPrsiiekrygkevleealeellnealeeaieeeklepv.gqpei.e.....leegk 98 
                  +++lk+k+++evpa+ ++k +e+a+++  ++   pGFRkG+vP + + k+ ++++ + ++ + + +++ ++ + e+l  + +q +i +     ++++k
  AHX11646.1   7 YSQNLKRKFEIEVPASLIDKGFEEAIRSRMQRNIYPGFRKGRVPFDFVAKQ-EEGLIDSVIVDQVYRHWCDIKDRENLVIFnDQENIaKietdgYKKEK 104
                 45689**********************************************.55588888888888888889999998655455666632234545555 PP

                 ..EEEEEEEEE--EEEE.XCCCSEEEEEXHHHHHHHHHH CS
   Trigger_N  99 .dleftvevevkPevelgdykglevekeevevtdeevde 136
                  +++ftve+e++P+v   d+++++v++ +  v+++++d 
  AHX11646.1 105 aNVSFTVECELLPDVPEIDFSKMTVKARTFIVSQNDIDL 143
                 58*************998*********999*******95 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.68
                 .EEEEEEEE CS
   Trigger_N  99 dleftveve 107
                 d e++  ++
  AHX11646.1 272 DTEIKKIIT 280
                 233333333 PP

  == domain 3  score: -1.9 bits;  conditional E-value: 0.64
                 --CCCHHHHCTCC.CHHHHHHHHHHCCCCCCCCCS..-EE CS
   Trigger_N  49 vPrsiiekrygke.vleealeellnealeeaieeeklepv 87 
                 vP s++e++  k+ ++ +  + + ++  +ea++ +kl+ +
  AHX11646.1 306 VPDSLVEQQ--KHyIKMDTPRIADDKLQDEALRRAKLSLI 343
                 677777777..44466665555544444566666665433 PP

  == domain 4  score: -2.6 bits;  conditional E-value: 1
                 HHHHHHHHCCCCCCCCCS. CS
   Trigger_N  65 ealeellnealeeaieeek 83 
                  + +e  ++++ee++ ++k
  AHX11646.1 408 TVQRESTESTVEEILAAQK 426
                 4444444444444443333 PP

>> Trigger_C  Bacterial trigger factor protein (TF) C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.8   0.0   0.00025       1.5      29      60 ..       7      38 ..       2      48 .. 0.84
   2 !   37.8   4.1   3.1e-13   1.8e-09       3     161 ..     269     406 ..     267     407 .. 0.94
   3 ?   -3.5   1.0       1.5   9.1e+03      11      25 ..     419     433 ..     412     438 .. 0.36

  Alignments for each domain:
  == domain 1  score: 8.8 bits;  conditional E-value: 0.00025
                CHCCCGCGEEEEE-HHHHHHHHHHHHHHHHHC CS
   Trigger_C 29 lldkLvekaeidiPeslveeeidrllrqakqq 60
                  ++L +k+ei++P sl+++ +++++r   q+
  AHX11646.1  7 YSQNLKRKFEIEVPASLIDKGFEEAIRSRMQR 38
                568999*****************999887665 PP

  == domain 2  score: 37.8 bits;  conditional E-value: 3.1e-13
                 HHHHHHHCCCCHHHHHHHHHHHHHCCCHCCCGCGEEEEE-HHHHHHHHHHHHHHHHHCT...TSSHHCHHHHHCTHCCCHCHHCHHHHHHHHHHHHHHH CS
   Trigger_C   3 eeLkedlrkqleeekeeatkeelkealldkLvekaeidiPeslveeeidrllrqakqqleqqGldleeylelsgsseeelreelkeeAekrVklgLvle 101
                 eeL ++++k + +e e +++e l++++ ++L ek+++ +P+slve++ + +  +                     +   ++++l++eA +r kl L+++
  AHX11646.1 269 EELDTEIKKIITSECEIKLNEDLRRQIESNL-EKYDFLVPDSLVEQQKHYIKMD---------------------TPRIADDKLQDEALRRAKLSLIFA 345
                 89************************99997.99**********9987665444.....................477899****************** PP

                 HHHHHTT----HHHHHHHHHHHCCCTTSXHHHHHHHHHHXHHHH.HHHHHHHHHHHHHHHC CS
   Trigger_C 102 eiakeekievteeelkeeleelasqygmepeevkeflkkneqls.alkedileekvvdlll 161
                 + a +++i+ + +++ ++l+ ++ + g + e + + +++n++   ++  +++e k++ +ll
  AHX11646.1 346 QFATKKEISLDKADVARHLMTVSAAAGLDLEYLANIYRNNKDFAnSVTLRLMEGKIITALL 406
                 ********************************************9************9997 PP

  == domain 3  score: -3.5 bits;  conditional E-value: 1.5
                 CCCHHHHHHHHHHHH CS
   Trigger_C  11 kqleeekeeatkeel 25 
                 +++ +++++++++ +
  AHX11646.1 419 EEILAAQKQEIEADK 433
                 222222222222222 PP

>> FKBP_C  FKBP-type peptidyl-prolyl cis-trans isomerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.9   0.0      0.73   4.4e+03      31      53 ..      11      33 ..       4      39 .. 0.70
   2 !   42.8   0.0     8e-15   4.8e-11       4      80 ..     163     236 ..     160     252 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.9 bits;  conditional E-value: 0.73
                HTSEEEEETTSSSSCHHHHHHHT CS
      FKBP_C 31 rakplefkvGsgqvikGfeeale 53
                 ++++e++v +  + kGfeea++
  AHX11646.1 11 LKRKFEIEVPASLIDKGFEEAIR 33
                45667777777777789999886 PP

  == domain 2  score: 42.8 bits;  conditional E-value: 8e-15
                 BB-TTCEEEEEEEEEETTSSEEEEHCCHTSEEEEETTSSSSCHHHHHHHTTSBTT-EEEEEEEGGGTTTTTTBCTTT CS
      FKBP_C   4 eakegdtVtvhykgkledgkvfdssrsrakplefkvGsgqvikGfeealegmkvGekrtltippelaYgekglaggv 80 
                  a++gd+V ++ +g++ +gk f++   +  ++++++G+g++i  + ++l gmk Gek+ +++ +++ Y+++++ag++
  AHX11646.1 163 AAEDGDRVVLDLNGTV-HGKPFKGG--QLMDFQCRIGDGKIISSLNDGLIGMKSGEKKVISVAFPEDYHDREVAGKE 236
                 589*************.********..9********************************************98844 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       753  (0.041999); expected 358.6 (0.02)
Passed bias filter:                      350  (0.0195214); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.24s 00:00:00.75 Elapsed: 00:00:00.41
# Mc/sec: 3252.70
//
Query:       AHX11647.1  [L=196]
Description: clp protease family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.9e-82  274.2   0.1    5.7e-82  274.0   0.1    1.0  1  CLP_protease  Clp protease


Domain annotation for each model (and alignments):
>> CLP_protease  Clp protease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  274.0   0.1   3.2e-86   5.7e-82       1     181 [.       7     187 ..       7     188 .. 0.99

  Alignments for each domain:
  == domain 1  score: 274.0 bits;  conditional E-value: 3.2e-86
                   XSSSECHHHHHHHHTTTEEEEES-BSHHHHHHHHHHHHHHHHH-SSS-EEEEEEE--B-HHHHHHHHHHHHHSSS-EEEEEEEEEETHHHHHHHTS- CS
  CLP_protease   1 skgeraydiysrllkeriiflgseiddevankiiaqLllLeaedpdkdillyinspGGsvtaglaIydtmqyikpdvsticlGlaaSmgslllaage 97 
                   s+geraydi+srllkeriifl ++i+d +a+ ++aqL++Leae+pdkdi++yinspGG vtagl+Iydtmqyi+p vst+c+G+aaS++sl+laag+
    AHX11647.1   7 SRGERAYDIFSRLLKERIIFLVGPIEDGMASLVVAQLIFLEAESPDKDIFMYINSPGGVVTAGLSIYDTMQYIRPSVSTVCVGQAASAASLILAAGA 103
                   5899********************************************************************************************* PP

                   TTGEEEETTEEEEES-TEEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHCSTEEEEHHHHHHHTSSSEE-SS CS
  CLP_protease  98 kgkRfalpnarimihqPlggaqgqasdieieaeellkikerlneilakhtgqslekiekdldrdtflsaeeAveyGLideviek 181
                   +gkRfalp++rim+hqP+gg++gqa+d+ei+++e+lk+k+ +nei++kht+q+++kie+ l+rdtflsaeeA  +GLid+ i+k
    AHX11647.1 104 EGKRFALPHSRIMVHQPSGGIRGQATDMEIHVREILKLKRMINEIYQKHTKQTIKKIEALLERDTFLSAEEARGFGLIDDTITK 187
                   *******************************************************************************98876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       961  (0.0536003); expected 358.6 (0.02)
Passed bias filter:                      654  (0.0364772); expected 358.6 (0.02)
Passed Vit filter:                        49  (0.002733); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 1461.95
//
Query:       AHX11648.1  [L=402]
Description: ATP-dependent Clp protease, ATP-binding subunit ClpX [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.5e-48  165.2   0.0    2.5e-48  164.4   0.0    1.4  1  AAA_2            AAA domain (Cdc48 subfamily)
      2e-17   63.9   0.0    7.8e-17   61.9   0.0    1.9  2  AAA              ATPase family associated with various cellul
      1e-15   57.5   0.1    2.3e-15   56.4   0.1    1.6  1  ClpB_D2-small    C-terminal, D2-small domain, of ClpB protein
    1.8e-14   53.3   3.4    1.8e-14   53.3   3.4    2.2  2  zf-C4_ClpX       ClpX C4-type zinc finger
      8e-08   32.4   0.0    1.7e-06   28.1   0.0    2.8  3  AAA_5            AAA domain (dynein-related subfamily)
    5.6e-06   26.5   0.0    1.3e-05   25.3   0.0    1.5  1  Sigma54_activ_2  Sigma-54 interaction domain
    8.8e-06   25.5   0.0     0.0063   16.2   0.0    2.3  2  Sigma54_activat  Sigma-54 interaction domain
    1.2e-05   25.6   0.5     0.0002   21.7   0.1    2.6  2  AAA_22           AAA domain
     0.0001   21.5   0.1    0.00017   20.7   0.1    1.4  1  MCM              MCM P-loop domain
    0.00042   19.8   0.0      0.017   14.5   0.0    2.6  3  Mg_chelatase     Magnesium chelatase, subunit ChlI
    0.00045   19.8   0.0    0.00094   18.7   0.0    1.4  1  AAA_7            P-loop containing dynein motor region
    0.00047   20.2   0.0    0.00097   19.2   0.0    1.5  1  AAA_14           AAA domain
    0.00057   19.7   0.0     0.0019   18.0   0.0    1.9  1  RuvB_N           Holliday junction DNA helicase RuvB P-loop d
    0.00099   18.9   0.6       0.02   14.6   0.1    2.2  3  AAA_15           AAA ATPase domain
      0.002   17.9   0.0     0.0032   17.2   0.0    1.3  1  AAA_24           AAA domain
     0.0063   17.0   0.0      0.011   16.2   0.0    1.5  1  AAA_23           AAA domain
  ------ inclusion threshold ------
      0.011   16.2   0.1      0.057   13.8   0.0    2.0  2  AAA_16           AAA ATPase domain
      0.013   15.2   0.0      0.029   14.1   0.0    1.5  1  IstB_IS21        IstB-like ATP binding protein
      0.013   15.4   0.0      0.034   14.1   0.0    1.7  1  Rad17            Rad17 P-loop domain
      0.014   15.9   0.0      0.031   14.8   0.0    1.6  1  ABC_tran         ABC transporter
      0.018   15.5   0.0      0.043   14.2   0.0    1.7  1  RNA_helicase     RNA helicase
      0.018   14.4   2.7        0.2   10.9   0.1    2.7  3  ATPase           KaiC
      0.028   14.4   0.0      0.077   13.0   0.0    1.7  1  TsaE             Threonylcarbamoyl adenosine biosynthesis pro
      0.035   13.2   0.0      0.058   12.4   0.0    1.3  1  T2SSE            Type II/IV secretion system protein
       0.05   13.5   0.0       0.17   11.8   0.0    1.9  2  NACHT            NACHT domain
      0.054   12.9   0.0       0.11   11.9   0.0    1.4  1  PhoH             PhoH-like protein
      0.061   13.1   0.1        0.7    9.6   0.0    2.3  2  DEAD             DEAD/DEAH box helicase
       0.08   12.7   0.0        0.2   11.4   0.0    1.6  1  AAA_29           P-loop containing region of AAA domain
        0.1   13.1   0.0       0.21   12.1   0.0    1.6  1  AAA_18           AAA domain
       0.12   11.2   0.0       0.24   10.3   0.0    1.3  1  AAA_10           AAA-like domain
       0.15   12.2   0.0       0.34   11.1   0.0    1.6  1  AAA_33           AAA domain
       0.17   11.5   0.1       0.64    9.6   0.0    1.8  2  Terminase_6      Terminase-like family


Domain annotation for each model (and alignments):
>> AAA_2  AAA domain (Cdc48 subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  164.4   0.0   4.5e-51   2.5e-48       3     170 ..     108     302 ..     106     303 .. 0.97

  Alignments for each domain:
  == domain 1  score: 164.4 bits;  conditional E-value: 4.5e-51
                 ---EEEE--TTSSHHHHHHHHHHHTT-....-EEEEEGGG---....----THHHHHHHHHTTT-HHHHTTSEEEEETGGG----...---------HH CS
       AAA_2   3 iisilllgptgvGktelakalaellfvkkekkliradaselle....eeevehlvsrligappgyvgaeegGivllDEidKihpk...essgadvSreg 94 
                 ++++l++gptg+Gkt+ ak+la++l+v    ++++ da++++e    +++ve+++ +l+++++++v+a+++Gi+++DEidKi++k   +s+++dvS+eg
  AHX11648.1 108 KSNVLIIGPTGCGKTLFAKTLARFLNV----PFAICDATSITEagyvGDDVENILRMLLQSADYNVEAAQKGIIYIDEIDKISKKsdgPSITRDVSGEG 202
                 789***********************8....********************************************************9*********** PP

                 HHHHHHHHHH--EE-.........----.--EE-TT-EEEEEE--TTHHHHTTTS-S..............TTTTSGGG--HHHHHHTT--HHHHTT-- CS
       AAA_2  95 VqrdLLqileggtlt.........dkqg.rkvdtknilfImtgafgsskisdesrsk..............eeeeekkkeeveeelkkglipEllgRlp 169
                 Vq++LL+i+eg+ ++         ++q+  ++dt+nilfI++gaf + + + ++r k              +++e  kk e+e+++k+glipE++gRlp
  AHX11648.1 203 VQQALLKIMEGTIASvppqggrkhPNQElIQIDTTNILFICGGAFVGLDSIVANRFKgnvmgfeselrgsrSTTEILKKVEPEDLIKFGLIPEFIGRLP 301
                 ************************99999*******************9999999889***********99999999*********************9 PP

                 E CS
       AAA_2 170 e 170
                 +
  AHX11648.1 302 V 302
                 7 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       5.6   3.1e+03      38      56 ..      15      33 ..       4      43 .. 0.72
   2 !   61.9   0.0   1.4e-19   7.8e-17       1     110 [.     111     238 ..     111     255 .. 0.84

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 5.6
                STTHHHHHHHHHHHHHHHT CS
         AAA 38 yvgesekkirelfkeakek 56
                + ge+e+k+++l++ a++ 
  AHX11648.1 15 FCGETEDKVQKLIAGASAF 33
                789********99877544 PP

  == domain 2  score: 61.9 bits;  conditional E-value: 1.4e-19
                 EEEESSTTSSHHHHHHHHHHHHTHEEEEEETTTCS.SSSTTHHHHHH.HHHHHHHHHTS...TSEEEEEETGGGHHHHH...TTCCCHHHHHHHHHHHH CS
         AAA   1 vllyGppGtGKTllakavakelgvefleisgsell.skyvgesekki.relfkeakeka...kpsilfiDEidalaksr...sgseseeeervvnqLlt 91 
                 vl++Gp G+GKTl+ak +a+ l+v+f   ++++++   yvg+  ++i r+l+++a  +    ++ i+ iDEid++ k++   s + + ++e v+++Ll+
  AHX11648.1 111 VLIIGPTGCGKTLFAKTLARFLNVPFAICDATSITeAGYVGDDVENIlRMLLQSADYNVeaaQKGIIYIDEIDKISKKSdgpSITRDVSGEGVQQALLK 209
                 799********************************667**998887636777777444466677**************999888899999********* PP

                 HHHHTTTS..........SSTEEEEEEES CS
         AAA  92 eldgvkkk..........eskvivigatn 110
                  ++g   +          ++++i i +tn
  AHX11648.1 210 IMEGTIASvppqggrkhpNQELIQIDTTN 238
                 ***98877777777777755566666665 PP

>> ClpB_D2-small  C-terminal, D2-small domain, of ClpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.4   0.1   4.2e-18   2.3e-15       1      73 [.     309     385 ..     309     389 .. 0.95

  Alignments for each domain:
  == domain 1  score: 56.4 bits;  conditional E-value: 4.2e-18
                    SCHHHHHHHHHH...HHHHHHHHSCT.TTEEEEEHHHHHHHHHHHTSBTTTBTCCHHHHHHHHTHHHHHHHHHTTSS CS
  ClpB_D2-small   1 LtkeelkkIvdl...alkklekrlke.rgvelevtdealdalaekgydpeyGARpLrriiqreiedplaeeilsgel 73 
                    Lt+++l++I+     al k+++rl e ++++l+++d+al+ +a++ + ++ GAR+Lr i++ ++ d ++e+++++++
     AHX11648.1 309 LTEDNLVDILSVpnnALVKQYARLFEmDNIKLSFSDDALRTIARESIRRKIGARGLRAIMEATLRDYMFELPSKDDV 385
                    899*******99999*********99899******************************************999886 PP

>> zf-C4_ClpX  ClpX C4-type zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   3.4   3.2e-17   1.8e-14       2      38 ..      12      47 ..      11      48 .. 0.94
   2 ?   -1.9   0.0       5.8   3.3e+03      14      22 ..     110     118 ..     107     140 .. 0.62

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 3.2e-17
  zf-C4_ClpX  2 rCSFCgksesevkklIagpngvyICdeCvelcneiie 38
                +CSFCg +e++v+klIag + ++ICd+C+ lc+++++
  AHX11648.1 12 QCSFCGETEDKVQKLIAGAS-AFICDRCIVLCSNVLN 47
                6*****************97.7************997 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 5.8
  zf-C4_ClpX  14 kklIagpng 22 
                 + lI gp+g
  AHX11648.1 110 NVLIIGPTG 118
                 556777766 PP

>> AAA_5  AAA domain (dynein-related subfamily)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.0   3.1e-09   1.7e-06       1      79 [.     110     187 ..     110     190 .. 0.84
   2 ?   -1.0   0.0       2.9   1.6e+03      81     118 ..     203     241 ..     197     248 .. 0.82
   3 ?   -0.0   0.0       1.4   7.9e+02      65      89 ..     300     325 ..     266     367 .. 0.66

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 3.1e-09
                 EEEEE--SSSSHHHHHHHGGGGBS--EEEEE--TT--HHHHH--B--.........--------G-SEEEEESGGG--H CS
       AAA_5   1 dvlLvGppGtgKselaerlaaalnreveyvqltrdtteedlkgrreikngttslvdsplvraaregeilvlDEveraes 79 
                 +vl++Gp+G+gK+ +a+ la++ln ++ +   t+ t++  +   +e +  +  l+   +  +a ++ i+++DE++++++
  AHX11648.1 110 NVLIIGPTGCGKTLFAKTLARFLNVPFAICDATSITEAGYVGDDVE-NILRMLLQSADYNVEAAQKGIIYIDEIDKISK 187
                 69********************************999988888777.34445666666666677899*********986 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 2.9
                 HHHHHHHHHHSSEEE..-SSSEEE---.......-EEEE CS
       AAA_5  81 vlnsLlslleerrllleeggelvkakndd.llerfrvia 118
                 v+++Ll+++e    ++++ g++ + +++  ++ ++++++
  AHX11648.1 203 VQQALLKIMEGTIASVPPQGGRKHPNQELiQIDTTNILF 241
                 89999************9999999988876666666655 PP

  == domain 3  score: -0.0 bits;  conditional E-value: 1.4
                 G-SEEEEESGGG--.HHHHHHHHHHH CS
       AAA_5  65 egeilvlDEverae.sevlnsLlsll 89 
                  + ++vlDE+++ +  ++l++ ++ l
  AHX11648.1 300 LPVVAVLDELTEDNlVDILSVPNNAL 325
                 66788888888655555555555554 PP

>> Sigma54_activ_2  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   2.3e-08   1.3e-05      15      84 ..     102     188 ..      95     190 .. 0.73

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 2.3e-08
                      HHHHT-SS-EEEEEETT--HHHHHHCC--TTS-EE--SSTTHHHH-H..............HHHHHH.......TTTSEEEEEE-TT--HH CS
  Sigma54_activ_2  15 eqaaqsklpvfltGekGsgkelvArlLhknsgpwleifvverlaklp..............ldlleq.......akggtLylkdiadlska 84 
                      + ++ sk++v+++G+ G+gk+l+A++L+ +     +i +  +  ++               +    +       a+ g++y+ +i+++sk+
       AHX11648.1 102 KDIEISKSNVLIIGPTGCGKTLFAKTLARFLNVPFAICDATSITEAGyvgddvenilrmllQ----SadynveaAQKGIIYIDEIDKISKK 188
                      678899**********************9987766666664444322555666667544440....334444448*************996 PP

>> Sigma54_activat  Sigma-54 interaction domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   1.1e-05    0.0063      14      44 ..     100     130 ..      88     147 .. 0.82
   2 !    6.8   0.0    0.0086       4.8      89     108 ..     169     188 ..     163     191 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 1.1e-05
                      HHHHHCTSSS-EEEECSTTSSHHHHHHHHHH CS
  Sigma54_activat  14 qikkvaktdlsvlitGesGtGKellaraihe 44 
                      ++k +  ++++vli G +G+GK+l+a+++ +
       AHX11648.1 100 KTKDIEISKSNVLIIGPTGCGKTLFAKTLAR 130
                      5567777899****************99865 PP

  == domain 2  score: 6.8 bits;  conditional E-value: 0.0086
                      HHHTTTSEEEEETGGGS-HH CS
  Sigma54_activat  89 fekadgGtlfLDeigelple 108
                      +e+a++G++++Dei +++ +
       AHX11648.1 169 VEAAQKGIIYIDEIDKISKK 188
                      89*************99865 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.1   3.5e-07    0.0002       5     103 ..     108     185 ..     105     198 .. 0.74
   2 ?   -2.0   0.0         7   3.9e+03      59      66 ..     349     356 ..     310     394 .. 0.51

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 3.5e-07
      AAA_22   5 agilvvtGesGtGKTtllrrlleqldeeakaeeerpevvfvtlpsstsskdllrellralglelkaerlsseellealeqalraravielliiDEaqhl 103
                 ++ ++++G++G+GKT+ +++l++ l         +++++ ++++s t+   +  ++ ++l             ll+    +++a+++ +++ iDE++++
  AHX11648.1 108 KSNVLIIGPTGCGKTLFAKTLARFL---------NVPFAICDATSITEAGYVGDDVENILR-----------MLLQSADYNVEAAQK-GIIYIDEIDKI 185
                 67899********************.........999998888888855555555555555...........344555556666666.66666666666 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 7
      AAA_22  59 ellralgl 66 
                  ++r+  +
  AHX11648.1 349 TIARESIR 356
                 22222222 PP

>> MCM  MCM P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.7   0.1   3.1e-07   0.00017      49     136 ..     100     188 ..      65     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 20.7 bits;  conditional E-value: 3.1e-07
                 SSSSBBCSS-EEEEEESSTSTHHHHHHHHHHHSSSEEEEESS.SSSSSHSSSEEEEESSSSSEEEEET.HHHHTTTSEEEEESGGGSTCH CS
         MCM  49 edktklrgdinvllvgdpgtaKsqlLkyveklapravytsgk.gssaagLtaavvrdeetgefvleaG.alvladkGvcciDefdkmkee 136
                 + k   +++ nvl++g  g++K+ + k+++++++    ++ + + ++ag +   v +   + +   a   +  a+kG+++iDe+dk++++
  AHX11648.1 100 KTKDIEISKSNVLIIGPTGCGKTLFAKTLARFLNVPFAICDAtSITEAGYVGDDVEN-ILRMLLQSADyNVEAAQKGIIYIDEIDKISKK 188
                 2223357999*********************99988777655055889988887744.44444444441466789***********9986 PP

>> Mg_chelatase  Magnesium chelatase, subunit ChlI
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.0       4.4   2.5e+03       5      20 ..      73      88 ..      71      97 .. 0.81
   2 !   14.5   0.0     3e-05     0.017      22      46 ..     108     132 ..      95     147 .. 0.87
   3 ?    2.1   0.0      0.19   1.1e+02     101     121 ..     168     188 ..     162     190 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 4.4
  Mg_chelatase  5 vkGqeeakraleiaaa 20
                  ++ qe+akr l +a+ 
    AHX11648.1 73 ITAQEDAKRILSVAVY 88
                  7889*********986 PP

  == domain 2  score: 14.5 bits;  conditional E-value: 3e-05
  Mg_chelatase  22 gHnlllvGppGsGKtmlakrlpsll 46 
                   + n+l++Gp G+GKt+ ak l+  l
    AHX11648.1 108 KSNVLIIGPTGCGKTLFAKTLARFL 132
                   569*****************99877 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.19
  Mg_chelatase 101 eislahnGvLfLDElpefkrk 121
                   ++  a++G++++DE+ ++++k
    AHX11648.1 168 NVEAAQKGIIYIDEIDKISKK 188
                   57889**********999876 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.7e-06   0.00094      20     110 ..      95     183 ..      90     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.7e-06
       AAA_7  20 vrysyllelllknkkpvllvGptGtGKtviikdllkkldkekylsltinfsaqtsanqlqdiiesklekrrk.gvygPpggkklvvFvDDln 110
                 +r++y ++ +  +k +vl++GptG+GKt+ +k+l + l+   + ++++  ++ t+a  + d +e+ l    +   y   + +k ++++D+++
  AHX11648.1  95 IRNQYKTKDIEISKSNVLIIGPTGCGKTLFAKTLARFLN---VPFAICDATSITEAGYVGDDVENILRMLLQsADYNVEAAQKGIIYIDEID 183
                 577788888888999*******************99999...77777788888888888888888887654426788889999999999886 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.0   1.7e-06   0.00097       4      78 ..     110     187 ..     107     215 .. 0.70

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 1.7e-06
      AAA_14   4 ilvitGaRrvGKTtllkqlikellvkkesilyinldderdkkla..dpekllelilek.lke...ekktylflDEiqevpe 78 
                  ++i G+  +GKT ++k+l++ l      +   +  + +++ +   d e++l+++l++  ++    +k ++++DEi ++++
  AHX11648.1 110 NVLIIGPTGCGKTLFAKTLARFLN---VPFAICDATSITEAGYVgdDVENILRMLLQSaDYNveaAQKGIIYIDEIDKISK 187
                 589****************97766...33444444444443333224557788888875344778899********99954 PP

>> RuvB_N  Holliday junction DNA helicase RuvB P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.0   0.0   3.4e-06    0.0019      31      99 ..     106     188 ..      68     192 .. 0.74

  Alignments for each domain:
  == domain 1  score: 18.0 bits;  conditional E-value: 3.4e-06
      RuvB_N  31 ealdhvllyGpPGlGkttlakiiakelgvklkitsgPvlekag....dlaalltnl..........eekdvlfideihrlsra 99 
                  +   vl++Gp G Gkt +ak +a+ l+v + i  +  + +ag    d+  +l  l           +k +++idei ++s++
  AHX11648.1 106 ISKSNVLIIGPTGCGKTLFAKTLARFLNVPFAICDATSITEAGyvgdDVENILRMLlqsadynveaAQKGIIYIDEIDKISKK 188
                 45678****************************99999999864444666776544222222222135679999999999876 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.1   3.5e-05      0.02      14      49 ..      99     134 ..      95     157 .. 0.87
   2 ?    0.4   0.0      0.76   4.3e+02     293     333 ..     146     183 ..     136     185 .. 0.89
   3 ?    1.4   0.0      0.38   2.1e+02     281     316 ..     180     218 ..     151     236 .. 0.69

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.5e-05
      AAA_15  14 lkdveidlseeltvliGkNnsGKSsilealdlFlnn 49 
                 +k  +i++s++  ++iG+ ++GK+ +++ l  Fln 
  AHX11648.1  99 YKTKDIEISKSNVLIIGPTGCGKTLFAKTLARFLNV 134
                 7777899999899*********************95 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.76
      AAA_15 293 plnknGsGvqrllllillileaekkdekeeknvilliEEPE 333
                 ++ ++G+ v ++l ++l+ ++++      ++  i+ i+E++
  AHX11648.1 146 EAGYVGDDVENILRMLLQSADYNVE---AAQKGIIYIDEID 183
                 567999*****************99...9999999***986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.38
      AAA_15 281 neeieik...ddeelplnknGsGvqrllllillileaek 316
                 +e ++i+   d+ +++ +  G Gvq++ll i++ + a+ 
  AHX11648.1 180 DEIDKISkksDGPSITRDVSGEGVQQALLKIMEGTIASV 218
                 333333377799999999999999999999998887765 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   5.6e-06    0.0032       2      79 ..     108     187 ..     107     203 .. 0.67

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 5.6e-06
      AAA_24   2 klkiliyGpsgiGKTtlakelgpkplfi.........dtekGlksldadkfpdieswedfldevvel.aaeladyktlviDtidelee 79 
                 k ++li+Gp g GKT +ak+l  ++l +          te+G+    +d++++i  + ++l+ ++++ +a++    ++ iD id++ +
  AHX11648.1 108 KSNVLIIGPTGCGKTLFAKTL-ARFLNVpfaicdatsITEAGY---VGDDVENI--LRMLLQSADYNvEAAQ--KGIIYIDEIDKISK 187
                 5689*****************.666666444455555566666...34444444..5677777777643333..35677777777765 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     2e-05     0.011       9      35 ..      98     124 ..      88     214 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 2e-05
      AAA_23   9 sfrdqeidFskgltlItGpNGaGKTTi 35 
                 +++ ++i+ sk  +lI+Gp+G+GKT +
  AHX11648.1  98 QYKTKDIEISKSNVLIIGPTGCGKTLF 124
                 567888*******************65 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0    0.0001     0.057      25      48 ..     109     132 ..      95     150 .. 0.84
   2 ?   -1.6   0.0       5.5   3.1e+03      67      88 ..     340     362 ..     300     390 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 0.0001
      AAA_16  25 elvllsGesGvGKsslvrellral 48 
                 ++vl++G+ G+GK+  +++l+r l
  AHX11648.1 109 SNVLIIGPTGCGKTLFAKTLARFL 132
                 89*****************99866 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 5.5
      AAA_16  67 ipysa.laqalareellrqllde 88 
                 +++s   ++++are++ r+++++
  AHX11648.1 340 LSFSDdALRTIARESIRRKIGAR 362
                 45555577777777777777766 PP

>> IstB_IS21  IstB-like ATP binding protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   5.1e-05     0.029      46      68 ..     107     129 ..      95     133 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 5.1e-05
   IstB_IS21  46 kkenivllGpsGvGKshlaialg 68 
                 +k n++++Gp+G GK+ +a +l+
  AHX11648.1 107 SKSNVLIIGPTGCGKTLFAKTLA 129
                 578****************9997 PP

>> Rad17  Rad17 P-loop domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.0   6.1e-05     0.034      29      70 ..      93     133 ..      66     155 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 6.1e-05
       Rad17  29 eevkewlkadvLesrkkriLLisGPsGCgkstvvkvLskelg 70 
                   +++  k++ +e  k + +Li GP+GCgk+   k L++ l 
  AHX11648.1  93 CFIRNQYKTKDIEISKSN-VLIIGPTGCGKTLFAKTLARFLN 133
                 557777788888888555.5678**************99775 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.5e-05     0.031      12      36 ..     109     133 ..     101     199 .. 0.84

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.5e-05
                 SEEEEEESTTSSHHHHHHHHTTSS- CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  12 ekvaivGenGaGKStLlkllagllk 36 
                 + v i+G++G+GK+ ++k+la+ l+
  AHX11648.1 109 SNVLIIGPTGCGKTLFAKTLARFLN 133
                 5789****************99876 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.2   0.0   7.6e-05     0.043       1      25 [.     111     135 ..     111     197 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.2 bits;  conditional E-value: 7.6e-05
  RNA_helicase   1 iwlyGpsgeGKStlakeLakallkk 25 
                   +++ Gp+g+GK+++ak+La+ l   
    AHX11648.1 111 VLIIGPTGCGKTLFAKTLARFLNVP 135
                   5799**************9987754 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.1   0.00037       0.2      19      38 ..     108     127 ..     106     132 .. 0.88
   2 ?    2.4   0.1      0.15        85      83     141 ..     136     196 ..     132     200 .. 0.75
   3 ?   -2.1   0.0       3.5   1.9e+03     144     163 ..     372     392 ..     339     400 .. 0.64

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00037
      ATPase  19 grvvlitGepGtGKtifalq 38 
                 ++ vli G +G+GKt+fa++
  AHX11648.1 108 KSNVLIIGPTGCGKTLFAKT 127
                 6889*************986 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.15
      ATPase  83 laiidasesaee.saeekdkedleelieelaeaikeikakrvviDsitgl.ayeekeavaR 141
                 +ai da++ +e  +  ++ ++ l+ l+++  + +++ +   + iD i+ + ++++ ++ +R
  AHX11648.1 136 FAICDATSITEAgYVGDDVENILRMLLQSADYNVEAAQKGIIYIDEIDKIsKKSDGPSITR 196
                 67778777665403444778888999999999******************55555565555 PP

  == domain 3  score: -2.1 bits;  conditional E-value: 3.5
      ATPase 144 lrqlvrvl.kklgvTailvse 163
                 lr  + +l +k +vT++l+++
  AHX11648.1 372 LRDYMFELpSKDDVTSLLITD 392
                 333333444566677777666 PP

>> TsaE  Threonylcarbamoyl adenosine biosynthesis protein TsaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   0.00014     0.077      19      47 ..     108     137 ..      86     149 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 0.00014
                 TEEEEEEESTTSSHHHHHHHHHHHTT--.- CS
        TsaE  19 gdvilLeGdLGaGKTtlvrglakalgve.e 47 
                 ++ +l+ G+ G+GKT +++ la+ l+v  +
  AHX11648.1 108 KSNVLIIGPTGCGKTLFAKTLARFLNVPfA 137
                 45699******************9988654 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0    0.0001     0.058     128     154 ..     107     133 ..      75     146 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 0.0001
       T2SSE 128 erglilvsGgTgsGKttllyallkein 154
                 ++ ++l+ G+Tg GKt ++ +l  ++n
  AHX11648.1 107 SKSNVLIIGPTGCGKTLFAKTLARFLN 133
                 5889***************99998887 PP

>> NACHT  NACHT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0003      0.17       3      22 ..     111     130 ..     109     137 .. 0.89
   2 ?   -2.4   0.0       7.2     4e+03      77      98 ..     169     190 ..     158     215 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0003
                 EEEEC-TTTCHHHHHHHHHH CS
       NACHT   3 vilqGeaGsGKTtLlqklal 22 
                 v++ G+ G+GKT +++ la+
  AHX11648.1 111 VLIIGPTGCGKTLFAKTLAR 130
                 89***************997 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 7.2
                 CCSCCCEEEEEE-STT-SS-TC CS
       NACHT  77 lelperlLlilDglDelvtdlg 98 
                 +e +++  + +D +D+++++ +
  AHX11648.1 169 VEAAQKGIIYIDEIDKISKKSD 190
                 6778888899999999987544 PP

>> PhoH  PhoH-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0    0.0002      0.11      15      40 ..     104     129 ..      94     133 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 0.0002
                 HHHH-SEEEEE--TTSSTTHHHHHHH CS
        PhoH  15 alkkndivfaiGpaGtGKtylavala 40 
                 +  +++ v +iGp+G+GKt++a +la
  AHX11648.1 104 IEISKSNVLIIGPTGCGKTLFAKTLA 129
                 333777899************98876 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0012       0.7       4      31 ..      98     125 ..      95     133 .. 0.81
   2 ?    0.4   0.0      0.84   4.7e+02     119     144 ..     171     196 ..     151     204 .. 0.76

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0012
                 HHHHHHHHHTTCEEEEEESTTSSHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD   4 QaeaiplilgggdvlvaaeTGsGKTlaf 31 
                 Q ++ ++ +++ +vl+ ++TG GKTl +
  AHX11648.1  98 QYKTKDIEISKSNVLIIGPTGCGKTLFA 125
                 555555666889*************975 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.84
                 CTTEEEEEEETHHHHHHTTTHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 119 lsqvrflVlDEadrlldqgfsdfinr 144
                   q  ++ +DE+d++++++ ++ i r
  AHX11648.1 171 AAQKGIIYIDEIDKISKKSDGPSITR 196
                 556677889*******9998888876 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   0.00035       0.2      12      36 ..      99     122 ..      92     128 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00035
      AAA_29  12 fdghtieidlkgatlltGpsGsGKS 36 
                 ++ ++iei+ + ++l++Gp+G GK+
  AHX11648.1  99 YKTKDIEISKS-NVLIIGPTGCGKT 122
                 66788999966.5***********6 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   0.00037      0.21       1      25 [.     111     151 ..     111     213 .. 0.69

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00037
      AAA_18   1 IlltGtpGvGKttlakeLskrlgf................g 25 
                 +l+ G+ G+GKt +ak L++ l++                g
  AHX11648.1 111 VLIIGPTGCGKTLFAKTLARFLNVpfaicdatsiteagyvG 151
                 79****************99887777766666666664442 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00042      0.24       6      45 ..      96     132 ..      92     139 .. 0.76

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00042
      AAA_10   6 kpllanqevkgsktnasasliiGdlGnGKSvlakllvlyi 45 
                 + ++  ++++ sk+   ++liiG++G GK ++ak+l  ++
  AHX11648.1  96 RNQYKTKDIEISKS---NVLIIGPTGCGKTLFAKTLARFL 132
                 55556666666555...457***************98876 PP

>> AAA_33  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0    0.0006      0.34       2      23 ..     111     132 ..     111     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.0006
      AAA_33   2 vllvGlpGsGKstlaerllkkl 23 
                 vl++G+ G+GK+ +a+ l++ l
  AHX11648.1 111 VLIIGPTGCGKTLFAKTLARFL 132
                 789**************99765 PP

>> Terminase_6  Terminase-like family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.0       2.9   1.6e+03       2      20 ..     113     130 ..     112     148 .. 0.80
   2 ?    9.6   0.0    0.0011      0.64      90     128 ..     167     205 ..     155     224 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 2.9
                  EEE-SSS-HHHHHHHHHHH CS
  Terminase_6   2 ilggrqsGKTfagarellr 20 
                  i g+ ++GKT  +a +l+r
   AHX11648.1 113 IIGPTGCGKTL-FAKTLAR 130
                  78999****95.5555555 PP

  == domain 2  score: 9.6 bits;  conditional E-value: 0.0011
                  HHHHTS--SEEEEESGGGSTTHHHHHHHHHHHHCSTT-- CS
  Terminase_6  90 ggiqGaqidliyfDElteipksqelekvtrlratkgtdt 128
                  +++ +aq  +iy+DE+ +i+k+ +  ++tr ++++g++ 
   AHX11648.1 167 YNVEAAQKGIIYIDEIDKISKKSDGPSITRDVSGEGVQQ 205
                  566777888************************999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (402 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       716  (0.0399353); expected 358.6 (0.02)
Passed bias filter:                      627  (0.0349713); expected 358.6 (0.02)
Passed Vit filter:                       117  (0.00652574); expected 17.9 (0.001)
Passed Fwd filter:                        32  (0.00178482); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              32  [number of targets reported over threshold]
# CPU time: 0.60u 0.29s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2756.81
//
Query:       AHX11649.1  [L=256]
Description: rod shape-determining MreC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      1e-10   41.7   0.2    1.8e-10   40.9   0.2    1.4  1  MreC      rod shape-determining protein MreC


Domain annotation for each model (and alignments):
>> MreC  rod shape-determining protein MreC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   40.9   0.2     1e-14   1.8e-10      12     118 ..     131     230 ..     124     251 .. 0.81

  Alignments for each domain:
  == domain 1  score: 40.9 bits;  conditional E-value: 1e-14
                 EEEES--GGGT--TT-EEEETTEEEEEEEEE-SS-EEEEETTSCCE.EEEEEE.CTTEEEEEEEETTTTEEEEEEE.CT-..--TT-EEEEE-TTSSS- CS
        MreC  12 sltIdkGskdgvkkgmpVvsgkglVGkVtevgknssrVllitdssssvsvkvkrtgergilegkddekkeleleylpkeaadvkkgdlvvTsglggvfp 110
                 +++  +G + +vk+++ Vv++kg++Gk+++v++n  + +l+t++ ++++v    t++r i++g + e k+l ++yl+    ++  g+lv+++  g    
  AHX11649.1 131 TFMAIRGGNMNVKPDQLVVNEKGVIGKIISVENNLITGMLVTHPHFRIPVISAATQHRFIISG-TGECKRLAVSYLEG---SLIDGELVLSTIGG---S 222
                 555568999*****************************************44469999***99.45678899998843...47888888776544...3 PP

                 CCEEEEEE CS
        MreC 111 kglpvGtV 118
                 ++lp+++ 
  AHX11649.1 223 ENLPIARF 230
                 77887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      482  (0.0268838); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.23s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 1966.84
//
Query:       AHX11650.1  [L=661]
Description: glycine--tRNA ligase, beta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   2.3e-141  472.3   0.0   2.8e-141  472.1   0.0    1.1  1  tRNA_synt_2f  Glycyl-tRNA synthetase beta subunit
    5.4e-06   26.6   0.0    1.4e-05   25.3   0.0    1.6  1  DALR_1        DALR anticodon binding domain


Domain annotation for each model (and alignments):
>> tRNA_synt_2f  Glycyl-tRNA synthetase beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  472.1   0.0  3.2e-145  2.8e-141      34     533 ..       3     522 ..       1     523 [. 0.96

  Alignments for each domain:
  == domain 1  score: 472.1 bits;  conditional E-value: 3.2e-145
  tRNA_synt_2f  34 rlsyeevevfatpRRLallveglaekqadkeeekkgppvkvafdadgkptkaaegflrkqgveveeleveekkkgeylfakkekkgretaelLaell 130
                   +l++++vevf++ RR+a++v++++++ + +  ++kgp       + g+  k +e+f++++gv+v +l +++ +++ey+fa ++++  ++ ++L+++ 
    AHX11650.1   3 NLKVGTVEVFVSCRRIAVIVHDVDTNFTLSGLDRKGP-------SLGSGIKIVEKFASSAGVTVPDLYTRTVGSKEYYFAPSRESNITVVQVLKKIT 92 
                   68899********************************.......4566669******************99999*********************** PP

  tRNA_synt_2f 131 eelikklpfpksMrWgsselrFvRPvrwlvallgeevvpveiaglksgrttrghrfla..eeveiksaddYaekleeakVivdaeeRkekIleqlea 225
                   e+++ ++ +p+sMrWg+ +++++RP+++++++lg+evvpv++++ ++ ++trg   ++  +e++i sa++Y++ l+++++i++++eR+++I+eq+++
    AHX11650.1  93 EDILMGFAWPRSMRWGKYNFTWIRPIKSITCMLGGEVVPVQFHHYSAANVTRGSGATSdfREITIGSAEEYVSLLRRNSIILSQAERRNIIKEQIAK 189
                   ******************************************************9996699************************************ PP

  tRNA_synt_2f 226 lakeagleveedeeLleevtaLvEwPvvllGsfdeefLelPeevlittmkehqkyfpvrdkegkLlpkFivvsnieskdeeaviaGnerVlraRLsD 322
                   +++e+++ v+++++Ll+ev+++ E P+++lGsfde+fL+lPee++ t++ +hqk+fpv++ + kLl+kFi+vs  +   ++a ++G+erV++aRL+D
    AHX11650.1 190 IEAEHNFCVQVTDSLLDEVVGISESPNAMLGSFDEDFLRLPEELIKTVIISHQKVFPVYQ-NRKLLNKFIAVSSLA---NDAPVRGYERVITARLAD 282
                   ***99******************************************************7.9*************4...456789************ PP

  tRNA_synt_2f 323 AkFFyeeDlkkplesrvekLkkvvFhekLGslldkverieklaeela....eekleeaeraaeLaKaDLvtemVgeFpeLqGimGryYakadgeke. 414
                   A      D+k pl ++++kLk+++Fh+kLGs  +k+ ri +la+ +a    ++++ ++e+aae+aK+DL+t  V +FpeL G++G+yY k +ge++ 
    AHX11650.1 283 AVSMVLIDTKIPLVDYAPKLKQLIFHKKLGSFSEKTGRIVALAKFVAlwvpNASIIKVEKAAEIAKVDLLTTFVRDFPELAGFVGSYYLKLSGEDDc 379
                   **********************************************95442222349*************************************876 PP

  tRNA_synt_2f 415 eVaeAieehylprgagdelPetkvgavvaladkldtlvglfaigekptGskDPfaLRRaalgvirillekklrldlkellekalealk......... 502
                   e+ +A++++ylp  a d +P+++v++++aladk+d+lvgl++++ek t+++DP +LRRaa+g++ri++e++++++lk +l ka++ ++         
    AHX11650.1 380 EIINALRDQYLPVDAADVCPAAPVTVTLALADKMDNLVGLISANEKVTSTRDPLGLRRAAIGILRIIIENNINVPLKVFLMKAIDLYPaslfrslid 476
                   9***********************************************************************************99999******** PP

  tRNA_synt_2f 503 ...............vleelleFfaeRlkvllreegiradlvdavl 533
                                  v+  +leFf eRlk+ll ++g+  +++++v 
    AHX11650.1 477 risinpdeekqrksdVMMFILEFFSERLKALLLKQGVGIEVFNSVA 522
                   ************99988999**********************9996 PP

>> DALR_1  DALR anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.3   0.0   1.5e-09   1.4e-05       5     105 ..     554     651 ..     551     655 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.3 bits;  conditional E-value: 1.5e-09
                 HHHHHHHHHHTTCTTCCCCHCCHCCS-SHHHHHHHHHHHTHHHHHHHHHHHT-THHHHHHHHHHHHHHHHHHHHCTSTTSCTHHH.HHHHHHHHHHHHH CS
      DALR_1   5 haRiksilrkaeeegekleeealalleeeeekeLlkalaqfpevleeaaeelephklaeylyeLaatfhkfYnkervlkeeeeelaaaRLaLvkavrqv 103
                 h Ri+ il+  + + +++ +++ +   ++ee+ L+ +   f+ v ++++++ + +k ++ l  La   + f +++ ++   ++el+++R+ L++ ++++
  AHX11650.1 554 HKRISGILETTDVQLKSKYNKKVF--VSDEERMLAESFESFQGVFTKSLKNGDFEKALSELSGLAGPLTLFMDNVIINA-TDPELKRNRIGLLNTISET 649
                 99*******999988766555555..59****************************************99987776665.555567********99888 PP

                 HH CS
      DALR_1 104 La 105
                 ++
  AHX11650.1 650 VS 651
                 65 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (661 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.61u 0.26s 00:00:00.87 Elapsed: 00:00:00.41
# Mc/sec: 4861.67
//
Query:       AHX11651.1  [L=291]
Description: glycine--tRNA ligase, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.6e-122  408.1   0.0   1.8e-122  407.9   0.0    1.0  1  tRNA-synt_2e   Glycyl-tRNA synthetase alpha subunit
     0.0042   16.9   0.4     0.0073   16.1   0.4    1.3  1  N-glycanase_C  Peptide-N-glycosidase F, C terminal


Domain annotation for each model (and alignments):
>> tRNA-synt_2e  Glycyl-tRNA synthetase alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  407.9   0.0  2.1e-126  1.8e-122       3     277 ..      12     287 ..      10     288 .. 0.98

  Alignments for each domain:
  == domain 1  score: 407.9 bits;  conditional E-value: 2.1e-126
                   HHHHHHHHHHHCTT-EE----SS--SSGGGSHHHHTCCCSSS-EEEEEEEEEE-GGG--TT-STT--SEEEEEEEEEES--TTHHHHHHHHHHHCT- CS
  tRNA-synt_2e   3 elilklqkfwaeqgcvilqpydlevGagtlhpatflralgpepwkvayvepsrRptDgrygenpnrlqkyyqfqvilkPspeniqelyleslealgi 99 
                    li kl+++w++ gc il py  e Ga+tlhpat++ ++++++ k+ayv+p+ Rp+Dgryg+npnrl++++q+qv++kPsp+++qelyl sle++gi
    AHX11651.1  12 GLIKKLEEYWSDYGCSILLPYTSELGAATLHPATIFSCVSKRDAKIAYVQPVIRPADGRYGKNPNRLYQHHQYQVLIKPSPDDLQELYLGSLEHIGI 108
                   699********************************************************************************************** PP

                   -CCCS-EEEEEEEEEEGGGTEEEEEEEEEETTCEEEEEEEEEEETTEE-SS--EEEEEEHHHHHHHHCT-SSGGG-ECCT.TEEHHHHHHHHHHHHH CS
  tRNA-synt_2e 100 dlkehdirfveDdWesptlGawGlGwevwldGmeitqftYfqqvgglelkpvsveityGleRlamylqevdnvydlewne.kvtygdvflqneveqs 195
                   d+++hdirfveDdWe+p++GawGlGwevw+dGmei+qftY+qqvgg+ lk +++e++yGleR+amy+q+vdnv dl++++  ++y++++ qne+++s
    AHX11651.1 109 DVRSHDIRFVEDDWENPSVGAWGLGWEVWCDGMEISQFTYMQQVGGIALKVIPGELAYGLERIAMYMQNVDNVGDLVFAKdGTKYSQIYAQNEYQFS 205
                   ******************************************************************************6637*************** PP

                   HHHHCTS-HHHHHHHHHHHHHHHHHHHCCT-HHHHHHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHHHHHHHH CS
  tRNA-synt_2e 196 aynfeeadvelllklfeeyekeakrllekklvlpaydlvlkashtfnlldargaisvterakyiarvrklakkvaeayleqr 277
                   +  +e+ d  lll+ f +   +ak +lekkl+l ayd+++kash++n ld+rg isv+erakyi +vr+++k+++e +++q+
    AHX11651.1 206 VAALEAYDYPLLLNRFADNAVQAKIFLEKKLPLVAYDHCVKASHILNFLDSRGFISVSERAKYILEVREIVKQCCELFITQE 287
                   ******************************************************************************9986 PP

>> N-glycanase_C  Peptide-N-glycosidase F, C terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   8.1e-07    0.0073      77      98 ..     124     145 ..     112     155 .. 0.86

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 8.1e-07
                    .TT--EEES-BSS--TT-EE-- CS
  N-glycanase_C  77 vPnsgvwllsRsnWCpGsevkp 98 
                    +P+ g+w l+++ WC+G+e++ 
     AHX11651.1 124 NPSVGAWGLGWEVWCDGMEISQ 145
                    6888***************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       391  (0.0218082); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.22s 00:00:00.64 Elapsed: 00:00:00.37
# Mc/sec: 2355.74
//
Query:       AHX11652.1  [L=397]
Description: degT/DnrJ/EryC1/StrS aminotransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.1e-69  233.5   0.0    4.6e-69  233.3   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      2e-09   37.2   0.0    7.5e-09   35.4   0.0    1.8  2  DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
    0.00037   19.6   0.0     0.0009   18.3   0.0    1.6  2  Aminotran_5      Aminotransferase class-V
    0.00066   18.3   0.0     0.0011   17.6   0.0    1.3  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  233.3   0.0     1e-72   4.6e-69       1     363 []      29     389 ..      29     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 233.3 bits;  conditional E-value: 1e-72
                    SEEEESSSSSTTSTTSSHHHHHHHHHHHHHHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EE CS
  Aminotran_1_2   1 tdvinLgsneylgdsgkptlpevakaekegalaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdei 96 
                    +dvi L+++e+++     t+p   + +++  + +    +y+p  g   l+e++ k + r+++lk+  +  ++v++Ga++++  +  +l lnpgde+
     AHX11652.1  29 KDVISLCIGEPDFS----TPPLGQEMAIQ--AIKDCDDSYPPVSGTNLLREEIVKKFARDNALKYSVD-DIIVSNGAKQVLYNVLSAL-LNPGDEV 116
                    589***********....77766677766..66667789*****************************.*******************.******* PP

                    EEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHT.TEEEEEEETTT CS
  Aminotran_1_2  97 lvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakky.nlllfvDeaYa 191
                    ++ +p++ sy++++rl+ ++ v ++  s edf++d+eale al+e      ktk i+++sp+NP+G+ +t+ el+kl+d+ + y  +++++D++Y+
     AHX11652.1 117 ILIAPYWVSYSEMVRLASATPVVVS--STEDFRIDFEALESALNE------KTKAIILNSPNNPSGVCYTESELRKLADVLRMYpQVYIVSDDIYE 204
                    *************************..67****************......********************************************* PP

                    TCBSSSSHTHHHHGGSTTSTT..EEEEEESSSTTSSGGG-EEEEEE.EHHHHHHHHHHHHHHTS..SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 192 gfvfgsldavatranveeepn..llivgslsKafGlaGeRvGyilg.naavvsqlrklsrpfls..ssllqaavaaalsdallkqseleemrqrlq 282
                    +  + ++++ + +anv+++    ++iv++ sK ++++G+R+Gy+++ ++++ s +r l+ + +   ++++qaa++ al+  ++    l e+   ++
     AHX11652.1 205 HITYSHSSFLN-IANVAPDLRqrIVIVNGASKCYAMTGWRIGYAAItDKELMSLVRVLQEHSTGgaCTIAQAAAVGALRSGPE---LLRERLHVFE 296
                    *****889977.********9*************************888**************9****************998...59******** PP

                    HHHHHHHHHHHHS.TEEEECCSCSSEEEEEETHH............CHHHHHHHHHHTCTEEEEEGGGGTSTTEEEEECTTS-HHHHHHHHHHH CS
  Aminotran_1_2 283 krrkelrdeLael.glkvlasqsgmflltdlsae............takelskkLleevgvyvtpgtsftvpgrlRitvAglteeeleelveal 363
                    +rr++ ++ L ++ +lk+ +++++++l+  ++ +            t+++l + Ll+e+ v+v+ g++f+v g +Ri++ +l+ e le++++++
     AHX11652.1 297 SRRDKAFAILSSApYLKCSKPDGAFYLFICCKDLlgkktstgleikTDSDLTEYLLNEHSVAVVSGSEFGVAGYFRISY-ALSIELLEQACKRI 389
                    ***********99***************999999*********************************************.************98 PP

>> DegT_DnrJ_EryC1  DegT/DnrJ/EryC1/StrS aminotransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   35.4   0.0   1.7e-12   7.5e-09      22     117 ..      73     166 ..      51     190 .. 0.83
   2 ?   -1.6   0.0      0.28   1.3e+03      30      48 ..     345     363 ..     337     364 .. 0.89

  Alignments for each domain:
  == domain 1  score: 35.4 bits;  conditional E-value: 1.7e-12
                      SHHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHHTTTTTT-EEEEESSS-THHHHHHHHTT-EEEEE-B-TTTSSB-GGGCGGG--TTEEEE CS
  DegT_DnrJ_EryC1  22 gpeveeFEkafaaylgvkhaiavssGtaAlhlaLralgvgpgdeVIvpsltFvatanavlelgakpvfvDvdpdtynidpaaieaaitertkaI 115
                      ++ v++F+++ a    v+    vs+G + ++       ++pgdeVI  +  +v+  ++v+ + a+pv v  + +++ id +a+e+a++e+tkaI
       AHX11652.1  73 EEIVKKFARDNALKYSVDDI-IVSNGAKQVLYNVLSALLNPGDEVILIAPYWVSYSEMVRLASATPVVVSST-EDFRIDFEALESALNEKTKAI 164
                      55666777776666666654.4777777776666666799*****************************988.99******************* PP

                      EE CS
  DegT_DnrJ_EryC1 116 lp 117
                      ++
       AHX11652.1 165 IL 166
                      95 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 0.28
                      HHHHHHHT-SEEEEESSHH CS
  DegT_DnrJ_EryC1  30 kafaaylgvkhaiavssGt 48 
                      +++ +yl ++h++av sG+
       AHX11652.1 345 SDLTEYLLNEHSVAVVSGS 363
                      57899************97 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0     2e-07    0.0009      69     165 ..      96     186 ..      73     201 .. 0.77
   2 ?   -2.4   0.0       0.4   1.8e+03     320     358 ..     344     374 ..     341     378 .. 0.73

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 2e-07
                  SHHHHHHHHHHHCCCC.-TTTSEEEEETTSHGGGTHHHHHHHHHHTEEEEEEEBETTSCBEGGGHHHH--TTEEEEEEESBETTTTEB--HHHHHHHH CS
  Aminotran_5  69 Gtteainlvalslars.lkpgdeivvteaehhanlvpwqelakrtgakvkvipldeegeldldelekllnektklvaithvsnvtGtiqpveeigkla 165
                  +++   + v+++++ + l+pgde+++ +    +    +++l     a+ +v++ +e+ ++d ++le++lnektk+++++  +n +G++    e+ kla
   AHX11652.1  96 NGA---KQVLYNVLSAlLNPGDEVILIAPYWVSYS-EMVRL---ASATPVVVSSTEDFRIDFEALESALNEKTKAIILNSPNNPSGVCYTESELRKLA 186
                  443...334555555559*****999887666666.44444...45666788999********************************98777777665 PP

  == domain 2  score: -2.4 bits;  conditional E-value: 0.4
                  SHHHHHHHHHHTTEEEEEE-TTTHHHHHHTT.S-EEEEE CS
  Aminotran_5 320 haedvatlLdeegIavrsGhhcaqplmkrlalegtvRaS 358
                  +++  + lL+e+ +av sG++          ++g +R+S
   AHX11652.1 344 DSDLTEYLLNEHSVAVVSGSEFG--------VAGYFRIS 374
                  55666778899999999999876........66666665 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.6   0.0   2.4e-07    0.0011      72     150 ..      93     173 ..      77     205 .. 0.72

  Alignments for each domain:
  == domain 1  score: 17.6 bits;  conditional E-value: 2.4e-07
                      EESSHHHH.HHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCEEEEEST.TSHHHHHHHCCTTEEEEEEESS-TTT CS
  Cys_Met_Meta_PP  72 avssGmaA.iaaailallkaGdeivvsddlYggtqrllkkvlkklgievkfvdt.sdleelekaikentklvylEtptnpl 150
                      +vs G    + +++ all+ Gde+++    + + +++++       + ++  d   d+e+le+a++e+tk++ l +p np 
       AHX11652.1  93 IVSNGAKQvLYNVLSALLNPGDEVILIAPYWVSYSEMVRLASATPVVVSSTEDFrIDFEALESALNEKTKAIILNSPNNPS 173
                      5566654414578899**********99877777777666665555555555544699**********************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (397 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       527  (0.0293937); expected 358.6 (0.02)
Passed bias filter:                      502  (0.0279993); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.40
# Mc/sec: 2993.05
//
Query:       AHX11653.1  [L=151]
Description: single-stranded DNA-binding protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-36  124.4   2.0    2.4e-36  123.9   2.0    1.1  1  SSB       Single-strand binding protein family


Domain annotation for each model (and alignments):
>> SSB  Single-strand binding protein family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  123.9   2.0   1.3e-40   2.4e-36       1      99 [.       2     102 ..       2     107 .. 0.97

  Alignments for each domain:
  == domain 1  score: 123.9 bits;  conditional E-value: 1.3e-40
                 ECEEEEEEEESSS-EEEEETTSEEEEEEEEEEEEEEEE.TTCCEEEEEEEEEEEEEHH.HHHHHHHH--TT-EEEEEEEEEEEEEECTTSCEEEEEEEE CS
         SSB   1 vnkvilvGrlgkdpelrqtesGnavarftlatnrrfkd.qegekdeetewhrvvvfgk.laevvaeylkkGslvyveGrlqtrkyedqegqkrysteiv 97 
                 +nkvil+G+lg+dpe+r++ + ++va+f+lat++++ d ++ge+ ++tewh++vvf++ l +v+++y++kG++vy+eG+lqtrk++d+++++ry+te+v
  AHX11653.1   2 INKVILIGNLGRDPEVRTMSNSKQVATFSLATTENWSDkNTGERVSKTEWHQIVVFNEsLIKVISNYVSKGTRVYIEGSLQTRKWTDNNNVERYTTEVV 100
                 7*************************************999*********************************************************9 PP

                 EE CS
         SSB  98 ae 99 
                  +
  AHX11653.1 101 LN 102
                 87 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       650  (0.0362541); expected 358.6 (0.02)
Passed bias filter:                      388  (0.0216409); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.27s 00:00:00.64 Elapsed: 00:00:00.42
# Mc/sec: 1071.02
//
Query:       AHX11654.1  [L=199]
Description: COQ9 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.5e-21   73.4   0.1    2.1e-20   72.3   0.1    1.6  1  COQ9      COQ9


Domain annotation for each model (and alignments):
>> COQ9  COQ9
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.3   0.1   1.1e-24   2.1e-20       1      76 [.     108     183 ..     108     184 .. 0.98

  Alignments for each domain:
  == domain 1  score: 72.3 bits;  conditional E-value: 1.1e-24
        COQ9   1 PqnaptslrelarlaDdiwraagDkstDfnwYtkRatLsavyastelymlqdksedfedtwaFldrriddvmalek 76 
                 P+n+ +sl+  +rl+Ddiw+a++D+s  f++Y++R tL+ + as ++ +++d s++ ++t++Fl++ri+++ ++ k
  AHX11654.1 108 PRNSLSSLQASYRLVDDIWHAVNDTSIGFTFYSRRGTLAVLNASLMVKLANDYSHELNETHSFLRERIKNIVSFSK 183
                 999*********************************************************************9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (199 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       554  (0.0308997); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1434.67
//
Query:       AHX11655.1  [L=213]
Description: fructose-6-phosphate aldolase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-54  184.6   0.1      1e-53  182.6   0.1    1.7  1  TAL_FSA   Transaldolase/Fructose-6-phosphate aldolase


Domain annotation for each model (and alignments):
>> TAL_FSA  Transaldolase/Fructose-6-phosphate aldolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  182.6   0.1   5.7e-58     1e-53       1     241 [.       2     199 ..       2     212 .. 0.94

  Alignments for each domain:
  == domain 1  score: 182.6 bits;  conditional E-value: 5.7e-58
                 EEEE---HHHHHHHHHTT---EEE--HHHHHH..TTS.-HHHHHHHHHHH........................H-S-EEEE-S-...-SHHHHHHHHH CS
     TAL_FSA   1 lvlDtadrelikklleekgiqgvTtNPsliekaikykalydeaieeikkegkkvkeaydkLavedilealdllgadgrvslEVdarlsddteatieeAr 99 
                 +++D+a++++i+ +le++++ gvTtNP+li+k  +++ + +++i+ei+++                      +  +g+vs+EV +    + +++i+e+ 
  AHX11655.1   2 FFIDSAELKEIELALEWGIVSGVTTNPTLIRK--SGR-EHKDVIKEICNI----------------------V--KGPVSAEVIS---LTSKEMIDEGL 70 
                 69******************************..545.789999999988......................6..**********...99********* PP

                 HHHTT-T..TEEEEEESSHHHHHHHHHHHHTT--EEEEEE-SHHHHHHHHHHT-SEEEEBHHHHHTTT............S-HHHHHHHHHHHHHHHT- CS
     TAL_FSA 100 rlialyerenvlIKiPateeGikAikeLkkeGinvnvTliFsleqalaaaeagasviSpFvgRiddllkkleekdklkgkddgvalvkeiynyykklgy 198
                 rl ++++  nv+IK+P+t++GikA++ Lk++G + n+Tl+Fs++qa++aa  ga++iSpF+gR+dd++            ++gv l++ei ++y++   
  AHX11655.1  71 RLSEIAQ--NVVIKLPCTRDGIKAASLLKAHGCKLNITLCFSAAQAILAASVGADYISPFIGRLDDIG------------HQGVLLIEEIAQLYESKY- 154
                 ******9..***********************************************************............89*************975. PP

                 S-EEEEBS--SHHHHH..HHHT-SEEEE-HHHHHHHT--HHH... CS
     TAL_FSA 199 sTkvmaasfrnveeve..elagcdtvTippkllealakhgktsek 241
                 +Tk++aas+r+ve+v+   ++g+++vT+p k+l+++ +h++t++ 
  AHX11655.1 155 DTKILAASIRSVEHVLssFKLGAHVVTAPMKILDQMFDHPLTHKG 199
                 9***************9999*********************9544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (213 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1659.00
//
Query:       AHX11656.1  [L=97]
Description: ATP synthase, Delta/Epsilon chain, beta-sandwich domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.4e-11   42.5   0.0    5.3e-11   42.3   0.0    1.1  1  ATP-synt_DE_N  ATP synthase, Delta/Epsilon chain, beta-sandwi


Domain annotation for each model (and alignments):
>> ATP-synt_DE_N  ATP synthase, Delta/Epsilon chain, beta-sandwich domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.3   0.0   2.9e-15   5.3e-11       4      73 ..       2      71 ..       1      78 [. 0.92

  Alignments for each domain:
  == domain 1  score: 42.3 bits;  conditional E-value: 2.9e-15
                   EEEESSSEEEEEEEEEEEEEESSSEEEE-TT--SEEEEEESEEEEEEEGGGEEEEEEESSEEEEEETTEE CS
  ATP-synt_DE_N  4 eivtpervvfsgeveevvaptteGelgilpgHaplitaLkpgelriktedgeeesiavsgGflevqdnkv 73
                   +i+tp+      +v+++  +t +G +++l++H++++ +Lk g++ i  e+g+++ + v+g++l+v + + 
     AHX11656.1  2 NIITPDDGSALSKVKSLSGNTVTGRFTVLAQHEDYLFSLKDGPVSILFEGGTKKQFLVEGAILRVHGGSY 71
                   79****999999*****************************************************87655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (97 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       245  (0.013665); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 824.07
//
Query:       AHX11657.1  [L=474]
Description: ATP synthase F1, beta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.4e-61  206.6   0.0    4.6e-61  206.2   0.0    1.2  1  ATP-synt_ab    ATP synthase alpha/beta family, nucleotide-bin
    4.4e-19   68.8   0.1    9.4e-19   67.7   0.1    1.6  1  ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel do
     0.0017   17.8   0.2     0.0048   16.3   0.1    1.8  2  ATPase         KaiC
     0.0096   15.1   0.6      0.034   13.3   0.1    1.9  2  NB-ARC         NB-ARC domain
  ------ inclusion threshold ------
      0.011   16.2   0.0      0.031   14.7   0.0    1.8  1  AAA_16         AAA ATPase domain
      0.011   15.6   0.1      0.022   14.7   0.1    1.4  1  RsgA_GTPase    RsgA GTPase
      0.018   14.9   0.1       0.16   11.8   0.0    2.2  2  T3SS_ATPase_C  T3SS EscN ATPase C-terminal domain
       0.03   14.3   0.0      0.052   13.5   0.0    1.4  1  ATPase_2       ATPase domain predominantly from Archaea
      0.077   13.0   0.1         13    5.7   0.1    2.3  2  ResIII         Type III restriction enzyme, res subunit
       0.15   12.6   0.1       0.37   11.3   0.1    1.7  1  ABC_tran       ABC transporter
        0.2   12.1   0.0       0.45   10.9   0.0    1.6  1  RNA_helicase   RNA helicase


Domain annotation for each model (and alignments):
>> ATP-synt_ab  ATP synthase alpha/beta family, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.2   0.0   2.8e-64   4.6e-61       1     212 [.     133     352 ..     133     353 .. 0.95

  Alignments for each domain:
  == domain 1  score: 206.2 bits;  conditional E-value: 2.8e-64
                  SSHHHHHHS-EBTT-EEEEEESTTSSHHHHHHHHHHHSSTS.S.EEEEEEESEEHHHHHHHHHHCHH......SS.GGGGEEEEEEETTS-HHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.x.xxxxxxxxxxxxxxxxxxxxxxx......xx.xxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab   1 GirvlDalfpivqGqrtlipgafgvGktvisqslskqsnsd.d.aiiyvgiGergnevaevleefpe......gt.imkrtvlvantsnepvaareas 89 
                  Gi+v+D+l p+ +G++++++g++gvGktv++ +l+++  ++    ++++g+Ger++e +++++e+ e      ++   +++vlv+ ++nep+ ar ++
   AHX11657.1 133 GIKVIDLLAPYSKGGKVGLFGGAGVGKTVLIMELINNIAKAyGgFSVFAGVGERTREGNDLYHEMIEsgvidrENpEKSKVVLVYGQMNEPPGARAKV 230
                  99*****************************9999998777536***********************5555432246669****************** PP

                  HHHHHHHHHHHHH.TTSEEEEEEETHHHHHHHHHHHHHHTTTSBEGGGSBTTHHHHHHHHHTTSEEETSSEEEEEEEEEEE-GGCSTTSHHHHHHHHH CS
                  xxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab  90 iytgitlAEyfrd.qgknvlliadslsrwaeAlreislrlgempadqgypaylgaklaslyERagkapdrtGsvtivaavspaggDfsdpvttatlgi 186
                  ++ ++t+AEyfrd +g+nvl+++d+++r+++A  e+s++lg++p++ gy+++l++++ +l+ER++++  r+Gs+t+v+a++++++D++dp + + +++
   AHX11657.1 231 ALSALTMAEYFRDkEGQNVLFFVDNIFRFTQAGAELSTLLGRIPSAVGYQPTLATDMGKLQERITST--RNGSITSVQAIYVPADDLTDPAPATSFAH 326
                  *************99****************************************************..99*************************** PP

                  SSEEEEB-HHHHHTTBSSSBCTTTEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxx RF
  ATP-synt_ab 187 tdgfivLdkklaqrkhfPainvlvSv 212
                  +d+++vL++++a+ +++Pa+++l+S+
   AHX11657.1 327 LDSTTVLSRQIAELGIYPAVDPLAST 352
                  ***********************996 PP

>> ATP-synt_ab_N  ATP synthase alpha/beta family, beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   67.7   0.1   5.8e-22   9.4e-19       1      69 []       8      75 ..       8      75 .. 0.94

  Alignments for each domain:
  == domain 1  score: 67.7 bits;  conditional E-value: 5.8e-22
                   EEEEETTEEEEESSTSCETCTTEEEEECCETCSTEEEEEEEEEETTEEEEEESS-STTBBTTSEEEEES CS
  ATP-synt_ab_N  1 ivqviGpvvdvefgigrlpgiynalevelvefgtlllgvalnlgedkVrvivmgstdGlsrGteVkrTG 69
                   i++v+Gp vd++f+ g+lp+i nal +e ++++tl l+va++lg++ Vr+++m+stdGl r+ +V +TG
     AHX11657.1  8 IIRVVGPTVDIKFEDGNLPKIENALLCE-NNGKTLYLEVAQQLGDGIVRAVAMDSTDGLTRNRKVHDTG 75
                   789*************************.55567779*******************************9 PP

>> ATPase  KaiC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1     3e-06    0.0048       2      87 ..     131     217 ..     130     266 .. 0.75
   2 ?   -2.6   0.0       1.8   2.9e+03      35      65 ..     412     441 ..     411     448 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 3e-06
      ATPase   2 ktgIeglDeilkgGipegrvvlitGepGtGKtifalqFlikgaekygepgvfvtveepa...edlrenakslGw.dlekleeegklaiid 87 
                 +tgI+ +D +    + +g  v + G++G GKt++ ++ + + a+ yg   vf  v e+    +dl++++ + G+ d e+ e++ k++++ 
  AHX11657.1 131 ETGIKVIDLLA--PYSKGGKVGLFGGAGVGKTVLIMELINNIAKAYGGFSVFAGVGERTregNDLYHEMIESGViDRENPEKS-KVVLVY 217
                 79999999996..899999**************************************99999999999999997255555554.555543 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.8
      ATPase  35 falqFlikgaekygepgvfvtveepaedlre 65 
                 +++ F +  + + g+pg fv++  +   ++e
  AHX11657.1 412 LSQPFHVAEVFT-GQPGKFVSLKDTIAGFKE 441
                 677788888777.9*******9998877776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.3   0.1   2.1e-05     0.034      22      56 ..     148     182 ..     134     222 .. 0.84
   2 ?   -0.5   0.1      0.35   5.8e+02      65     101 ..     378     413 ..     352     415 .. 0.64

  Alignments for each domain:
  == domain 1  score: 13.3 bits;  conditional E-value: 2.1e-05
                 EEEEEESTTSSHHHHHHHHCCSHCCCCCCBTEEEE CS
      NB-ARC  22 vvalvGmgGvGKttlakqilnksdevegrFdsvaw 56 
                  v+l G +GvGKt+l+ + +n+ ++  g F ++a 
  AHX11657.1 148 KVGLFGGAGVGKTVLIMELINNIAKAYGGFSVFAG 182
                 489*******************9999999988875 PP

  == domain 2  score: -0.5 bits;  conditional E-value: 0.35
                 HHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCC CS
      NB-ARC  65 seeiletilkeLslseddleekeeveslkrklvrlLl 101
                 s++ l++i++ L+ +e   e k +v+ ++rk++r+L 
  AHX11657.1 378 SYKSLQDIIAILGMEELSEEDKLTVY-RARKIQRFLS 413
                 33334558888888877777777777.8888888886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.0   1.9e-05     0.031      27     154 ..     149     266 ..     135     281 .. 0.57

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.9e-05
      AAA_16  27 vllsGesGvGKsslvrellralekdggif..lrgkcdqlesaipysa.laqalareellrqlldeaesaeleawrekleealaavpelagaeasrllel 122
                 v l G +GvGK+ l+ el + + k++g f  ++g  ++ +++      + +++ +++++  ++ e+++  +         ++++ +e +ga a+  l +
  AHX11657.1 149 VGLFGGAGVGKTVLIMELINNIAKAYGGFsvFAGVGERTREGN---DlYHEMI-ESGVIDRENPEKSK-VV--------LVYGQMNEPPGARAKVALSA 234
                 667899*******************877765555555553332...2266666.43555555555333.22........22222233333333333333 PP

      AAA_16 123 lkrllallsrderp.lvlvlDdlqwadeaslql 154
                 l+ +  + + +e + +++++D++ ++ +a ++l
  AHX11657.1 235 LTMAE-YFRDKEGQnVLFFVDNIFRFTQAGAEL 266
                 33333.333333333777777777777666666 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.7   0.1   1.4e-05     0.022      89     157 ..     136     204 ..     122     206 .. 0.87

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.4e-05
                  THHHHHHHCTTSEEEEECSTTSSHHHHHHHHCTT-----S--------------SEEEEEETTTEEEES CS
  RsgA_GTPase  89 gleelkellkdktsvlvGqSGvGKStLinallpelelktgevseklgrGkhTTtavellelaegglliD 157
                   ++ l+++ k+  + l G  GvGK+ Li +l+++   + g  s   g G  T     l++   ++ +iD
   AHX11657.1 136 VIDLLAPYSKGGKVGLFGGAGVGKTVLIMELINNIAKAYGGFSVFAGVGERTREGNDLYHEMIESGVID 204
                  46677888888888999***********************************99999998777777776 PP

>> T3SS_ATPase_C  T3SS EscN ATPase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0    0.0001      0.16       3      28 ..     363     388 ..     361     391 .. 0.95
   2 ?    0.2   0.0      0.41   6.7e+02      46      58 ..     405     417 ..     397     423 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.0001
  T3SS_ATPase_C   3 pehlqaarklrellatyqenedLini 28 
                    +eh++ a+k++ +l+ y++ +d+i i
     AHX11657.1 363 QEHYEVAQKVKGILQSYKSLQDIIAI 388
                    79**********************87 PP

  == domain 2  score: 0.2 bits;  conditional E-value: 0.41
  T3SS_ATPase_C  46 rpainafLkQgvd 58 
                      +i++fL Q+ +
     AHX11657.1 405 ARKIQRFLSQPFH 417
                    679*******876 PP

>> ATPase_2  ATPase domain predominantly from Archaea
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   3.2e-05     0.052      25     133 ..     151     262 ..     131     278 .. 0.69

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 3.2e-05
    ATPase_2  25 iYGpegsGKtaLlkeiienl.edkdkyviyyialreesi..skldefie......eeeekkklekalgiavpkaeleeilkeksklvfkaielllekik 114
                 ++G  g+GKt L++e+i+n  + ++   ++    ++ ++  + + e+ie      e+ ek+k+  + g+  +   +      + k + +a++ +     
  AHX11657.1 151 LFGGAGVGKTVLIMELINNIaKAYGGFSVFAGVGERTREgnDLYHEMIEsgvidrENPEKSKVVLVYGQMNEPPGA------RAKVALSALTMAEYFRD 243
                 79*****************966677777776655554441145777777777655444444444444333333333......45777788888888888 PP

    ATPase_2 115 kkgkkiiiiiDelqklidl 133
                 k+g+ +  ++D +++  + 
  AHX11657.1 244 KEGQNVLFFVDNIFRFTQA 262
                 8888899999999887755 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    5.7   0.1    0.0083        13      33      53 ..     155     175 ..     124     183 .. 0.86
   2 ?    5.0   0.0     0.014        23      39      71 ..     231     263 ..     229     324 .. 0.76

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0083
                 TTSTHHHHHHHHHHHH-S... CS
      ResIII  33 TGtGKTlvaaklierllkkgk 53 
                  G+GKT+++++li +++k+++
  AHX11657.1 155 AGVGKTVLIMELINNIAKAYG 175
                 59**************99876 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.014
                 HHHHHHHHHH-S.....-EEEEESSHHHHHHHH CS
      ResIII  39 lvaaklierllkkgkeekflflvprkslleqtl 71 
                  ++a +++++++ ++ +++lf+v+++    q+ 
  AHX11657.1 231 ALSALTMAEYFRDKEGQNVLFFVDNIFRFTQAG 263
                 56789999***999999*******986666655 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.1   0.00023      0.37       9      40 ..     144     175 ..     140     236 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00023
                 ETTSEEEEEESTTSSHHHHHHHHTTSS--SEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran   9 kegekvaivGenGaGKStLlkllagllkpteG 40 
                 ++g kv+++G  G GK+ L++ l+++  ++ G
  AHX11657.1 144 SKGGKVGLFGGAGVGKTVLIMELINNIAKAYG 175
                 6899****************998888776555 PP

>> RNA_helicase  RNA helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.9   0.0   0.00028      0.45       3      26 ..     151     174 ..     149     216 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 0.00028
  RNA_helicase   3 lyGpsgeGKStlakeLakallkkl 26 
                   l+G +g+GK++l+ eL+++++k++
    AHX11657.1 151 LFGGAGVGKTVLIMELINNIAKAY 174
                   79*******************887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (474 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       462  (0.0257683); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        63  (0.00351386); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.53u 0.23s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3583.39
//
Query:       AHX11658.1  [L=43]
Description: hypothetical protein NHE_0726 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (43 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       289  (0.0161191); expected 358.6 (0.02)
Passed bias filter:                      183  (0.0102069); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.25s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 340.28
//
Query:       AHX11659.1  [L=851]
Description: hypothetical protein NHE_0727 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (851 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       533  (0.0297284); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.63u 0.26s 00:00:00.89 Elapsed: 00:00:00.40
# Mc/sec: 6343.25
//
Query:       AHX11660.1  [L=753]
Description: cagE, TrbE, VirB, component of type IV transporter system family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.8e-06   26.3   0.0    1.7e-05   25.0   0.0    1.7  1  CagE_TrbE_VirB  CagE, TrbE, VirB family, component of type IV


Domain annotation for each model (and alignments):
>> CagE_TrbE_VirB  CagE, TrbE, VirB family, component of type IV transporter system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0   9.4e-10   1.7e-05       7     200 ..     168     360 ..     140     363 .. 0.86

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 9.4e-10
  CagE_TrbE_VirB   7 eerellfselleflnflin.Gene.pvklpsgsmlldeliatskvpfgkdkfiirtakdekfasilsikeYpeetrsslldsllsldieliites 99 
                     e   l  +ell f ++l++ G+ + +  + ++   +d l    k++fg ++f+i+  k + f+    +k + + +++  +  +l  ++  iite 
      AHX11660.1 168 EAAPLAEDELLYFFSSLLGvGKVNmESSVRDI--AVDLLSD-RKIFFGFNTFEIQG-KTKLFGTSFRVKSFRNPSSPEFIGEVLGISCRMIITEV 258
                     55566778999999999998887756666666..7777777.9999*****99864.67899999999999999********************* PP

  CagE_TrbE_VirB 100 fskiskqkalsklkkkqsrllsiedkaksqiteledlidevasgdva.lGayhlslvlfaedkekLdkavseatkllnakGivavketigmepaF 193
                     +  ++   ++sk+++  + +  ++d+  ++ +  ++  ++ a g ++ ++     + +f e+   L ++++e+ +   + G++ v+ ++ +e+ F
      AHX11660.1 259 ITAATAGAVKSKFEEGIELMKVVKDEKYLDASCKSKIAAQFADGKFEnFCRRSFDVTIFSESADGLSSSIEECGRVFIKHGFIIVRDDLLLEDVF 353
                     **************86666666666666666666677777788888559********************************************** PP

  CagE_TrbE_VirB 194 fsqlPgn 200
                     + +lPg 
      AHX11660.1 354 WQKLPGS 360
                     *****96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (753 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       485  (0.0270511); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.61u 0.28s 00:00:00.89 Elapsed: 00:00:00.43
# Mc/sec: 5240.48
//
Query:       AHX11661.1  [L=100]
Description: trbC/VIRB2 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.2e-15   56.1   9.2    3.6e-15   56.0   9.2    1.0  1  TrbC      TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.0   9.2     2e-19   3.6e-15      19      99 .]       2      84 ..       1      84 [. 0.94

  Alignments for each domain:
  == domain 1  score: 56.0 bits;  conditional E-value: 2e-19
        TrbC 19 lvllllaspalAqaagg..dpvetvlqnivdfltgplakviatiaiivaGimlafgrlswrtlvmvviGiviifgAssivsti 99
                +++ + a+ a A++++g  + v+ v++niv++l+gp++++iat++ii++G+ ++ g+ s+++l+ v++Gi+++fgA++i+ +i
  AHX11661.1  2 VFFCFGAQFACADEPTGddSIVSYVICNIVKQLSGPISQAIATLVIIITGYSFFVGKVSIGMLFIVAAGIMFVFGAQTIMGWI 84
                566778888999999889889999********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       882  (0.049194); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 790.39
//
Query:       AHX11662.1  [L=108]
Description: trbC/VIRB2 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.6e-15   56.0  10.9    4.2e-15   55.8  10.9    1.1  1  TrbC      TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.8  10.9   2.4e-19   4.2e-15      19      99 .]       3      84 ..       1      84 [. 0.90

  Alignments for each domain:
  == domain 1  score: 55.8 bits;  conditional E-value: 2.4e-19
        TrbC 19 lvllllaspalAqaagg.dpvetvlqnivdfltgplakviatiaiivaGimlafgrlswrtlvmvviGiviifgAssivsti 99
                ++++ + +   A+ +++ + v+ v++niv++l+gp++++iat++ii++G+ ++ g+ s+++l+ v++Gi+++fgA++i+ +i
  AHX11662.1  3 FFCFGVQFVDAAAVPNNdNVVSRVICNIVKQLSGPISQAIATLVIIITGYSFFVGKVSIGMLFIVAAGIMFVFGAQTIMGWI 84
                55666666677777777899***********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (108 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       696  (0.0388198); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.37
# Mc/sec: 882.67
//
Query:       AHX11663.1  [L=107]
Description: trbC/VIRB2 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-17   63.4   6.9      2e-17   63.2   6.9    1.1  1  TrbC      TrbC/VIRB2 family


Domain annotation for each model (and alignments):
>> TrbC  TrbC/VIRB2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   63.2   6.9   1.1e-21     2e-17      19      99 .]       2      85 ..       1      85 [. 0.96

  Alignments for each domain:
  == domain 1  score: 63.2 bits;  conditional E-value: 1.1e-21
        TrbC 19 lvllllaspalAqaagg...dpvetvlqnivdfltgplakviatiaiivaGimlafgrlswrtlvmvviGiviifgAssivsti 99
                l +l+ +++a+A +++g   + v+ v++niv++l+gp++++iat++ii++G+ ++ g+ s+++l+ v++Gi+++fgA++i+ +i
  AHX11663.1  2 LCCLFTTDQAYAKKSSGsddSIVSYVICNIVKQLSGPISQAIATLVIIITGYSFFVGKVSIGMLFIVAAGIMFVFGAQTIMGWI 85
                6789**********999**99999*********************************************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       743  (0.0414412); expected 358.6 (0.02)
Passed bias filter:                      312  (0.017402); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.22s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 844.98
//
Query:       AHX11664.1  [L=596]
Description: GTP-binding protein LepA [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.3e-52  176.8   0.2      5e-52  176.3   0.2    1.3  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    8.8e-46  154.5   0.5    1.6e-45  153.7   0.5    1.4  1  LepA_C        GTP-binding protein LepA C-terminus
      1e-20   73.5   0.0    2.7e-20   72.2   0.0    1.8  1  EFG_C         Elongation factor G C-terminus
    8.1e-11   42.2   2.0    9.1e-11   42.0   0.4    2.0  2  GTP_EFTU_D2   Elongation factor Tu domain 2
    2.3e-06   27.6   0.0    7.6e-06   25.9   0.0    1.9  1  EFG_II        Elongation Factor G, domain II
    7.5e-06   26.0   0.0    1.5e-05   25.0   0.0    1.5  1  MMR_HSR1      50S ribosome-binding GTPase
    0.00011   21.8   0.0     0.0002   21.0   0.0    1.4  1  Ras           Ras family
     0.0034   16.7   0.2        2.2    7.5   0.2    2.4  2  Septin        Septin
     0.0062   16.0   0.0      0.013   14.9   0.0    1.6  1  SRPRB         Signal recognition particle receptor beta subun
  ------ inclusion threshold ------
       0.01   16.1   0.0      0.049   13.9   0.0    2.0  1  Roc           Ras of Complex, Roc, domain of DAPkinase
      0.011   15.8   0.0      0.024   14.6   0.0    1.6  1  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
      0.026   14.3   0.0      0.051   13.4   0.0    1.4  1  RF3_C         Class II release factor RF3, C-terminal domain


Domain annotation for each model (and alignments):
>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  176.3   0.2   3.3e-55     5e-52       2     193 ..       3     181 ..       2     182 .. 0.95

  Alignments for each domain:
  == domain 1  score: 176.3 bits;  conditional E-value: 3.3e-55
                 CEEEEEEEESTTSSHHHHHHHHHHHTTSSCHHHHHHHHHSTHCHSHHHHHHTSCSSCEEEEEE...TTCSSEEEEEEEESSSGGGHHHHHHHHHT-SEE CS
    GTP_EFTU   2 rirnigiighvDhGKtTLtdrLlyktgaiskkgekaeeervlDtlkeErergiTiksaaisle...ketkkylinliDtPGHvdFskevirglrvlDga 97 
                 +irn++ii+h+DhGK+TL drL++++ ai+ +++ka+    lD++k ErergiTiks+++ l+   k+++ y +nl+DtPGHvdFs ev+r+l++++g 
  AHX11664.1   3 NIRNFAIIAHIDHGKSTLADRLMEECCAIDPRKMKAQ---LLDSMKIERERGITIKSQTVMLKyraKNGQGYILNLMDTPGHVDFSYEVSRSLAACEGS 98 
                 89*****************************888775...9**********************9877******************************** PP

                 EEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGSTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHHHHSH CS
    GTP_EFTU  98 vlvvdaveGvepqteevlrlalkegvpiivfiNKmDrlkaelkeiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealvellp 193
                 +lvvda++Gve+qt  +++ a++++  ii +iNK+D   ae ++++ ++++ +          g +++   + v +Sa++g g+++lle +v+++p
  AHX11664.1  99 LLVVDATQGVEAQTLANVYKAIDNDQTIIPVINKVDLDSAEPERVKAQIREVI----------GISTD---NAVEVSAKTGLGITDLLESIVKYIP 181
                 **************************************************877..........33333...589********************98 PP

>> LepA_C  GTP-binding protein LepA C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  153.7   0.5   1.1e-48   1.6e-45       1     107 []     487     593 ..     487     593 .. 0.99

  Alignments for each domain:
  == domain 1  score: 153.7 bits;  conditional E-value: 1.1e-48
                 ESSCB-GGG-EEEETTTHHHHHHHHHHHHHHHS---SS-EEEEEEETTEEEEEEEE----XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
      LepA_C   1 ingekvdaLslivhrskaeergrklvekLkeliprqlfevaiqaaigskviaretikalrkdvlaklyggditrkkKllekqkegkkrlkkignveipq 99 
                 inge++daLs++v r +a++rgr+++e+Lk+liprq++++aiqaaig+kv+aret++++rkdv+aklyggd tr++Kllekqk+gkkr+++ig+ +ipq
  AHX11664.1 487 INGEEADALSILVYRPSADRRGREICERLKDLIPRQQYKIAIQAAIGGKVVARETVNPYRKDVTAKLYGGDRTRRMKLLEKQKKGKKRMHSIGKANIPQ 585
                 8************************************************************************************************** PP

                 XXXXXXXX CS
      LepA_C 100 eaflavlk 107
                 +af++ lk
  AHX11664.1 586 KAFIEALK 593
                 ****9986 PP

>> EFG_C  Elongation factor G C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.2   0.0   1.8e-23   2.7e-20       2      87 ..     399     484 ..     398     486 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.2 bits;  conditional E-value: 1.8e-23
                 EEEEEEEEEEEEECCCCCCHHHHHHHCT-EEEEEEEE.TTEEEEEEEEEGGG-T.THHHCHHHCTTTS-EEEEEEEEEEE--HHHHH CS
       EFG_C   2 llEPivkveievpeeyvgkvisdlssrrGeiedmeqdasgrviieaeiPlaeli.gfateLrslTkGegsfsmefsgYeevpgdkld 87 
                 + EP+ k+ i+ p +y+g+vi++++++rGe++d  +  ++ +i+++++Pl+e++ +f+++L+s++kG++s+++e s+Y+  + +kl+
  AHX11664.1 399 IEEPWIKASIMLPGDYIGEVINLCNEKRGEQIDLGYV-DNKAILTYRLPLSEIVfDFYDRLKSMSKGYASLDWEISEYQANDLVKLS 484
                 78***********************************.*****************************************98877765 PP

>> GTP_EFTU_D2  Elongation factor Tu domain 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         9   1.3e+04      44      65 ..     134     155 ..     130     162 .. 0.77
   2 !   42.0   0.4   6.1e-14   9.1e-11       1      73 [.     205     274 ..     205     275 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9
                  EESEEETTSEEEEEEEESSCCS CS
  GTP_EFTU_D2  44 dedeavaganaGvivaikgled 65 
                  d+d a+++ ++ +i  ++g+++
   AHX11664.1 134 DLDSAEPERVKAQIREVIGIST 155
                  7888889999999888888887 PP

  == domain 2  score: 42.0 bits;  conditional E-value: 6.1e-14
                  EEEEEEEEEESEEETTEEEEEECTCTTSEEEEEEEEEEEEETEEESEEETTSEEEEEEEESSCCSGSSTTCEE CS
  GTP_EFTU_D2   1 GtvalgrvysGtlkkGdevrilgndtskkeivtrissletfhededeavaganaGvivaikgledaiivGdtl 73 
                  G+v+l+rv +Gt+k G+++++  ++t+ +  v++++    +++++ e+ ag+ + + + ik+++d+  +Gdt+
   AHX11664.1 205 GVVILVRVKNGTIKSGMNIEM--MSTKHRYAVETVGIFTPEKKNVPELKAGEIGFFTASIKDVSDC-NIGDTI 274
                  89*******************..999777899****99999************************5.*****8 PP

>> EFG_II  Elongation Factor G, domain II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   5.1e-09   7.6e-06       3      72 ..     292     364 ..     292     367 .. 0.87

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 5.1e-09
      EFG_II   3 ePvislaiepkskadedklskaLarlleEDptlrverdeeT...ketilsGmGelHleivverlkreykveve 72 
                 +Pv+++++ p s ++ +kl ++L++l+  D ++++e +  +   + +    +G lHle+++erl +e+++ + 
  AHX11664.1 292 QPVVFCSLFPVSADEFEKLRQSLEKLHLNDSSFTFEPEASSalgHGFRCGFLGMLHLEVITERLDEEFDLALV 364
                 6*********************************998888744345556668****************99876 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.0   0.0     1e-08   1.5e-05       3     114 .]       8     132 ..       6     132 .. 0.71

  Alignments for each domain:
  == domain 1  score: 25.0 bits;  conditional E-value: 1e-08
                 EEEESTTSSHHHHHHHHHT...............STEEESSSTTSSSSEEEEEEEETTEE.....EEEEECGGCSSHHHHHHHHHHHHHHHHCTSEEEE CS
    MMR_HSR1   3 aivGrpNvGKStLinaltg...............ekaivsdkpgtTrdinegrvklkgke.....ielvDtpGliegaseekglgkaflaleeadlill 81 
                 ai+ +   GKStL  +l++               +  +++++ g T++ ++  +k++ k+     ++l+DtpG ++    + +++++++    ++  ll
  AHX11664.1   8 AIIAHIDHGKSTLADRLMEeccaidprkmkaqllDSMKIERERGITIKSQTVMLKYRAKNgqgyiLNLMDTPGHVD---FSYEVSRSLA---ACEGSLL 100
                 66677788**********7777777777766544477999999*******9999944333445559*******655...2224444444...489**** PP

                 EEETTTTCSHHHHHHHHHHHHH..TTSEEEEEEES CS
    MMR_HSR1  82 vvdaseeklkpldeeleellee..akkplilvlnk 114
                 vvda+++ +  + ++l+++ +   +++ +i v+nk
  AHX11664.1 101 VVDATQG-V--EAQTLANVYKAidNDQTIIPVINK 132
                 ***8844.5..445666665445466777889998 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.0   0.0   1.4e-07    0.0002      31     160 ..      53     180 ..      36     181 .. 0.76

  Alignments for each domain:
  == domain 1  score: 21.0 bits;  conditional E-value: 1.4e-07
                 TSSEEEEEEEEEET...TEEEEEEEEEETTSGGGHHHHHHHHTTESEEEEEEETTBHHHHHTHHHHHHHHHHHSTTTSEEEEEEETTTGGG..G-SS-H CS
         Ras  31 Tigvdfytkeievd...gkevkleiwDTAGqeefkslrelyyrdaegillvyditsresfenvkkwveeikrvaeenvpivLvGnKvDlee..kravst 124
                 Ti  +  + +   +   g+ + l+++DT G  +f+   + ++  +eg llv d t+    +++++ ++ i +  +    i+ v nKvDl++   + v++
  AHX11664.1  53 TIKSQTVMLKY--RaknGQGYILNLMDTPGHVDFSYEVSRSLAACEGSLLVVDATQGVEAQTLANVYKAIDNDQT----IIPVINKVDLDSaePERVKA 145
                 44333333333..233588999**********************************9999999999988877655....78889*****9843344544 PP

                 HHHHHHHHHHTSEEEEEBTTTTCTHHHHHHHHHHHH CS
         Ras 125 eegeelakelglkfletSAktnenveeafeellrei 160
                 +   e+      + +e+SAkt  ++++++e++++ i
  AHX11664.1 146 QIR-EVIGISTDNAVEVSAKTGLGITDLLESIVKYI 180
                 443.34444445679***************999865 PP

>> Septin  Septin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0    0.0028       4.1      13      75 ..      13      84 ..       6      92 .. 0.74
   2 !    7.5   0.2    0.0014       2.2     134     170 ..     116     151 ..     106     164 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0028
                TTSSCCCCCCTTSSSS----......--------------S-EEEEEEEE...ETTCEEEEEEEE---BSSS CS
      Septin 13 sglGkttlintlfetdliee......ekleeasekkkktveikkkkvvie...edgvklnltviDtpgfGda 75
                   Gk+tl + l+e+    +      + l++ + + ++ ++ik+++v+++   ++g+   l+++Dtpg+ d+
  AHX11664.1 13 IDHGKSTLADRLMEECCAIDprkmkaQLLDSMKIERERGITIKSQTVMLKyraKNGQGYILNLMDTPGHVDF 84
                5679****9999998765555555434444444477888999999999973335689999********9886 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0014
                 HHHHHTTTS-EEEEESSGGGS-HHHHHHHHHHHHHHH CS
      Septin 134 lmkklsekvnliPviaKaDtltkeElkefKkkireel 170
                 + k++++   +iPvi K D l + E +++K +ire +
  AHX11664.1 116 VYKAIDNDQTIIPVINKVD-LDSAEPERVKAQIREVI 151
                 5688999999*********.7999**********987 PP

>> SRPRB  Signal recognition particle receptor beta subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   8.8e-06     0.013      26      86 ..      37     105 ..       3     146 .. 0.74

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 8.8e-06
                 S...........S---B---SS-EEETTG...GGTT-SEEEETT-GCCSHHHHHHHHHHGGEEEEEEEEETT CS
       SRPRB  26 d...........svkktvtSqessaalkvksekgskltliDfPGheklrqklleklkaksslkglvfvvDSt 86 
                 +           +   t  Sq  ++ ++ k+ +g  l+l+D PGh+ + ++++ +    +   g + vvD+t
  AHX11664.1  37 KaqlldsmkierERGITIKSQTVMLKYRAKNGQGYILNLMDTPGHVDFSYEVSRS---LAACEGSLLVVDAT 105
                 04444444443456678999999999999**********************9998...56677888888877 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.0   3.3e-05     0.049      11     120 .]      16     135 ..       8     135 .. 0.70

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.3e-05
                 SHHHHHHCHCT-CC.............C-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHHCTSCEEEEEEEGHHHHCHH CS
         Roc  11 GKtsllkrfvedkf.............sekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplylreaalailvydsrssenlk 96 
                 GK++l++r++e+               s k +   g+++++++v+ +k     k+ + + ln+ Dt G+ +f+   +  l + +  +lv+d+++  +++
  AHX11664.1  16 GKSTLADRLMEECCaidprkmkaqlldSMKIERERGITIKSQTVM-LKY--RAKNGQGYILNLMDTPGHVDFSYEVSRSLAACEGSLLVVDATQGVEAQ 111
                 777777777765442211111111111122334456666665553.333..334567799**************999999************9999999 PP

                 HHHHHHHHHCSSS-EEEEEE-TTT CS
         Roc  97 eWlkelkkvagkspvilvgnkiDl 120
                 +  +  k+  +++ +i v+nk+Dl
  AHX11664.1 112 TLANVYKAIDNDQTIIPVINKVDL 135
                 99999999999999999*****95 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0   1.6e-05     0.024      58     103 ..     126     179 ..     104     181 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 1.6e-05
  MMR_HSR1_Xtn  58 clyvlNKiDl..isleeldelare......pnsvviSaekelnldeLkekiwee 103
                    + v+NK+Dl  ++ e +++  re      +n+v +Sa+++l++ +L+e i ++
    AHX11664.1 126 IIPVINKVDLdsAEPERVKAQIREvigistDNAVEVSAKTGLGITDLLESIVKY 179
                   46799****95444455554444478888779******************9887 PP

>> RF3_C  Class II release factor RF3, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.4e-05     0.051       7      80 ..     291     367 ..     285     383 .. 0.82

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.4e-05
                 E--SEEEEEEESSGGGHHHHHHHHHHHHHCTSSEEEEET.TS...S-EEEEESSTHHHHHHHHHHHHHH---EEEEE CS
       RF3_C   7 FaPElfarvrlkdplkrkqlrkgleqLaeEGavqvfkeeeag...eelilgaVGqLQfeVveeRlknEYgvevrles 80 
                  +P +f ++    + +  +lr+ le+L+       f++e+++   + +  g +G L +eV++eRl++E+++ + l+ 
  AHX11664.1 291 LQPVVFCSLFPVSADEFEKLRQSLEKLHLNDSSFTFEPEASSalgHGFRCGFLGMLHLEVITERLDEEFDLALVLTA 367
                 56778888888888888999999999999999999988876555456999*******************99887765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (596 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      434  (0.0242066); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.57u 0.27s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4248.20
//
Query:       AHX11665.1  [L=505]
Description: lysine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
     4e-120  401.0   0.0   5.3e-120  400.6   0.0    1.1  1  tRNA-synt_1f  tRNA synthetases class I (K)
     0.0043   15.8   0.0     0.0075   15.1   0.0    1.3  1  tRNA-synt_1g  tRNA synthetases class I (M)
  ------ inclusion threshold ------
      0.038   12.3   0.0      0.052   11.8   0.0    1.1  1  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
      0.052   12.9   0.0        2.2    7.5   0.0    2.2  2  tRNA-synt_1b  tRNA synthetases class I (W and Y)


Domain annotation for each model (and alignments):
>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  400.6   0.0  1.2e-123  5.3e-120       2     340 ..       6     334 ..       5     350 .. 0.96

  Alignments for each domain:
  == domain 1  score: 400.6 bits;  conditional E-value: 1.2e-123
  tRNA-synt_1f   2 aWadklaeklieerkkkkaekdevvvesGispSGliHiGnlrevltadlvaralrkrgee..vrlilisDdmDglRkvpenlpek.llekylgkplt 95 
                   aW+ ++a+kl+ +  k+    +++++e+G++pSGl+HiG+++ev+++ +v++al+ ++    ++li++sDdmDglRkvp+n+p+   +ekylg++lt
    AHX11665.1   6 AWPIEEAKKLLPRIGKH----KTIIFETGYGPSGLPHIGTFGEVVRTIMVMKALEYLSPGvdMKLICFSDDMDGLRKVPDNVPNPeEVEKYLGHALT 98 
                   8**********555444....79********************************9955444*********************************** PP

  tRNA-synt_1f  96 siPdpkgkhesyaehfnaelvesLdelgievefisatelYksglydeaikealenrekikeilekyrgeereetyspylpvcekcgrvdttevvevd 192
                   siPdp+ +hesy+ h+na+l+++Ld +g+++ef+sate+Y+ gl+de+++ +l+n+++i +++ +++g+er++tysp+lpv  + grv++++v+e++
    AHX11665.1  99 SIPDPFRTHESYGAHMNARLMSFLDLFGFQYEFKSATECYQRGLFDEQLLLVLRNNRRILDLILPTLGDERQQTYSPFLPV--RDGRVLQAKVMELK 193
                   *********************************************************************************..89***********9 PP

  tRNA-synt_1f 193 aeeeeieYkceecGeeeevdiregngKLqWkvdwamrWaalgVdfEpaGkDhaaaGgSvdvsskiaeilggeaPekvvYelillkggekmssSkGnv 289
                     e++i Y++ + G  +e+ +++g +KLqWkvdw+mrWaalgVdfE +GkD++    S+ +s+kia+ilg ++Pe  vYel+l+++g+k+s+SkGn+
    AHX11665.1 194 --ENSIIYEDPSTGALMESGVTGGACKLQWKVDWGMRWAALGVDFEFHGKDLTP---SAVLSAKIAKILGSTPPELSVYELFLDEEGKKISKSKGNG 285
                   ..99**************************************************...**************************************** PP

  tRNA-synt_1f 290 ltledwlevaepevlrflilrrkPkkakkldldleilrlvdeYdklerkyf 340
                   lt+e+wl++a+ e+l+f++++ +Pk+ak+l++d  i++ vd+Y ++ +++ 
    AHX11665.1 286 LTIEEWLTYAPWESLAFFMFQ-HPKRAKRLYFD-IIPKNVDDYLRFLQSFS 334
                   *********************.***********.***********998875 PP

>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   1.7e-06    0.0075     312     362 ..     262     312 ..     220     319 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 1.7e-06
                   -S-EEEE--EEE--------------HHHHHHHH-HHHHHHHHHHHS-TTS CS
  tRNA-synt_1g 312 pkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYylaaeapekk 362
                   p+  v + +l  egkK+SkS+g++ +++e+l++ + + l +++ ++ ++ k
    AHX11665.1 262 PELSVYELFLDEEGKKISKSKGNGLTIEEWLTYAPWESLAFFMFQHPKRAK 312
                   333344559999******************************998766555 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   1.2e-05     0.052     550     591 ..     264     305 ..     234     328 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 1.2e-05
  tRNA-synt_1 550 vlvhglvrdeeGrKmSKslgNvidpldvikkygadalRltli 591
                  + v  l +deeG+K+SKs+gN +  ++ ++    ++l +++ 
   AHX11665.1 264 LSVYELFLDEEGKKISKSKGNGLTIEEWLTYAPWESLAFFMF 305
                  5567799**************998777777666666666665 PP

>> tRNA-synt_1b  tRNA synthetases class I (W and Y)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.0   0.1     0.012        53       3      26 ..      22      45 ..      20      66 .. 0.83
   2 ?    7.5   0.0    0.0005       2.2     146     206 ..     229     284 ..     226     299 .. 0.91

  Alignments for each domain:
  == domain 1  score: 3.0 bits;  conditional E-value: 0.012
                  HS--EEEEEEETSSS-BGGGHHHH CS
  tRNA-synt_1b  3 erplrvysGidPTgklHlGylvpl 26
                  ++ +++ +G  P+g +H+G ++ +
    AHX11665.1 22 HKTIIFETGYGPSGLPHIGTFGEV 45
                  67788899***********99865 PP

  == domain 2  score: 7.5 bits;  conditional E-value: 0.0005
                   HHHTCHSEEEEEGGGHHHHHHHHHHHHHHHHHSTTSS-EEEEET-BBSTTSSSBTTCETTC CS
  tRNA-synt_1b 146 illlkadlvpgGsDQkqnielgrdlarrfnkkevfkkpegltvplltgldGekKmSKSagn 206
                   +++l +d+++ G+D     +l  ++a+ ++++    +pe  + +l  + +G+ K+SKS+gn
    AHX11665.1 229 WAALGVDFEFHGKDLTPSAVLSAKIAKILGST----PPELSVYELFLDEEGK-KISKSKGN 284
                   578899999**********************9....9***9***********.******** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (505 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       381  (0.0212505); expected 358.6 (0.02)
Passed bias filter:                      377  (0.0210274); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.29s 00:00:00.77 Elapsed: 00:00:00.41
# Mc/sec: 3658.16
//
Query:       AHX11666.1  [L=157]
Description: hypothetical protein NHE_0734 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (157 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       520  (0.0290033); expected 358.6 (0.02)
Passed bias filter:                      440  (0.0245412); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1241.85
//
Query:       AHX11667.1  [L=248]
Description: thiF family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.5e-58  195.6   0.1    1.1e-57  195.2   0.1    1.0  1  ThiF             ThiF family
      0.003   17.6   0.1      0.017   15.2   0.0    1.9  2  Shikimate_DH     Shikimate / quinate 5-dehydrogenase
     0.0038   17.5   0.9       0.13   12.5   0.2    2.8  2  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
  ------ inclusion threshold ------
      0.079   12.4   0.0        0.3   10.5   0.0    1.6  2  DUF373           Domain of unknown function (DUF373)
       0.09   13.2   0.0       0.21   12.1   0.0    1.6  1  NAD_binding_7    Putative NAD(P)-binding


Domain annotation for each model (and alignments):
>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  195.2   0.1   3.1e-61   1.1e-57       4     240 ..       8     237 ..       3     241 .. 0.92

  Alignments for each domain:
  == domain 1  score: 195.2 bits;  conditional E-value: 3.1e-61
                 HHHHHHHHHHHHHHTSEEEEE--SHHHHHHHHHHHHHTTTEEEEEESSB--GGGGGTBTTS-GGGTTSBHHHHHHHHHHHT-TTSEEEEEES-CCGCCS CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF   4 qlallgedgqekLrdskvllvGaGglGsellknLalsGvgkltlvDnDkielsNlnRqflfreediGkpKaevaaealqeinpdveveavteritdetv 102
                 + al+g+ gq ++ d+kvl++G+GglG+ +l nL+++Gvg++ +vD+D+i+ sNlnRqflf  ++i k K+++a+++l+++npd+++ ++++ri+d + 
  AHX11667.1   8 HFALFGKTGQYAILDAKVLVIGVGGLGCSVLYNLVGAGVGEIAIVDFDRISESNLNRQFLFDNASIHKLKVDAAQTRLKAFNPDCKIHRYPARIQDCS- 105
                 5678******************************************************************************************9943. PP

                 -HHHHTT-SEEEEESSSHHHHHHHHHHHHHHT-EEEEEEEETTEEEEEEEEE...CCS-ECTSS-TGGS.EECCCCEEHHHHHHCTE-B-HHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 103 leellesvDlVvdalDniearrlvnracvkkgiplieagtlgfegqvvviip...gktgcyeCldpsstedptekkvplctsiagnipaiatttavvag 198
                   e+++++ ++vd++Dn+e+r+++nr+c+  ++pli++++ g++g+v vi +    + +cy+C  +   e+p+++   +c +  g   +i++++ v+++
  AHX11667.1 106 --EIISEYEIIVDCSDNFETRFYLNRLCHLLKKPLISGAVIGYSGYVIVIKSfvsIEASCYQCFCY---EKPKQAIDHSC-EGGG---VIGAAVNVIGS 195
                 ..9***********************************************5566699*******98...***********.7777...*********** PP

                 HHHHHHHHHH.TTBCGGGCCEEEECCTTTTEEEEECCEEEEEE CS
                 xxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF 199 laalellkll.sgkeklenslltqvdllesrfenvelerakks 240
                 ++  ++++ +   +++ ++++  + d+l+++f++  + +++ +
  AHX11667.1 196 IQSMKVIQEIlRLHPEDSGTFI-FCDVLLNKFRRATILKDPSC 237
                 *******988533444555555.9***********99888855 PP

>> Shikimate_DH  Shikimate / quinate 5-dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   4.6e-06     0.017      11      68 ..      21      80 ..      13      89 .. 0.77
   2 ?    0.3   0.0      0.19   6.7e+02      63      84 ..      98     119 ..      78     137 .. 0.75

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 4.6e-06
                  TT-EEEEES-SHHHHHHHHHHHCCT-CEEEEEESSHHHHHHHHHHH..T.ET-EEEEGCG CS
  Shikimate_DH 11 kekkvlliGaGemaelvakhLlakgvkkvvvaNRtlerakelaeel..kgeeiealklee 68
                   ++kvl+iG G ++  v+ +L+ +gv +++++  ++   ++l +++  ++++i+ lk++ 
    AHX11667.1 21 LDAKVLVIGVGGLGCSVLYNLVGAGVGEIAIVDFDRISESNLNRQFlfDNASIHKLKVDA 80
                  589*****************************9888888888888833344444444455 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.19
                   EEEGCGHHHHHHT-SEEEE-SS CS
  Shikimate_DH  63 alkleelkellaeadvvisata 84 
                     ++++ +e+++e+++++ +  
    AHX11667.1  98 PARIQDCSEIISEYEIIVDCSD 119
                   56799999********998765 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.2   3.7e-05      0.13       1      64 [.      25      86 ..      25     144 .. 0.74
   2 ?   -0.1   0.0       0.3   1.1e+03      63      87 ..     176     203 ..     168     207 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 3.7e-05
                     EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHH CS
  Sacchrp_dh_NADP  1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLa 64
                     vl+iG G+ G +v+  l+  +    ei+++d+++ +  +l  + l  ++++++l ++  +  L+
       AHX11667.1 25 VLVIGVGGLGCSVLYNLVGAGVG--EIAIVDFDRISESNLNRQFLFDNASIHKLKVDAAQTRLK 86
                     89*****************9976..***********9999988855555555554444444343 PP

  == domain 2  score: -0.1 bits;  conditional E-value: 0.3
                      HHHHHTTS...SEEEE-SSGGGHHHHHH CS
  Sacchrp_dh_NADP  63 Laallkeg...dlvvnlsppissldvlk 87 
                      ++  +++g   ++ vn++++i+s++v++
       AHX11667.1 176 IDHSCEGGgviGAAVNVIGSIQSMKVIQ 203
                      5556666666677899999999999987 PP

>> DUF373  Domain of unknown function (DUF373)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.5   0.0   8.4e-05       0.3     117     173 ..     101     159 ..      99     170 .. 0.90
   2 ?   -1.3   0.0      0.33   1.2e+03      18      44 ..     187     213 ..     175     217 .. 0.75

  Alignments for each domain:
  == domain 1  score: 10.5 bits;  conditional E-value: 8.4e-05
      DUF373 117 iqsrvkvdsvkrVvVkqsrniEstyyll..kkalkdpelrktiLvplGlllliyallll 173
                 iq   +++s   ++V  s n E+ +yl    ++lk p ++  ++++ G +++i +++++
  AHX11667.1 101 IQDCSEIISEYEIIVDCSDNFETRFYLNrlCHLLKKPLISGAVIGYSGYVIVIKSFVSI 159
                 77778999999****************8779**********************999987 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 0.33
      DUF373  18 gvktPvvGreavleaavklaladPeDS 44 
                 g    v+G  + +++++++    PeDS
  AHX11667.1 187 GAAVNVIGSIQSMKVIQEILRLHPEDS 213
                 455568888888888888888888888 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.8e-05      0.21       7      87 ..      22     136 ..      18     140 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.8e-05
  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleag.akvtvvapevkeele.................................elvklaeeelekdlegadlviaa 68 
                    + kvlv+G G ++ + +++l+ ag  ++ +v+ +  +e++                                  ++ ++ +++++ ++++++++ +
     AHX11667.1  22 DAKVLVIGVGGLGCSVLYNLVGAGvGEIAIVDFDRISESNlnrqflfdnasihklkvdaaqtrlkafnpdckiHRYPARIQDCSEIISEYEIIVDC 117
                    789*********************779***9999544433777777777767665555555444444443333333334444666699999***** PP

  NAD_binding_7  69 tddrelneriaeaakarri 87 
                     d+ e +  + ++++  ++
     AHX11667.1 118 SDNFETRFYLNRLCHLLKK 136
                    *999999888888886655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (248 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       637  (0.035529); expected 358.6 (0.02)
Passed bias filter:                      439  (0.0244855); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.37
# Mc/sec: 1988.34
//
Query:       AHX11668.1  [L=333]
Description: pyridine nucleotide-disulfide oxidoreductase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.2e-30  106.8   0.0    1.4e-30  106.5   0.0    1.0  1  Pyr_redox_2     Pyridine nucleotide-disulphide oxidoreductase
    5.6e-25   88.2   0.5    2.1e-20   73.2   0.0    2.1  2  Pyr_redox_3     Pyridine nucleotide-disulphide oxidoreductase
    4.5e-12   46.4   1.0    5.2e-09   36.5   0.0    2.6  2  Pyr_redox       Pyridine nucleotide-disulphide oxidoreductase
    1.4e-09   37.2   0.8    0.00039   19.2   0.2    2.8  3  HI0933_like     HI0933-like protein
    1.8e-06   27.6   0.0    2.5e-06   27.1   0.0    1.3  1  FAD_oxidored    FAD dependent oxidoreductase
    7.4e-06   25.8   1.1      0.078   12.5   0.7    2.5  2  DAO             FAD dependent oxidoreductase
     0.0002   20.6   0.3     0.0033   16.6   0.0    2.5  3  K_oxygenase     L-lysine 6-monooxygenase (NADPH-requiring)
    0.00026   21.2   0.0    0.00062   20.0   0.0    1.6  1  NAD_binding_8   NAD(P)-binding Rossmann-like domain
     0.0007   18.8   0.2       0.49    9.4   0.1    2.2  2  GIDA            Glucose inhibited division protein A
     0.0012   18.1   0.3       0.11   11.5   0.2    2.8  3  FAD_binding_2   FAD binding domain
     0.0012   18.7   0.0     0.0024   17.8   0.0    1.4  1  DUF5076         Domain of unknown function (DUF5076)
     0.0015   17.9   0.6     0.0045   16.3   0.2    2.0  2  Thi4            Thi4 family
     0.0043   16.4   0.4      0.014   14.7   0.2    1.8  2  FAD_binding_3   FAD binding domain
     0.0045   17.0   1.1      0.093   12.7   0.0    2.5  2  NAD_binding_9   FAD-NAD(P)-binding
  ------ inclusion threshold ------
      0.047   13.0   0.0      0.094   12.0   0.0    1.5  1  AlaDh_PNT_C     Alanine dehydrogenase/PNT, C-terminal domain
       0.08   11.3   0.0       0.12   10.8   0.0    1.1  1  FMO-like        Flavin-binding monooxygenase-like
      0.082   13.4   0.0        1.3    9.6   0.0    2.2  2  XdhC_C          XdhC Rossmann domain
       0.11   11.5   0.2        3.2    6.7   0.2    2.2  2  Lycopene_cycl   Lycopene cyclase protein
       0.12   12.8   0.0          9    6.7   0.0    2.6  2  Transposase_20  Transposase IS116/IS110/IS902 family


Domain annotation for each model (and alignments):
>> Pyr_redox_2  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  106.5   0.0   1.5e-33   1.4e-30       2     281 ..       4     290 ..       3     302 .. 0.80

  Alignments for each domain:
  == domain 1  score: 106.5 bits;  conditional E-value: 1.5e-33
                  SEEEE--SHHHHHHHHHHHHHTS-EEEEETTHCHHHCSHHH...HCHHHHHHHHHHHHH........HHHHCHHHHCCCCHCCTCEEEEESCEEEEET CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxx........xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2   2 dvvviGgGpAGlaaaltlaqagakvtlvelegtclnggcll...skallgvaedaeias........evvkklnqgielllgeevvkidpgkkkvkle 88 
                  d++++G+Gp G+ +a +++  g+k+++++     ++g+c      k +  +++ ++i +        ++ ++++  ++  +g+ v++++++   +++ 
   AHX11668.1   4 DIIIVGAGPVGIFTAFQAGMLGMKTHIID-SLPSVGGQCTAlypEKFIYDIPGYKQITAaslisnlvDQADRFSPTYH--TGQFVTHLEKADDSFTV- 97 
                  89**************************5.555555555544447777777777776668889977766666666655..4533****99999****. PP

                  EEECTCEEEEEESEEEE---EEE-BC.TCTTC.TTBEECCSECHHHHHHCCSS-TSEEEEES-SHHHHHHHHHHHHHT-EEEEEESSSSSSTTS-HHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Pyr_redox_2  89 kkkegdeekiaydklvlAtGssprdl.gipGvaenvgklvrtldsaealklkllpkrivvvGgGyiGvElAaalaklgkevtlveardrllraldkel 185
                    k++++ +i+ +++++A G+ ++d  +ip +  + +++ + + s++ ++l  + k +++ GgG  + +    la+++k+v+++++r+++ r ld+ +
   AHX11668.1  98 --KTSKGLEIQSKAVIIAAGAGAFDYnKIPIDSSEIYEGKSLFYSVQDVELFRN-KTVAIAGGGDSAADWGVILADIAKQVYVIHRRSKF-RCLDSTF 191
                  ..456799***************9999666444444455555555555554444.4789*******************************.7****** PP

                  HHHHHHHHHHT.TEEEEESCEEEEEEETTE...EEEEEETTSCE..EEESEEEE-S-EEES-HHCSHCCT-EEEETTEEE--TTS.BESSTTEEE-GG CS
                  xxxxxxxxxxx.xxxxxxxxxxxxxxxxxx...xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxx RF
  Pyr_redox_2 186 saaleealeke.Gvevklgtsvkeidgnge...klevvledgee..idadlvvvavGvrpstelleeklglelderggivvdefl.rtnvpgiyaiGD 276
                  ++   + le+  +v++++ +++++i+g g+   ++e+++ +ge+  +++d+++   G++ps + l e+  l +  +  i+vd+ +  tn++g+ya+GD
   AHX11668.1 192 TQL--RNLENTgKVRIVTPCQITDIEGIGTqitRIELTTLSGESmmLETDYLLAFFGLKPSLNHL-ENWSLDI-INHSIKVDPIScSTNIDGVYAVGD 285
                  *99..88888878***************997775554444444456****************999.99****9.999******883688********* PP

                  GCTEC CS
                  xxxxx RF
  Pyr_redox_2 277 vaggk 281
                  va+ +
   AHX11668.1 286 VASYE 290
                  **333 PP

>> Pyr_redox_3  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.4   0.3   3.5e-05     0.033       1      29 [.       6      33 ..       6      50 .. 0.82
   2 !   73.2   0.0   2.3e-23   2.1e-20      91     305 .]      72     284 ..      52     284 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.5e-05
  Pyr_redox_3  1 iIiGaGPaGlaaaielkkagledylilEk 29
                 iI+GaGP G+ +a ++  +g++   i++ 
   AHX11668.1  6 IIVGAGPVGIFTAFQAGMLGMK-THIIDS 33
                 8********************6.568886 PP

  == domain 2  score: 73.2 bits;  conditional E-value: 2.3e-23
  Pyr_redox_3  91 aksfelpiklfeeVesvkkedegfevetske.tyeAkkviiAtGe..fdkPnklnipGeek..lvkhyskvkefhkyagqkvvViGgknSavDaAlel 183
                  a++f    ++ + V+ ++k+d++f+v+tsk+ ++++k viiA+G   fd+ +   i  +e    +  ++ v++++ ++++ v++ Gg++Sa+D  + l
   AHX11668.1  72 ADRFSPTYHTGQFVTHLEKADDSFTVKTSKGlEIQSKAVIIAAGAgaFDYNKI-PIDSSEIyeGKSLFYSVQDVELFRNKTVAIAGGGDSAADWGVIL 168
                  6666667789999******************9**********87611555443.34444422246688999*************************** PP

  Pyr_redox_3 184 vrkgaeVtvvtrgseiekeesdpsyslkpdienrleelvkeekikvlfnaevkeik...ekeeeykvktedgkkvevkddvvla.tGykpdlsflkks 277
                  ++  ++V v++r+s+ +  +          +  +l++l +++k+++++  ++++i+   ++ ++++++t +g+++  ++d++la  G kp+l+ l++ 
   AHX11668.1 169 ADIAKQVYVIHRRSKFRCLD---------STFTQLRNLENTGKVRIVTPCQITDIEgigTQITRIELTTLSGESMMLETDYLLAfFGLKPSLNHLENW 257
                  *************9665554.........455567777777888888887777776222566677899****************99**********86 PP

  Pyr_redox_3 278 lfeldedgrpvlteeteetnvpglflaG 305
                   +++  +  +++++  ++tn++g++ +G
   AHX11668.1 258 SLDI-INHSIKVDPISCSTNIDGVYAVG 284
                  6655.6899****************998 PP

>> Pyr_redox  Pyridine nucleotide-disulphide oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.1    0.0048       4.6       2      35 ..       5      38 ..       4      45 .. 0.90
   2 !   36.5   0.0   5.5e-12   5.2e-09       2      78 ..     152     226 ..     151     232 .. 0.89

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.0048
                EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSS CS
   Pyr_redox  2 vvvvGgGyiglElAgalaelgkkVtvversdkll 35
                +++vG+G +g+  A  +  lg k+++++  + + 
  AHX11668.1  5 IIIVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVG 38
                89*************************9998876 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 5.5e-12
                 EEEECSSHHHHHHHHHHHHTTSEEEEEESSSSSSTTSSHHHHHHHHHHHHHT.TEEEECSEEEEEEEEETTSEEEEEE CS
   Pyr_redox   2 vvvvGgGyiglElAgalaelgkkVtvversdkllrllDeeaskilqeklekn.gievllntkveeiegsedgvesvkl 78 
                 v++ GgG+++ +++ +la+++k+V+v++r++k++  lD ++ ++  ++le+  ++++++  +++ ieg + ++++++l
  AHX11668.1 152 VAIAGGGDSAADWGVILADIAKQVYVIHRRSKFR-CLDSTFTQL--RNLENTgKVRIVTPCQITDIEGIGTQITRIEL 226
                 89********************************.888887764..66777788**************9998887877 PP

>> HI0933_like  HI0933-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.2   0.2   4.1e-07   0.00039       2      36 ..       4      38 ..       3      42 .. 0.94
   2 !   15.3   0.0   6.6e-06    0.0062     107     165 ..      60     117 ..      56     121 .. 0.92
   3 ?   -1.5   0.0      0.81   7.7e+02     140     171 ..     134     165 ..     123     174 .. 0.77

  Alignments for each domain:
  == domain 1  score: 19.2 bits;  conditional E-value: 4.1e-07
                 SEEEE--SHHHHHHHHHHHHTT--EEEE-SSSSS- CS
  HI0933_like  2 dviviGgGaAGlmaAisaakrgkrVlllekakklg 36
                 d+i++G+G+ G+++A +a+  g ++ ++++ +++g
   AHX11668.1  4 DIIIVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVG 38
                 89***************************999887 PP

  == domain 2  score: 15.3 bits;  conditional E-value: 6.6e-06
                  -CHHHHHHHHHHHHHHT-EEE-S--EEEEECETTE.EEEEE.TTEEEEESEEEE----S CS
  HI0933_like 107 kaedivdallkelkeagvklrletevksvekeedgkfrvktkseeeleadklvlAtGGl 165
                  +a+++++ l+ ++++   ++++ + v+++ek +d+ f+vkt+++ e++++++++A G  
   AHX11668.1  60 TAASLISNLVDQADRFSPTYHTGQFVTHLEKADDS-FTVKTSKGLEIQSKAVIIAAGAG 117
                  7999*************************998888.*****9**************976 PP

  == domain 3  score: -1.5 bits;  conditional E-value: 0.81
                  TE.EEEEE.TTEEEEESEEEE----SS-GGGT CS
  HI0933_like 140 dgkfrvktkseeeleadklvlAtGGlSiPklG 171
                  ++++  ++++ e ++ +++ +A GG S++  G
   AHX11668.1 134 GKSLFYSVQDVELFRNKTVAIAGGGDSAADWG 165
                  44455566678889999999*****9999877 PP

>> FAD_oxidored  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.1   0.0   2.6e-09   2.5e-06       1      41 [.       4      44 ..       4     101 .. 0.88

  Alignments for each domain:
  == domain 1  score: 27.1 bits;  conditional E-value: 2.6e-09
  FAD_oxidored  1 DvvVvGGgpaGvaAAiaAaraGakvlLveergvlGGlltsg 41
                  D+++vG+gp G+  A +A   G k+ +++  + +GG+ t+ 
    AHX11668.1  4 DIIIVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVGGQCTAL 44
                  9*************************************985 PP

>> DAO  FAD dependent oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.5   0.7   8.2e-05     0.078       1      33 [.       4      38 ..       4      45 .. 0.83
   2 !   11.0   0.0   0.00024      0.22     138     204 ..      54     118 ..      40     154 .. 0.80

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 8.2e-05
                EEEEECTSHHHHHHHHHHHHTT..EEEEESSSSTT CS
         DAO  1 dvviiGGGiiGlstAyeLarrg..Vtllekgdiag 33
                d++i+G+G +G++tA+++   g  + ++++ + +g
  AHX11668.1  4 DIIIVGAGPVGIFTAFQAGMLGmkTHIIDSLPSVG 38
                8****************966678888888876666 PP

  == domain 2  score: 11.0 bits;  conditional E-value: 0.00024
                 TTEEEEEHHHHHHHHHHHHHHTT-EEEESECEEEEEEEETCEEEEEEECT.EEE.EEEEEEEE--GGGH CS
         DAO 138 pdtgqvdpakltaalaraaealGveilegtevtgleeedgkvwgverttp.gen.daadavVnaaGaws 204
                 p+  q+ +a l+  l ++a +   + ++g  vt+le+ d+   +v  +t+ g + ++ +av++aaGa++
  AHX11668.1  54 PGYKQITAASLISNLVDQADRFSPTYHTGQFVTHLEKADD-SFTV--KTSkGLEiQS-KAVIIAAGAGA 118
                 6677888999999999999999999****99****87664.5999..6777998555.99*******96 PP

>> K_oxygenase  L-lysine 6-monooxygenase (NADPH-requiring)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.1      0.44   4.1e+02       3      15 ..       3      15 ..       1      36 [. 0.79
   2 !   16.6   0.0   3.5e-06    0.0033     107     234 ..      73     190 ..      68     196 .. 0.75
   3 ?    0.2   0.0      0.34   3.2e+02     287     334 ..     195     241 ..     190     247 .. 0.80

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.44
  K_oxygenase  3 lDligiGiGpsnL 15
                  D+i++G+Gp  +
   AHX11668.1  3 TDIIIVGAGPVGI 15
                 79********876 PP

  == domain 2  score: 16.6 bits;  conditional E-value: 3.5e-06
  K_oxygenase 107 sqleeqvrfgeeveevepdeeeeeelltveskdaegeeeelearnlvlgvG....tepkiPevleklegkervvHsseylerkeellakkriaVvGsG 200
                  ++++ + + g+ v+++e  ++     +tv++     +  e+++++++++ G       kiP    ++ + + ++ s +  e      ++k++a+ G+G
   AHX11668.1  73 DRFSPTYHTGQFVTHLEKADD----SFTVKT----SKGLEIQSKAVIIAAGagafDYNKIPIDSSEIYEGKSLFYSVQDVEL----FRNKTVAIAGGG 158
                  566666777888888887775....699998....35678888888888883233346788888888877778877665555....589********* PP

  K_oxygenase 201 qSaaeifedllrrqkkvelklvtrsealepldds 234
                   Saa+    l++ +k  ++ ++ r+++++ ld++
   AHX11668.1 159 DSAADWGVILADIAK--QVYVIHRRSKFRCLDST 190
                  *****8777766655..999*********99976 PP

  == domain 3  score: 0.2 bits;  conditional E-value: 0.34
  K_oxygenase 287 qkvkgeerlrllpnrevesaeaegkgeveltlrneesgeeetlevdav 334
                  ++++++ ++r+++ ++++++e  g++ ++++l+   sge+  le+d++
   AHX11668.1 195 RNLENTGKVRIVTPCQITDIEGIGTQITRIELTT-LSGESMMLETDYL 241
                  56777889**************999877777766.7788888888877 PP

>> NAD_binding_8  NAD(P)-binding Rossmann-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.0   0.0   6.5e-07   0.00062       1      37 [.       7      43 ..       7      58 .. 0.91

  Alignments for each domain:
  == domain 1  score: 20.0 bits;  conditional E-value: 6.5e-07
                   EE--SHHHHHHHHHHHCCTEEEEEE-SSSSSSGGG-E CS
  NAD_binding_8  1 IvGaGlsGlvaAylLakagfdvlllekrdrlGGraas 37
                   IvGaG  G  +A  +   g + +++++ +++GG+++ 
     AHX11668.1  7 IVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVGGQCTA 43
                   9**********************************85 PP

>> GIDA  Glucose inhibited division protein A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.4   0.1   0.00052      0.49       1      28 [.       4      31 ..       4      50 .. 0.88
   2 !    7.4   0.0    0.0022       2.1     119     167 ..      86     135 ..      81     151 .. 0.79

  Alignments for each domain:
  == domain 1  score: 9.4 bits;  conditional E-value: 0.00052
                CEEEE-SSHHHHHHHHHHHHTT--EEEE CS
        GIDA  1 dviViGgGhAGceAAlaaarlGakvlLi 28
                d+i++G+G  G+  A++a  lG+k+ +i
  AHX11668.1  4 DIIIVGAGPVGIFTAFQAGMLGMKTHII 31
                79***********************998 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.0022
                 EEEEECTTEEEEEEETTS-EEEECEEEE--TT..-BT-EEEETTEEEESSC CS
        GIDA 119 eeliveekkvkgvvtedgetikakavviatGt..flkgkihigekelsaGr 167
                 ++l+ + +    v+t++g +i++kav+ia+G+  f   ki i ++e+ +G+
  AHX11668.1  86 THLE-KADDSFTVKTSKGLEIQSKAVIIAAGAgaFDYNKIPIDSSEIYEGK 135
                 5553.34566689****************9987788888888888887776 PP

>> FAD_binding_2  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.5   0.2   0.00012      0.11       1      38 [.       4      41 ..       4      44 .. 0.94
   2 ?   -0.9   0.0      0.69   6.5e+02     139     201 ..      60     116 ..      52     124 .. 0.68
   3 ?    3.1   0.0     0.044        41     389     403 ..     274     288 ..     262     299 .. 0.83

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 0.00012
                   SEEEE--SHHHHHHHHHHHHTTT-EEEEESSSGGGSGG CS
  FAD_binding_2  1 DviViGsGlAGLaAAleaaeaGlkvavvekeqefggat 38
                   D+i++G+G  G   A +a   G k+ +++  +++gg+ 
     AHX11668.1  4 DIIIVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVGGQC 41
                   9**********************************964 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.69
                    HHHHHHHHHHHHHHTCTEEEEESEEEEEEEECTTEEEEEEEEETTTTCEEEEEESEEEE---- CS
  FAD_binding_2 139 tghallarlvesarkagvdfqerteadeLivedgrvtGavvenpesgrevrirakavvlatgG 201
                    t   l+  lv++a++   ++++  ++++L   d+  t   v   ++++  +i++kav++a+g+
     AHX11668.1  60 TAASLISNLVDQADRFSPTYHTGQFVTHLEKADDSFT---V---KTSKGLEIQSKAVIIAAGA 116
                    5556666667777666677777777777755444333...3...4666678999999999986 PP

  == domain 3  score: 3.1 bits;  conditional E-value: 0.044
                    EESSBTEEE-STCEE CS
  FAD_binding_2 389 gqpipGLYAaGevaa 403
                     ++i+G YA+G va+
     AHX11668.1 274 STNIDGVYAVGDVAS 288
                    579**********94 PP

>> DUF5076  Domain of unknown function (DUF5076)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   2.5e-06    0.0024      27      73 ..     150     195 ..     146     200 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.5e-06
                 EEEEE-S--.--HHHHHHHHHHHHHHHHHHHHHTSSS-HHHHHHHHH CS
     DUF5076  27 lhvalnrglweepeaWGilLadlarhiaralaeedelseeealeril 73 
                   va++ g  + +++WG++Lad+a+++  ++ +++    ++++ +++
  AHX11668.1 150 KTVAIAGGG-DSAADWGVILADIAKQVYVIHRRSKFRCLDSTFTQLR 195
                 578999998.9****************99999988777777777665 PP

>> Thi4  Thi4 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.2   4.7e-06    0.0045      17      55 ..       2      39 ..       1      43 [. 0.92
   2 ?   -1.5   0.0       1.3   1.2e+03      10      49 ..     142     180 ..     138     184 .. 0.75

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 4.7e-06
                EEEEEEE--SHHHHHHHHHHHHCTTS-EEEEESSSS--T CS
        Thi4 17 esDvvivGaGssGLtaayylakkpdlkvailersvspGG 55
                 +D++ivGaG+ G+ +a+  +   ++k+ i+++  s+GG
  AHX11668.1  2 HTDIIIVGAGPVGIFTAFQAGML-GMKTHIIDSLPSVGG 39
                79*****************9999.*********999999 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.3
                 HHHHHHTEEEEEEE--SHHHHHHHHHHHHCTTS-EEEEES CS
        Thi4  10 edllkyaesDvvivGaGssGLtaayylakkpdlkvailer 49 
                 +d+  + +  v+i G+G s    + +la     +v ++ r
  AHX11668.1 142 QDVELFRNKTVAIAGGGDSAADWGVILADI-AKQVYVIHR 180
                 677778888999999999998888888876.556666655 PP

>> FAD_binding_3  FAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.2   1.5e-05     0.014       2      33 ..       3      34 ..       2      41 .. 0.93
   2 ?   -1.2   0.0      0.96   9.1e+02       3      35 ..     151     183 ..     149     190 .. 0.91

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 1.5e-05
                   EEEEEE--SHHHHHHHHHHHHTTHHEEEEESS CS
  FAD_binding_3  2 tdVlIVGaGpaGlmlallLseaGvrvvlvekr 33
                   td++IVGaGp+G+ +a    + G ++++++  
     AHX11668.1  3 TDIIIVGAGPVGIFTAFQAGMLGMKTHIIDSL 34
                   89***************************975 PP

  == domain 2  score: -1.2 bits;  conditional E-value: 0.96
                    EEEEE--SHHHHHHHHHHHHTTHHEEEEESSSS CS
  FAD_binding_3   3 dVlIVGaGpaGlmlallLseaGvrvvlvekrst 35 
                    +V+I G+G + +  + +L+    +v ++ +rs+
     AHX11668.1 151 TVAIAGGGDSAADWGVILADIAKQVYVIHRRSK 183
                    699****************99999****99987 PP

>> NAD_binding_9  FAD-NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.3      0.16   1.5e+02       2      15 ..       7      20 ..       6      42 .. 0.85
   2 !   12.7   0.0   9.9e-05     0.093     103     155 ..      64     116 ..      61     117 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.16
  NAD_binding_9  2 ivGaGprGlavler 15
                   ivGaGp G+ ++ +
     AHX11668.1  7 IVGAGPVGIFTAFQ 20
                   9*******998865 PP

  == domain 2  score: 12.7 bits;  conditional E-value: 9.9e-05
  NAD_binding_9 103 lfeellarlpegvtvevhraevvdleeradgqavlladgaslaadaVvLAlGh 155
                    l+++l++++ +     +  + v+ le+++d+++v +++g +++ +aV++A G 
     AHX11668.1  64 LISNLVDQADRFSPTYHTGQFVTHLEKADDSFTVKTSKGLEIQSKAVIIAAGA 116
                    567888888776666777889*****************************995 PP

>> AlaDh_PNT_C  Alanine dehydrogenase/PNT, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.0    0.0001     0.094      29      93 ..       3      73 ..       1      81 [. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.0001
                 -EEEEESTSHHHHHHHHHHHHTT-EEEEEESSHHHHHHHHH.TTTCECEE.....HCHHHHHHHHHHHH-S CS
  AlaDh_PNT_C 29 akvlviGgGvaGlqAiatakglgakVtvlDvrparleqles.lgakfvev.....lksqeellaeavkead 93
                   ++++G+G +G+  +  a  lg k+ ++D  p++  q  + + +kf+       +   ++l+++ v +ad
   AHX11668.1  3 TDIIIVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVGGQCTAlYPEKFIYDipgykQITAASLISNLVDQAD 73
                 5789******************************9999999888888765566655555555666666655 PP

>> FMO-like  Flavin-binding monooxygenase-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00012      0.12     145     215 ..     115     181 ..      90     190 .. 0.77

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00012
    FMO-like 145 ctGhhvnphlplesfpGiekfkGqy.fhsrdykepevfkgkrvlviGlGnsggdiavelsrtaeqvllstrs 215
                  +G + + ++p++s    e + G+  f+s   ++ e f++k v + G G+s++d  v l+  a+qv++  r+
  AHX11668.1 115 GAGAFDYNKIPIDSS---EIYEGKSlFYS--VQDVELFRNKTVAIAGGGDSAADWGVILADIAKQVYVIHRR 181
                 346677888888885...55666651444..45689******************************998776 PP

>> XdhC_C  XdhC Rossmann domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.6   0.0    0.0014       1.3       2      35 ..       6      45 ..       5     121 .. 0.71
   2 ?    1.7   0.0      0.36   3.4e+02       1      34 [.     152     185 ..     152     240 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.6 bits;  conditional E-value: 0.0014
                EEE--STTHHHHHHHHHHHTEEEEEEES-GGGG......- CS
      XdhC_C  2 vifGaghvaqalarlaaalgfrvtvvdpreefa......t 35
                +i+Gag+v+   a  a +lg++++++d+ +++        
  AHX11668.1  6 IIVGAGPVGIFTAFQAGMLGMKTHIIDSLPSVGgqctalY 45
                8**************************9886555555550 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.36
                 EEEE--STTHHHHHHHHHHHTEEEEEEES-GGGG CS
      XdhC_C   1 lvifGaghvaqalarlaaalgfrvtvvdpreefa 34 
                 ++i G+g+ a+    ++a +  +v+v+  r++f+
  AHX11668.1 152 VAIAGGGDSAADWGVILADIAKQVYVIHRRSKFR 185
                 5799**************************9887 PP

>> Lycopene_cycl  Lycopene cyclase protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.2    0.0034       3.2       1      36 [.       4      37 ..       4      42 .. 0.90
   2 ?    2.4   0.0     0.068        64      80     143 ..      55     118 ..      44     127 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0034
  Lycopene_cycl  1 DvvviGaGpAglslAarlteakpglkvvlieaspsl 36
                   D++++GaGp g+  A +      g+k  +i++ ps+
     AHX11668.1  4 DIIIVGAGPVGIFTAFQA--GMLGMKTHIIDSLPSV 37
                   9***************99..9999999999987765 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.068
  Lycopene_cycl  80 aYgrvsskrlkeellerlvengvklleak.vesveeeeageslvvleggrkirarlvvdarglas 143
                     Y++++ + l ++l  +      +++ ++ v++ e++++   +v ++ g +i++++v+ a g+++
     AHX11668.1  55 GYKQITAASLISNLVDQADRFSPTYHTGQfVTHLEKADD-SFTVKTSKGLEIQSKAVIIAAGAGA 118
                    577777777777777776655666666654777777777.899999****************875 PP

>> Transposase_20  Transposase IS116/IS110/IS902 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0096         9       6      29 ..      52      76 ..      48      85 .. 0.84
   2 ?    3.1   0.0      0.13   1.2e+02       4      44 ..     211     251 ..     210     253 .. 0.86

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0096
  Transposase_20  6 sipGiGpvtaaallaei.gdlrrfk 29
                     ipG  ++taa l++ + ++ +rf+
      AHX11668.1 52 DIPGYKQITAASLISNLvDQADRFS 76
                    79**************966668886 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.13
  Transposase_20   4 LesipGiGpvtaaallaeigdlrrfksakqlaayaGlapve 44 
                     ++ i GiG++++   l ++   +     + l a++Gl p+ 
      AHX11668.1 211 ITDIEGIGTQITRIELTTLSGESMMLETDYLLAFFGLKPSL 251
                     57899999999988888997778999999*********986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              19  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2474.25
//
Query:       AHX11669.1  [L=413]
Description: histidine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.4e-36  125.6   0.0    3.5e-36  125.1   0.0    1.2  1  tRNA-synt_His   Histidyl-tRNA synthetase
    1.6e-13   51.0   0.0      4e-13   49.7   0.0    1.6  1  tRNA-synt_2b    tRNA synthetase class II core domain (G, H, P
    5.7e-06   26.0   0.1    1.3e-05   24.8   0.0    1.6  2  tRNA-synt_2d    tRNA synthetases class II core domain (F)
    0.00085   19.4   0.0     0.0019   18.3   0.0    1.6  1  HGTP_anticodon  Anticodon binding domain
  ------ inclusion threshold ------
      0.093   11.8   0.0        3.8    6.5   0.0    2.2  2  tRNA-synt_2     tRNA synthetases class II (D, K and N)


Domain annotation for each model (and alignments):
>> tRNA-synt_His  Histidyl-tRNA synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  125.1   0.0   9.7e-40   3.5e-36       1     310 []      10     310 ..      10     310 .. 0.90

  Alignments for each domain:
  == domain 1  score: 125.1 bits;  conditional E-value: 9.7e-40
                    T---EETCHHHHHHHHHHHHHHHHHHTT-EEEE--SEEEHHHHCTTSTCCHH....HS-EEE-TTSSEEEE-SSSHHHHHHHHHHHHH.TSS-EEE CS
  tRNA-synt_His   1 glrdllpeeaekieelrrrlldlfeswGYelVspPllEyldslltgagedld....qtfklvDqsgrllglRaDiTpqvaRiaahrln.rerplRl 91 
                    g++dl  ++ ek++ +++   dl  ++ +++  +P++Ey++ + ++ ge +d    +++ + D+sg ++ lR+++T+ ++R+   +++  ++p +l
     AHX11669.1  10 GTKDLFGQNLEKMRFIEKVARDLSIRYLFSELATPIIEYTELFIRNLGETSDvvskEIYSFEDKSGHNICLRPEFTAAIVRAFVGNFQhTPSPVKL 105
                    6789999999*************************************9999888878******************************99******* PP

                    EEEEEEEESS-SSTT--CCEEEEEEEEESS-SHHHHHHHHHHHHHHHHHHCTSSSEEEEEEETCHHHHHHHHTT--HHHHHHHHHHHHCT-HHHHH CS
  tRNA-synt_His  92 cYaGsvlrtrpdglgrsreplQvGaEliGaegleadlEvlslllealeaaagvkelrldlghvglvralleaaglsesleeallaalarkdlaelk 187
                     ++G+++r ++ + gr r++ Qv  E+iG+++   d+E + l+++ l + +g+ e +l +++ g+ +        +e  + al +++++ +    +
     AHX11669.1 106 FSFGPLFRYERPQKGRYRQFHQVNFEWIGVDSFLWDVEAIVLAVSFL-RELGI-ENKLRINSLGCSK-------ARERYRCALIDYFKQYKSDLSA 192
                    ***********************************************.6***9.779999*****99.......5689999999999887766554 PP

                    HHHHCCTTHHHCCHCC...HCCHCCCHHHHCHCCHCTHHHHHHHHHHHHHHHHHHHHHHHH-TTEEE-TT--TTTTT--SEEEEEEETT-SS..-S CS
  tRNA-synt_His 188 elaaeaglkealrellkalelygdaevleealealaaapalqaaldeleelaallealakpevrvtlDlaelrgyeYytGlvFaayaegvgq..ai 281
                    + + +  l+++ +++l++     d+e +e a + l + +     l ++++++ +l++++   +++++D  ++rg++Yy+Gl+F++ + + g+  a+
     AHX11669.1 193 DSLLR--LERNPLRILDSK-DPADKEIIECAPKILEHHT--DISLVHFDSICGVLREME---IDFSIDYRLVRGLDYYSGLIFECTSADIGAqdAL 280
                    44443..778889999886.3457788888866555554..56799***********95...************************98766444** PP

                    EEEEEECTTTGGG.T---EEEEEEEEHHHH CS
  tRNA-synt_His 282 arGGrYdelgaaf.grarpAtGfsldleal 310
                    ++GGrY++l++++ g++ +++Gf+  +e+l
     AHX11669.1 281 LGGGRYEQLVENLgGKKVSSIGFAAGIERL 310
                    *************99***********9987 PP

>> tRNA-synt_2b  tRNA synthetase class II core domain (G, H, P, S and T)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.7   0.0   1.1e-16     4e-13       1     174 [.      68     313 ..      68     318 .. 0.80

  Alignments for each domain:
  == domain 1  score: 49.7 bits;  conditional E-value: 1.1e-16
                   EEEEETTSEEEEE-SSSHHHHHHHHHHHEEEBGGSSEEEEEEEEEEBTTTSTBCTTTB-SEEEEEEEEEEESGGGHHHHHHHHHHHHHHHHHHTT.S CS
                   xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b   1 YkledrndreyiLkPtneetfvelirdevlrskrLPlklyqiqtkyRdEksdsrGLlRvreFhqkdgyvfhaeaslddslrdlikaisriferlgle 97 
                   Y +ed+ +++ +L+P+ ++++v+++  +  +    P+kl+ +++++R+E++ ++G  R+r+Fhq + + ++ ++ l+d+  + i ++  ++++lg+e
    AHX11669.1  68 YSFEDKSGHNICLRPEFTAAIVRAFVGN-FQHTPSPVKLFSFGPLFRYERP-QKG--RYRQFHQVNFEWIGVDSFLWDV--EAIVLAVSFLRELGIE 158
                   99************************99.666667****************.***..*****************99986..78899999*******9 PP

                   CEEEEEEGTTSC..................................................................................... CS
                   xxxxxxxxxxxx..................................................................................... RF
  tRNA-synt_2b  98 fraiielmsaks..................................................................................... 109
                    +  i++ +  +                                                                                     
    AHX11669.1 159 NKLRINSLGCSKareryrcalidyfkqyksdlsadsllrlernplrildskdpadkeiiecapkilehhtdislvhfdsicgvlremeidfsidyrl 255
                   8766666554446678889998888888888888888888888888888888888888877777777777777777777777777777777777777 PP

                   ...BTTSEEEEEEEEETTTSEEEEEEEEEEEETHHHHHTTEEEECTTSSEEEEEEEEEEEEHHHHHHH CS
                   ...xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2b 110 ...adykdkkefeavsesltkgieigtiqklgtrlserlgatvldennreksvimicaaigveRllsa 174
                      +dy+  + fe +s  ++++      ++++++l+e lg++          v  i++a g+eRl+ a
    AHX11669.1 256 vrgLDYYSGLIFECTSADIGAQD-ALLGGGRYEQLVENLGGKK---------VSSIGFAAGIERLVEA 313
                   77777777777777777777766.3334555677777777654.........7778888899998866 PP

>> tRNA-synt_2d  tRNA synthetases class II core domain (F)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.8   0.0   3.7e-09   1.3e-05      67     162 ..      67     164 ..       9     166 .. 0.76
   2 ?   -3.0   0.0       1.2   4.2e+03     200     222 ..     290     311 ..     283     314 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.8 bits;  conditional E-value: 3.7e-09
                   SEBTCTSSS-ECESEEE-SSTHHHHHHHH....TTS-SSEEEEEEEEEEBSST-SSSB-SEEEEEEEEEEETT--HHHHHHH..HHHHHHHHCTSTE CS
  tRNA-synt_2d  67 tFylkkpekaveekllLRthttavqirtl....ekkkppikiisigrvfRrdavDathlaeFhqveglvvdenvsladlkgv..leellkklfgaev 157
                    + + +++    ++  LR   ta  +r+     ++   p+k++s+g  fR +   + +  +Fhqv++ +++ +  l d+ ++  + ++l++l g e 
    AHX11669.1  67 IYSF-EDK--SGHNICLRPEFTAAIVRAFvgnfQHTPSPVKLFSFGPLFRYERPQKGRYRQFHQVNFEWIGVDSFLWDVEAIvlAVSFLREL-GIEN 159
                   3444.333..36789*************9999999999***************************999999998888876541157899999.9999 PP

                   EEEEE CS
  tRNA-synt_2d 158 kvrfr 162
                   k+r++
    AHX11669.1 160 KLRIN 164
                   99975 PP

  == domain 2  score: -3.0 bits;  conditional E-value: 1.2
                   HHHTT-.TTSEEEEEEEEHHHHH CS
  tRNA-synt_2d 200 leavgideevsgfafGlGveRla 222
                   +e++g  ++vs ++f  G+eRl 
    AHX11669.1 290 VENLGG-KKVSSIGFAAGIERLV 311
                   566666.899999999999*985 PP

>> HGTP_anticodon  Anticodon binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.0   5.2e-07    0.0019       2      93 ..     325     410 ..     324     411 .. 0.93

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 5.2e-07
                     EEEEESSSSHHHHHHHHHHHHHHHHTTTSEEEEESSSSTHHHHHHHHHHTT-SEEEEE-HHHHHHTEEEEEETTTCEEEEEETTHHHHHHHH CS
  HGTP_anticodon   2 vvviplnekaeeleeyakklaeeLraagirvelddsnesigkkireadllgipfavvvGekelekgtvtvrdrdtreqervsldelveklke 93 
                     v v+p++e    ++  a kl  +Lr +g+rv++++ + s++ +++++++    ++v+ Ge+el ++++ ++ ++t+ +++ s+d l+ klke
      AHX11669.1 325 VSVVPIGE---VAQRKAVKLVFALRTEGFRVDMYY-GLSLRSRMKRSENS--FLTVIFGEDELSRNECIIKLMETGIEYTASFDGLAVKLKE 410
                     78******...899*******************96.99999999999876..6899*******99*******************99999987 PP

>> tRNA-synt_2  tRNA synthetases class II (D, K and N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.5   0.0    0.0011       3.8      93     122 ..     104     132 ..     100     151 .. 0.90
   2 ?    2.8   0.0     0.014        50     270     305 ..     286     321 ..     282     328 .. 0.84

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0011
                  EEEEEEEEE--S--BTTB-S-CEEEEEEEE CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2  93 rvfqiaraFRaEdsrtdrhlaEFtqieaem 122
                  + f++++ FR E+ ++ r   +F q+++e+
   AHX11669.1 104 KLFSFGPLFRYERPQKGRYR-QFHQVNFEW 132
                  78*****************9.*******98 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.014
                  GHHHHHHHHCT--SEEEEEEEHHHHHHHHCT-SSGG CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  tRNA-synt_2 270 fswylealeyGapphgGlglGldRlvmlllgsesIr 305
                  +++++e l    ++  G++ G++Rlv   + + sI 
   AHX11669.1 286 YEQLVENLGGKKVSSIGFAAGIERLVEATTVEVSIC 321
                  6777777877888899**********9999998885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       399  (0.0222544); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.49u 0.26s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 2939.23
//
Query:       AHX11670.1  [L=86]
Description: bolA-like family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-22   78.8   0.0    3.1e-22   78.6   0.0    1.0  1  BolA      BolA-like protein


Domain annotation for each model (and alignments):
>> BolA  BolA-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   78.6   0.0   1.7e-26   3.1e-22       1      76 []       7      82 ..       7      82 .. 0.97

  Alignments for each domain:
  == domain 1  score: 78.6 bits;  conditional E-value: 1.7e-26
        BolA  1 LtealkpehlevedeShkhaghaeaggetHFkvvivseaFegkslvarhRlvyalLkeelakgiHALslktktpee 76
                +++al+ ++++v++ S++h gh++ ++++HF+vv+vs++F+g+++v rh++  ++L++ l++g+HA+s+k++t +e
  AHX11670.1  7 IRSALNVVYCDVKNTSEEHFGHTGYSKNSHFEVVVVSSDFDGLTRVVRHKMLFKILEKYLNNGVHAISMKLWTVDE 82
                6789******************8888***********************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (86 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       442  (0.0246528); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.25s 00:00:00.58 Elapsed: 00:00:00.38
# Mc/sec: 670.01
//
Query:       AHX11671.1  [L=331]
Description: sugar (and other) transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-15   56.9  30.2    4.7e-10   38.9   6.3    2.0  2  Sugar_tr  Sugar (and other) transporter
    1.8e-08   33.7  34.9    1.8e-08   33.7  34.9    2.0  2  MFS_1     Major Facilitator Superfamily
  ------ inclusion threshold ------
        4.9    7.8   6.6         11    6.6   5.6    2.2  1  DUF5592   Family of unknown function (DUF5592)


Domain annotation for each model (and alignments):
>> Sugar_tr  Sugar (and other) transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.9   6.3   7.8e-14   4.7e-10      87     202 ..      11     127 ..       1     132 [. 0.84
   2 !   25.6  15.4   8.8e-10   5.3e-06     239     434 ..     130     322 ..     122     329 .. 0.81

  Alignments for each domain:
  == domain 1  score: 38.9 bits;  conditional E-value: 7.8e-14
                 HHHHHHHH-TTTT....SS-TGGGGGHHHHHHHHHHHHHHHHHHHHTTS-SCCHHHHHHHHHHHHHHHHHHHHHHHHHH.HTSS-....TTHHHHHHHC CS
    Sugar_tr  87 vigavlqaaakgk....nsvevlivgRvlvGigvGlasvlvPmyisEiApkklRgalvslyqlaitfGilvaaifglgl.nktsn....adgwrillgl 176
                 +  +             ++v +l++ R+l G+++G++ +   +++ E +p+k+Rg+++s+  l+ ++G  +++++ l+  + +s+     +gwri++  
  AHX11671.1  11 ILPTY-------HtagiSAVIMLVLVRMLQGFALGGEVGN-VLFLIECSPPKYRGFFGSFEVLSAIIGAAMSSVVVLICnALISQeeflIWGWRIPFIA 101
                 33333.......1333469*****************9765.69************************************8888889***9********* PP

                 CHHHHHHHHHHGGGS---HHHHHHTT CS
    Sugar_tr 177 qlvpallllilllflPESPrylvekg 202
                   ++ ++ +i++    E+P +  +k+
  AHX11671.1 102 GTAIGIIGSIFRACSGETPVFENSKK 127
                 *******************9976665 PP

  == domain 2  score: 25.6 bits;  conditional E-value: 8.8e-10
                 ...HTTHHHHSH...HHHHHHHHHHHHHHTTHHHHHHHTTTHHHHSS-THH..HHHHHHHHHHHHHHHHHHHHHHHHS-SHHHHHHHHHHHHHHHHHHH CS
    Sugar_tr 239 kaswkellssktvrqrlligvvlqifqqltGinaimyysptifenlglsks..llvtiivgvvnfvatfvaiflvdrfGRRtllllGaagmaicfvilg 335
                 +  + +l+++  ++++l+++++++++   + + ++ ++  +++ ++g+s+    l+ +++  +  ++t+ a++++d fGR+ l+ll aa+ +i f++  
  AHX11671.1 130 SLPLATLFRK--YKKALFVAIGIDSLEETSLYLFLVFLNVYFTTKMGFSDItfELIHLLFLGLLGIFTLLAALFSDFFGRK-LMLLIAAVSSIIFAYP- 224
                 4455667777..89************************************997788999999999****************.5555666666666666. PP

                 ..HHHHTTSS...CHHHHHHHHHHHHHHHTTTTHHHHHHHHHHSHTTTHHHHHHHHHHHH.HHHHHHHHHHHHHHHCHHH...T-HHHHHHHHHHHHHH CS
    Sugar_tr 336 ivalllvakskaasivaivfialfialfalgwgpvpwvlvsElfpqsvRskalaiavavn.wlanflisllfpiiteaig...ggyvflvfaglavlfi 430
                  ++ll++++      ++i++  lf+ + +l++gpv    v E+ p +v +++la++ +++  l+      +   + +a+g   +g + l+ +gl+ lf 
  AHX11671.1 225 -IFLLMESG---LFPCIIIAKTLFVLIVGLSLGPVS-TAVYEILPVEVSYTGLALSRNISsALFGGMAPAFAVLLISASGtssAGAIPLIIVGLVTLFS 318
                 .37787777...699********************9.7779***************9865267888888887777777775666666666666666666 PP

                 HHHH CS
    Sugar_tr 431 ifvf 434
                 +  +
  AHX11671.1 319 LCFY 322
                 6555 PP

>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.7  34.9   3.1e-12   1.8e-08      69     341 ..       6     277 ..       1     286 [. 0.77
   2 !   12.8  28.8   6.9e-06     0.041      15     173 ..     161     323 ..     157     329 .. 0.85

  Alignments for each domain:
  == domain 1  score: 33.7 bits;  conditional E-value: 3.1e-12
       MFS_1  69 lllfalglllllf..a..sslwlllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg........Wravfy 155
                 ++l+a+    +++  a  s + +l+++r+lqG++ g+ + + + ++ + +p++ rg+  ++  +++ +Ga++  ++  ++ ++++        Wr +f+
  AHX11671.1   6 VALLAIL---PTYhtAgiSAVIMLVLVRMLQGFALGGEV-GNVLFLIECSPPKYRGFFGSFEVLSAIIGAAMSSVVVLICNALISqeefliwgWRIPFI 100
                 3333333...333222535566************96555.5556667788888*************************999999999999999****** PP

       MFS_1 156 ilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawkallkdpvlwillialllfffgfsglltllplylqevlgls..glllaglllal 252
                 + +++++++ +    +  ++  ++  +++k+     +  pl++++++ +k  ++  ++ +  l  + ++++l++l +y+ + +g+s  + +++   l +
  AHX11671.1 101 AGTAIGIIGSI----FRACSGETPVFENSKKT----VSLPLATLFRKYKKALFV--AIGIDSLEETSLYLFLVFLNVYFTTKMGFSdiT-FELI-HLLF 187
                 *********66....77778888888888888....888999977777776655..44444455669999****************854.3333.4777 PP

       MFS_1 253 lalvgailallagrlsdrlgrrrrlllallllllaalglallavtssavllll....vlvliGfglgfvfpsllalasdlappeeagtasglf 341
                 l+l+g++  lla+ +sd +gr+ +ll+a ++ +++a  ++ll  +   +++++    +++++G+ lg v++++  ++   +  +++g a++ +
  AHX11671.1 188 LGLLGIFT-LLAALFSDFFGRKLMLLIAAVSSIIFAYPIFLLMESGLFPCIIIaktlFVLIVGLSLGPVSTAVYEILPVEV--SYTGLALSRN 277
                 77777665.7888888*****999999999999999999999999888888888986777799999999999999999888..6777666655 PP

  == domain 2  score: 12.8 bits;  conditional E-value: 6.9e-06
       MFS_1  15 lgpalplalaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllllfa...sslw.lllvlrvlqGlgagalfpagaal 109
                 ++++l  + ++  g+s  ++ l+  l+  + ++++l+++ +sd fGr+ +ll+++++++++ ++++f    s+l+  ++++  l  l  g+++  + ++
  AHX11671.1 161 FLVFLNVYFTTKMGFSDITFELIHLLFLGLLGIFTLLAALFSDFFGRKLMLLIAAVSSIIF-AYPIFLlmeSGLFpCIIIAKTLFVLIVGLSLGPVSTA 258
                 5555555999999************************************************.666653367999999********************** PP

       MFS_1 110 iadwfpke..ergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllp 173
                 + ++ p e    g+a++   +++ +G  ++p+++ ll+s+ g +++  i  i+  l+ ++ l+++ 
  AHX11671.1 259 VYEILPVEvsYTGLALSRNISSALFGG-MAPAFAVLLISASGTSSAGAIPLIIVGLVTLFSLCFYK 323
                 *******63366777777666666666.789***************99999999999997777774 PP

>> DUF5592  Family of unknown function (DUF5592)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.6   5.6    0.0019        11      15      78 ..     181     247 ..     166     250 .. 0.77

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0019
     DUF5592  15 kaiyLtDlllllvlllltmklsslvhaslvvlfyifviilv...iflviksktNpklrnykalyLal 78 
                   i+L  l+ll ++ ll+  +s  + ++l  l++ ++ i+    ifl++ s   p     k+l+  +
  AHX11671.1 181 ELIHLLFLGLLGIFTLLAALFSDFFGRKLMLLIAAVSSIIFaypIFLLMESGLFPCIIIAKTLFVLI 247
                 44566666667777778889*************9998776434589999999888888888888766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (331 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       863  (0.0481343); expected 358.6 (0.02)
Passed bias filter:                      310  (0.0172904); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.52u 0.26s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 2344.02
//
Query:       AHX11672.1  [L=177]
Description: hypothetical protein NHE_0740 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (177 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.39u 0.21s 00:00:00.60 Elapsed: 00:00:00.36
# Mc/sec: 1463.26
//
Query:       AHX11673.1  [L=247]
Description: signal peptidase I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.8e-19   68.8   0.1    4.5e-19   68.2   0.1    1.3  1  Peptidase_S24  Peptidase S24-like
    3.4e-08   33.4   0.0     0.0017   18.1   0.0    2.7  2  Peptidase_S26  Signal peptidase, peptidase S26


Domain annotation for each model (and alignments):
>> Peptidase_S24  Peptidase S24-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.2   0.1     5e-23   4.5e-19       2      70 .]      39     128 ..      38     128 .. 0.98

  Alignments for each domain:
  == domain 1  score: 68.2 bits;  conditional E-value: 5e-23
                    XXSSTTCCTXXTTXEEEEECTS........................---TTSEEEEEETTCE.-EEEEEEEEETTEEEEE.SSTT.STEEEECTC CS
  Peptidase_S24   2 vpGdSMeptlldGdlilVdkfs........................epkrGdivvfrlpgee.eayiKrviglpgdrvllasnne.ypplyingk 70 
                    +p++SM+ tll Gd+i+ +k++                        +pkrGdivvfr p++  ++yiKrviglpgdr++       +++ ying+
     AHX11673.1  39 IPSGSMKSTLLVGDYIVTSKYAygysrysfpfapsfikgnprifydSPKRGDIVVFRNPHKAsTNYIKRVIGLPGDRIQ-----LiNGDTYINGE 128
                    8******************************************************************************.....779*****985 PP

>> Peptidase_S26  Signal peptidase, peptidase S26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   0.0   1.2e-05      0.11      50      79 ..     102     131 ..      76     153 .. 0.78
   2 !   18.1   0.0   1.9e-07    0.0017      96     137 ..     174     218 ..     163     219 .. 0.91

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 1.2e-05
  Peptidase_S26  50 vpllKrVlalagqevcvadgavtidgvavs 79 
                    +  +KrV++l+g++++  +g+  i+g ++ 
     AHX11673.1 102 TNYIKRVIGLPGDRIQLINGDTYINGEPLK 131
                    4569**********************7764 PP

  == domain 2  score: 18.1 bits;  conditional E-value: 1.9e-07
  Peptidase_S26  96 gcrvlaegelfllskevadSfDsRY...fGpvpassvigvarpvl 137
                    g + ++ +++f+++++ ++S DsR+   +G +pa+ ++g+a+ vl
     AHX11673.1 174 GVYYVPRNHFFVMGDNRDNSTDSRFlsaVGFIPAEYLVGRAERVL 218
                    567899*******************9999************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       398  (0.0221987); expected 358.6 (0.02)
Passed bias filter:                      383  (0.021362); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1894.67
//
Query:       AHX11674.1  [L=413]
Description: radical SAM methylthiotransferase, MiaB/RimO family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
      2e-21   77.1   0.0    6.9e-21   75.3   0.0    1.9  2  Radical_SAM  Radical SAM superfamily
    1.6e-14   53.7   0.1    5.1e-14   52.1   0.1    1.8  1  UPF0004      Uncharacterized protein family UPF0004
       0.01   16.2   0.1       0.27   11.6   0.0    2.7  3  DUF2183      Uncharacterized conserved protein (DUF2183)


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.0      0.56   3.3e+03      32      59 ..      45      72 ..      38      81 .. 0.57
   2 !   75.3   0.0   1.1e-24   6.9e-21       2     167 .]     135     307 ..     134     307 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.56
                 HHHHHHHHHHH.HHTTSEEEEEESSTGGG CS
                 xxxxxxxxxxx.xxxxxxxxxxxxxxxxx RF
  Radical_SAM 32 eeileevkelk.aekgvkevilgggepll 59
                 +++++ +++ + +++  k +i++g  + l
   AHX11674.1 45 RQVKQRIRRCHrEDP-NKKIIVVGCGVQL 72
                 567777777754444.4444444433444 PP

  == domain 2  score: 75.3 bits;  conditional E-value: 1.1e-24
                  EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS......TTHHHHHHHHHHTC.CCTEEEEEEECSSCHG.. CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx......xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxx.. RF
  Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly......pdfvellerlakla.vpgiritvetngtlpd.. 90 
                  ++++gC ++C+fCa++     +g+ rs++ve +++ev+e+ ae gv ev+l+g + ++y      ++   +l r++     +  r+++++  +  +  
   AHX11674.1 135 EIQNGCDHDCTFCAITL---ARGKNRSVPVEVLIAEVREM-AEAGVLEVVLTGVDITDYgkdlfgKPSLSYLIRAILDNvPELPRLRLSSVDVA-Eld 227
                  689*************9...8*******************.899***************66666633333333333333444444444444444.146 PP

                  HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET..EEEEEEEBTTTSHHHHHHHHHHH CS
                  xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  91 eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr..vvdrivglpGendeeleellell 167
                  +e++ +++  +  + +++l+l+++d+  +lk+m+r+h+++++ +   +  +++       d+i g+p e++e++ ++++l+
   AHX11674.1 228 DEFIGLFVSEPrlMPHIHLSLQSGDEM-ILKRMKRRHNLKQIRDFYSRVSSLRSVTafGADIIAGFPTETEEMFLNTYRLI 307
                  *********99***************8.***********99999999999986555889******************9986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   52.1   0.1   8.6e-18   5.1e-14       4      88 ..       4      79 ..       2      88 .. 0.89

  Alignments for each domain:
  == domain 1  score: 52.1 bits;  conditional E-value: 8.6e-18
                EE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTST.--EEEEEEHHHHS-HHHHHH CS
     UPF0004  4 ietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalkkpekkvvvlGCmaqrekeellk 88
                ++t+GC+ N ++s+ + + L+++        +  +++++nTCav+++ae++v q++r+++++  p+kk++v+GC +q ++e  l+
  AHX11674.1  4 VITFGCRLNFYESDLIKDFLSSN--------NGEEIIVINTCAVTNEAERQVKQRIRRCHRED-PNKKIIVVGCGVQLDPEGYLA 79
                79******************875........45589*************************99.*************99887665 PP

>> DUF2183  Uncharacterized conserved protein (DUF2183)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.6   0.0   4.6e-05      0.27      46      84 ..      42      80 ..      17      86 .. 0.81
   2 ?    1.3   0.0     0.073   4.4e+02      55      78 ..      90     114 ..      84     121 .. 0.78
   3 ?   -3.1   0.0       1.7     1e+04      45      58 ..     258     271 ..     237     281 .. 0.53

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 4.6e-05
     DUF2183 46 staehKraeiekiletfperkfiliGDsgqkdpeiYaei 84
                +++++ +++i++ +++ p++k+i++G   q dpe Y +i
  AHX11674.1 42 EAERQVKQRIRRCHREDPNKKIIVVGCGVQLDPEGYLAI 80
                344555689***************************876 PP

  == domain 2  score: 1.3 bits;  conditional E-value: 0.073
     DUF2183  55 ieki.letfperkfiliGDsgqkdp 78 
                 iek+ le++ + k il+GD +  d 
  AHX11674.1  90 IEKLqLENYKSEKRILVGDISAVDK 114
                 66643689999********887665 PP

  == domain 3  score: -3.1 bits;  conditional E-value: 1.7
     DUF2183  45 kstaehKraeieki 58 
                 + +++h +++i++ 
  AHX11674.1 258 RMKRRHNLKQIRDF 271
                 22444444444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (413 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       705  (0.0393218); expected 358.6 (0.02)
Passed bias filter:                      614  (0.0342462); expected 358.6 (0.02)
Passed Vit filter:                        53  (0.0029561); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 3128.53
//
Query:       AHX11675.1  [L=39]
Description: hypothetical protein NHE_0743 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       269  (0.0150036); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.37
# Mc/sec: 313.53
//
Query:       AHX11676.1  [L=55]
Description: hypothetical protein NHE_0744 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (55 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      242  (0.0134977); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.39
# Mc/sec: 420.93
//
Query:       AHX11677.1  [L=433]
Description: hypothetical protein NHE_0745 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.034   14.2   0.0        0.5   10.4   0.0    2.4  2  Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-


Domain annotation for each model (and alignments):
>> Octopine_DH  NAD/NADP octopine/nopaline dehydrogenase, alpha-helical domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.4   0.0   2.8e-05       0.5      85     121 ..      29      69 ..       9      75 .. 0.77
   2 ?    0.7   0.0     0.028   4.9e+02      57      98 ..     323     367 ..     314     373 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.4 bits;  conditional E-value: 2.8e-05
  Octopine_DH  85 k...dksslaevirtneaykgika.PmsldhRyltEDipyg 121
                  +   d ++lae i+ n+a + i   P+ +++Ry+t D+p+ 
   AHX11677.1  29 SktiDLEQLAELINLNNASSYILLdPSRVQQRYFTKDFPFI 69 
                  13448999999999988887776659999**********96 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.028
  Octopine_DH  57 Erlaiakalgl.evl..plaerlldaYgdeikdksslaevirt.ne 98 
                  E  ai k+lg+ ++    l+e+ l++Y+ ++++k +l++ +++ n+
   AHX11677.1 323 ESNAISKELGYlDIVsaGLKED-LNNYDTQSQEKIKLYKLFQSpNK 367
                  7778999997766652245555.6778889999999***9999776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       673  (0.037537); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.23s 00:00:00.75 Elapsed: 00:00:00.42
# Mc/sec: 3116.62
//
Query:       AHX11678.1  [L=183]
Description: hypothetical protein NHE_0746 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
  ------ inclusion threshold ------
       0.02   14.9   0.8      0.036   14.1   0.8    1.5  1  SK_channel  Calcium-activated SK potassium channel
        0.2   11.9   0.2        0.2   11.9   0.2    2.1  3  DUF2560     Protein of unknown function (DUF2560)


Domain annotation for each model (and alignments):
>> SK_channel  Calcium-activated SK potassium channel
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.1   0.8     4e-06     0.036      48     103 ..       2      57 ..       1      62 [. 0.87

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 4e-06
  SK_channel  48 vslalkvlislsTviLLvlivlyhaaeiqlflidngaedwrvalsserilkillEl 103
                 + + lk ++ ls+++LL+++v++++++ +  ++   +++w v  + + i k+  E+
  AHX11678.1   2 AKHYLKHIVLLSSILLLCFVVFHYTNQFKETITLLKINQWEVSKQRSDIDKMKAEI 57 
                 5689************************9999999999999988888877777665 PP

>> DUF2560  Protein of unknown function (DUF2560)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.2   2.2e-05       0.2       7      63 ..      51     109 ..      46     112 .. 0.85
   2 ?   -3.4   0.0       1.3   1.2e+04      27      41 ..     122     136 ..     118     139 .. 0.72
   3 ?   -1.6   0.1      0.36   3.2e+03       9      18 ..     166     175 ..     162     177 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.2e-05
     DUF2560   7 qqfkLelykLvlnqnAAAeeAf.qFigtDeLkleLFkihyqkggansdiv.aRtveAvR 63 
                  ++k e+ kL+  ++ A +  f + +++  L +eL ++ y+  + n +i  +  +eA R
  AHX11678.1  51 DKMKAEIKKLITEDSLATQVIFsNSVENLTLLFELIRDDYELENYNFQIEnSEKIEALR 109
                 69******************994479999***********9999998885256677777 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 1.3
     DUF2560  27 AfqFigtDeLkleLF 41 
                  + F  + ++k+ +F
  AHX11678.1 122 SLSFSVDSKMKFYMF 136
                 567777888898888 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.36
     DUF2560   9 fkLelykLvl 18 
                 +kLe+y L +
  AHX11678.1 166 LKLEIYTLKM 175
                 6888888755 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (183 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1177  (0.0656478); expected 358.6 (0.02)
Passed bias filter:                      556  (0.0310112); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 1372.42
//
Query:       AHX11679.1  [L=256]
Description: hypothetical protein NHE_0747 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.044   13.4   0.1      0.067   12.8   0.1    1.2  1  Dip       gp37/Dip protein


Domain annotation for each model (and alignments):
>> Dip  gp37/Dip protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.1   3.7e-06     0.067      13      58 ..     115     160 ..     106     179 .. 0.89

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 3.7e-06
                 HHHTTSTTB-S------EEEEEEEETTTTEEEEEEEESSSCEEEEE CS
         Dip  13 qalskldglhhphkledisvhwvfnpvdisvfvtcatmsshnthyt 58 
                  a  +l+gl+h  +l  i     f    is++ t+at+ +hn h  
  AHX11679.1 115 LAAKNLQGLKHKLRLSRICTAVFFFYSAISIIATAATFITHNVHAK 160
                 567789*************************************964 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1003  (0.0559429); expected 358.6 (0.02)
Passed bias filter:                      640  (0.0356964); expected 358.6 (0.02)
Passed Vit filter:                        64  (0.00356964); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 1901.30
//
Query:       AHX11680.1  [L=323]
Description: ferrochelatase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.6e-89  300.1   0.0    1.9e-89  299.9   0.0    1.0  1  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  299.9   0.0     1e-93   1.9e-89       1     315 [.       3     301 ..       3     303 .. 0.96

  Alignments for each domain:
  == domain 1  score: 299.9 bits;  conditional E-value: 1e-93
                     .EEEEEEE----SSCCCHHHHHHHHCT-TTTS-S-TTTHHHHHHHHHHHHHHHHHHHHHHTTSS-SHHHHHHHHHHHHHHHHHHH---EEEEEEE CS
  Ferrochelatase   1 ktavLLlnlGgPekpedvrpflenllsdrrvielplllqkllaklilkerlekvaekYekigggSPlneitrkqaealekelaergidvkvylam 95 
                     k av+LlnlGgP++ e+v pfl nl+ drr+++lp +++ lla++i+ +r  +++  Y ++gg+SP++  trkqa+al++ l+     ++v++am
      AHX11680.1   3 KRAVVLLNLGGPDSIEAVGPFLFNLFYDRRILDLPNPFRYLLARWISYKRCTEARSIYGRLGGKSPILLETRKQAAALCEVLGGG---YEVFVAM 94 
                     68********************************************************************************985...******* PP

                     SSSSSBHHHHHHHHHCTT-SEEEEEES-SS--TTTHHHHHHHHHHHHHHTT-SSEEEEE---TT-HHHHHHHHHHHHHHHTTS-.HC.C-EEEEE CS
  Ferrochelatase  96 rywePsiedaleelkadgvervvvlplyPqysasttgssleeleralkkkreapevrvirqfydhpgyiealaesikealeelp.eekkakllfs 189
                     ryw+P+i++ + +l++ ++ +v++lplyPq+s++t+ ss+e++ + l+      ++rv++++y hp +iea++e+i  +++ +   + k ++lfs
      AHX11680.1  95 RYWHPFIHESIPRLNSGEFSEVILLPLYPQFSSATSLSSIEQCLDLLRV-----PTRVVCCYYSHPLFIEAHVEMILSYYNVALdFG-KPVILFS 183
                     **********************************************965.....79*************************875344.69***** PP

                     EE--BHHHHT.TT-SHHHHHHHHHHHHHHHTTT-S.-EEEEEE---SSS-BSSSBHHHHHHHHCCC.-S-EEEE-TT-SS--HHHHIIIIIIIIT CS
  Ferrochelatase 190 aHglPeravkkkgdpYqqqveetarlvaealglke.evelayqSrvGpeeWlePdtddtleelaekgvkaivvvpigFvsDhlEtleeldieare 283
                     aHglP ++v ++gdpYq q+e+ ++ +++++g+ke ++e++yqS+vG  +WlePdt ++++++ +   +++vvvpi+Fvs+h+Etl+eld e+  
      AHX11680.1 184 AHGLPLKMV-EEGDPYQFQIESCVERIVSRIGIKElDWEICYQSKVGGRKWLEPDTITVIKKYSN---RSLVVVPIAFVSEHSETLVELDLEYSV 274
                     *********.57***************************************************99...77************************* PP

                     TSTT..CCCEEE----TT-HHHHHHHHHHHHH CS
  Ferrochelatase 284 laeeaggekfvrvptlndspafiealadlvee 315
                     lae+     f rvp+l  +++f+e+la+l+ e
      AHX11680.1 275 LAEH-----FFRVPALSVHAKFVECLAQLCSE 301
                     9986.....9******************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (323 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       405  (0.0225891); expected 358.6 (0.02)
Passed bias filter:                      316  (0.0176251); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.27s 00:00:00.70 Elapsed: 00:00:00.42
# Mc/sec: 2290.23
//
Query:       AHX11681.1  [L=316]
Description: hypothetical protein NHE_0749 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (316 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       719  (0.0401026); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2398.73
//
Query:       AHX11682.1  [L=53]
Description: ribosomal S20 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.8e-11   43.9   0.9      3e-11   43.8   0.9    1.0  1  Ribosomal_S20p  Ribosomal protein S20


Domain annotation for each model (and alignments):
>> Ribosomal_S20p  Ribosomal protein S20
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.8   0.9   1.7e-15     3e-11      35      82 .]       2      50 ..       1      50 [. 0.95

  Alignments for each domain:
  == domain 1  score: 43.8 bits;  conditional E-value: 1.7e-15
                    HHHHHC.-HHHHHHHHHHHHHHHHHHHCTTSSTCCHHHHHHHHHHHHHH CS
  Ribosomal_S20p 35 raaiea.dkekaqealkkaiskidkaakkgvihkNtAaRkkSrlakkin 82
                    r+ai++ +k+ a eal++a+ ++++ ++k v+hkN+AaR  Srl+k+i+
      AHX11682.1  2 REAIATgTKDVAVEALRVAQPEVHRGVTKRVLHKNKAARIISRLSKHIK 50
                    8899778***************************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (53 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       383  (0.021362); expected 358.6 (0.02)
Passed bias filter:                      262  (0.0146132); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.26s 00:00:00.59 Elapsed: 00:00:00.40
# Mc/sec: 395.56
//
Query:       AHX11683.1  [L=439]
Description: UDP-N-acetylmuramate--alanine ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.5e-17   63.7   0.0    6.9e-17   61.6   0.0    2.1  2  Mur_ligase    Mur ligase family, catalytic domain
    1.1e-16   60.9   0.0    5.5e-14   52.2   0.0    2.9  3  Mur_ligase_C  Mur ligase family, glutamate ligase domain
    1.6e-16   60.9   0.0    3.7e-16   59.7   0.0    1.6  1  Mur_ligase_M  Mur ligase middle domain
     0.0087   16.1   0.5          3    7.9   0.0    2.9  3  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain


Domain annotation for each model (and alignments):
>> Mur_ligase  Mur ligase family, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.6   0.0   1.5e-20   6.9e-17       2      86 ..       6     100 ..       5     102 .. 0.95
   2 ?   -1.4   0.0      0.68     3e+03      23      48 ..     370     398 ..     368     415 .. 0.70

  Alignments for each domain:
  == domain 1  score: 61.6 bits;  conditional E-value: 1.5e-20
                 EEEESTTSCCHHHHHHHHHHTTSEEEEEESSHC.....HHHTT-EEEES-....HGGGGEE-T.S-TTCHHHHHHHHTTEEEEEHHHHHHHHHHC CS
  Mur_ligase   2 ihfigidgrgmsagalflalkGykvdGsdfies.....lialGaaavvgh....daanivvss.iskdnpeleaakepgipvesraeaLaelaar 86 
                 +h+igi+g+gms++a+ l ++Gy+v+Gsd+ +      l  +G+++v+g     da+ i++s+ +++d+pel++a+ +g p+ +r e+L  l+++
  AHX11683.1   6 LHIIGICGIGMSGIAQALKNQGYTVQGSDADPGdtahlLARAGIRVVHGLsyigDADFIIYSNaVPEDHPELQYARLLGKPLLRRWEILKFLLQD 100
                 69*********************************************998888899999****************************99988876 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.68
                 TSEEEEEESSHC...HHHTT-EEEES-HG CS
  Mur_ligase  23 GykvdGsdfies...lialGaaavvghda 48 
                 G+k  G d ++    ++++Ga+ v+  + 
  AHX11683.1 370 GEKPNGYDSEQLccsAREQGATKVFHAKN 398
                 55566666666677799999987655444 PP

>> Mur_ligase_C  Mur ligase family, glutamate ligase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.3   0.0    0.0051        23      37      79 ..      97     135 ..      90     144 .. 0.78
   2 !   52.2   0.0   1.2e-17   5.5e-14       1      87 [.     293     373 ..     293     377 .. 0.93
   3 ?   -2.3   0.0       1.2   5.4e+03      56      78 ..     398     419 ..     393     425 .. 0.68

  Alignments for each domain:
  == domain 1  score: 5.3 bits;  conditional E-value: 0.0051
                   HSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSE.EEEEE CS
  Mur_ligase_C  37 iapdkrlilvfgpggelgertrtfhdefgrlasalads.lvvlg 79 
                   + +dk++i+v g+  + g+ t t  +++g+++ ++  +  +++g
    AHX11683.1  97 LLQDKEVIVVSGC--H-GKTTTT--AMIGEILTDAGKDpTIICG 135
                   46799********..7.445555..*******998888777766 PP

  == domain 2  score: 52.2 bits;  conditional E-value: 1.2e-17
                   CTTSSEEEEETTTEEEEEET--SHHHHHHHHHHHHHHSSSSEEEEEEEESTT.CCSCHCTHHHHHHHHCCHSSEEEEEESS-TTSTH CS
  Mur_ligase_C   1 vkgRlevvgeadgvtvidDyahnpdslsaalkalreiapdkrlilvfgpggelgertrtfhdefgrlasaladslvvlgdypraeds 87 
                   v +R+  +ge  g +v+ Dyah+pd++  + +al ++   ++lilv++p  ++++r ++f+++   l  + +  l++l++yp++e++
    AHX11683.1 293 VFRRMTFIGELLGSKVFTDYAHHPDEILSTADALSHM---GKLILVVQP--HRYSRVAKFFERYSSLWRK-VNALIFLDIYPAGEKP 373
                   569*******************************666...9********..******************9.6678888******986 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 1.2
                   SCHCTHHHHHHHHCCHSSEEEEE CS
  Mur_ligase_C  56 rtrtfhdefgrlasaladslvvl 78 
                   ++++ +d++ ++  +  +++v++
    AHX11683.1 398 NDKETYDRIVEINTK-GAIIVFM 419
                   577888888888888.5554443 PP

>> Mur_ligase_M  Mur ligase middle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   59.7   0.0   8.2e-20   3.7e-16       1     191 [.     106     272 ..     106     273 .. 0.78

  Alignments for each domain:
  == domain 1  score: 59.7 bits;  conditional E-value: 8.2e-20
                   EESSS-HHHHHHHHHHHHHCTEE.EEETTCSS-THHHHHHHHHHHHHTT-SEEEEE--HCHHHCTTTCCHCBESEEEE---TSTTHHHHSSHHHHHH CS
  Mur_ligase_M   1 vTGtnGKTTtteliaailekagk.vigtvgttnneiglpktlaemekkeaeyavlEvsshglgekrlegllkpdvavitnispdHldfhgtlenyae 96 
                   v G +GKTTtt +i +il++agk  + + g   +        ++++  +  ++v+E  ++    +   +ll+ d av+tni+ dH+++h+++ n  +
    AHX11683.1 106 VSGCHGKTTTTAMIGEILTDAGKdPTIICGGVMQRF-----GNNVRLGKSSLYVVEGDES----DDTFSLLPRDFAVVTNIGDDHMEYHQDVWNLEK 193
                   79*******************884666666533333.....34444478899*******9....455555999************************ PP

                   HHHHHHHTSETTCEEEEETTSC...CHHHHHCTCCTCEEEEESSSTSECEEEEEEEEETTEEEEEEEEETTEEEE.EEESSCSCHHHHHHHHHHHH CS
  Mur_ligase_M  97 aKaelferlkeegiavinaddpyakelikklkkakvkvvtfglekeaedlraknieeksegteiellevkggele.ieipllGkhnvyNalaaiaa 191
                    + +++++ k    a+i + +          + +++  + ++le++a+  r + +e   eg ++++  +k +e++ + ++ lG +nv+Na+aaia+
    AHX11683.1 194 KFLRFISNTK----AIIPNLKC-------FFSVEGF-RYDYDLESNAS--RIAMVEP--EGLKMRFR-YKLDEYHdFLLNALGLFNVKNAMAAIAC 272
                   *******999....67763333.......3334433.47899999994..4555555..78887666.87777776999***************97 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.9   0.0   0.00067         3      18      41 ..      18      41 ..      16      59 .. 0.83
   2 !    5.0   0.3    0.0055        25      10      28 ..     110     128 ..     103     133 .. 0.87
   3 ?   -2.5   0.0       1.1     5e+03      34      55 ..     221     279 ..     218     359 .. 0.59

  Alignments for each domain:
  == domain 1  score: 7.9 bits;  conditional E-value: 0.00067
                HHHHHHHHTT--EEEEEEEESSCC CS
                xxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA 18 nLaralarrglrVllvDaDpqann 41
                ++a+al+++g+ V+  DaDp  ++
  AHX11683.1 18 GIAQALKNQGYTVQGSDADPGDTA 41
                689*****************9444 PP

  == domain 2  score: 5.0 bits;  conditional E-value: 0.0055
                 SSHHHHHHHHHHHHHHTT- CS
                 xxxxxxxxxxxxxxxxxxx RF
        CbiA  10 vGKTtlaanLaralarrgl 28 
                  GKTt++a ++ +l ++g+
  AHX11683.1 110 HGKTTTTAMIGEILTDAGK 128
                 6*************99987 PP

  == domain 3  score: -2.5 bits;  conditional E-value: 1.1
                 EEEESSCCCCH....HTTEB-HHHH.....................................C CS
                 xxxxxxxxxxx....xxxxxxxxxx.....................................x RF
        CbiA  34 DaDpqannlai....leglendiep.....................................d 55 
                 D D ++n+++i     egl+                                          +
  AHX11683.1 221 DYDLESNASRIamvePEGLK----MrfrykldeyhdfllnalglfnvknamaaiactyscgvG 279
                 66666666665333322222....122223334444444444444444444444444444442 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (439 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       402  (0.0224218); expected 358.6 (0.02)
Passed bias filter:                      384  (0.0214178); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3324.67
//
Query:       AHX11684.1  [L=238]
Description: orotidine 5'-phosphate decarboxylase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    7.9e-32  110.7   0.0    8.9e-32  110.5   0.0    1.0  1  OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS famil


Domain annotation for each model (and alignments):
>> OMPdecase  Orotidine 5'-phosphate decarboxylase / HUMPS family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  110.5   0.0     5e-36   8.9e-32       2     225 .]       4     221 ..       3     221 .. 0.93

  Alignments for each domain:
  == domain 1  score: 110.5 bits;  conditional E-value: 5e-36
                 EEEEEE-SSSHHHHHHHHHHHGGGSSEEEEEHHHHHHHTHH.HHTHHHHHHHHHTSEEEEEEEE-S-HHHHHHHHHSTCHHHHTTESEEEEEGTGHHHH CS
   OMPdecase   2 nLclalDvatarelleladkvgpsivvlKthydlvegwgfegtgaklaalarkhgflifeDrKfaDIGntvekqatagsarikewadivtvhavaGkas 100
                 +++ a+D ++     +l+  + ++i v+K + +++++ g      + ++++++ g +if+D+K++DI+ntv+k ++  ++r + ++ ++tvh+  Gk++
  AHX11684.1   4 KIVCAIDNPDFGYSYSLVASISDHIHVVKLGSEFFSSCG-----ISGVEKIASIGLPIFLDLKLHDIPNTVSKTIE--VIRKIRGIKFLTVHITGGKEM 95 
                 678899*****99**************************.....9******************************9..99******************* PP

                 HHHHHHHHHHTTS.EEEEEESTSSGGHHHHHH.H..SHHHHHHHHHHHHHHHTTESEEECCCHTH.HHHHH.TTCSCEEEHHHTTEEEEECTTCCGGGH CS
   OMPdecase 101 vkalaeaaekwgnrgllilaqmsskgnlmlqe.k..gytqacveaarehkaedfvmGfvaqetln.ateed.addfihltpgigleqggdgkgqqyntp 194
                 + a+ +a+  ++  +ll +  ++s  +++l + +  +   + v++++   ++++++G++++ ++    +++ ++dfi++ pgi     +   +q++   
  AHX11684.1  96 ILAARRALVNTK-ICLLGVSALTSLSQEDLISnRirEPLPEYVKNLSLFGKNCGLDGVICSVQESlLVRQAcGKDFIIVAPGISS---SSLSDQKRVVD 190
                 ***********7.9******************757899**************************984445569**********96...88888888877 PP

                 HHHHHHTTCSEEEESHHHHTSSSHHHHHHHH CS
   OMPdecase 195 ekligiagadiiivGRgIlkagdpveeaery 225
                      +++ad++++GR+I++a+ p   a+r+
  AHX11684.1 191 IFNLPVNEADYVVIGRAITQAPCPLDVARRI 221
                 77778899****************9999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (238 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       316  (0.0176251); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1936.94
//
Query:       AHX11685.1  [L=225]
Description: integral membrane TerC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.3e-33  116.2  18.4    1.8e-33  115.7  18.4    1.2  1  TerC           Integral membrane protein TerC family
    6.6e-05   22.8  14.8    9.1e-05   22.4  14.8    1.3  1  DUF475         Protein of unknown function (DUF475)
  ------ inclusion threshold ------
       0.99    9.4   6.5       0.74    9.8   1.0    2.8  2  TB2_DP1_HVA22  TB2/DP1, HVA22 family


Domain annotation for each model (and alignments):
>> TerC  Integral membrane protein TerC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.7  18.4     3e-37   1.8e-33       3     180 ..      11     189 ..       9     190 .. 0.90

  Alignments for each domain:
  == domain 1  score: 115.7 bits;  conditional E-value: 3e-37
        TerC   3 lvlleivLsiDNlvviallvkklpeeqqkkalllGilgAlvlRillillavallel.........f.dlilligglfLlytavkellekrlenklvkee 91 
                 l++leivL+iDN+++i++++++l+e+  + ++++G+ +Al++R++++++++ ll+l         + d+i++igglfL +++++e++++      + + 
  AHX11685.1  11 LLFLEIVLGIDNIIFISVVTSRLHEN--SGIRYFGLGLALFFRLVALFSVSTLLKLkqpvfyalsIqDVIFIIGGLFLSFKGLSEIIHDA-----KPKI 102
                 789********************876..6899************************99998887626*******************9854.....2333 PP

        TerC  92 kkkkkktkstllavviqielaDlvfslDSvlaavaitsdlfivitavilsilvlrflakllakllerfptlkylalalllligvklvle 180
                 +++ k+ +   l++v+ i+++Dlvfs+DS l+a+ait++++++ +a+ + i+++ +++++++k+++ fp lk+lal+++  ig+ l+++
  AHX11685.1 103 NNEFKVYS--KLSAVLYIAFIDLVFSIDSLLTALAITQNMLLIALAFSVTIVFMGVASDVVSKWITLFPELKTLALVFITSIGIVLLFD 189
                 33333333..3689999*********************************************************************986 PP

>> DUF475  Protein of unknown function (DUF475)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.4  14.8   1.5e-08   9.1e-05      81     225 ..       6     154 ..       2     211 .. 0.83

  Alignments for each domain:
  == domain 1  score: 22.4 bits;  conditional E-value: 1.5e-08
      DUF475  81 gmflllvfldfllddrdikWlkwiekplak...lgklda.vsvvivlvlllllaallakkaeqrqkvllagllgll..tyllvdglerlfekdeaakaa 173
                 ++f +l+fl+ +l  ++i +++++   l++   ++ ++  +     lv+l  +++ll+ k+  ++++++  ++ ++  ++l  +gl++++++++  ++ 
  AHX11685.1   6 SAFCILLFLEIVLGIDNIIFISVVTSRLHEnsgIRYFGLgLALFFRLVALFSVSTLLKLKQPVFYALSIQDVIFIIggLFLSFKGLSEIIHDAK--PKI 102
                 789*********************99998722245555424556677888899999999************99999555888899****99954..555 PP

      DUF475 174 avraagkaglalflylevldasfsfdGviGafaitkdivlialGlgigamfv 225
                   +    + l + ly+ ++d  fs+d ++ a+ait++++lial ++++ +f+
  AHX11685.1 103 NNEFKVYSKLSAVLYIAFIDLVFSIDSLLTALAITQNMLLIALAFSVTIVFM 154
                 667778889999**********************************999997 PP

>> TB2_DP1_HVA22  TB2/DP1, HVA22 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.3      0.05     3e+02      20      37 ..       1      18 [.       1      29 [. 0.82
   2 ?    9.8   1.0   0.00012      0.74      26      58 ..     146     179 ..     132     188 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.05
  TB2_DP1_HVA22 20 wltYWvvfafltvvesla 37
                   +l+Y+  f++l+++e ++
     AHX11685.1  1 MLDYFSAFCILLFLEIVL 18
                   589***********9987 PP

  == domain 2  score: 9.8 bits;  conditional E-value: 0.00012
  TB2_DP1_HVA22  26 vfafltvvesla.dvllswiPfYylfKllfllwl 58 
                     f++  v+  +a dv+ +wi+++ ++K+l+l+++
     AHX11685.1 146 AFSVTIVFMGVAsDVVSKWITLFPELKTLALVFI 179
                    577778888888799999*************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       822  (0.0458475); expected 358.6 (0.02)
Passed bias filter:                      252  (0.0140554); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.38
# Mc/sec: 1782.51
//
Query:       AHX11686.1  [L=37]
Description: hypothetical protein NHE_0754 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       334  (0.018629); expected 358.6 (0.02)
Passed bias filter:                      139  (0.0077528); expected 358.6 (0.02)
Passed Vit filter:                         8  (0.000446204); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.34
# Mc/sec: 321.81
//
Query:       AHX11687.1  [L=504]
Description: propionyl-CoA carboxylase, beta subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
   4.7e-171  569.7   0.0   5.7e-171  569.5   0.0    1.0  1  Carboxyl_trans  Carboxyl transferase domain
    0.00015   21.3   0.0    0.00037   20.1   0.0    1.5  1  MdcE            Malonate decarboxylase gamma subunit (MdcE)


Domain annotation for each model (and alignments):
>> Carboxyl_trans  Carboxyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  569.5   0.0  6.4e-175  5.7e-171       5     494 .]      24     502 ..      21     502 .. 0.97

  Alignments for each domain:
  == domain 1  score: 569.5 bits;  conditional E-value: 6.4e-175
                     TCEEEEEEEEHTTSGGGEBEHHHHHHHHHHHHHHHHHT...EEEEEEEESBETTEEHHHHTTEEEEESSTTSGGGCEEECHHHHHHHHHTEEEEE CS
  Carboxyl_trans   5 rGkltareridllldpgsFgeledlffhrvtelgrkkklp.rdgvvtgsGaviGravevvaqdktvlggslgpakgekllkaqeeaikageplig 98 
                     + kl a er+++l+d+g F+ ++dl++hr++++g++k+++ +dgv+tg+G ++Gr+v+ ++qd+ vlggsl+++++ k++k++++a+k++ p+ig
      AHX11687.1  24 NSKLSASERLEILFDNGEFTRIDDLVQHRCMNFGLEKRIVdGDGVITGYGYIKGRKVFAYSQDFSVLGGSLSEKNAGKICKIMDLAAKTRSPIIG 118
                     5688899****************************66554289**************************************************** PP

                     EEEE-ESSSGHHSSHHHHHHHHHHHHHHHHHHHCS-EEEEESSEEETHHHHHHHHTSEEEEETTEEEEESSTHHHHHHHHSSCC-SSCHHHHSHH CS
  Carboxyl_trans  99 indsgGaegriqegveslrgsGkifgenskasgeIpqislvtgrcaGggaYlpalgdrvimveetskifltGpdvikkvlgreevtseelgGatq 193
                     indsgGa  riqegv+sl+g+G+if++n+++sg++pq+sl++g+caGg++Y+pal+d+++mv++ts++f+tGp+v+k+vl  e+ t++elgG ++
      AHX11687.1 119 INDSGGA--RIQEGVDSLAGYGEIFRRNVQLSGVVPQLSLIMGPCAGGAVYSPALTDFIFMVKNTSYMFVTGPKVVKTVLR-EDLTQDELGGTDV 210
                     *******..***********************************************************************9.************* PP

                     HHTTTTSSSEEESSHHHHHHHHHHHHTTS-SSTTSGGSS----ECSSGSSSH.....HCS-CTTTS---HHHHHHCEECTTC-EEESTTSSTTEE CS
  Carboxyl_trans 194 hmtksGvahltaeddeealelirkllsylPkkasnnresaPivetadepdrd...lieivPdnakkpyDvreviarlvdegeFlEikegyAktvV 285
                     h++ksGv++ ++++d e l ++r+++ +lP   +nn e++ + +++d++dr+   l+   P  ++ pyD++ +i +lvd+g F+E+ +++Ak+++
      AHX11687.1 211 HTKKSGVCDKAFANDAELLISVRDFIDFLP---QNNCEPSRKNSCNDPVDRQtewLNYSKPMVSNLPYDMKGIIGALVDDGYFFELGSEFAKNIL 302
                     ******************************...99999**************9988899************************************ PP

                     EEEEEETTEEEEEEEE--SEEETTEE-HHHHHHHHHHHHHHHHTT--EEEEE-BSEE--SHHHHHTTHHHHHHHHHHHHHT--S-EEEEE-TEEE CS
  Carboxyl_trans 286 vGfArlgGipvGvvAnetrveaGqvlfidsavKaarfirlcdaenlPlviladvrGflvGqrqeyggilkhGaklvdalaeakvPkitvilrkay 380
                     +GfAr+gG  +G+vAn++ v aG +l+i+s+ Ka rf+r+cda+n+P+++l+dv+Gfl+G+ qe++ i+khGakl++a+aea+vPk+t+i++kay
      AHX11687.1 303 TGFARIGGMNIGIVANQPLVLAG-CLDINSSRKAGRFVRFCDAFNIPILTLVDVPGFLPGSVQEQNAIIKHGAKLLYAYAEATVPKVTLIVKKAY 396
                     ***********************.*********************************************************************** PP

                     HHHHHTTTGGGSTTTTEEETTT-EEESS-HHHHHHHHSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSHHHHHHTTSSS CS
  Carboxyl_trans 381 GGayvvmdskingadlvaawptariaVlgpegaveilfrkekaaaemerkdlaaerkkklkeyeeellnpyvaaargfaDavidpsetraklvia 475
                     GGay+vm+sk++ +d+++awp+a++aV+gpe avei+f++e+ +          ++++   ey+ +++np+v a+rg++D +i+p++ r+k++ a
      AHX11687.1 397 GGAYIVMGSKHLASDVNLAWPEAEVAVMGPEAAVEIIFKREISTPG--------RAAELALEYKAKFANPKVPASRGYIDSIITPADSRRKIIEA 483
                     *****************************************98776........2367788********************************** PP

                     EEEHGGGHHHHHHHHHHHH CS
  Carboxyl_trans 476 lelewkkarklparkrrni 494
                      e++  k+ +  ++k++n+
      AHX11687.1 484 FEMLSGKESTTLWKKHDNL 502
                     ****************985 PP

>> MdcE  Malonate decarboxylase gamma subunit (MdcE)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   4.1e-08   0.00037      65     150 ..     347     432 ..     341     446 .. 0.88

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 4.1e-08
                 -EEEEEEEE--B--SHHHHHHTHHHHHHHHHHHHHHHHHHT--EEEEEEEEEEHHHHHHTT...TT-SEEEEEET-EEESS-HHHHHHH CS
        MdcE  65 rpilvlvDvasQrlgrrdEllGihealahlakalarArlaGhpvigllvGkavsGaflahg...lqanrlialpgvqvavmdkasaArv 150
                  pil lvDv++   g  +E   i +  a l  a+a A +   p ++l+v ka  Ga++ +g   l++++ +a p+++vavm+  +a  +
  AHX11687.1 347 IPILTLVDVPGFLPGSVQEQNAIIKHGAKLLYAYAEATV---PKVTLIVKKAYGGAYIVMGskhLASDVNLAWPEAEVAVMGPEAAVEI 432
                 59******************9999999999999999876...9***************887555889999************9988765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (504 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      329  (0.0183502); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.38
# Mc/sec: 3992.70
//
Query:       AHX11688.1  [L=169]
Description: hypothetical protein NHE_0756 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (169 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1147  (0.0639746); expected 358.6 (0.02)
Passed bias filter:                      492  (0.0274416); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1280.41
//
Query:       AHX11689.1  [L=425]
Description: outer membrane efflux family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-46  159.0   7.5    1.5e-26   93.4   5.5    2.0  2  OEP       Outer membrane efflux protein


Domain annotation for each model (and alignments):
>> OEP  Outer membrane efflux protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.7   0.0   2.6e-22   4.6e-18       1     187 [.      21     206 ..      21     207 .. 0.94
   2 !   93.4   5.5   8.1e-31   1.5e-26       1     179 [.     229     406 ..     229     414 .. 0.96

  Alignments for each domain:
  == domain 1  score: 65.7 bits;  conditional E-value: 2.6e-22
         OEP   1 ldellalalennpdlkaaeaeieaaeanlkaakaeflPtlslsgsygyegngsegggddggtgttsvgltlsqplfdggkrrarvkaakaqleaaeaql 99 
                 l ++l+ al+nn d++    + e +  + k+a ++ lPt +l++sy+  g+ ++  g ++ t+ + +g+ +  +l +  +  +r+ +ak +   a+  +
  AHX11689.1  21 LKDALRDALANNDDIAVISRQSELSSLQSKIALSDLLPTAALGLSYDLHGELWSPIGIGSLTN-PGIGIVVKHNLSSLIAPTSRLLMAKHDHLSAKFLH 118
                 67999***********************************************99888766444.49********************************* PP

         OEP 100 eqarqqlrlevaqaylqlllakeqlelaeealklaekalelaearykaGlislldvlqaqvrllqaraelaeaeqqlqlaraqLeyll 187
                 ++a+ ++ l+v +ayl++  ++e+l+l++e+++++e +l+++ +++k+G++++ +++ a++rl++a+++++ ae++ ++++  ++yl+
  AHX11689.1 119 ADAVHKILLQVIEAYLGVIESEETLALYKESIRALEMHLDAVHRALKLGESTKGELAYAKARLSSAKSQYLRAENSAEKSKDFFSYLT 206
                 *****************************************************88********************9988776655555 PP

  == domain 2  score: 93.4 bits;  conditional E-value: 8.1e-31
         OEP   1 ldellalalennpdlkaaeaeieaaeanlkaakaeflPtlslsgsygyegngsegggddggtgttsvgltlsqplfdggkrrarvkaakaqleaaeaql 99 
                 l+++++lal+nn  lka++   e+a+  +++a ++++P++s+ +s++y  ++    +   + ++ +  l++ +plf+ggk++  v++a  ++   e ++
  AHX11689.1 229 LNDVMKLALANNMTLKASKSSRESAKLKIAEAIGNWMPSVSVETSFQYAPSTRVVADGVRYLSS-QTVLNIGLPLFTGGKNSIVVAMAYENKALKEHEY 326
                 6899************************************************999887777776.9********************************* PP

         OEP 100 eqarqqlrlevaqaylqlllakeqlelaeealklaekalelaearykaGlislldvlqaqvrllqaraelaeaeqqlqla 179
                  +    l++ev++a++++++++ ++++ ++++++ + a++ +++ +++ l s l+v++a+ +ll+ar++l++a++ +++a
  AHX11689.1 327 SAKNKLLEQEVREAWNNYRNSESLVAASRDLVDAHDIAFKSIKQEAQLNLKSNLNVIDAELELLKARIQLRQAQSGRIIA 406
                 ***************************************************************************99887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (425 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1000  (0.0557756); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.52u 0.24s 00:00:00.76 Elapsed: 00:00:00.40
# Mc/sec: 3190.78
//
Query:       AHX11690.1  [L=421]
Description: 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-97  326.7   0.0      2e-97  326.4   0.0    1.0  1  GcpE      GcpE protein


Domain annotation for each model (and alignments):
>> GcpE  GcpE protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  326.4   0.0  1.1e-101     2e-97       4     350 ..      17     409 ..      14     410 .. 0.90

  Alignments for each domain:
  == domain 1  score: 326.4 bits;  conditional E-value: 1.1e-101
                 EEETTEEESTTS--EEEEE--S-TT-.......HHHHHHHHHHHHHCT-SEEEEEE-SHHHHHHHHHHHHHHHHTT-S.S-EEEEE-SSC.HHHHHHHH CS
        GcpE   4 vkvgkvkiGgeapiavqsMtntdtad.......veatvkqikrlaeaGaelvRvtvqdeeeaealkeikeklkkkglk.vplvaDihfnp.klaleaae 93 
                 v v  vk+Gg++p+ vqsMt+ +  d       +e+  +++ +la+aG+el+R+++++e++a+a+  i+e l+k+g++ +plv+  +++  ++ ++ ae
  AHX11690.1  17 VDVAGVKMGGGNPVIVQSMTSGTRVDpnnilaiAEDESREALALARAGSELIRIAINSEKAAAAIPYIREALDKAGFEsIPLVGCGQYEVkQILETQAE 115
                 89999***************99988877777777777889999********************************98659*********9445555555 PP

                 C..C-SEEEE-TTTSSSTTHHHHHHHHHHHHHHHHT-EEEEEEEGGG--HHHHHH.HCCTH.............HHHHHHHHHHHHHHHHTT--..GEE CS
        GcpE  94 a..gvdkvRiNPGnigdgkkkeekvkelveaakekgtaiRiGvNhGSLskrllsk.ygdtp.............ealvesalefleilekldfk..div 174
                 a  ++ k+RiNPGnig g+k+++++++++e + +++ +iRiGvN+GSL+++ll+k ++d++             +alv+sal +++ +e+l++k  +iv
  AHX11690.1 116 AirSLGKMRINPGNIGFGSKRDANFDKVIELICKYDLPIRIGVNWGSLDQSLLQKiMDDNAkmekpasysdvlrSALVQSALISAKRAEELGLKsdKIV 214
                 566799*************************************************5555545677799999999*******************9645** PP

                 EEEE-SSHHHHHHHHHHHHHH--S-EEE--TT-ECHHHHHHHHHHHHHHHHHTT--SEE---ECS-C....CHHHHHHHHHHHHTTS--SS-EEEE--- CS
        GcpE 175 iSlKasnvvvmveayrllaeeldyplHlGvTEAGegedgriksavgigaLLaegiGdTiRvSLtedp....eeEvkvakeiLqalrlrksktelisCPs 269
                 iS+K+sn ++++++y  lae  +yplHlG+TEAG+g+ g+ik+++++++LL++giGdTiR SLt++p    ++Ev+++++iLq+++lr + ++++sCP+
  AHX11690.1 215 ISCKVSNFQDLISVYSSLAELSNYPLHLGLTEAGMGNPGIIKTTAALAVLLHNGIGDTIRASLTQKPgesrVTEVETCQAILQSMGLRAFAPQITSCPG 313
                 *******************************************************************999999************************** PP

                 -TTS-C.HHHHHHHHHHHHC.CCHH.........CG-EEEEESSTCCHHHHCCCSSEEEE..EBT.TCE.EEEETTEEEECEESSCHHHHHHHHHH CS
        GcpE 270 CgRtlf.dlqelveeveeal.ehlk.........kglkiavmGCiVNGpgEaadAdlGiv..ggk.gkv.slykkkevvkkvpeeeavdellelik 350
                 CgRt+   +q+l+ ++++++ ++l+         +++k+avmGC+VNGpgE ++A++Gi+  g + +kv +++ +++  +k++ ++++++ +++i 
  AHX11690.1 314 CGRTSGdYFQRLTYDLNAYImDNLSewkqkyrgvEDFKLAVMGCVVNGPGEGKHANIGISlpGYNeKKVaAIFIDGKPARKLTGDNILEKSKQIIM 409
                 *****9557888888888874445345577888899***********************975555444359*******************999885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (421 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       632  (0.0352502); expected 358.6 (0.02)
Passed bias filter:                      584  (0.0325729); expected 358.6 (0.02)
Passed Vit filter:                        46  (0.00256568); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 2960.18
//
Query:       AHX11691.1  [L=241]
Description: inositol monophosphatase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    1.8e-10   40.8   0.0    1.5e-09   37.8   0.0    2.0  1  Inositol_P  Inositol monophosphatase family


Domain annotation for each model (and alignments):
>> Inositol_P  Inositol monophosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.8   0.0   8.4e-14   1.5e-09      69     211 ..      57     185 ..      13     191 .. 0.71

  Alignments for each domain:
  == domain 1  score: 37.8 bits;  conditional E-value: 8.4e-14
                 HHCHHHHCCCT.SSSSSEEEEEEEEETHHHHHHT-SG-EEEEEEEETTEEEEEEEEETTTTEEECEETTTEEEETC....EEEEECTTSEGGGTEEEEE CS
  Inositol_P  69 geetlakgekseltedgltwivDPiDGTknFvrgipqvaVsigllvegkpvlGviaqPllgqlysaakgkGaflng....eklplsrappiseallvtl 163
                  e +l++ + + ++++ + +++ P+DG  nF+rgip ++Vs+ l + ++pv+ vi +Pl  +++ a +  Ga+l++     +l+      i+ +  ++ 
  AHX11691.1  57 LERDLRDYN-IATGSQ-YKIVIFPVDGKENFLRGIPEFTVSVLLKKGDEPVICVIEAPLSYTTFYAERSYGAYLEDlggiVRLK------IKTFTDIG- 146
                 344444444.777888.99*******************************************************9944333333......33333322. PP

                 ESSSSSSHHHHCHHHHHHHCCCCCHEEEBESSHHHHHHHHHHTSTSEE CS
  Inositol_P 164 favssrkdtseasllekvesavsaegvrsvgssalklaavaeGkaday 211
                    +++   +        +++  +e +r +g   l+ a++a+G+ada 
  AHX11691.1 147 ---NTVALLNY-----PENQFSFRE-CRLLGCDSLSAAYLASGRADAL 185
                 ...11111111.....112222233.5567777777777777777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (241 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      293  (0.0163422); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.27s 00:00:00.68 Elapsed: 00:00:00.43
# Mc/sec: 1697.66
//
Query:       AHX11692.1  [L=1049]
Description: hypothetical protein NHE_0760 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
  ------ inclusion threshold ------
      0.031   13.6   0.1       0.18   11.1   0.0    2.0  2  Herpes_UL36  Herpesvirus UL36 tegument protein


Domain annotation for each model (and alignments):
>> Herpes_UL36  Herpesvirus UL36 tegument protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.1   0.0     1e-05      0.18     123     184 ..     136     203 ..     130     230 .. 0.68
   2 ?   -0.7   0.0     0.039     7e+02      46     120 ..     859     944 ..     838     947 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 1e-05
  Herpes_UL36 123 ile.aadasndgnidyhelvlelsgdLlqvpaLa...eyvdFyrrsYekfldir..aaLeelradvrr 184
                  il+  +++sndgni+  +lv+ +sg     +  +   + + F ++sY kf++i+  ++L+e  +   +
   AHX11692.1 136 ILRdDFQTSNDGNIEKFHLVQDVSGSDGADSSFTfcnGVLRFTHNSYLKFISILspDRLKEIESSLAE 203
                  554269******************98766555532228899***********9744577776544322 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.039
  Herpes_UL36  46 krArqvvaarakvvlsaletvlafNPYtaensqllP.............PlallksitWidaFsaaAdtytklFgvsvekllaLlria 120
                  + Ar  +    + +   + +vl+ N Y+ +n                  P  ll+ i+ +  F +    +  lF vs  +l a l+++
   AHX11692.1 859 SEARSLLCKFYTSIAVPVPAVLKGNSYAFKNDDTYKfskrvaksyhlslPGTLLRHIESF--FLVFIRFFSLLFNVSFARLSARLHLR 944
                  567777777777777788899999999999887433345666677777788888888643..45556788999999999998888876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1049 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       902  (0.0503096); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.75u 0.28s 00:00:01.03 Elapsed: 00:00:00.45
# Mc/sec: 7077.90
//
Query:       AHX11693.1  [L=321]
Description: pyruvate dehydrogenase (acetyl-transferring) E1 component, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    1.4e-86  290.2   0.0    1.7e-86  289.9   0.0    1.0  1  E1_dh           Dehydrogenase E1 component
    1.6e-06   27.5   0.2    2.4e-06   27.0   0.2    1.3  1  DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
     0.0044   16.8   2.2      0.022   14.6   2.4    1.9  2  TPP_enzyme_C    Thiamine pyrophosphate enzyme, C-terminal TPP


Domain annotation for each model (and alignments):
>> E1_dh  Dehydrogenase E1 component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  289.9   0.0   2.9e-90   1.7e-86       2     296 ..      15     308 ..      14     311 .. 0.97

  Alignments for each domain:
  == domain 1  score: 289.9 bits;  conditional E-value: 2.9e-90
                 HHHHHHHHHHHHHHHHHTTSS-S-----TT-HHHHHHHHHTS-TTSEEEESS--HHHHHHTT--HHHHHHHHTT-T....TTSSGTT-.-E..BTT..B CS
       E1_dh   2 klvllrrvedaldalykrkkrigfyhlsagqealkvgiaaalekeDliiteYReagvllarglsleeilaeltgkv....kgkggsrhelmyaekesri 96 
                 k+  +rr+e+++ +ly   +  gf+hl++gqea++vg++  l++eD++it+YR++gv++arg + e i++el g++     gkggs+h + + +++  +
  AHX11693.1  15 KMLFIRRFEERAGQLYGMGEVGGFCHLYIGQEAVAVGVEYCLTEEDSVITSYRDHGVMIARGSPPEVIMSELLGRAsgcsGGKGGSMH-VFDVNRN--F 110
                 8999************************************************************************9999999*****.9988888..* PP

                 EEE-SSTTTHHHHHHHHHHHHHHHTS---EEEEEEGGGTT-HHHHHHHHHHHHTT--EEEEEEEESEETTEEHHHH-S---GGG..TTTTS-EEEEETT CS
       E1_dh  97 lggngivgaqvplvaGialaakiegkkevailliGDgAanqGdvyealnlaalwklpvifvveNNkygisTeaekasaskeladrargvgipglrVdgn 195
                 +gg+givgaqv+l+ G+ala+k++g ++v+++++GDgAanqG+vye++n+a lw+lpv++ +eNN+y ++ ++   sa+  l+ r+r + ipg  Vdg+
  AHX11693.1 111 FGGHGIVGAQVSLGTGMALACKYRGSDSVSVVYFGDGAANQGQVYESFNMAVLWNLPVLYAIENNMYSMGSAVGDVSATALLSCRGRSFDIPGYSVDGM 209
                 *************************************************************************************************** PP

                 SHHHHHHHHHHHHHHHHTTT--EEEEEEE--SS-SSTTSHSHSSSHHHHHHHHHHHH-HHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHHHHHHHHHHS CS
       E1_dh 196 DplavyeAvkfAaeraregkgpllielvtYRyggHsesDdpstyrtreeveevrkkkdpiqrlkelLvkkgvvseeelkeiekevrkeveeavkkaesk 294
                 D ++v  ++k A  + r+g gp+++e+ tYR+ gHs+sD p tyr+++ev + +k  dpi+ l+++L ++g ++     ei+++v+ +v e v  a+s+
  AHX11693.1 210 DLMEVVRVTKDALAHIRSGCGPAIVEYNTYRFRGHSMSD-PATYRSKDEVAAYKKR-DPIEALEKQLLDSGNIAPAAIAEIRENVKRRVAECVTYAQSS 306
                 ***************************************.99***99999998877.************************************999987 PP

                 -- CS
       E1_dh 295 ke 296
                   
  AHX11693.1 307 AF 308
                 65 PP

>> DXP_synthase_N  1-deoxy-D-xylulose-5-phosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.2     4e-10   2.4e-06     113     185 ..     117     189 ..      92     232 .. 0.91

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 4e-10
  DXP_synthase_N 113 sstsisaalGlavardlkgekkkvvaviGDgaltgGmafealnnigelkkkllvilNdNemsisknvGalsky 185
                      ++ +s ++G+a a +++g+++  v   GDga   G  +e++n +   +  +l  + +N  s+ + vG +s++
      AHX11693.1 117 VGAQVSLGTGMALACKYRGSDSVSVVYFGDGAANQGQVYESFNMAVLWNLPVLYAIENNMYSMGSAVGDVSAT 189
                     47889*****************99*9******************************************99864 PP

>> TPP_enzyme_C  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   2.4   3.6e-06     0.022       3      84 ..      92     177 ..      90     184 .. 0.76
   2 ?   -1.0   0.0      0.23   1.4e+03     119     152 ..     198     235 ..     196     236 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 3.6e-06
                   SHHHHHHHHHHTTSSSSEEECETTTS-TTTHHHHHHHHHHH...ST.TSEEEEEEEHHHHHHT..GGGHHHHHHTT-SEEEEEEE-SB CS
  TPP_enzyme_C   3 GcltlwaarllkvkrprsyltsgglgtmGyglpaAiGakla...kp.drevvaivGDGgflmi..lqelatavrrnlpitvvvlnNeg 84 
                   Gc+ +    +  +   r+++   g+g  G +++ ++G++la   +  d+  v++ GDG+       + +  av  nlp+++ + nN +
    AHX11693.1  92 GCSGGKGGSMHVFDVNRNFFG--GHGIVGAQVSLGTGMALAckyRGsDSVSVVYFGDGAANQGqvYESFNMAVLWNLPVLYAIENNMY 177
                   555555555533444677776..*****************755422478999*******765555788888999999****9999975 PP

  == domain 2  score: -1.0 bits;  conditional E-value: 0.23
                   HTTSEEEEESSH.HHHHHHHHHHHH....CSSSEEEEE CS
  TPP_enzyme_C 119 alGakgarvekadveeleealkeal....ekkgpalie 152
                   ++ ++g++v+  d+ e+ ++ k+al    +  gpa++e
    AHX11693.1 198 SFDIPGYSVDGMDLMEVVRVTKDALahirSGCGPAIVE 235
                   77888899999999999999999986666666777765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (321 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      387  (0.0215851); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.47u 0.25s 00:00:00.72 Elapsed: 00:00:00.42
# Mc/sec: 2310.73
//
Query:       AHX11694.1  [L=280]
Description: ubiA prenyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.3e-38  130.0  19.8    1.1e-37  129.7  19.8    1.1  1  UbiA      UbiA prenyltransferase family


Domain annotation for each model (and alignments):
>> UbiA  UbiA prenyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  129.7  19.8   6.2e-42   1.1e-37       2     249 ..      22     266 ..      21     274 .. 0.90

  Alignments for each domain:
  == domain 1  score: 129.7 bits;  conditional E-value: 6.2e-42
        UbiA   2 lipalvglalaaggspdlllllllllgtllaaaaanalNdyfDreiDadmertpnRPlvsGrispkealifaivllilgllllalllnpltallgllal 100
                 ++pal+ +al +   + +l + ++llg++++++a++++Nd++D+++Da+ +rt  RP++sG i   e+l +  ++l++g++l  +ll+  +++lg++++
  AHX11694.1  22 FFPALFVIALLGADLLAALWIPFFLLGAFVIRSAGCIINDIADHKFDAKIARTSARPIASGSIRITETLPLLGIFLLIGFSLT-FLLGAEAIILGVATM 119
                 6899***9999999999999***************************************************************.*************** PP

        UbiA 101 llyvvYtglrlKrrtllgtvvggiafglppllgwaavtgslsllalllalavflltwaialandlrdregDrkagiktlpvvl.Grkaarillalllav 198
                 l   +Y+  + Kr+ +++++v++++f +++l++  av+g ++ +a+++++a+f++t+ ++++++++d+ gD++ g+++++++  G k+ +   ++ +a+
  AHX11694.1 120 LGTAIYP--FAKRYFYYPQIVLAAVFNTGALFASIAVSGAIHGTAFFVYIACFFWTLYYDTIYAHQDKLGDKELGLHSISLTGfGSKTWLK-KYSRIAL 215
                 999****..*********************************************************************9988655555555.3444455 PP

        UbiA 199 lllallllllalllllylllalllaalallraarlvrrrdakkaakff..lfl 249
                  +la  +++++  l l+++ +l+ + ++  +    ++ +d+++++ +f  +++
  AHX11694.1 216 SFLA--FAGVLPSLNLLYYCCLAGLFFMEEKFTESLDLDDPQSCWNAFnsMKM 266
                 5555..56777777777777777777777888999999999999999977554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (280 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      222  (0.0123822); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.27s 00:00:00.72 Elapsed: 00:00:00.40
# Mc/sec: 2090.16
//
Query:       AHX11695.1  [L=142]
Description: flavin reductase like domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      9e-24   84.3   0.0    1.2e-23   83.9   0.0    1.2  1  Flavin_Reduct  Flavin reductase like domain
  ------ inclusion threshold ------
       0.08   12.2   0.0      0.088   12.1   0.0    1.1  1  RE_NgoFVII     NgoFVII restriction endonuclease


Domain annotation for each model (and alignments):
>> Flavin_Reduct  Flavin reductase like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   1.3e-27   1.2e-23       1     154 [.       1     141 [.       1     142 [] 0.93

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 1.3e-27
                    HTTS-EE-EEEEE.EETTEEEEEEESSEEEEETTTTEEEEEEETTSHHHHHHHHHSEEEEEEEBCCGHHHHHHTCS...SCCCCCCCCCCCEEECT CS
  Flavin_Reduct   1 mrrvaqpvavvttsvpptsplgatlssftslsldPplvafslrlpsstadalkeagefvinllsesqealadafsqksgprtddksifagltwees 96 
                    m++++++vavvtt + ++++ g+t+ssf+++sldPpl + +l +     + + +++ fvin+l e  ++    fs++          f+   wee+
     AHX11695.1   1 MSHFPTGVAVVTT-RFEGKRYGMTISSFCPVSLDPPLALYCLSKTANRFQPFFKSNDFVINILDETSAETSVLFSKND---------FS--AWEEE 84 
                    899**********.7789999*************************99*9999***********************32.........33..69999 PP

                    CCCSEEETTCSEEEEEEEEEEECCTTEEEEEEEEEEEEESTTECTTBEECCCCCEEEE CS
  Flavin_Reduct  97 ptgapallgalasleCqvvgsvelgdhelfigeVvavkvgddadeepLlywrrryagl 154
                     +    l+ a   + C++  ++e gdh ++++ V ++k + + + +pL+y+++ y+++
     AHX11695.1  85 FDDNLELKKATWCIYCTTQYRYEGGDHKIIVALVRECKPHIS-KAPPLIYYKSDYHSM 141
                    999999*******************************98888.5589********987 PP

>> RE_NgoFVII  NgoFVII restriction endonuclease
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   9.8e-06     0.088      84     136 ..      38      89 ..      15     114 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 9.8e-06
                 EEEEEET.TEEEEEEESXXSXXTTSXXXSBXEEEEEE.HHHHHHHHHHHHHHH CS
  RE_NgoFVII  84 lYiwkkdgkplsAliGSANlssnglrtrqrEtlvdldtedafkeldeyiqsll 136
                 lY+ +k  + ++ +  S+++ +n l +   Et+v +  ++ f+  +e +++ l
  AHX11695.1  38 LYCLSKTANRFQPFFKSNDFVINILDETSAETSVLFS-KNDFSAWEEEFDDNL 89 
                 8**********************************99.777777777766544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (142 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      300  (0.0167327); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.37
# Mc/sec: 1156.91
//
Query:       AHX11696.1  [L=151]
Description: dihydrodipicolinate reductase, family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-13   51.4   0.0    3.3e-13   49.8   0.0    1.8  1  DapB_N    Dihydrodipicolinate reductase, N-terminus
    2.8e-06   27.3   0.0    3.9e-06   26.9   0.0    1.3  1  DapB_C    Dihydrodipicolinate reductase, C-terminus


Domain annotation for each model (and alignments):
>> DapB_N  Dihydrodipicolinate reductase, N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   49.8   0.0   3.7e-17   3.3e-13      12     124 .]       1      90 [.       1      90 [. 0.96

  Alignments for each domain:
  == domain 1  score: 49.8 bits;  conditional E-value: 3.7e-17
                 HHHHHHHHHHHSTTEEEEEEEETTCSTTTTTBHHHHSSSS--S-BEBSSHHHHHHH-SEEEE-S-HHHHHHHHHHHHHTT-EEEE--SS--HHHHHHHH CS
      DapB_N  12 mGkevvkaveeaedlelvaavdrkeselegkdagellglgklgvavtddleevlekadvliDFTtpeavlenlklalekgvklViGTTGlseeelaele 110
                 mGk+++k++ee++++ l+a + r++                     +ddl+++++k+ v+iDF+tp+ + ++l+ + +++ +lV GTT    ++ ++l+
  AHX11696.1   1 MGKAILKLIEEDPGACLAASYGRNS---------------------SDDLDDFIRKSSVIIDFSTPQLMSALLDGLNSNPRPLVSGTTAH--NNFEKLN 76 
                 9********************9998.....................7*****************************************86..7889*** PP

                 HHTTTSEEEE-S-- CS
      DapB_N 111 elakkigvviapNf 124
                 el+ k++v++apN+
  AHX11696.1  77 ELSTKTAVLWAPNM 90 
                 *************9 PP

>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.9   0.0   4.3e-10   3.9e-06       1      49 [.      93     140 ..      93     151 .] 0.86

  Alignments for each domain:
  == domain 1  score: 26.9 bits;  conditional E-value: 4.3e-10
                 HHHHHHHHHHHHCCCSTTT-EEEEEEEESTT--SSS-HHHHHHHHHHH. CS
      DapB_C   1 GvnlllklveeaakllkeaydveiiEkHhnkKaDaPSGTAlalaeaiae 49 
                 G nl++ ++e+  ++l++ ++  i E+Hh++K D  SGTA  + + +++
  AHX11696.1  93 GSNLMIGFIESNLSHLSK-FETYISEMHHKHKRDPLSGTATLMQDILEK 140
                 779999****99999998.*********************999888773 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       387  (0.0215851); expected 358.6 (0.02)
Passed bias filter:                      361  (0.020135); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.36
# Mc/sec: 1240.46
//
Query:       AHX11697.1  [L=57]
Description: dihydrodipicolinate reductase, family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.9e-15   56.3   0.0    3.1e-15   56.2   0.0    1.0  1  DapB_C    Dihydrodipicolinate reductase, C-terminus


Domain annotation for each model (and alignments):
>> DapB_C  Dihydrodipicolinate reductase, C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   56.2   0.0   1.7e-19   3.1e-15      70     121 .]       2      53 ..       1      53 [. 0.97

  Alignments for each domain:
  == domain 1  score: 56.2 bits;  conditional E-value: 1.7e-19
                 -CCCCEEEECTTEEEEEEEEEESCHHHHHHHHHHHHHH.HCTSSEESHHHHH CS
      DapB_C  70 vgehevlfagegevieikhealsreiFaeGallaaewlakkkkglysmedvL 121
                  g+h+++f g+ge++ei h+a++r  Fa Ga++aa++la++++glysm+dvL
  AHX11697.1   2 HGKHSIIFVGDGETLEIIHTAENRGAFALGAMKAARFLATAPSGLYSMKDVL 53 
                 699***********************************999**********8 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       217  (0.0121033); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 474.28
//
Query:       AHX11698.1  [L=255]
Description: phosphate ABC transporter, ATP-binding protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.5e-30  104.7   0.0    7.4e-30  104.2   0.0    1.2  1  ABC_tran     ABC transporter
    2.9e-12   47.0   0.0    5.9e-07   29.6   0.0    2.1  2  AAA_21       AAA domain, putative AbiEii toxin, Type IV TA sy
    2.1e-08   33.9   1.0    1.4e-06   27.9   1.0    2.1  1  SMC_N        RecF/RecN/SMC N terminal domain
    2.6e-07   30.7   0.1    0.00043   20.1   0.0    2.1  2  AAA_15       AAA ATPase domain
    0.00069   20.2   0.0     0.0019   18.7   0.0    1.7  2  AAA_23       AAA domain
     0.0012   18.8   0.1     0.0036   17.2   0.0    1.8  2  RsgA_GTPase  RsgA GTPase
     0.0033   17.2   0.0     0.0063   16.2   0.0    1.4  1  AAA_29       P-loop containing region of AAA domain
     0.0041   17.4   0.1     0.0081   16.4   0.1    1.7  1  AAA_22       AAA domain
     0.0053   17.2   0.0     0.0083   16.5   0.0    1.5  1  AAA_16       AAA ATPase domain
  ------ inclusion threshold ------
      0.035   13.5   0.0        1.1    8.6   0.0    2.9  3  TniB         Bacterial TniB protein
      0.039   12.6   0.0       0.13   10.9   0.0    1.7  2  AAA_13       AAA domain
       0.05   12.8   0.1       0.11   11.7   0.1    1.6  1  NB-ARC       NB-ARC domain
      0.085   12.4   0.0       0.19   11.3   0.0    1.6  1  Ras          Ras family
       0.11   12.7   0.3        0.3   11.3   0.1    1.8  2  DUF5442      Family of unknown function (DUF5442)


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.2   0.0   5.8e-33   7.4e-30       1     136 [.      24     180 ..      24     181 .. 0.94

  Alignments for each domain:
  == domain 1  score: 104.2 bits;  conditional E-value: 5.8e-33
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--.....SEEEEEETTCEGGG..B-HHHCCHCEEEE-SS--S-TTSBHHHH............. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxx............. RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkp.....teGeilldgkdlke..qeleslrkeigvlpqepqlfpeltvren............. 79 
                 lk+v+l+++  +++ ++G++G+GKStLl+++ ++ +        Gei +d++++     +   lr ++g+++q+p+ fp++ +++n             
  AHX11698.1  24 LKDVNLDIYSKSVTSLIGSSGCGKSTLLRCFNRMNDFvddckVTGEIIIDNHNICApeVDVVLLRTRVGMVFQKPNPFPKS-IYDNvaygprlqemtnk 121
                 79********************************9988888899**********998889999******************.99999******988876 PP

                 ..HHHTCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHHTSSEEEEESTT CS
                 ..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  80 ..esdeeiekalsklglkelkdtvvksspssLSgGqkqrvalarallkkpkllllDEpt 136
                   + de ++k l + gl +  ++++++++ +LSgGq+qr+++ara++ kp++ll+DEp+
  AHX11698.1 122 rgQLDEIVQKSLVRSGLWDEVHDNLHQNAMELSGGQQQRLCIARAIAVKPTILLMDEPC 180
                 66666669999999********************************************7 PP

>> AAA_21  AAA domain, putative AbiEii toxin, Type IV TA system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   7.6e-06    0.0097       1      26 [.      36      63 ..      36      82 .. 0.82
   2 !   29.6   0.0   4.6e-10   5.9e-07     232     298 ..     148     210 ..      89     212 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 7.6e-06
      AAA_21  1 lnvliGpNgsGKSnLLdaldllarl..d 26
                ++ liG  g+GKS+LL+++  + ++  d
  AHX11698.1 36 VTSLIGSSGCGKSTLLRCFNRMNDFvdD 63
                688****************999776552 PP

  == domain 2  score: 29.6 bits;  conditional E-value: 4.6e-10
      AAA_21 232 lparelSdGtkrllalltallralkkgsllliDEpEngLHPkllrrllellkelsrngaQviltTHS 298
                  +a elS G+++ l+++ a++  +   ++ll DEp + L+Pk+++++  l+ el++ +  +i++THS
  AHX11698.1 148 QNAMELSGGQQQRLCIARAIAVKP---TILLMDEPCSALDPKATKSIESLIIELKK-KFTIIIVTHS 210
                 478899*****9999999999877...*********************99977777.7********9 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.9   1.0   1.1e-09   1.4e-06      22     209 ..      32     221 ..      19     231 .. 0.65

  Alignments for each domain:
  == domain 1  score: 27.9 bits;  conditional E-value: 1.1e-09
                 TTSSEEEEEESTTSSHHHHHHHHHHHCTT.TTTTTTCHCCCCCC--.....BTTCSSTTEEEEEEEEEETTEESSSSSSCEEEEEEEETTSE....EEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxx RF
       SMC_N  22 fsksftaivGpNGSGKsnlldAilFvLGersakklrseklsdlihk.....skekasvkkaeveitfdnedkklkiekeevsisrrvkrkge....sey 111
                 +sks+t+++G+ G+GKs ll     +  + +  k+  e +   i +      +    + + +v ++f++++   k   ++v    r+++  +     + 
  AHX11698.1  32 YSKSVTSLIGSSGCGKSTLLRCFNRMNDFVDDCKVTGEII---IDNhnicaPEVDVVLLRTRVGMVFQKPNPFPKSIYDNVAYGPRLQEMTNkrgqLDE 127
                 4788999999999999999988844444434433333332...22233333566667778888888888887744445554444433333330011333 PP

                 EETTEEE-HHHHHHHHHCTT-STTCS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEE CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 112 kingkevtkkevsellesagiskelLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklv 209
                  ++++ v++    e+  + + +  +LSgG+++ + +a  +A++   p  + l+De  +aLD k +k + +l+ e +k++ +i+++++ ++ +  + +v
  AHX11698.1 128 IVQKSLVRSGLWDEVHDNLHQNAMELSGGQQQRLCIARAIAVK---P-TILLMDEPCSALDPKATKSIESLIIELKKKFTIIIVTHSMKQARSISDMV 221
                 3344444443223333333334448******988888877764...4.5889**********************************999888775444 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.1   0.0   3.3e-07   0.00043      14     101 ..      24     116 ..      18     154 .. 0.75
   2 !    9.2   0.1   0.00071      0.91     319     365 ..     166     210 ..     117     212 .. 0.82

  Alignments for each domain:
  == domain 1  score: 20.1 bits;  conditional E-value: 3.3e-07
      AAA_15  14 lkdveidlsee.ltvliGkNnsGKSsilealdlFlnnkekkn.kkvikiekedleifeniseskdikIdvefaek...ekakeyektlkskek 101
                 lkdv +d+ ++ +t liG  ++GKS++l+ ++ + +  ++ +   +i i+++++   e +    + ++ + f+++   +k+++++++  ++ +
  AHX11698.1  24 LKDVNLDIYSKsVTSLIGSSGCGKSTLLRCFNRMNDFVDDCKvTGEIIIDNHNICAPEVDVVLLRTRVGMVFQKPnpfPKSIYDNVAYGPRLQ 116
                 788888888778**********************99775555877888888888888888888888888888333555556555555555544 PP

  == domain 2  score: 9.2 bits;  conditional E-value: 0.00071
      AAA_15 319 ekeeknvilliEEPEahLHpqaqkvlikllkelandnktQviitTHS 365
                  +  k+ ill++EP   L p+a k++  l++el ++    +ii THS
  AHX11698.1 166 AIAVKPTILLMDEPCSALDPKATKSIESLIIELKKKFT--IIIVTHS 210
                 3455789******************************6..******9 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   1.5e-06    0.0019       3      39 ..      10      54 ..       8      57 .. 0.85
   2 ?   -2.0   0.0       3.3   4.2e+03      16      24 ..     197     205 ..     181     244 .. 0.51

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 1.5e-06
      AAA_23  3 kienfrsf.......rdqeidF.skgltlItGpNGaGKTTildAi 39
                +i+n++ f       +d+++d  sk +t ++G  G+GK+T+l+++
  AHX11698.1 10 SIRNLNVFyrakqvlKDVNLDIySKSVTSLIGSSGCGKSTLLRCF 54
                68888888877666677788889********************98 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 3.3
      AAA_23  16 dFskgltlI 24 
                 +++k++t+I
  AHX11698.1 197 ELKKKFTII 205
                 333333322 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   2.8e-06    0.0036      87     120 ..      21      55 ..       3      70 .. 0.74
   2 ?   -1.5   0.0       1.6     2e+03      83     104 ..     184     205 ..     159     234 .. 0.66

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.8e-06
                  HTTHHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
  RsgA_GTPase  87 kegleelkellkd.ktsvlvGqSGvGKStLinall 120
                  k+ l++++  + + +++ l+G+SG GKStL+  ++
   AHX11698.1  21 KQVLKDVNLDIYSkSVTSLIGSSGCGKSTLLRCFN 55 
                  45666666555554999*************98765 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 1.6
                  -TTTHTTHHHHHHHCTTSEEEE CS
  RsgA_GTPase  83 saktkegleelkellkdktsvl 104
                  + k ++++e+l  +lk+k++++
   AHX11698.1 184 DPKATKSIESLIIELKKKFTII 205
                  4444555555555555555444 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0     5e-06    0.0063      15      39 ..      27      51 ..      22      55 .. 0.84

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 5e-06
      AAA_29 15 htieidlkgatlltGpsGsGKSTll 39
                  ++i  k++t l+G sG GKSTll
  AHX11698.1 27 VNLDIYSKSVTSLIGSSGCGKSTLL 51
                5567777779**************8 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.4   0.1   6.3e-06    0.0081       4      30 ..      33      59 ..      30     178 .. 0.81

  Alignments for each domain:
  == domain 1  score: 16.4 bits;  conditional E-value: 6.3e-06
      AAA_22  4 tagilvvtGesGtGKTtllrrlleqld 30
                +++++ ++G sG+GK+tllr + + +d
  AHX11698.1 33 SKSVTSLIGSSGCGKSTLLRCFNRMND 59
                688999****************99886 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   6.5e-06    0.0083      25      46 ..      35      56 ..      16     202 .. 0.71

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 6.5e-06
      AAA_16 25 elvllsGesGvGKsslvrellr 46
                +++ l+G sG+GKs+l+r++ r
  AHX11698.1 35 SVTSLIGSSGCGKSTLLRCFNR 56
                67889**************986 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.6   0.0   0.00085       1.1      39      64 ..      38      63 ..      18     154 .. 0.78
   2 ?    1.4   0.1      0.14   1.8e+02     105     162 ..     156     211 ..     130     218 .. 0.67
   3 ?   -1.0   0.0      0.75   9.6e+02       4      24 ..     223     243 ..     221     245 .. 0.90

  Alignments for each domain:
  == domain 1  score: 8.6 bits;  conditional E-value: 0.00085
        TniB 39 llvGdsnnGKtmivekFarlhppekd 64
                 l+G s +GK+++++ F r++   +d
  AHX11698.1 38 SLIGSSGCGKSTLLRCFNRMNDFVDD 63
                689****************9976655 PP

  == domain 2  score: 1.4 bits;  conditional E-value: 0.14
        TniB 105 skleqqvlrllrelkvrvLiiDEihnllagsarkqreflnalksLgnelkipivlvGt 162
                  ++++ +++   ++k+ +L++DE  ++l  +a+k   +  ++  L+ ++ i iv+   
  AHX11698.1 156 GQQQRLCIARAIAVKPTILLMDEPCSALDPKATK--SIESLIIELKKKFTIIIVTHSM 211
                 455555666666788899*****99999655554..5555667777777777776555 PP

  == domain 3  score: -1.0 bits;  conditional E-value: 0.75
        TniB   4 yiradrwigyprakeilerLe 24 
                 yi++ r i+y + +e++++L+
  AHX11698.1 223 YIEKGRVIEYGETEEVFHKLK 243
                 8999************99996 PP

>> AAA_13  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.48   6.2e+02      23      40 ..      41      58 ..      36      82 .. 0.80
   2 ?   10.9   0.0    0.0001      0.13     526     579 ..     170     219 ..     163     247 .. 0.83

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.48
      AAA_13 23 GwNGaGKTtLSrllrsle 40
                G+ G GK+tL r ++ ++
  AHX11698.1 41 GSSGCGKSTLLRCFNRMN 58
                8889******99998874 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0001
      AAA_13 526 kdkivviDDPvSSLDsnslfivfsliksrllkkkkakQlfiLTHnleffkevkk 579
                 k +i  +D P S LD ++  ++ sli +     kk+  ++i TH+++  + +++
  AHX11698.1 170 KPTILLMDEPCSALDPKATKSIESLIIELK---KKF-TIIIVTHSMKQARSISD 219
                 899************************996...666.59999***998888776 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.1   8.4e-05      0.11      21     111 ..      35     178 ..      19     238 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 8.4e-05
                 EEEEEEESTTSSHHHHHHHHCCSHCCCCC.CBTEEEEE.......................................................EEESXX CS
      NB-ARC  21 lvvalvGmgGvGKttlakqilnksdeveg.rFdsvawv.......................................................vvsktd 63 
                  v +l G  G+GK+tl++  ++  d v+  +  + + +                                                        v k+ 
  AHX11698.1  35 SVTSLIGSSGCGKSTLLRCFNRMNDFVDDcKVTGEIIIdnhnicapevdvvllrtrvgmvfqkpnpfpksiydnvaygprlqemtnkrgqldeIVQKSL 133
                 5789*************9988887777764444445557788888888888888888888888888888888888888888888888888888888888 PP

                 HHHHHHHXXHHHHHCCCTTSSSS-STTSHHHHHHHHCCCTTEEEEEEE CS
      NB-ARC  64 kseeiletilkeLslseddleekeeveslkrklvrlLltkrfllvlDD 111
                   + +++++  +L+++  +l+  +++      + r++  k ++l++D 
  AHX11698.1 134 VRSGLWDEVHDNLHQNAMELSGGQQQR---LCIARAIAVKPTILLMDE 178
                 888888888888877766666555444...678888888888888885 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   0.00015      0.19       4      32 ..      39      68 ..      36      88 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 0.00015
                EEESTTSSHHHHHHHHHH.SSCSSSCTTTS CS
         Ras  4 lvGdsavGKtslllrfvk.dkFkeeyesTi 32
                l+G+s++GK++ll  f + ++F ++ + T 
  AHX11698.1 39 LIGSSGCGKSTLLRCFNRmNDFVDDCKVTG 68
                89**************86488999998885 PP

>> DUF5442  Family of unknown function (DUF5442)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.3   0.0         4   5.1e+03      77      92 ..      15      30 ..      11      41 .. 0.50
   2 ?   11.3   0.1   0.00024       0.3      13      49 ..     216     252 ..     205     254 .. 0.87

  Alignments for each domain:
  == domain 1  score: -2.3 bits;  conditional E-value: 4
     DUF5442 77 nyyykkdliptdpdee 92
                n +y+ + +  d + +
  AHX11698.1 15 NVFYRAKQVLKDVNLD 30
                5555544444444333 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
     DUF5442  13 gandflkfvakgaiikygdiseelkksekeklkeylk 49 
                 +  d++ ++ kg +i+yg+  e ++k + + + +y+ 
  AHX11698.1 216 SISDMVVYIEKGRVIEYGETEEVFHKLKGNSIGNYFT 252
                 55799***************99999999999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       685  (0.0382063); expected 358.6 (0.02)
Passed bias filter:                      554  (0.0308997); expected 358.6 (0.02)
Passed Vit filter:                        78  (0.00435049); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              14  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 1980.22
//
Query:       AHX11699.1  [L=40]
Description: hypothetical protein NHE_0771 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (40 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       103  (0.00574488); expected 358.6 (0.02)
Passed bias filter:                      101  (0.00563333); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.20s 00:00:00.53 Elapsed: 00:00:00.37
# Mc/sec: 321.29
//
Query:       AHX11700.1  [L=147]
Description: ssrA-binding protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.2e-54  182.0   1.5    6.4e-54  181.7   1.5    1.0  1  SmpB      SmpB protein


Domain annotation for each model (and alignments):
>> SmpB  SmpB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  181.7   1.5   3.6e-58   6.4e-54       1     141 [.       4     144 ..       4     145 .. 0.99

  Alignments for each domain:
  == domain 1  score: 181.7 bits;  conditional E-value: 3.6e-58
                 EEE-CHHHTTSEEEEEEEEEB---HHHHHHHHH--EESSSEEEEEESSCEEEEESEE---S--SS----TT--EEBB--HHHHHHHHHHHHHHT-EEEE CS
        SmpB   1 iakNkkarhdYeieetyeaGivLkGtEvkslragkvnlkdsyvkikngelfllnvhiseyekgnifnhdpkrkrkLLlhkkeikklagkveekgltlvp 99 
                 ia Nkkar+dY++ +++eaGivL GtEvksl+ ++++l++++v +++gel+l n+h+ +y+ ++ fnh p+r+rkLL+hk++++k++g ++ kgltlv 
  AHX11700.1   4 IAVNKKARFDYSLADEFEAGIVLLGTEVKSLKYQSASLNEAFVAFRKGELWLNNMHVPHYKPASRFNHVPTRSRKLLVHKRQLNKISGIIKMKGLTLVV 102
                 689************************************************************************************************ PP

                 EEEEE.ESSEEEEEEEEEEC--SS--XXXXXXXXXXXXXXXX CS
        SmpB 100 lklyfkkkglvKveialakgkklydkretlkerdakreiera 141
                 l++y+++kgl+K++ a a+gkk+ydkr+++k+rd++r+++r+
  AHX11700.1 103 LSIYVNDKGLIKLKFATARGKKKYDKRQDIKDRDWERKKARQ 144
                 **************************************9985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (147 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       443  (0.0247086); expected 358.6 (0.02)
Passed bias filter:                      271  (0.0151152); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 1170.78
//
Query:       AHX11701.1  [L=948]
Description: AIR synthase related, N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.4e-28   97.8   1.2    3.5e-23   82.5   0.1    2.6  2  AIRS_C          AIR synthase related protein, C-terminal doma
    9.8e-17   61.4   0.0    2.1e-11   44.3   0.0    2.7  2  AIRS            AIR synthase related protein, N-terminal doma
    1.2e-09   38.5   0.7    2.8e-09   37.3   0.7    1.7  1  FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransfe
  ------ inclusion threshold ------
       0.15   12.4   0.7       0.91   10.0   0.0    2.6  3  Propep_M14      Carboxypeptidase activation peptide


Domain annotation for each model (and alignments):
>> AIRS_C  AIR synthase related protein, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.5   0.1   7.7e-27   3.5e-23       2     153 ..     442     591 ..     441     594 .. 0.92
   2 !   13.6   0.1   1.2e-05     0.056      47     149 ..     833     920 ..     808     925 .. 0.80

  Alignments for each domain:
  == domain 1  score: 82.5 bits;  conditional E-value: 7.7e-27
                 TTEEEEEEET....SSCTCCHHHHHHHCHHHCTSHTTTSEHHHHHHHHHHHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHH CS
      AIRS_C   2 pGdvliltgs....lGlggagtslkrkileeeglddsavqlgdvlleptliyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpi 96 
                 +Gd+++  g+    +G++ga++s+++  ++e+ ++  +vqlgd+l  ++l ++  ++a++ gl +a++D ++GGL++++ em +    g+++ l+kv +
  AHX11701.1 442 DGDLIVIAGGrtgrDGIHGATFSSSA--ITESNVKGTEVQLGDPLTQKKLSDAIIREARDLGLYNAITDNGAGGLSSSVGEMGRR---GFTVALEKVSL 535
                 69999999999**********99988..5666665559********************************************665...7********** PP

                 HHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEEEESSSEEE CS
      AIRS_C  97 fdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGevtakeelsv 153
                  ++  sp+e+++se+++r+ +avp+e+ + + ++++++g+ e +vIGe  +++++ +
  AHX11701.1 536 KANGLSPWEIWISESQERMTFAVPKENLKVFQDVMQKHGV-ESSVIGEFNNSGRGII 591
                 ***99***********************************.8*******99988655 PP

  == domain 2  score: 13.6 bits;  conditional E-value: 1.2e-05
                 HHHHHHHHHHHHTTECEEEE--TTHHHHHHHHHHHTTTEEEEEECGTHHHHHHHHHHHHHHHCSTTTEEEEEEEHGGHHHHHHHHHHTTCCCEEEEEEE CS
      AIRS_C  47 liyvkralaalkglvkaahDvTgGGLlgalaemapasgvgaeidldkvpifdelesplemllsensGrllvavppeeadavlaileeeglpeaavIGev 145
                 + + ++ + ++  lv +a  v  GG l a+a m+ a++ gae+++d  + +d+         ++ s   +v+++pe+a+ +++i+++      ++ G+v
  AHX11701.1 833 VFDNYCVALRN-RLVASAISVNQGGRLTAIAKMVIANNYGAELSID--ENVDN---------FARSREIIVTIAPENAQVFKEIFADKA---IREAGRV 916
                 45555555554.88999999999***********************..66665.........345666889***************975...6899999 PP

                 EESS CS
      AIRS_C 146 take 149
                 t+++
  AHX11701.1 917 TDSK 920
                 9976 PP

>> AIRS  AIR synthase related protein, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   44.3   0.0   4.6e-15   2.1e-11       3      94 .]     297     426 ..     295     426 .. 0.92
   2 !   14.2   0.0   1.2e-05     0.052      21      94 .]     701     800 ..     681     800 .. 0.86

  Alignments for each domain:
  == domain 1  score: 44.3 bits;  conditional E-value: 4.6e-15
                 SE.........EEEEEEEEE.EECCTCCCCHHHHHHHHHHHHHH..TTTEEEEEEEEEEEEC........................HHHHHHHHHHHHH CS
        AIRS   3 aa.........vvvttdshnrpvlvepvhfiGakavavnlsDla..amGArPlalllslalp........................wleevvrglaeaa 66 
                 a+         v+v++++hn+p+++ep+ + + +++ ++ +D++    GA+P+a  +++++                         +l+++++g++ ++
  AHX11701.1 297 AGaiwfddehlVCVKVETHNSPSALEPFGG-AMTGILGVNRDILgfGLGAKPIANYYTFCIDdpdteevnlyrdshkteakldslsILRGIIQGVNTGG 394
                 55555555555799****************.************977899****9999999999************************************ PP

                 HHTT-EEEEEEEEEESS....EEEEEEEEEEE CS
        AIRS  67 eelgvplvgGdtsfsne....ptisvtavGlv 94 
                 ++ g+p+  G + fs++    p++ v+++G++
  AHX11701.1 395 NCSGIPTPQGALYFSDAfrakPLVFVGCTGII 426
                 ***************9999***********86 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                 CCCHHHHHHHHHHHHHHTTTEEEE..EEEEEEEEC.........HHHHHHHHHHHHHHHTT-EEEEEEEEEESS................EEEEEEEEE CS
        AIRS  21 vhfiGakavavnlsDlaamGArPl..alllslalp.........wleevvrglaeaaeelgvplvgGdtsfsne................ptisvtavG 92 
                 +   ++ ++ +++++l++ GA P   all++++++          l+e  r +++   ++ +p ++G+ s  n+                p + +ta+G
  AHX11701.1 701 YME-TYNSIEQAIRNLVTIGANPGkiALLDNFCWSdsnnpeklwLLKESGRACHDFSIAFSTPFISGKDSMFNDfngydasgekisisnaPALLITAIG 798
                 555.678899*************76699***************99999*******************99966666667777778888888999999999 PP

                 EE CS
        AIRS  93 lv 94 
                 ++
  AHX11701.1 799 II 800
                 85 PP

>> FGAR-AT_linker  Formylglycinamide ribonucleotide amidotransferase linker domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.3   0.7   6.3e-13   2.8e-09       1      49 [.     204     254 ..     204     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 37.3 bits;  conditional E-value: 6.3e-13
  FGAR-AT_linker   1 LeeankelglaLsdeEidylqeaf..eklgrnPtdvElemfaqvwSEHCrH 49 
                     Lee n ++ l Ls+    +++++f  e+      d+Ele +aq+wSEHC+H
      AHX11701.1 204 LEEVNVKNALNLSKIQLGAIAKHFqsEERRNYIHDIELEAIAQTWSEHCKH 254
                     7999********************7655666799****************9 PP

>> Propep_M14  Carboxypeptidase activation peptide
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.0   0.0    0.0002      0.91      24      62 ..     541     580 ..     529     582 .. 0.80
   2 ?   -3.5   0.0       3.3   1.5e+04      46      65 ..     630     649 ..     626     649 .. 0.85
   3 ?   -1.6   0.0      0.85   3.8e+03      34      56 ..     887     909 ..     878     911 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.0 bits;  conditional E-value: 0.0002
  Propep_M14  24 dfWk.ppsklgepvdilVppekledfeelLeslgisyevl 62 
                 + W    s+++e + + Vp e+l+ f++ ++++g++ +v+
  AHX11701.1 541 SPWEiWISESQERMTFAVPKENLKVFQDVMQKHGVESSVI 580
                 4455335788999**********************99986 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.3
  Propep_M14  46 edfeelLeslgisyevlieD 65 
                  ++ee L++++i  + +i++
  AHX11701.1 630 TSLEEALSDKNIRSKEFIAN 649
                 578999******99998887 PP

  == domain 3  score: -1.6 bits;  conditional E-value: 0.85
  Propep_M14  34 epvdilVppekledfeelLeslg 56 
                 +++ + ++pe+ + f+e++ ++ 
  AHX11701.1 887 REIIVTIAPENAQVFKEIFADKA 909
                 45557789999999998877665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (948 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       521  (0.0290591); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        36  (0.00200792); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.70u 0.28s 00:00:00.98 Elapsed: 00:00:00.46
# Mc/sec: 6210.50
//
Query:       AHX11702.1  [L=92]
Description: bacterial SH3 domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.1e-08   33.9   0.3    5.3e-05   23.0   0.1    2.3  2  SH3_4     Bacterial SH3 domain
  ------ inclusion threshold ------
      0.047   14.0   0.2       0.09   13.1   0.2    1.5  1  SH3_3     Bacterial SH3 domain


Domain annotation for each model (and alignments):
>> SH3_4  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.1   5.9e-09   5.3e-05      33      55 ..       4      26 ..       2      27 .. 0.90
   2 !    9.0   0.0   0.00013       1.2      19      40 ..      52      73 ..      49      79 .. 0.90

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 5.9e-09
       SH3_4 33 kgnWcrvrDadGatGWiyqsllw 55
                 ++W  vrD++G+tGWi++s ++
  AHX11702.1  4 FEDWTYVRDIEGDTGWINSSFIS 26
                69****************99776 PP

  == domain 2  score: 9.0 bits;  conditional E-value: 0.00013
       SH3_4 19 ayleaGvpvrvvackgnWcrvr 40
                +++e+Gv + v++c+g+ crv+
  AHX11702.1 52 VTIEPGVFLLVKKCNGDLCRVV 73
                5789****************97 PP

>> SH3_3  Bacterial SH3 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.2     1e-05      0.09      33      55 .]       6      26 ..       2      26 .. 0.89

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1e-05
       SH3_3 33 ggeWykvrtddgteGwvssgyls 55
                +  W  vr+  g +Gw++s+++s
  AHX11702.1  6 D--WTYVRDIEGDTGWINSSFIS 26
                4..*****************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (92 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       279  (0.0155614); expected 358.6 (0.02)
Passed bias filter:                      247  (0.0137766); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 703.92
//
Query:       AHX11703.1  [L=435]
Description: major Facilitator Superfamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    8.4e-18   64.4  40.4    7.5e-11   41.5  28.6    2.1  2  MFS_1        Major Facilitator Superfamily
    2.8e-07   29.4  12.9    2.3e-05   23.1   3.4    2.4  2  Acatn        Acetyl-coenzyme A transporter 1
  ------ inclusion threshold ------
       0.27   11.5   0.0       0.27   11.5   0.0    3.0  3  DUF423       Protein of unknown function (DUF423)


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.5  28.6   1.3e-14   7.5e-11       4     310 ..      18     345 ..      15     348 .. 0.77
   2 !   27.8  10.4   1.8e-10   1.1e-06      65     178 ..     316     432 ..     308     435 .] 0.85

  Alignments for each domain:
  == domain 1  score: 41.5 bits;  conditional E-value: 1.3e-14
       MFS_1   4 aaflsalarsi....lgpalplalaedlgispseigl..lltlyalgaavaslplGrl.....sdrfGrrrvlllglllfalglllllfa.....sslw 86 
                 a+f+ ++a++i    + p+l  +la++ g++ s+ig   l+t+ ++  +++++++        ++rfG +r +++ l  f++ ++++l a       ++
  AHX11703.1  18 ATFFLGFASNIpvvlVVPTLNTWLAKA-GVNYSSIGVfsLITIPYIIKFLFAPFFDKYtvpllGTRFGQKRGWIFLLQPFVVLSIIGL-AntnpiDRIY 114
                 677777777775444666666444444.8999999998899999999999999986543444488******99999999999955555.4444445588 PP

       MFS_1  87 lllvlrvlqGlgagalfpagaaliadwfpkeergraigllsagfslGailgpllggllasslg...........Wravfyilaivsllafvlfllllpe 174
                 l+ ++ +  +l++++   ++ ++   +  ++e+  + + + +g  +++++  +++ +++++l            W  v+++ +++s+ a + +++++ e
  AHX11703.1 115 LMGIFAMAVALFSSFQDIIIDSYRISMLRPKEQLIGSSSVLLGGRFAYLISGAVALFVVDYLCdvkglcnnsinWKIVYIFSGFLSFSASI-VVFFMGE 212
                 8888888999999*******************************************877776677788888888***************88.5688899 PP

       MFS_1 175 epperkrkspkeee.kgtgpaplvp.......awkallkdpvlwillialllfffgfsglltllplylqevlglsglllaglllallalvgailallag 265
                 ++p+++  +  + e +       +p       + ++l++++ lw++++++++ ++   ++++ +p+    + g+s l +++++   ++l++    +l+g
  AHX11703.1 213 PNPRKSEANNLTHEhE-----LSFPlhmitvpLQEILWSKNGLWVVVLVIIYRSCDSLIATMISPF--LVDTGFS-LTEIAIVAKTFGLFS---LVLGG 300
                 9999999999999553.....44444445588899999***9998999999998777777777777..8999999.888887788888887...66677 PP

       MFS_1 266 rlsdrlgrrrrlllallllllaalglallavtssavllllvlvli 310
                 ++  r+  +  ++++l+++ ++ +   ++ v + +v + l+l+ i
  AHX11703.1 301 FIGARIVYKSGIMMGLIVGGVVQMVSNVMFVVQAKVGYNLPLLYI 345
                 777776666777777777777777666666666777777766555 PP

  == domain 2  score: 27.8 bits;  conditional E-value: 1.8e-10
       MFS_1  65 lllglllfalglllllfa.....sslwlllvlrvlqGlgagalfpagaaliadwfpk.eergraigllsagfslGailgpllggllasslgWravfyil 157
                 l++g ++  ++ ++++ +      +l+ll++  +   ++++++++a++ +i++++++ +  g +++++s+ + +  ++ p+++g +a+ +gW  +f + 
  AHX11703.1 316 LIVGGVVQMVSNVMFV-VqakvgYNLPLLYITIATENICGSIATTAILGYISEIASRaRFSGTVYAVFSSISLIDRAILPIIAGTIADKFGWVILFNVS 413
                 4566666666633333.1346679999******************************999*************************************** PP

       MFS_1 158 aivsllafvlfllllpeeppe 178
                  ++++ a+   l+++++++++
  AHX11703.1 414 VVIGIPALA--LVFFLRKYSQ 432
                 *******55..5999888776 PP

>> Acatn  Acetyl-coenzyme A transporter 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.1   3.4   3.8e-09   2.3e-05      10      81 ..      24      97 ..      17     112 .. 0.74
   2 !   11.8   1.7     1e-05     0.062     119     211 ..     113     207 ..     104     231 .. 0.79

  Alignments for each domain:
  == domain 1  score: 23.1 bits;  conditional E-value: 3.8e-09
       Acatn 10 llqGiPvGLafgtiPflLkslaketsftelgvfslatyPyslkilWsPivDslys....kkiGrrrsWiiPvqlvs 81
                +   iPv L   t+   L      + ++++gvfsl t Py +k l++P  D   +     + G++r Wi  +q   
  AHX11703.1 24 FASNIPVVLVVPTLNTWLAK--AGVNYSSIGVFSLITIPYIIKFLFAPFFDKYTVpllgTRFGQKRGWIFLLQPFV 97
                66778999986665544433..4799*************************86542222789999****9888543 PP

  == domain 2  score: 11.8 bits;  conditional E-value: 1e-05
       Acatn 119 lsLtlvflvLv.llcatqDiavDgWaltiLskkslsyastaqtvGlnlGyflsftvflslnssdfvnkylrkvpleyglvs.lsgylklaGllyl 211
                 + L  +f++ v l+ + qDi +D++ + +L +k     s +  +G  + y++s +v l++ +     k l + + +  +v  +sg+l ++  +++
  AHX11703.1 113 IYLMGIFAMAVaLFSSFQDIIIDSYRISMLRPKEQLIGSSSVLLGGRFAYLISGAVALFVVDYLCDVKGLCNNSINWKIVYiFSGFLSFSASIVV 207
                 45666777766155678******************************************999999999999999998888525677776655543 PP

>> DUF423  Protein of unknown function (DUF423)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.1       1.6   9.8e+03      54      66 ..     115     127 ..      97     128 .. 0.59
   2 ?   11.5   0.0   4.4e-05      0.27      27      74 ..     162     210 ..     159     219 .. 0.90
   3 ?   -0.4   0.3      0.22   1.3e+03      63      72 ..     372     381 ..     308     399 .. 0.71

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 1.6
      DUF423  54 agllflaGivlFS 66 
                  + +f++ ++lFS
  AHX11703.1 115 LMGIFAMAVALFS 127
                 3456777777777 PP

  == domain 2  score: 11.5 bits;  conditional E-value: 4.4e-05
      DUF423  27 Yqlyhalallavalla.skaaasrllklagllflaGivlFSgslyllal 74 
                 Y +  a+al++v  l+  k   ++ +++  + ++ G + FS s+++  +
  AHX11703.1 162 YLISGAVALFVVDYLCdVKGLCNNSINWKIVYIFSGFLSFSASIVVFFM 210
                 888889********999778999*********************98766 PP

  == domain 3  score: -0.4 bits;  conditional E-value: 0.22
      DUF423  63 vlFSgslyll 72 
                 + FSg++y++
  AHX11703.1 372 ARFSGTVYAV 381
                 4577777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (435 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       603  (0.0336327); expected 358.6 (0.02)
Passed bias filter:                      210  (0.0117129); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.24s 00:00:00.79 Elapsed: 00:00:00.41
# Mc/sec: 3198.71
//
Query:       AHX11704.1  [L=652]
Description: hlyD secretion family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-79  265.9   1.0    3.9e-79  265.0   1.0    1.4  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
    1.4e-41  141.5   0.0    4.4e-41  139.9   0.0    1.9  1  Biotin_carb_N    Biotin carboxylase, N-terminal domain
    7.5e-34  116.1   0.0    3.4e-33  114.0   0.0    2.2  2  Biotin_carb_C    Biotin carboxylase C-terminal domain
    1.9e-20   72.4   1.2    2.6e-19   68.8   1.1    2.8  2  Biotin_lipoyl    Biotin-requiring enzyme
      3e-13   49.8   0.1    5.9e-13   48.8   0.1    1.4  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    6.4e-10   38.7   0.0    0.00039   20.2   0.0    3.0  3  Biotin_lipoyl_2  Biotin-lipoyl like
    6.4e-08   32.4   0.1    1.3e-07   31.3   0.1    1.4  1  ATP-grasp        ATP-grasp domain
    2.9e-07   30.3   1.6    7.2e-07   29.0   0.3    2.2  2  RimK             RimK-like ATP-grasp domain
    2.9e-06   26.7   0.1     0.0091   15.2   0.0    2.5  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    0.00022   21.9   0.1       0.35   11.6   0.0    3.3  3  HlyD_3           HlyD family secretion protein
    0.00097   19.2   0.1     0.0019   18.3   0.1    1.5  1  ATP-grasp_3      ATP-grasp domain
     0.0024   17.6   0.2         10    5.9   0.0    3.7  3  PTS_EIIA_1       phosphoenolpyruvate-dependent sugar phosphot
      0.007   16.7   0.0      0.025   14.9   0.0    1.9  2  PCC_BT           Propionyl-coenzyme A carboxylase BT domain
  ------ inclusion threshold ------
      0.017   13.9   0.1        3.8    6.1   0.0    2.5  3  Oxidored_nitro   Nitrogenase component 1 type Oxidoreductase
      0.031   14.5   1.1        1.2    9.4   0.1    3.1  3  Peptidase_M23    Peptidase family M23
      0.036   13.8   0.0      0.086   12.6   0.0    1.6  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
      0.096   12.7   0.2        1.9    8.5   0.2    2.9  2  RnfC_N           RnfC Barrel sandwich hybrid domain


Domain annotation for each model (and alignments):
>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  265.0   1.0   3.7e-82   3.9e-79       2     210 ..     117     324 ..     116     325 .. 0.99

  Alignments for each domain:
  == domain 1  score: 265.0 bits;  conditional E-value: 3.7e-82
                  HHHHHHHHHHTT-BBSSEECSSBSSHHHHHHHHHHH-SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEE CS
  CPSase_L_D2   2 kesakealkkinvpvvpssaapvetleealaiakeigyPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvev 99 
                  k+ ak+++k++ v+++p+  + v++  +al+iakeig+Pv+ika++g+GGkGmr+++ eeel+++++ a +ea + f +++v++ek++k+p++iE+++
   AHX11704.1 117 KVMAKKIAKEASVNLIPGYVGEVSDYTHALSIAKEIGFPVLIKASAGGGGKGMRLVHREEELRDAMNLACSEALSFFKDQRVFIEKYIKNPRHIEIQI 214
                  7899********************************************************************************************** PP

                  EEETTS-EEEEEEEEECCECTCCCCEEEES-SS--HHHHHHHHHHHHHHHHHHT-EEEEEEEEEEETTTTEEEEEEEESS--CCHHHHHHHHS--HHH CS
  CPSase_L_D2 100 lrDakgnvitvcerenslqlrtqkvievAPsqtLtdeerqalreaavkvvrevgvvgagtveflldpkskeyyviEvNtRlsvesalaekaTGldlvk 197
                  l+D++gn+i ++ere+s+q+r+qk+ie+APs +L+++ r+++ +++++++++v++++agtve++ld+ ++++y++E+NtR++ve++++e++TG+d+v+
   AHX11704.1 215 LADKQGNIICLGERECSIQRRHQKIIEEAPSIALHRALRKEMYNQSIRLAKSVNYTSAGTVEYILDQ-ENNFYFMEMNTRIQVEHPVTEMITGIDIVE 311
                  ******************************************************************8.9***************************** PP

                  HHHHHHTT--GCG CS
  CPSase_L_D2 198 eaakialgekLee 210
                  e+++ia g  L++
   AHX11704.1 312 EMIRIAEGDALSK 324
                  *********9986 PP

>> Biotin_carb_N  Biotin carboxylase, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  139.9   0.0   4.2e-44   4.4e-41       2     110 .]       3     111 ..       2     111 .. 0.98

  Alignments for each domain:
  == domain 1  score: 139.9 bits;  conditional E-value: 4.2e-44
                    --EEEE---HHHHHHHHHHHHHTT-EEEEEEEGGGTTSHHHHHSSEEEEEESSTTCCGGG-HHHHHHHHHHTT-SEEE--SSTTTT-HHHHHHHHH CS
  Biotin_carb_N   2 ikkvlianrGeiAvriiravrelgietvavyseedanslhvreadeavelgpasasesYlniekivkaakesgadavhpGyGflsEnaefaeavee 97 
                    i+kvlianrGeiA riir++r+lg ++vavys+ d  +++vr+adeav++g+++a++sY n+e++++a++++gadavhpGyGflsEn+efa  +e+
     AHX11704.1   3 IQKVLIANRGEIASRIIRTLRKLGKKSVAVYSDLDVGAEYVRHADEAVHIGGSTAKDSYNNMEALLSAITKTGADAVHPGYGFLSENPEFALCLEK 98 
                    89********************************************************************************************** PP

                    TT-EESSS-HHHH CS
  Biotin_carb_N  98 agivfiGPsaeal 110
                    ++i+fiGPs++++
     AHX11704.1  99 HNIIFIGPSSDCI 111
                    *********9875 PP

>> Biotin_carb_C  Biotin carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.7   3.9e+03      34      65 ..      47      79 ..      19      92 .. 0.67
   2 !  114.0   0.0   3.2e-36   3.4e-33       1     107 [.     337     441 ..     337     442 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.7
                   EE---.TT-EE-TTS-SEEEEEEEEESSHHHHH CS
  Biotin_carb_C 34 dsgve.egsevspyyDsllaKlivhgetreeal 65
                   d++v+  gs+ +  y ++ a l +  +t ++a+
     AHX11704.1 47 DEAVHiGGSTAKDSYNNMEALLSAITKTGADAV 79
                   455553456666677777776666666666665 PP

  == domain 2  score: 114.0 bits;  conditional E-value: 3.2e-36
                    EEEEESEETTTTTEE--CE-SEEE---STTEEEEE---TT-EE-TTS-SEEEEEEEEESSHHHHHHHHHHHHHT-EEESS-BSHHHHHHHHH-HHH CS
  Biotin_carb_C   1 eaRinaEdpeknflpssGkvtelelpegpgvRvdsgveegsevspyyDsllaKlivhgetreealarlrraLaelrieGvktnieflrailedeef 96 
                    eaR++aEdp +nf+p+sG v++++ p  ++ Rv+s++ +gs+v ++yD+++aK+ivh+++r++a++++ +aL+++ i G+k+n+ fl++++++e+f
     AHX11704.1 337 EARVYAEDPMNNFMPTSGFVAKMDSP--TNARVESSICAGSDVGMFYDPMVAKIIVHAKSRADAINEMCEALRRTCIVGLKNNLVFLESVFRHEDF 430
                    89************************..899***************************************************************** PP

                    HHT---TTTCC CS
  Biotin_carb_C  97 akgeldtkfle 107
                    ++g++dt+f+e
     AHX11704.1 431 ISGNVDTHFVE 441
                    *********98 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.0      0.92   9.7e+02      45      60 ..     267     282 ..     263     284 .. 0.84
   2 !   68.8   1.1   2.4e-22   2.6e-19       8      72 ..     584     648 ..     578     649 .. 0.91

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.92
                    EEBSSSEEEEEESSTT CS
  Biotin_lipoyl  45 ieapkaGvvkeilvke 60 
                    +++ +aG+v++il +e
     AHX11704.1 267 VNYTSAGTVEYILDQE 282
                    88999*******9876 PP

  == domain 2  score: 68.8 bits;  conditional E-value: 2.4e-22
                    SEEEEEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEEE-TTCEEEE CS
  Biotin_lipoyl   8 iGesveeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdtvevgdllak 72 
                    ++ +++ g +++v+v++Gd Vk+g++l+++eamKm+++i+++  G+v++++v++G+++++gd+l+k
     AHX11704.1 584 VSATMT-GmIANVYVAAGDIVKQGDPLCVIEAMKMQNTITSERGGTVEKVYVEKGQNISEGDPLLK 648
                    556666.67899****************************************************97 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.8   0.1   5.6e-16   5.9e-13      30     174 ..     147     292 ..     135     294 .. 0.85

  Alignments for each domain:
  == domain 1  score: 48.8 bits;  conditional E-value: 5.6e-16
                      HHHHHC-SSEEEEESSSSTTTTEEEESSGGGHHHHHHHH......HTT-SCEEEEE--.ESEEEEEEEEETSSCEEEEEEEEE-SSSSS-HHHH CS
  Dala_Dala_lig_C  30 kveeelgypvfVKpareGSSvGvskveseeelkeaieea......fkydekvlvEeai.egreievavlgneklevsevgeivvkkgfydyeak 116
                      ++ +e+g+pv++K++  G   G+  v+ eeel++a++ a      f +d++v++E++i + r ie+ +l + + ++  +ge+  +  + + ++k
       AHX11704.1 147 SIAKEIGFPVLIKASAGGGGKGMRLVHREEELRDAMNLAcsealsFFKDQRVFIEKYIkNPRHIEIQILADKQGNIICLGERECS--IQRRHQK 238
                      68899******************************9876222222458**********999*******************99775..6688999 PP

                      HC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTEEEEEEEES CS
  Dala_Dala_lig_C 117 ysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteegeivlnEvNt 174
                       ++++ ++ +  +l ke++++    +++  k ++ +  + v ++l++e+++++ E+Nt
       AHX11704.1 239 IIEEAPSIALHRALRKEMYNQ----SIRLAKSVNYTSAGTVEYILDQENNFYFMEMNT 292
                      988888877777777777766....66666788999999******************9 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.0   0.0       3.1   3.3e+03      18      37 ..     514     533 ..     510     535 .. 0.80
   2 !   20.2   0.0   3.7e-07   0.00039       4      40 ..     583     619 ..     580     623 .. 0.90
   3 !   15.8   0.0   8.9e-06    0.0094       4      32 ..     620     648 ..     618     652 .] 0.88

  Alignments for each domain:
  == domain 1  score: -2.0 bits;  conditional E-value: 3.1
  Biotin_lipoyl_2  18 VkdGqrVkaGdvLaelDsra 37 
                      V+  q V +G  Lael+++a
       AHX11704.1 514 VEWQQDVREGLFLAELNKEA 533
                      566699999999***99987 PP

  == domain 2  score: 20.2 bits;  conditional E-value: 3.7e-07
  Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLaelDsralql 40 
                      +++a   G +a ++V  G+ Vk+Gd L +++  + q+
       AHX11704.1 583 QVSATMTGMIANVYVAAGDIVKQGDPLCVIEAMKMQN 619
                      6888899***********************9988876 PP

  == domain 3  score: 15.8 bits;  conditional E-value: 8.9e-06
  Biotin_lipoyl_2   4 sIaapvsGrVaqlnVkdGqrVkaGdvLae 32 
                      +I++   G+V++++V+ Gq + +Gd L+ 
       AHX11704.1 620 TITSERGGTVEKVYVEKGQNISEGDPLLK 648
                      57778889******************986 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.3   0.1   1.2e-10   1.3e-07      14     159 ..     139     293 ..     129     295 .. 0.84

  Alignments for each domain:
  == domain 1  score: 31.3 bits;  conditional E-value: 1.2e-10
                 ECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC........GTTCEEEEE----SEEEEEEEEEETTC-EEE--EEE.EEEETT CS
   ATP-grasp  14 veskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqaleal........keekvivEefvpfekElsvlvvrsaeGetafypvve.tvqedg 103
                 v++ +++ ++a+e+g+pv++K +  g  GkG  +v+ ee+l++a++ +        k+++v +E++++  + + + +  +++G++ ++   e  +q++ 
  AHX11704.1 139 VSDYTHALSIAKEIGFPVLIK-ASAGGGGKGMRLVHREEELRDAMNLAcsealsffKDQRVFIEKYIKNPRHIEIQILADKQGNIICLGEREcSIQRRH 236
                 56666777889**********.777789*****************99999*********************************9988865542566655 PP

                 EEEEEEECE.E-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS CS
   ATP-grasp 104 ilrlsvapa.evsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapR 159
                    +  ap+ +++++  k+  ++  ++++++++    +vE  + ++++ ++ E+  R
  AHX11704.1 237 QKIIEEAPSiALHRALRKEMYNQSIRLAKSVNYTSAGTVEYILDQENNFYFMEMNTR 293
                 5555555541566778899999999***************99998888999998877 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.3   6.8e-10   7.2e-07      32     186 ..     147     315 ..     113     317 .. 0.72
   2 ?   -4.0   0.1       8.6   9.1e+03     142     162 ..     593     613 ..     577     622 .. 0.64

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 6.8e-10
                 HHHHTT-..-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH.........GGG--EEEEE--SS-SEEEEEEEET.TEEEEEEEEE--.SSS----T.T CS
        RimK  32 kliekik.lrfPvvvKsvegsqGikvvlakkeqklkqvlea.........lkeailvqeyieeaenediRvlvvd.devvaalrrvsk.eGdFRsnl.h 117
                 ++    k ++fPv++K + g  G ++ l + e++l++ ++           ++++++ +yi++    +i +l  + ++++   +r +  +      + +
  AHX11704.1 147 SIA---KeIGFPVLIKASAGGGGKGMRLVHREEELRDAMNLacsealsffKDQRVFIEKYIKNPRHIEIQILADKqGNIICLGERECSiQRRHQKIIeE 242
                 222...2468****************************98665666666555666**************999864144555444443302222222312 PP

                 TT-EEEE----HHHHHHHHHHHHHCT-SEEE.EE.EEEETTEEEEEEEESS--SHH..HHHHHT--HHHHHHH CS
        RimK 118 rGgvaeklqlseeekelAikaakamelvvaG.vD.llrakrgllvlEvnsspglek..iektlgidiakklie 186
                   ++a +  l +e  +  i+ ak ++   aG v+ +l+++++++++E+n+  ++e+   e+ +gidi +++i+
  AHX11704.1 243 APSIALHRALRKEMYNQSIRLAKSVNYTSAGtVEyILDQENNFYFMEMNTRIQVEHpvTEMITGIDIVEEMIR 315
                 34556677899999999*************95669*****************999644799**********97 PP

  == domain 2  score: -4.0 bits;  conditional E-value: 8.6
                 CT-SEEEEEEEEETTEEEEEE CS
        RimK 142 melvvaGvDllrakrgllvlE 162
                  ++ va  D++++ + l v+E
  AHX11704.1 593 ANVYVAAGDIVKQGDPLCVIE 613
                 344555668888888888887 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.2   0.0   8.6e-06    0.0091      18      58 ..     580     619 ..     575     623 .. 0.87
   2 !    9.9   0.0   0.00037      0.39      21      50 ..     620     648 ..     616     652 .] 0.70

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 8.6e-06
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23  18 rlarvsarveGwveklyvnatgdkVkkGqpLaelyspelva 58 
                 +  +vsa+++G++ ++yv   gd Vk+G+pL  +++ ++ +
  AHX11704.1 580 QSEQVSATMTGMIANVYVA-AGDIVKQGDPLCVIEAMKMQN 619
                 56799*************9.9*************9988766 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00037
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23  21 rvsarveGwveklyvnatgdkVkkGqpLae 50 
                 +++++  G vek+yv+  g+++++G+pL++
  AHX11704.1 620 TITSERGGTVEKVYVE-KGQNISEGDPLLK 648
                 5667777778888887.7888888887776 PP

>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.7   0.0       9.5     1e+04      60      78 ..     262     280 ..     254     302 .. 0.65
   2 ?    6.5   0.0     0.012        13       2      31 ..     584     613 ..     583     617 .. 0.90
   3 !   11.6   0.0   0.00033      0.35       1      29 [.     620     648 ..     620     651 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.7 bits;  conditional E-value: 9.5
      HlyD_3  60 kldqgsdytlkgkierisp 78 
                 +l ++ +yt  g++e+i +
  AHX11704.1 262 RLAKSVNYTSAGTVEYILD 280
                 4445566788888888865 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.012
      HlyD_3   2 lrApvdGvvvelnveegevvqagdelleii 31 
                 + A  +G ++ + v +g++v +gd+l  i 
  AHX11704.1 584 VSATMTGMIANVYVAAGDIVKQGDPLCVIE 613
                 678999*******************99885 PP

  == domain 3  score: 11.6 bits;  conditional E-value: 0.00033
      HlyD_3   1 tlrApvdGvvvelnveegevvqagdelle 29 
                 t+++ ++G+v ++ ve+g+ +++gd+ll+
  AHX11704.1 620 TITSERGGTVEKVYVEKGQNISEGDPLLK 648
                 799************************97 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.3   0.1   1.8e-06    0.0019       2     159 ..     115     295 ..     114     297 .. 0.80

  Alignments for each domain:
  == domain 1  score: 18.3 bits;  conditional E-value: 1.8e-06
                  TSHHHHHHHHTTT.S-.--............-EESS--SSSEEEEESS-------B--SS--TTE...................EEEE---S.EEEEE CS
  ATP-grasp_3   2 sdKlktykkLkeagvk.vP.......tkle.aeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve............lvqefieG.kplSv 77 
                  s+K+   k  kea+v+ +P       ++++  + ++e   ++ +K + G+gg+++r+v+ +ee+  a++  +             + ++i+  +++ +
   AHX11704.1 115 SNKVMAKKIAKEASVNlIPgyvgevsDYTHaLSIAKEIGFPVLIKASAGGGGKGMRLVHREEELRDAMNLACsealsffkdqrvFIEKYIKNpRHIEI 212
                  566666666666666534677766643333034555668899***********************999999899*********9999999854899** PP

                  EEEE.SSSEEE.EEEEEEEEET....TEEEEEEES----HHHHHHHHHHHHHTTSTT--EEEEEEEEESS..SEEEEEEESS-- CS
  ATP-grasp_3  78 sllsdgekvlv.lavnrqliekaekefvyaGnvtpietelkeevvelaeevvekleglaGyvGvDlvlkd.eepyviEvNPRlt 159
                  ++l+d++ + + l   +  i++++++++    ++  +  l++e+++   ++ +++ +  +   v+ +l + ++ y++E N R++
   AHX11704.1 213 QILADKQGNIIcLGERECSIQRRHQKIIEEAPSIALHRALRKEMYNQSIRLAKSV-NYTSAGTVEYILDQeNNFYFMEMNTRIQ 295
                  ****987765504444456777777788888888888899***************.9999999****9987999********98 PP

>> PTS_EIIA_1  phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.1   0.0       0.3   3.2e+02      42      71 ..     130     159 ..     111     163 .. 0.80
   2 !    5.9   0.0    0.0095        10      79     110 ..     588     619 ..     582     625 .. 0.83
   3 ?    5.8   0.0      0.01        11      81     104 ..     627     650 ..     619     651 .. 0.84

  Alignments for each domain:
  == domain 1  score: 1.1 bits;  conditional E-value: 0.3
                 ES--EEEEE--SSSSEEEEESSSS-EEEEE CS
  PTS_EIIA_1  42 apvdGkvekvfptkHaigiktddgvevlih 71 
                   + G v  v +  Ha+ i ++ g  vli+
  AHX11704.1 130 NLIPGYVGEVSDYTHALSIAKEIGFPVLIK 159
                 55678999999****************997 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0095
                 TTTTTEEES----SEE-SEEEEEEE-HHHHGG CS
  PTS_EIIA_1  79 lkgegFellvkegdkVkagdklvevdleaikk 110
                 + g   +++v++gd Vk+gd+l+ ++  ++++
  AHX11704.1 588 MTGMIANVYVAAGDIVKQGDPLCVIEAMKMQN 619
                 567777899**************998888776 PP

  == domain 3  score: 5.8 bits;  conditional E-value: 0.01
                 TTTEEES----SEE-SEEEEEEE- CS
  PTS_EIIA_1  81 gegFellvkegdkVkagdklvevd 104
                 g++ +++v++g+++++gd+l++++
  AHX11704.1 627 GTVEKVYVEKGQNISEGDPLLKFS 650
                 6666899**************996 PP

>> PCC_BT  Propionyl-coenzyme A carboxylase BT domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.0       9.4   9.9e+03     103     115 ..     331     343 ..     320     351 .. 0.80
   2 !   14.9   0.0   2.3e-05     0.025      30     108 ..     479     555 ..     469     568 .. 0.85

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 9.4
      PCC_BT 103 ykGtkfkvkVltp 115
                 ++G +f+++V+ +
  AHX11704.1 331 FNGWSFEARVYAE 343
                 7899999999976 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 2.3e-05
      PCC_BT  30 eekdwvvtvdgedetvtvkveeaadevevkvdgksvkvssdwklgqplirgtvdgesvtvqvlskkaggfrLqykGtkf 108
                 ee+d+v++++++ ++v+v+++  ++e+ +++ g s+ v+ +    + l+ +++++e+++v++++ ++ + r+ ykG ++
  AHX11704.1 479 EEQDFVIRLGKHVYEVRVTYN--SGELNFMFAGVSYLVEWQQDVREGLFLAELNKEAFIVRIINTDKFQKRVEYKGFSI 555
                 678888888887777766655..667888888********************************************986 PP

>> Oxidored_nitro  Nitrogenase component 1 type Oxidoreductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.1   0.0    0.0036       3.8     249     318 ..       4      68 ..       1      89 [. 0.81
   2 ?    5.1   0.0    0.0073       7.7     133     183 ..     115     164 ..      97     182 .. 0.77
   3 ?   -2.9   0.0       2.1   2.2e+03     101     138 ..     530     566 ..     523     607 .. 0.71

  Alignments for each domain:
  == domain 1  score: 6.1 bits;  conditional E-value: 0.0036
                     HHHHHHHHHHHHHHHHHHHHHHTT-EEEEECSSHHHHHHHHHHHHHT-EEEEEEESSS-HHHHHHHHHHS CS
  Oxidored_nitro 249 periaeerarlldaladyheylagkrvaiygdpdrvvalarllkelGmevvaagtetahrddeerlkael 318
                     +++++++r++++ +++ +  +l++k va+y d d    ++r       e v++g +ta +d +  ++a l
      AHX11704.1   4 QKVLIANRGEIASRIIRTLRKLGKKSVAVYSDLDVGAEYVRHAD----EAVHIGGSTA-KDSYNNMEALL 68 
                     5688999***************************9999999888....6667766666.34444566655 PP

  == domain 2  score: 5.1 bits;  conditional E-value: 0.0073
                     HHHCTT-TT---SSEEEEEEETTCGHGHHHHHHHHHHHHTEEEEEEECTSB CS
  Oxidored_nitro 133 vrklvgkkgekeprkvnilgeynlgpgdlrelkelleklGlevnavftggt 183
                      +k+++ k+  ++ +vn++++y  + +d+ +   + +++G+ v   ++ g 
      AHX11704.1 115 SNKVMA-KKIAKEASVNLIPGYVGEVSDYTHALSIAKEIGFPVLIKASAGG 164
                     444544.5556788********7778**************97776666555 PP

  == domain 3  score: -2.9 bits;  conditional E-value: 2.1
                     HHHHTSSEEEEEE--TT.SSSHHHHHHHHHHHHHHHCTT CS
  Oxidored_nitro 101 eeelgeipvipvstpgf.ggsqseGydaalealvrklvg 138
                     ++e     v  ++t  f +  +++G+++++ a+  ++ +
      AHX11704.1 530 NKEA--FIVRIINTDKFqKRVEYKGFSILCAAFPATVYA 566
                     4444..458889999999999999999999888777755 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0         2   2.1e+03      19      70 ..     270     329 ..     261     338 .. 0.66
   2 ?    9.4   0.1    0.0011       1.2      18      73 ..     558     613 ..     549     625 .. 0.72
   3 ?    2.0   0.1      0.23   2.5e+02      51      69 ..     628     646 ..     611     650 .. 0.78

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 2
                    SSSEEEEEEEEET......TTEEEEEEEE.CTCEEEEEEEESE.ESS-TTEEE-TTCEEE CS
  Peptidase_M23  19 aadGtVvfagkke......gyGnvviidh.gdgystlyahlsk.isvkegqkVkaGqvIG 70 
                    +++GtV ++ ++e      ++ + ++++h  ++++t +  +++ i++ eg+  ++ + I 
     AHX11704.1 270 TSAGTVEYILDQEnnfyfmEMNTRIQVEHpVTEMITGIDIVEEmIRIAEGDALSKKTSIT 329
                    567888666554444565566777777774344777777776645588888888777775 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.0011
                    ESSSEEEEEEEEETTTEEEEEEEECTC.EEEEEEEESEESS-TTEEE-TTCEEEEEB CS
  Peptidase_M23  18 AaadGtVvfagkkegyGnvviidhgdg.ystlyahlskisvkegqkVkaGqvIGtvg 73 
                    Aa   tV+ +    + +n v + ++++   t+ + + ++ v +g+ Vk+G+++  + 
     AHX11704.1 558 AAFPATVYAKYSL-AQDNAVDVLQSEQvSATMTGMIANVYVAAGDIVKQGDPLCVIE 613
                    5666666655444.55788877777772556666677799***********997766 PP

  == domain 3  score: 2.0 bits;  conditional E-value: 0.23
                    EESEESS-TTEEE-TTCEE CS
  Peptidase_M23  51 hlskisvkegqkVkaGqvI 69 
                     ++k+ v++gq++++G+++
     AHX11704.1 628 TVEKVYVEKGQNISEGDPL 646
                    4677889999999999976 PP

>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.6   0.0   8.2e-05     0.086       2      90 ..     116     205 ..     115     238 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.6 bits;  conditional E-value: 8.2e-05
                 BHHHHHHHHHHTT--B-..-EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE--- CS
      GARS_A   2 sKsfakdllkkagipta..eyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelle 90 
                 +K  ak++ k+a ++       +++d+ +a ++ +e ++++  +Ka+   +gKg+ +++ eee  +a++   ++       ++v iE++++
  AHX11704.1 116 NKVMAKKIAKEASVNLIpgYVGEVSDYTHALSIAKEIGFPV-LIKASAGGGGKGMRLVHREEELRDAMNLACSEALSFFKDQRVFIEKYIK 205
                 788999999999998543345699*****************.9*******************99999988887766666788999999886 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.2   1.2e+03      46      82 ..     316     361 ..     310     372 .. 0.69
   2 ?    8.5   0.2    0.0018       1.9      38      81 ..     589     633 ..     583     647 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.2
      RnfC_N  46 vkvgdkVlkGqkiaeaeg.fvsapvha........svsGtVkaiek 82 
                 +++gd   k   i++ +g  + a v+a        ++sG V ++++
  AHX11704.1 316 IAEGDALSKKTSITKFNGwSFEARVYAedpmnnfmPTSGFVAKMDS 361
                 5678888888888888887668888875544444467777766665 PP

  == domain 2  score: 8.5 bits;  conditional E-value: 0.0018
      RnfC_N  38 iGapakplvkvgdkVlkGqkiaeaeg.fvsapvhasvsGtVkaie 81 
                  G+ a++ v+ gd V++G+ +   e+  ++  + +   GtV ++ 
  AHX11704.1 589 TGMIANVYVAAGDIVKQGDPLCVIEAmKMQNTITSERGGTVEKVY 633
                 68999****************999985568899999999*99885 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (652 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       718  (0.0400469); expected 358.6 (0.02)
Passed bias filter:                      581  (0.0324056); expected 358.6 (0.02)
Passed Vit filter:                        66  (0.00368119); expected 17.9 (0.001)
Passed Fwd filter:                        17  (0.000948185); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.64u 0.26s 00:00:00.90 Elapsed: 00:00:00.40
# Mc/sec: 4905.84
//
Query:       AHX11705.1  [L=293]
Description: ribose-phosphate diphosphokinase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.6e-23   81.1   0.0    8.7e-22   77.2   0.0    2.2  2  Pribosyltran_N  N-terminal domain of ribose phosphate pyropho
    7.6e-21   75.0   4.1      7e-18   65.3   0.6    2.9  3  Pribosyl_synth  Phosphoribosyl synthetase-associated domain
    2.4e-14   53.1   1.6    1.9e-13   50.2   0.4    2.2  2  Pribosyltran    Phosphoribosyl transferase domain


Domain annotation for each model (and alignments):
>> Pribosyltran_N  N-terminal domain of ribose phosphate pyrophosphokinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.2   0.0   1.5e-25   8.7e-22       1     112 [.       1     113 [.       1     116 [. 0.96
   2 ?    1.6   0.0     0.042   2.5e+02      13      57 ..     170     215 ..     165     254 .. 0.79

  Alignments for each domain:
  == domain 1  score: 77.2 bits;  conditional E-value: 1.5e-25
  Pribosyltran_N   1 lkifagssskeLaekiakrlgvelgkakvsrfadgEikveiee..svrgkdvfiiqslskpvndnlmelllmidalrrasakritaViPylgysr 93 
                     +k++ gs s eL++k+a  lg + + a+++rf+dgE +v +++   + g++v +i sl+++   +++e ll++dal+r   + i++V Py++y r
      AHX11705.1   1 MKVILGSRSGELGQKVATLLGASRIAAEINRFPDGESNVIVNDpeLLPGDKVLVIESLCND--GDIIEFLLIVDALNRRGIRDIVLVAPYFAYTR 93 
                     899************************************999865788***********99..89****************************** PP

  Pribosyltran_N  94 qdrk.ksrepisaklvaklL 112
                      dr  +s ++i ak++a+l 
      AHX11705.1  94 ADRIvSSGSAIGAKVIADLV 113
                     ****999**********986 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.042
  Pribosyltran_N  13 aekiakrlgvelgkakvsrfadgEikv.eieesvrgkdvfiiqsls 57 
                     a+++a+ lg++l+ ++  r + g  ++ +i  +v g++++i+ +++
      AHX11705.1 170 AKSLAEGLGLSLVIMNKYRSSPGVSEItDIIGEVEGRECVIVDDIV 215
                     678888889999988888888886654268889********99986 PP

>> Pribosyl_synth  Phosphoribosyl synthetase-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0      0.12   6.9e+02      95     149 ..      63     117 ..      47     130 .. 0.78
   2 !    8.9   0.0   0.00023       1.4       4      32 ..     156     184 ..     154     191 .. 0.89
   3 !   65.3   0.6   1.2e-21     7e-18      76     174 ..     198     293 .]     187     293 .] 0.95

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.12
                     S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HH CS
  Pribosyl_synth  95 dvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntiphei 149
                     d+  f+   + l+ rG   i+ +a +  ++ ++  +   sai   v+++ + + i
      AHX11705.1  63 DIIEFLLIVDALNRRGIRDIVLVAPYFAYTRADRIVSSGSAIGAKVIADLVGQRI 117
                     4557888899999999999999999999999888888889998888888777766 PP

  == domain 2  score: 8.9 bits;  conditional E-value: 0.00023
                     GEEEEESSGGGHHHHHHHHHHTT-EEEEE CS
  Pribosyl_synth   4 navivakspgsakkatsyaerlrlglavi 32 
                     + viva + g++k+a+s ae l l+l ++
      AHX11705.1 156 DVVIVAPDLGAVKRAKSLAEGLGLSLVIM 184
                     579*********************99876 PP

  == domain 3  score: 65.3 bits;  conditional E-value: 1.2e-21
                     -EES--TTSEEEEEEEEE-S-HHHHHHHHHHHHTT--EEEEEEEEE---TTHHHHHHHSS--EEEEESSS--HHHHHT-TTEEEE--HHHHHHHH CS
  Pribosyl_synth  76 tvvGdvgGriaiivddliddvesfvaaaevlkerGaykiyvlathGllssdaprlleesaidevvvtntipheiqklrcskiktvdislllaeai 170
                      ++G+v+Gr  +ivdd++    ++ +aae l+e Ga  + +++thG+ls +a +++  s+ide+++t++ip      +  ki+    + l+a+ i
      AHX11705.1 198 DIIGEVEGRECVIVDDIVCGGGTLCNAAEKLNELGAKSVLAFVTHGVLSGKAQQRIMGSCIDEIIITDSIPVRK---NEGKIRIASAAELIAKEI 289
                     599********************************************************************765...7789************** PP

                     HHHH CS
  Pribosyl_synth 171 rrih 174
                     r i+
      AHX11705.1 290 RSIY 293
                     *997 PP

>> Pribosyltran  Phosphoribosyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.9   0.0     0.024   1.5e+02      67     102 ..      36      64 ..       7     109 .. 0.65
   2 !   50.2   0.4   3.2e-17   1.9e-13      28     124 ..     154     242 ..     142     267 .. 0.85

  Alignments for each domain:
  == domain 1  score: 1.9 bits;  conditional E-value: 0.024
                   T--EE............EE----TTSEEEEE-SEESSSHH CS
  Pribosyltran  67 gseeaargssdes....rlledpagkkVliVDDildtGgT 102
                               s    +++e++ g kVl+++ ++  G  
    AHX11705.1  36 E-----------SnvivNDPELLPGDKVLVIESLCNDGDI 64 
                   2...........0233348999999999999999988864 PP

  == domain 2  score: 50.2 bits;  conditional E-value: 3.2e-17
                   GGGEEEEEEETTTHHHHHHHHHHSTT-EE-EEEEEE-TTT--EE........EE----TTSEEEEE-SEESSSHHHHHHHHHHHCC-BSEEEEEEEE CS
  Pribosyltran  28 gkpdvvvgiargGvpfakiladeLevplayvrkvkyrpdgseeaargssdesrlledpagkkVliVDDildtGgTllaalelLkekgpeevriavlv 124
                   ++ +v+v+++ g+v +ak la  L++ l++++k + +p++se +           ++++g+ ++iVDDi+  GgTl++a+e L e g+++v + v +
    AHX11705.1 154 HSDVVIVAPDLGAVKRAKSLAEGLGLSLVIMNKYRSSPGVSEITD--------IIGEVEGRECVIVDDIVCGGGTLCNAAEKLNELGAKSVLAFVTH 242
                   4569*********************99999888887777777665........789*********************************99777766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (293 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      303  (0.0169); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.39
# Mc/sec: 2270.90
//
Query:       AHX11706.1  [L=180]
Description: NifU family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-29  101.6   0.1    3.6e-29  100.7   0.1    1.5  1  NifU      NifU-like domain
    5.2e-28   96.9   0.0    8.7e-28   96.2   0.0    1.3  1  Nfu_N     Scaffold protein Nfu/NifU N terminal
  ------ inclusion threshold ------
       0.17   12.1   0.5       0.27   11.5   0.1    1.5  2  PcfK      PcfK-like protein


Domain annotation for each model (and alignments):
>> NifU  NifU-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.7   0.1     6e-33   3.6e-29       1      67 []     112     178 ..     112     178 .. 0.99

  Alignments for each domain:
  == domain 1  score: 100.7 bits;  conditional E-value: 6e-33
                 HHHHHHH.HGGG--GG--EEEEEEEETTEEEEEEESGGGG-....THHHHHHHHHHHHH-TT--EEE CS
        NifU   1 ieevleeeirPaLasdGGdielvdvdegvVkvrlqGaCsgCpsstvtlkegiekaLkeevpevkeVe 67 
                 i+e++++++rPa+++dGG+i + ++++g+V+++lqGaC+gCpss+vtlk+gie++L+++vpevkeV+
  AHX11706.1 112 IKEIIDTKVRPAVMEDGGNIVFRGYKDGIVYLKLQGACAGCPSSAVTLKDGIENMLQYYVPEVKEVQ 178
                 89***************************************************************96 PP

>> Nfu_N  Scaffold protein Nfu/NifU N terminal
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.2   0.0   1.5e-31   8.7e-28       1      86 [.       3      88 ..       3      89 .. 0.97

  Alignments for each domain:
  == domain 1  score: 96.2 bits;  conditional E-value: 1.5e-31
       Nfu_N  1 iqteeTPNpnalkFlpgkellpegstaefksaeea.asplakkLfkiegVksVfigsdFitvtkeddvdWeelkpevlevikefles 86
                iqte+TPNpn+lkF+pg+++l+ ++ +++ s+eea +  +a+ L++++gV++V++g+dFi+++k+ d+dWe lkp++++vi e++++
  AHX11706.1  3 IQTESTPNPNSLKFFPGRQVLE-NGVIDIASEEEAsRCRIAEMLWEVQGVSGVMLGEDFISINKNVDADWEILKPQIFSVIVEYFTT 88
                9*********************.899*******999************************************************986 PP

>> PcfK  PcfK-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.1   4.5e-05      0.27      60      93 ..      76     111 ..      64     126 .. 0.69
   2 ?   -3.2   0.0       1.7   9.9e+03      35      49 ..     163     177 ..     162     179 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 4.5e-05
        PcfK  60 devyewaveYfeeddievtk..eeekaekradavsk 93 
                  ++++ +veYf+ d+++v+   +ee +e   +a ++
  AHX11706.1  76 PQIFSVIVEYFTTDSTAVQVdeAEEDIECTDAASKR 111
                 58*************999884333333333333333 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.7
        PcfK  35 leeclkYileeakkl 49 
                 +e++l+Y + e+k+ 
  AHX11706.1 163 IENMLQYYVPEVKEV 177
                 678889999999985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (180 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       470  (0.0262145); expected 358.6 (0.02)
Passed bias filter:                      380  (0.0211947); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1448.76
//
Query:       AHX11707.1  [L=129]
Description: dnaJ domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-09   38.3   0.2    2.6e-09   37.1   0.0    1.7  2  DnaJ             DnaJ domain
     0.0002   21.4   0.4    0.00062   19.8   0.1    1.8  2  Pam16            Pam16
     0.0078   16.7   0.5      0.011   16.1   0.5    1.4  1  SCIMP            SCIMP protein
  ------ inclusion threshold ------
      0.022   15.0   0.3      0.027   14.8   0.3    1.2  1  DUF4358          Domain of unknown function (DUF4358)
      0.025   13.7   1.5      0.029   13.5   1.5    1.0  1  AI-2E_transport  AI-2E family transporter
      0.028   15.4   2.6      0.038   15.0   2.6    1.4  1  DUF4834          Domain of unknown function (DUF4834)
      0.029   14.5   0.8      0.093   12.9   0.8    1.9  1  DUF2852          Protein of unknown function (DUF2852)
      0.037   14.2   0.5      0.045   13.9   0.5    1.3  1  Popeye           Popeye protein conserved region
       0.05   13.3   0.3      0.063   13.0   0.3    1.3  1  Lectin_N         Hepatic lectin, N-terminal domain
      0.081   13.4   0.2       0.12   12.8   0.2    1.4  1  SIT              SHP2-interacting transmembrane adaptor prote


Domain annotation for each model (and alignments):
>> DnaJ  DnaJ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0       2.7   4.8e+03      40      49 ..      34      43 ..      28      50 .. 0.68
   2 !   37.1   0.0   1.5e-12   2.6e-09       4      54 ..      82     128 ..      81     129 .] 0.86

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 2.7
                HHHHHHHHHH CS
        DnaJ 40 eekFkeineA 49
                +++F +i +A
  AHX11707.1 34 SKNFSQIYDA 43
                5678888776 PP

  == domain 2  score: 37.1 bits;  conditional E-value: 1.5e-12
                 HHHTSSTTG-HHHHHHHHHHHHHHHSTTTSCCHHHHHHHHH.HHHHHHHHHT CS
        DnaJ   4 eiLgvskdasedeIkkaYrklalkyHPDknpkdpeaeekFk.eineAyevLs 54 
                 eiLgvs da++ eI kaY+ l++k+HPDk       ++ F  ++n+A ++L+
  AHX11707.1  82 EILGVSVDATKTEINKAYHALVQKVHPDKG-----GSHYFTqQLNKARDTLM 128
                 79***************************9.....44555438888888886 PP

>> Pam16  Pam16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.7   0.1     0.066   1.2e+02      72      93 ..      48      69 ..      30      81 .. 0.79
   2 !   19.8   0.1   3.5e-07   0.00062      46     107 ..      66     127 ..      60     129 .] 0.90

  Alignments for each domain:
  == domain 1  score: 2.7 bits;  conditional E-value: 0.066
                HHHHHHHHHHHHHHT-CCCTS- CS
       Pam16 72 reevekryehlfevndkskGGs 93
                +e+ + ++e l++   k+  Gs
  AHX11707.1 48 MEKGNFNFENLYNFQQKDSQGS 69
                7888899**********98887 PP

  == domain 2  score: 19.8 bits;  conditional E-value: 3.5e-07
                 XXXXXXXXXX-HHHHHHHHT--G--SHHHHHHHHHHHHHHT-CCCTS-HHHHHHHHHHHHHH CS
       Pam16  46 eaaksnlkGisleeslkilnveedlnreevekryehlfevndkskGGslylqskvfrakerl 107
                 +++ s  + +s  ++ +il v+ d  + e++k y+ l +    +kGGs y+  ++ +a++ l
  AHX11707.1  66 SQGSSTTSRMSKAQAREILGVSVDATKTEINKAYHALVQKVHPDKGGSHYFTQQLNKARDTL 127
                 5678888899999**************************99**********99999988765 PP

>> SCIMP  SCIMP protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.5   6.4e-06     0.011      11      67 ..       7      64 ..       1     115 [. 0.63

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.4e-06
       SCIMP 11 ilavaiivvsvvlglilycvcrrllrqGkkw.eiakslkqkerdeekmyenvlnqspv 67
                ++ + ii++ v l ++l  ++r++lr  k++ +i  ++ +  +  +  +en  n +++
  AHX11707.1  7 LILSLIIILPVLLVIVLALIYRKKLRFSKNFsQIYDAVYEMMEKGNFNFENLYNFQQK 64
                233568888999******************9458888888888888889998874332 PP

>> DUF4358  Domain of unknown function (DUF4358)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.3   1.5e-05     0.027       6      85 ..      45     123 ..      41     129 .] 0.76

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 1.5e-05
     DUF4358   6 eidlkeldeddlkklygldkddvedyvayvsassasadevlivkakdeedaeevkkaleerledqkks..fedYlpeqyakl 85 
                 + +++e  + ++++ly+++++d ++    + +s+a+a e+l v ++ +++  e++ka  + +++   +   ++Y  +q +k+
  AHX11707.1  45 Y-EMMEKGNFNFENLYNFQQKDSQGSSTTSRMSKAQAREILGVSVDATKT--EINKAYHALVQKVHPDkgGSHYFTQQLNKA 123
                 4.78999999**********************************887644..666666666655543300334666666665 PP

>> AI-2E_transport  AI-2E family transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   1.5   1.6e-05     0.029      52     139 ..       3      89 ..       1     103 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.6e-05
  AI-2E_transport  52 avllvlllllvllvllvlllvplliaqltqlvkslpayidslqnilnelpslleelenliqalkqslskilsnilssilnsllsllas 139
                       ++l++l+l+++l +l+++++ l+     ++ k++++++d + + +++   ++e l+n  q+ +++ s++ s++ +  +  +l++  +
       AHX11707.1   3 YIILLILSLIIILPVLLVIVLALIYRKKLRFSKNFSQIYDAVYEMMEKGNFNFENLYN-FQQKDSQGSSTTSRMSKAQAREILGVSVD 89 
                      566777777777777888888899999999**************************94.55555555555555555444444444333 PP

>> DUF4834  Domain of unknown function (DUF4834)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.0   2.6   2.1e-05     0.038       3      67 ..       4      76 ..       2     119 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 2.1e-05
     DUF4834  3 fLlfilifiiailviglsilsvilrtvfglgsrkkss........ksaqkqfgnstnsnqqksqsrsetkeeg 67
                ++l il +ii++ v+ +++l+ i+r+ + ++++ ++         ++ + +f+n +n +q+ sq +s+t++  
  AHX11707.1  4 IILLILSLIIILPVLLVIVLALIYRKKLRFSKNFSQIydavyemmEKGNFNFENLYNFQQKDSQGSSTTSRMS 76
                7888999999999**************8888777776777775553333333444444444444222222222 PP

>> DUF2852  Protein of unknown function (DUF2852)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.8   5.2e-05     0.093       9      42 ..       3      59 ..       1     127 [. 0.65

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 5.2e-05
     DUF2852  9 eialivlgfilfWPlglallayllwskrlaaak.......................a 42
                 i l++l++i++ P+ l+++  l+++k+l+ +k                        
  AHX11707.1  3 YIILLILSLIIILPVLLVIVLALIYRKKLRFSKnfsqiydavyemmekgnfnfenlY 59
                6999*********************99996666333333333333332222222220 PP

>> Popeye  Popeye protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.5   2.5e-05     0.045      60     114 ..      13      67 ..       4     123 .. 0.72

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 2.5e-05
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
      Popeye  60 lvlinlaqllyllyklrpvkfekeleelYkklFqplkvsrkeFkklvseeeakil 114
                 ++l  l+ ++  l+ +++ +f+k+++++Y+++++ ++  + +F++l + ++++ +
  AHX11707.1  13 IILPVLLVIVLALIYRKKLRFSKNFSQIYDAVYEMMEKGNFNFENLYNFQQKDSQ 67 
                 3444455555666667899*************************99997777655 PP

>> Lectin_N  Hepatic lectin, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.3   3.5e-05     0.063      29      93 ..       9      79 ..       1     106 [. 0.71

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 3.5e-05
    Lectin_N 29 lllslglsllLLVvvcVigsqnsqLqreLetLketfs......nfssstlaeiqalssqggslsekvtsle 93
                l l++ l +lL++v++ i  ++ ++ ++++ + +++       nf  + l ++q+ +sqg+s+  +++  +
  AHX11707.1  9 LSLIIILPVLLVIVLALIYRKKLRFSKNFSQIYDAVYemmekgNFNFENLYNFQQKDSQGSSTTSRMSKAQ 79
                33455678899999**************9998887761112335566666666666667766666665544 PP

>> SIT  SHP2-interacting transmembrane adaptor protein, SIT
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.2   6.7e-05      0.12       3      82 ..       8      81 ..       2     108 .. 0.62

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.7e-05
         SIT  3 lllilallLlllviasllawrmkkrqkkaaeysseqisredeevlq.PieddicYanLnlqqtgtspesseekcyeqmkss 82
                +l ++ +l +llvi+  l +r+k r  k+ +  ++        v +   +++  + nL + q++ s++ss+ + +++++++
  AHX11707.1  8 ILSLIIILPVLLVIVLALIYRKKLRFSKNFSQIYDA-------VYEmMEKGNFNFENLYNFQQKDSQGSSTTSRMSKAQAR 81
                333334555677777778999999999986664444.......555344578999***99887666665555444443333 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (129 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1934  (0.10787); expected 358.6 (0.02)
Passed bias filter:                     1076  (0.0600145); expected 358.6 (0.02)
Passed Vit filter:                       138  (0.00769703); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.36
# Mc/sec: 1067.24
//
Query:       AHX11708.1  [L=57]
Description: hypothetical protein NHE_0780 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (57 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       282  (0.0157287); expected 358.6 (0.02)
Passed bias filter:                      209  (0.0116571); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.28u 0.24s 00:00:00.52 Elapsed: 00:00:00.34
# Mc/sec: 505.90
//
Query:       AHX11709.1  [L=151]
Description: NADH-quinone oxidoreductase subunit I [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.1e-15   55.8  16.0    3.2e-09   36.2   4.4    2.2  2  Fer4             4Fe-4S binding domain
    2.1e-13   50.6   9.8    3.2e-13   50.1   9.8    1.3  1  Fer4_7           4Fe-4S dicluster domain
    1.7e-11   44.9   5.0    6.3e-06   27.0   0.1    2.2  2  Fer4_16          4Fe-4S double cluster binding domain
    2.3e-11   43.7   2.3    6.7e-05   22.9   0.2    2.1  2  Fer4_21          4Fe-4S dicluster domain
    2.4e-10   40.3  20.7    7.6e-07   29.2  12.4    2.1  2  Fer4_10          4Fe-4S dicluster domain
    1.3e-09   38.1  10.0      2e-09   37.4  10.0    1.3  1  Fer4_9           4Fe-4S dicluster domain
      6e-09   36.2  18.1    2.9e-05   24.4  11.5    2.1  3  Fer4_8           4Fe-4S dicluster domain
    8.3e-08   32.0  17.7    0.00023   21.1   5.4    2.2  2  Fer4_6           4Fe-4S binding domain
    1.3e-07   31.3  11.1     0.0013   18.7   1.9    2.2  2  Fer4_2           4Fe-4S binding domain
      2e-06   27.9  10.7    0.00017   21.8   1.8    2.2  2  Fer4_4           4Fe-4S binding domain
    3.9e-05   24.1  11.7     0.0035   17.9  12.4    2.3  2  Fer4_17          4Fe-4S dicluster domain
     0.0017   18.6   5.6       0.11   12.7   0.5    2.2  2  c-SKI_SMAD_bind  c-SKI Smad4 binding domain
     0.0023   18.4  14.9       0.15   12.6   2.9    2.4  2  Fer4_13          4Fe-4S single cluster domain of Ferredoxin I
     0.0033   18.2  16.5     0.0087   16.9   4.2    2.2  2  Fer4_3           4Fe-4S binding domain
      0.004   17.3   8.2       0.16   12.2   1.0    2.2  2  Fer4_18          4Fe-4S dicluster domain
  ------ inclusion threshold ------
      0.015   15.5   4.6       0.18   12.0   0.3    2.2  2  ETF_QO           Electron transfer flavoprotein-ubiquinone ox
       0.17   12.7  11.4        1.5    9.7   1.7    2.3  3  Fer4_22          4Fe-4S dicluster domain


Domain annotation for each model (and alignments):
>> Fer4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.5   3.8   7.2e-09   7.6e-06       5      24 .]      48      67 ..      45      67 .. 0.96
   2 !   36.2   4.4   3.1e-12   3.2e-09       2      23 ..      85     106 ..      84     107 .. 0.94

  Alignments for each domain:
  == domain 1  score: 25.5 bits;  conditional E-value: 7.2e-09
                TTTSSS-THHHHHSTTTEEE CS
        Fer4  5 eekCigCGaCvevCPvgAIt 24
                ee+Ci+C++C+ +CP  AIt
  AHX11709.1 48 EERCIACKLCEAICPAQAIT 67
                79*****************7 PP

  == domain 2  score: 36.2 bits;  conditional E-value: 3.1e-12
                 EEETTTSSS-THHHHHSTTTEE CS
        Fer4   2 videekCigCGaCvevCPvgAI 23 
                  id+ kCi+CG+C e+CPv+AI
  AHX11709.1  85 DIDMTKCIYCGLCQEACPVDAI 106
                 69*******************9 PP

>> Fer4_7  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   50.1   9.8     3e-16   3.2e-13       1      52 []      50     105 ..      50     105 .. 0.87

  Alignments for each domain:
  == domain 1  score: 50.1 bits;  conditional E-value: 3e-16
      Fer4_7   1 rCigCgaCvaaCpvkaieldeeenek....gtekveidpekClgCgaCvavCPtga 52 
                 rCi C+ C+a Cp++ai+++ + +e+    +  +++id++kC++Cg C+++CP++a
  AHX11709.1  50 RCIACKLCEAICPAQAITIEAAPRESdgsrRATRYDIDMTKCIYCGLCQEACPVDA 105
                 8*****************99765555444466999*******************97 PP

>> Fer4_16  4Fe-4S double cluster binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.5   1.4   1.3e-06    0.0014       1      22 [.      50      71 ..      50      88 .. 0.78
   2 !   27.0   0.1   5.9e-09   6.3e-06       1      40 [.      90     128 ..      90     144 .. 0.69

  Alignments for each domain:
  == domain 1  score: 19.5 bits;  conditional E-value: 1.3e-06
     Fer4_16  1 rCgtCgkCaevCPtnaikekke 22
                rC+ C+ C  +CP++ai+ +++
  AHX11709.1 50 RCIACKLCEAICPAQAITIEAA 71
                6****************97733 PP

  == domain 2  score: 27.0 bits;  conditional E-value: 5.9e-09
     Fer4_16   1 rCgtCgkCaevCPtnaikekkekeiearecisy.ntaekkd 40 
                 +C+ Cg C e+CP++ai e  ++e++  ++  +    +kk+
  AHX11709.1  90 KCIYCGLCQEACPVDAIVEGPNFEFA--RENREdLIYNKKK 128
                 5*******************555554..3333313333333 PP

>> Fer4_21  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.9   0.2   6.3e-08   6.7e-05      33      58 ..      43      67 ..      32      68 .. 0.82
   2 !   20.7   0.2   3.2e-07   0.00034      35      57 ..      85     106 ..      71     118 .. 0.72

  Alignments for each domain:
  == domain 1  score: 22.9 bits;  conditional E-value: 6.3e-08
     Fer4_21 33 vlkvvedeCvGCnlCssvCPvedcie 58
                ++k  e++C++C+lC ++CP  ++i+
  AHX11709.1 43 RYKSGEERCIACKLCEAICPA-QAIT 67
                456679**************5.8887 PP

  == domain 2  score: 20.7 bits;  conditional E-value: 3.2e-07
     Fer4_21  35 kvvedeCvGCnlCssvCPvedci 57 
                  +   +C+ C lC + CPv d+i
  AHX11709.1  85 DIDMTKCIYCGLCQEACPV-DAI 106
                 4555677777777777777.443 PP

>> Fer4_10  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.2  12.4   7.2e-10   7.6e-07       6      56 .]      48     102 ..      43     102 .. 0.76
   2 !   22.7   1.2   7.3e-08   7.7e-05       4      24 ..      86     115 ..      83     136 .. 0.73

  Alignments for each domain:
  == domain 1  score: 29.2 bits;  conditional E-value: 7.2e-10
     Fer4_10   6 ddtCirCgkCvkaCPadl....tsvgakgeaseeeavrkkvekCtgcgaCveaCP 56 
                 +++Ci C+ C + CPa++     + + ++   +  + ++++ kC+ cg C+eaCP
  AHX11709.1  48 EERCIACKLCEAICPAQAitieAAPRESDGSRRATRYDIDMTKCIYCGLCQEACP 102
                 789*************9986543333334444444455699*************9 PP

  == domain 2  score: 22.7 bits;  conditional E-value: 7.3e-08
     Fer4_10   4 idddtCirCgkCvkaCPadl.........t 24 
                 id  +Ci Cg C++aCP+d+          
  AHX11709.1  86 IDMTKCIYCGLCQEACPVDAivegpnfefA 115
                 8999**************765555544441 PP

>> Fer4_9  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4  10.0   1.9e-12     2e-09       1      51 []      50     106 ..      50     106 .. 0.94

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 1.9e-12
      Fer4_9   1 kCtgCgaCveaCpagvvvedaaerkarlraase......eaCigCgaCveaCpkgai 51 
                 +C+ C+ C++ Cpa++++ +aa+r+    ++        ++Ci Cg C eaCp +ai
  AHX11709.1  50 RCIACKLCEAICPAQAITIEAAPRESDGSRRATrydidmTKCIYCGLCQEACPVDAI 106
                 6************************9998777799*******************987 PP

>> Fer4_8  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.8   2.6   0.00024      0.26      49      63 ..      49      63 ..      29      66 .. 0.68
   2 !   24.4  11.5   2.7e-08   2.9e-05       3      64 ..      49     104 ..      47     105 .. 0.79
   3 !   22.3   0.5   1.2e-07   0.00013       2      29 ..      88     126 ..      87     147 .. 0.65

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00024
      Fer4_8 49 wsCttcgaCtevCpv 63
                ++C +c+ C+  Cp 
  AHX11709.1 49 ERCIACKLCEAICPA 63
                455555555555554 PP

  == domain 2  score: 24.4 bits;  conditional E-value: 2.7e-08
      Fer4_8   3 ekCieCgaCqsaCpvlrrtk.khlldargeaaedvqeeqvleeeealwsCttcgaCtevCpvg 64 
                 e+Ci C +C++ Cp+   t    + ++ g + +  + +        + +C  cg C+e+Cpv+
  AHX11709.1  49 ERCIACKLCEAICPAQAITIeAAPRESDGSRRA-TRYDID------MTKCIYCGLCQEACPVD 104
                 68************8888875566666666555.444444......8**************96 PP

  == domain 3  score: 22.3 bits;  conditional E-value: 1.2e-07
      Fer4_8   2 lekCieCgaCqsaCp...........vlrrtkkhlldar 29 
                 + kCi Cg+Cq+aCp           ++r+ +++l +++
  AHX11709.1  88 MTKCIYCGLCQEACPvdaivegpnfeFARENREDLIYNK 126
                 789***********9666555555444444444444433 PP

>> Fer4_6  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.1   5.4   2.1e-07   0.00023       6      24 .]      48      66 ..      48      66 .. 0.95
   2 !   16.8   4.4   4.9e-06    0.0052       4      24 .]      86     106 ..      85     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 21.1 bits;  conditional E-value: 2.1e-07
      Fer4_6  6 pdkCigCgdCvrvCPegai 24
                +++Ci C  C+++CP++ai
  AHX11709.1 48 EERCIACKLCEAICPAQAI 66
                589***************8 PP

  == domain 2  score: 16.8 bits;  conditional E-value: 4.9e-06
      Fer4_6   4 idpdkCigCgdCvrvCPegai 24 
                 id  kCi Cg C  +CP +ai
  AHX11709.1  86 IDMTKCIYCGLCQEACPVDAI 106
                 8999**************998 PP

>> Fer4_2  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   2.0   2.4e-06    0.0025       6      22 .]      47      63 ..      42      63 .. 0.85
   2 !   18.7   1.9   1.2e-06    0.0013       4      21 ..      85     102 ..      82     103 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 2.4e-06
      Fer4_2  6 dtdrCigCgaCvsaCPa 22
                 ++rCi+C+ C   CPa
  AHX11709.1 47 GEERCIACKLCEAICPA 63
                689********999**8 PP

  == domain 2  score: 18.7 bits;  conditional E-value: 1.2e-06
      Fer4_2   4 vvdtdrCigCgaCvsaCP 21 
                  +d  +Ci Cg C+ aCP
  AHX11709.1  85 DIDMTKCIYCGLCQEACP 102
                 57888************* PP

>> Fer4_4  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.8   1.8   1.6e-07   0.00017       2      17 .]      49      64 ..      48      70 .. 0.93
   2 !   10.9   1.8    0.0005      0.53       3      16 ..      90     103 ..      88     109 .. 0.91

  Alignments for each domain:
  == domain 1  score: 21.8 bits;  conditional E-value: 1.6e-07
      Fer4_4  2 erCigCgsCvaaCPqg 17
                erCi C+ C+a+CP +
  AHX11709.1 49 ERCIACKLCEAICPAQ 64
                8*************65 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.0005
      Fer4_4   3 rCigCgsCvaaCPq 16 
                 +Ci Cg C  aCP+
  AHX11709.1  90 KCIYCGLCQEACPV 103
                 8************7 PP

>> Fer4_17  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.9   2.8   0.00012      0.13      42      58 ..      47      63 ..      27      66 .. 0.82
   2 !   17.9  12.4   3.3e-06    0.0035       1      58 [.      50     103 ..      50     106 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00012
     Fer4_17 42 kaslCieCgeCerkCPq 58
                  ++Ci C++Ce+ CP+
  AHX11709.1 47 GEERCIACKLCEAICPA 63
                5589************7 PP

  == domain 2  score: 17.9 bits;  conditional E-value: 3.3e-06
     Fer4_17   1 rCiqCgyClpeCpsyeaydnepkkllraaklglleeaekeekaslCieCgeCerkCPq 58 
                 rCi C+ C++ Cp  +++ +  + +++    g+ +++  +  + +Ci Cg+C+++CP 
  AHX11709.1  50 RCIACKLCEAICPAQAITIE--AAPRES--DGSRRATRYDIDMTKCIYCGLCQEACPV 103
                 7************9888555..222222..2223333334689**************6 PP

>> c-SKI_SMAD_bind  c-SKI Smad4 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.7   0.5    0.0001      0.11      13      41 ..      36      64 ..      30      71 .. 0.85
   2 !    8.2   0.5    0.0027       2.9      12      38 ..      75     101 ..      69     109 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 0.0001
  c-SKI_SMAD_bind 13 kGlfvpelyssseakCikCleCkllfspq 41
                     +G  + ++y+s e +Ci C+ C+++  +q
       AHX11709.1 36 RGEHALRRYKSGEERCIACKLCEAICPAQ 64
                     7888899****************987766 PP

  == domain 2  score: 8.2 bits;  conditional E-value: 0.0027
  c-SKI_SMAD_bind  12 ckGlfvpelyssseakCikCleCkllf 38 
                      ++G   +++y  + +kCi C  C+   
       AHX11709.1  75 SDGSRRATRYDIDMTKCIYCGLCQEAC 101
                      67888999***************9765 PP

>> Fer4_13  4Fe-4S single cluster domain of Ferredoxin I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.1   4.3   0.00041      0.43       4      18 ..      49      63 ..      48      64 .. 0.91
   2 !   12.6   2.9   0.00014      0.15       1      17 [.      86     102 ..      86     106 .. 0.95

  Alignments for each domain:
  == domain 1  score: 11.1 bits;  conditional E-value: 0.00041
     Fer4_13  4 dtCiacgaCvelaPd 18
                ++Ciac++C +++P 
  AHX11709.1 49 ERCIACKLCEAICPA 63
                89************5 PP

  == domain 2  score: 12.6 bits;  conditional E-value: 0.00014
     Fer4_13   1 VDrdtCiacgaCvelaP 17 
                 +D  +Ci cg+C e++P
  AHX11709.1  86 IDMTKCIYCGLCQEACP 102
                 7999************9 PP

>> Fer4_3  4Fe-4S binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.2   4.4      0.01        11       1      12 [.      51      62 ..      51      65 .. 0.90
   2 !   16.9   4.2   8.2e-06    0.0087       1      15 []      91     105 ..      91     105 .. 0.97

  Alignments for each domain:
  == domain 1  score: 7.2 bits;  conditional E-value: 0.01
      Fer4_3  1 CtgCgaCvevCP 12
                C+ C +C+  CP
  AHX11709.1 51 CIACKLCEAICP 62
                9*********** PP

  == domain 2  score: 16.9 bits;  conditional E-value: 8.2e-06
      Fer4_3   1 CtgCgaCvevCPvgA 15 
                 C+ Cg+C e+CPv+A
  AHX11709.1  91 CIYCGLCQEACPVDA 105
                 9************98 PP

>> Fer4_18  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   1.0   0.00015      0.16      53      74 ..      43      64 ..      17      71 .. 0.80
   2 !    9.5   1.2     0.001       1.1      50      74 ..      80     104 ..      65     113 .. 0.73

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00015
     Fer4_18 53 rkekgagdcidcescvkvcPtg 74
                r ++g+  ci+c+ c ++cP +
  AHX11709.1 43 RYKSGEERCIACKLCEAICPAQ 64
                45677889************75 PP

  == domain 2  score: 9.5 bits;  conditional E-value: 0.001
     Fer4_18  50 keerkekgagdcidcescvkvcPtg 74 
                 + +r + ++++ci c+ c + cP++
  AHX11709.1  80 RATRYDIDMTKCIYCGLCQEACPVD 104
                 5555566778899999999999875 PP

>> ETF_QO  Electron transfer flavoprotein-ubiquinone oxidoreductase, 4Fe-4S
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.3   0.00017      0.18      67     100 ..      43      77 ..      34      81 .. 0.79
   2 ?    6.5   0.3    0.0083       8.8      62      90 ..      78     106 ..      70     111 .. 0.81

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 0.00017
                 EEEE-CCC--S--HHHHH-TT--EEE-.--STT-C CS
      ETF_QO  67 klqinaqnCvhCktCdikdpsqniewv.vPeGggG 100
                 +++   + C+ Ck C+   p q i+ + +P  ++G
  AHX11709.1  43 RYKSGEERCIACKLCEAICPAQAITIEaAPRESDG 77 
                 55666789****************98625776666 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0083
                 TTSSEEEEE-CCC--S--HHHHH-TT--E CS
      ETF_QO  62 eakekklqinaqnCvhCktCdikdpsqni 90 
                 + +++++ i+ + C++C  C+   p + i
  AHX11709.1  78 SRRATRYDIDMTKCIYCGLCQEACPVDAI 106
                 5678899*************977777665 PP

>> Fer4_22  4Fe-4S dicluster domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   2.6     0.007       7.4      80      94 ..      49      63 ..      17      66 .. 0.72
   2 ?    7.7   2.3     0.006       6.4       1      15 [.      50      64 ..      50      85 .. 0.74
   3 ?    9.7   1.7    0.0014       1.5      76      94 ..      85     103 ..      77     105 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.007
     Fer4_22 80 sgCvGCgRCieacpv 94
                + C+ C  C++ cp+
  AHX11709.1 49 ERCIACKLCEAICPA 63
                555555555555554 PP

  == domain 2  score: 7.7 bits;  conditional E-value: 0.006
     Fer4_22  1 rClsCgaCtlvCptC 15
                rC++C  C ++Cp+ 
  AHX11709.1 50 RCIACKLCEAICPAQ 64
                7***********974 PP

  == domain 3  score: 9.7 bits;  conditional E-value: 0.0014
     Fer4_22  76 kfgesgCvGCgRCieacpv 94 
                  +++++C+ Cg C+eacpv
  AHX11709.1  85 DIDMTKCIYCGLCQEACPV 103
                 4578899999999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (151 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      294  (0.016398); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        19  (0.00105974); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              17  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1142.97
//
Query:       AHX11710.1  [L=295]
Description: tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.8e-61  204.7   4.6    7.3e-61  204.2   4.6    1.3  1  THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase,
    4.9e-37  126.7   0.6    7.8e-37  126.1   0.6    1.3  1  THF_DHG_CYH    Tetrahydrofolate dehydrogenase/cyclohydrolase,
  ------ inclusion threshold ------
      0.015   15.8   0.1      0.029   14.9   0.1    1.4  1  NLE            NLE (NUC135) domain


Domain annotation for each model (and alignments):
>> THF_DHG_CYH_C  Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  204.2   4.6   1.2e-64   7.3e-61       1     159 [.     123     282 ..     123     283 .. 0.96

  Alignments for each domain:
  == domain 1  score: 204.2 bits;  conditional E-value: 1.2e-64
                    SHHHHHHHHTT--.SS--HHHHHHHHHHHH.CT---TT-EEEEE---TTTHHHHHHHHHCTT-EEEEE-TTSCCHHHHHCCSSEEEE-SS-TT-B- CS
  THF_DHG_CYH_C   1 hplnlgrlvkgee.allpctpkgvvellke.tgielegkkvvvvGrsnivgkplallLleknatVtvchsktkdlaeitreadivvvavGkpelik 94 
                    hp+n+g+lv+g++  l pctp++ + l+k+  g +l+g ++vv+Grsnivgkp+a+lLl++++tVt++hsktkd++e+t +adivv+avG p+++k
     AHX11710.1 123 HPQNIGKLVLGKDaPLKPCTPTASIYLIKTvLGNDLKGLDAVVIGRSNIVGKPMATLLLHEDCTVTITHSKTKDIQEKTMHADIVVAAVGIPRFVK 218
                    899********662688************967999************************************************************* PP

                    GGGS-TT-EEEE---EEC-TTEEE-SB-HHHHCTTSSEE--TTTSCHHHHHHHHHHHHHHHHHCH CS
  THF_DHG_CYH_C  95 aemvkegavviDvGinrvekgklvGDvdfeevkevasaitPvpgGVGpmTvamllkntleaakrq 159
                    ++++k+ga+viDvGin+v + ++vGDvdf+ev+ +a++itPvp+GVGpmT+a l+ nt+ aa +q
     AHX11710.1 219 GNFIKSGATVIDVGINKV-DAEVVGDVDFQEVSGKAGFITPVPKGVGPMTIAFLMLNTVVAACMQ 282
                    ******************.9***************************************999875 PP

>> THF_DHG_CYH  Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.6   1.3e-40   7.8e-37       1     116 []       4     120 ..       4     120 .. 0.98

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 1.3e-40
                  E--HHHHHHHHHHHHHHHHHHHHHH.T---EEEEEEES--HHHHHHHHHHHHHHHHTT-EEEEEEE-TT--HHHHHHHHHHHHH-TT--EEEE-SS-S CS
  THF_DHG_CYH   1 lldGkalakeireelkeeveklkek.gvkpkLavilvgddpasevYvrnkkkaceevGieseliklpedvseeellklieelneddsvdGilvqlPlp 97 
                  ++dG+ +a+ei + ++e +++lk+     p+L vi vg++pas++Yvrnk+k++e+vGi+ ++i+lped+se+el++li++ln+d++v+Gil+qlP+p
   AHX11710.1   4 IIDGAGIAAEICSLIEEGISTLKADfDLVPRLRVIIVGNNPASQIYVRNKQKKAESVGIDAKTIALPEDTSESELVALIHQLNDDEKVNGILLQLPIP 101
                  79*********************96689********************************************************************** PP

                  TTS-HHHHHCCS-GGGBTT CS
  THF_DHG_CYH  98 khidekaileaispeKDVD 116
                  khid ++++ +i p+KDVD
   AHX11710.1 102 KHIDANKVIPSIRPDKDVD 120
                  ******************9 PP

>> NLE  NLE (NUC135) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.9   0.1   4.8e-06     0.029       2      44 ..      47      90 ..      47     103 .. 0.89

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 4.8e-06
         NLE  2 qvrFvtkded.eslavpgtplsvPasltrkqLselvnkLlkeek 44
                q++ ++k+++ es+ ++  ++++P ++++++L  l+++L ++ek
  AHX11710.1 47 QIYVRNKQKKaESVGIDAKTIALPEDTSESELVALIHQLNDDEK 90
                678889999******************************99443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (295 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       482  (0.0268838); expected 358.6 (0.02)
Passed bias filter:                      421  (0.0234815); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 2353.72
//
Query:       AHX11711.1  [L=407]
Description: hypothetical protein NHE_0783 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
     0.0011   19.1   1.8       0.24   11.4   0.0    3.7  3  COX4             Cytochrome c oxidase subunit IV
  ------ inclusion threshold ------
      0.016   15.6  34.5       0.29   11.5   0.6    5.9  6  RFXA_RFXANK_bdg  Regulatory factor X-associated C-terminal bi
       0.09   12.8   0.2        4.2    7.5   0.1    2.7  2  DUF3042          Protein of unknown function (DUF3042)
       0.31   11.3   5.0         19    5.7   0.2    4.0  5  SNAP-25          SNAP-25 family


Domain annotation for each model (and alignments):
>> COX4  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.4   0.0   5.3e-05      0.24      97     128 ..      46      77 ..      36      80 .. 0.89
   2 ?    3.2   0.1     0.018        82     104     128 ..     251     275 ..     238     278 .. 0.82
   3 ?    0.8   0.0     0.099   4.4e+02     111     128 ..     362     379 ..     347     381 .. 0.85

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 5.3e-05
        COX4  97 gpvpkTlskewqeaqlermldlkinpitGlss 128
                 g++p+T    w++ + +r+ d+  +pi+G ss
  AHX11711.1  46 GEAPSTALTHWKKLMAQRAVDQAEQPIQGTSS 77 
                 579***************************99 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.018
        COX4 104 skewqeaqlermldlkinpitGlss 128
                 ++  q +  +r++++  +pi+G ss
  AHX11711.1 251 DEIIQRQREQRAKKKAEQPIQGTSS 275
                 5556888899*************99 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.099
        COX4 111 qlermldlkinpitGlss 128
                   +r++++  +pi+G ss
  AHX11711.1 362 REQRAKKKAEQPIQGTSS 379
                 568999999*******98 PP

>> RFXA_RFXANK_bdg  Regulatory factor X-associated C-terminal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.4      0.33   1.5e+03       8      79 ..       8      86 ..       3     107 .. 0.45
   2 ?    3.1   1.9     0.026   1.2e+02       4      51 ..      89     141 ..      86     153 .. 0.69
   3 ?    5.6   0.8    0.0042        19      14      54 ..     164     204 ..     149     215 .. 0.83
   4 ?   10.5   1.5   0.00012      0.56      14      78 ..     224     283 ..     209     286 .. 0.85
   5 ?   11.5   0.6   6.5e-05      0.29       5      52 ..     288     336 ..     284     344 .. 0.83
   6 ?    8.7   1.1   0.00045         2      16      81 ..     330     389 ..     328     399 .. 0.79

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.33
  RFXA_RFXANK_bdg  8 tetttqsakqRkpwmckkhrnkmykdKykkkksDqalnskk.........elvkarlekkkeeepvsvtkqrtgsvGdrpa 79
                     t t++ s+k+  p ++    ++ y+++   + s  +l+  +         +   a+++ ++ e+p+    + ++++G+  a
       AHX11711.1  8 TPTKNDSKKRTAP-STPSPATSSYEEQSTSSGSSTVLAPGEapstalthwKKLMAQRAVDQAEQPIQ-GTSSSSAPGPSTA 86
                     5555555544443.44445555555555444333333333323222222223334444455556665.3334455555544 PP

  == domain 2  score: 3.1 bits;  conditional E-value: 0.026
  RFXA_RFXANK_bdg   4 yegctetttqsakqRk.pwmckk....hrnkmykdKykkkksDqalnskkelv 51 
                      +++++ tt+ + k+Rk +   k+     rn+  ++Ky   ++D++l++ +e+ 
       AHX11711.1  89 STSSRSTTVLAPKRRKlTPEEKRernrERNRKCSAKYYSAHRDEILQRRRESR 141
                      56777888888899987444454011156667777888889*****9999654 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0042
  RFXA_RFXANK_bdg  14 sakqRkpwmckkhrnkmykdKykkkksDqalnskkelvkar 54 
                       ++qR +     +r + y++Ky+  ++D+++++++e+    
       AHX11711.1 164 MQRQRESRARDPKRFREYEAKYRAAHRDEIIQRQRESRARD 204
                      56899999999999*******************99765544 PP

  == domain 4  score: 10.5 bits;  conditional E-value: 0.00012
  RFXA_RFXANK_bdg  14 sakqRkpwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrp 78 
                       ++qR +      + + y++Ky+  ++D+++++++    ++++kkk e+p+    + ++++G+  
       AHX11711.1 224 IQRQRESRARDPEKFREYEAKYRAAHRDEIIQRQR----EQRAKKKAEQPIQ-GTSSSSAPGPST 283
                      578999999999999******************99....8889999999999.445567777655 PP

  == domain 5  score: 11.5 bits;  conditional E-value: 6.5e-05
  RFXA_RFXANK_bdg   5 egctetttqsakqRk.pwmckkhrnkmykdKykkkksDqalnskkelvk 52 
                      +++  tt+ + k+Rk +   ++ rn+++++Ky+  ++D+++++++e+  
       AHX11711.1 288 TSSGSTTVLAPKRRKlTPEEQRERNRISQAKYRAAHHDEIMQRQRESRA 336
                      6677888999999998788899*********************996554 PP

  == domain 6  score: 8.7 bits;  conditional E-value: 0.00045
  RFXA_RFXANK_bdg  16 kqRkpwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrparP 81 
                      +qR +      + + y++Ky   ++D+++++ +    ++++kkk e+p+  t + ++++G+  ++P
       AHX11711.1 330 RQRESRARDPEKFREYRAKYYSAHHDEIIQRLR----EQRAKKKAEQPIQGT-SSSSAPGPS-GSP 389
                      68888888899999*****************99....888999999999944.455666654.344 PP

>> DUF3042  Protein of unknown function (DUF3042)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.1   0.00093       4.2      21      46 ..      95     120 ..      90     124 .. 0.91
   2 ?    2.1   0.0     0.043   1.9e+02      21      48 ..     293     321 ..     287     323 .. 0.81

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.00093
     DUF3042  21 gavfvfKkkviePiEekeakieenrk 46 
                 ++v++ K++ + P+E++e   e nrk
  AHX11711.1  95 TTVLAPKRRKLTPEEKRERNRERNRK 120
                 789999*******************9 PP

  == domain 2  score: 2.1 bits;  conditional E-value: 0.043
     DUF3042  21 gavfvfKkkviePiEe.keakieenrkkA 48 
                 ++v++ K++ + P+E+ + ++i + + +A
  AHX11711.1 293 TTVLAPKRRKLTPEEQrERNRISQAKYRA 321
                 789999*********95557888877777 PP

>> SNAP-25  SNAP-25 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.1   0.0      0.52   2.4e+03       4      37 ..     141     175 ..     140     183 .. 0.76
   2 ?    4.8   0.1     0.008        36       4      38 ..     171     206 ..     169     226 .. 0.84
   3 ?    1.8   0.0     0.069   3.1e+02       4      36 ..     201     234 ..     199     236 .. 0.85
   4 ?    5.7   0.2    0.0042        19       4      35 ..     231     263 ..     229     275 .. 0.79
   5 ?   -0.5   0.1      0.34   1.5e+03       4      29 ..     335     360 ..     316     383 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.1 bits;  conditional E-value: 0.52
     SNAP-25   4 rvksfekdkeYkktWgtnddgkVvssQP.srvvde 37 
                 r+++ e+  eY + +++   +++ ++Q  sr++d 
  AHX11711.1 141 RARDPERFCEYGAKYRAAHRDEIMQRQReSRARDP 175
                 56666777788888888999999999965777775 PP

  == domain 2  score: 4.8 bits;  conditional E-value: 0.008
     SNAP-25   4 rvksfekdkeYkktWgtnddgkVvssQP.srvvder 38 
                 r+++ ++ +eY++ +++   ++++++Q  sr++d +
  AHX11711.1 171 RARDPKRFREYEAKYRAAHRDEIIQRQReSRARDPE 206
                 6777788899*****************768988875 PP

  == domain 3  score: 1.8 bits;  conditional E-value: 0.069
     SNAP-25   4 rvksfekdkeYkktWgtnddgkVvssQP.srvvd 36 
                 r+++ ek  eY + +++   ++++++Q  sr++d
  AHX11711.1 201 RARDPEKFCEYGAKYRAAHRDEIIQRQReSRARD 234
                 778889999999***************6577777 PP

  == domain 4  score: 5.7 bits;  conditional E-value: 0.0042
     SNAP-25   4 rvksfekdkeYkktWgtnddgkVvssQP.srvv 35 
                 r+++ ek +eY++ +++   ++++++Q  +r+ 
  AHX11711.1 231 RARDPEKFREYEAKYRAAHRDEIIQRQReQRAK 263
                 889999*********************634444 PP

  == domain 5  score: -0.5 bits;  conditional E-value: 0.34
     SNAP-25   4 rvksfekdkeYkktWgtnddgkVvss 29 
                 r+++ ek +eY++ + +  +++++++
  AHX11711.1 335 RARDPEKFREYRAKYYSAHHDEIIQR 360
                 77788888888888888888888775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (407 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1525  (0.0850577); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                        21  (0.00117129); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.42
# Mc/sec: 2925.13
//
Query:       AHX11712.1  [L=403]
Description: hypothetical protein NHE_0785 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    0.00017   21.9  29.5      0.074   13.4   0.8    5.6  5  RFXA_RFXANK_bdg  Regulatory factor X-associated C-terminal bi
     0.0038   17.3   5.6       0.23   11.4   0.0    4.1  4  COX4             Cytochrome c oxidase subunit IV
  ------ inclusion threshold ------
      0.047   13.5   5.3        3.1    7.6   0.1    3.5  3  PPP1R35_C        Protein phosphatase 1 regulatory subunit 35 
       0.31   10.9   6.6        3.9    7.4   1.2    2.9  2  DUF896           Bacterial protein of unknown function (DUF89
        3.5    7.7  25.3        3.5    7.7   3.6    3.5  3  DUF4449          Protein of unknown function (DUF4449)


Domain annotation for each model (and alignments):
>> RFXA_RFXANK_bdg  Regulatory factor X-associated C-terminal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.3   2.2   0.00039       1.4      10      53 ..      40      84 ..      31     102 .. 0.76
   2 !    5.2   0.5     0.007        25      16      51 ..     107     142 ..      98     148 .. 0.82
   3 !    9.4   0.8   0.00036       1.3      15      78 ..     136     194 ..     133     198 .. 0.84
   4 ?    4.5   0.9     0.012        41      10      52 ..     204     247 ..     196     255 .. 0.78
   5 !   13.4   0.8   2.1e-05     0.074      14      78 ..     269     328 ..     260     333 .. 0.86

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00039
  RFXA_RFXANK_bdg 10 tttqsakqRk.pwmckkhrnkmykdKykkkksDqalnskkelvka 53
                      t+ + k+Rk +   k+ rn+++++Ky   ++D+++++++e+   
       AHX11712.1 40 STVLAPKRRKlTPEEKRERNRISQAKYYSAHRDEIMQRQRESRAR 84
                     555667889878889************************955443 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.007
  RFXA_RFXANK_bdg  16 kqRkpwmckkhrnkmykdKykkkksDqalnskkelv 51 
                      ++R +      + + yk+Ky+  ++D+++++++e+ 
       AHX11712.1 107 RRRESRARDPEKFREYKVKYRAAHRDEIIQRQRESR 142
                      566677778889999****************99654 PP

  == domain 3  score: 9.4 bits;  conditional E-value: 0.00036
  RFXA_RFXANK_bdg  15 akqRkpwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrp 78 
                      ++qR +      r + y+ Ky   ++D+++++++    ++++kkk e+p+    + ++++G+  
       AHX11712.1 136 QRQRESRARDPERFRGYRTKYYSAHRDEIIQRQR----EQRAKKKAEQPIQ-GTSSSSAPGPST 194
                      67899999999999******************99....8889999999999.445567777765 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.012
  RFXA_RFXANK_bdg  10 tttqsakqRk.pwmckkhrnkmykdKykkkksDqalnskkelvk 52 
                       t+ + k+Rk +   ++ rn+  ++Ky   ++D++l++ +e+  
       AHX11712.1 204 STVLAPKRRKlTPEEQRERNRKCSAKYYSAHRDEILQRRRESRA 247
                      556667888877788999*******************9996544 PP

  == domain 5  score: 13.4 bits;  conditional E-value: 2.1e-05
  RFXA_RFXANK_bdg  14 sakqRkpwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrp 78 
                       +kqR +     +r + y++Ky+  ++D++l++++    ++++kkk e+p+    + ++++G+  
       AHX11712.1 269 IQKQRESRARDPKRFREYEAKYRAAHHDEILQRQR----EQRAKKKAEQPIQ-GTSSSSAPGPST 328
                      689******************************99....8889999999999.445567777765 PP

>> COX4  Cytochrome c oxidase subunit IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.0      0.68   2.4e+03      42      61 ..      49      68 ..      41      84 .. 0.75
   2 ?    2.7   0.1     0.032   1.2e+02     107     128 ..     165     186 ..     155     189 .. 0.85
   3 ?    2.6   0.1     0.034   1.2e+02     108     128 ..     300     320 ..     284     323 .. 0.85
   4 !   11.4   0.0   6.5e-05      0.23      97     128 ..     344     375 ..     333     378 .. 0.89

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.68
        COX4 42 eLsleEkkalyrisFgqtlp 61
                +L+ eEk++  ris  + ++
  AHX11712.1 49 KLTPEEKRERNRISQAKYYS 68
                79999999877776555554 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.032
        COX4 107 wqeaqlermldlkinpitGlss 128
                  q +  +r++++  +pi+G ss
  AHX11712.1 165 IQRQREQRAKKKAEQPIQGTSS 186
                 57788899************99 PP

  == domain 3  score: 2.6 bits;  conditional E-value: 0.034
        COX4 108 qeaqlermldlkinpitGlss 128
                 q +  +r++++  +pi+G ss
  AHX11712.1 300 QRQREQRAKKKAEQPIQGTSS 320
                 7788899************99 PP

  == domain 4  score: 11.4 bits;  conditional E-value: 6.5e-05
        COX4  97 gpvpkTlskewqeaqlermldlkinpitGlss 128
                 g++p+T    w++ + +r+ d+  +pi+G ss
  AHX11712.1 344 GEAPSTALTHWKKLMAQRAVDQAEQPIQGTSS 375
                 589***************************99 PP

>> PPP1R35_C  Protein phosphatase 1 regulatory subunit 35 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1   0.00085       3.1      68     106 ..     161     199 ..     158     209 .. 0.87
   2 ?   -2.6   0.0       1.2   4.3e+03      77      94 ..     209     226 ..     203     229 .. 0.69
   3 ?    6.5   0.3    0.0019       6.8      68     106 ..     295     333 ..     265     370 .. 0.85

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.00085
   PPP1R35_C  68 eeelisqeaqqRlslapreakakpkkeklpePdlldFfd 106
                 ++e+i+++ +qR++++ +++ + ++ +++p+P+ +d+ +
  AHX11712.1 161 RDEIIQRQREQRAKKKAEQPIQGTSSSSAPGPSTADLST 199
                 68999999999999999999999999*******999976 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.2
   PPP1R35_C  77 qqRlslapreakakpkke 94 
                  +R++l p+e+++++ k+
  AHX11712.1 209 PKRRKLTPEEQRERNRKC 226
                 567778888777777665 PP

  == domain 3  score: 6.5 bits;  conditional E-value: 0.0019
   PPP1R35_C  68 eeelisqeaqqRlslapreakakpkkeklpePdlldFfd 106
                  +e+++++ +qR++++ +++ + ++ +++p+P+ +d+ +
  AHX11712.1 295 HDEILQRQREQRAKKKAEQPIQGTSSSSAPGPSTADLST 333
                 578888888888888888888888889*******99976 PP

>> DUF896  Bacterial protein of unknown function (DUF896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.4   1.2    0.0011       3.9      14      40 ..      46      73 ..      43      84 .. 0.81
   2 ?    5.2   0.4    0.0053        19      14      38 ..     210     235 ..     207     242 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.4 bits;  conditional E-value: 0.0011
      DUF896 14 ktegLTeeEkeeqkkLRk.eYlkafras 40
                k ++LT+eEk e++++ + +Y +a r +
  AHX11712.1 46 KRRKLTPEEKRERNRISQaKYYSAHRDE 73
                8899**********99653677777765 PP

  == domain 2  score: 5.2 bits;  conditional E-value: 0.0053
      DUF896  14 ktegLTeeEkeeqk.kLRkeYlkafr 38 
                 k ++LT+eE+ e++ k   +Y +a r
  AHX11712.1 210 KRRKLTPEEQRERNrKCSAKYYSAHR 235
                 8899********97245556665555 PP

>> DUF4449  Protein of unknown function (DUF4449)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.3   4.7    0.0027       9.5      60     121 ..      75     136 ..      54     138 .. 0.85
   2 ?    4.3   3.7     0.011        38      60     106 ..     135     178 ..     122     190 .. 0.80
   3 ?    7.7   3.6   0.00098       3.5      60     127 ..     239     306 ..     206     321 .. 0.78

  Alignments for each domain:
  == domain 1  score: 6.3 bits;  conditional E-value: 0.0027
     DUF4449  60 aerakeeaksdpenapniysryldalkkkftkkkekaeekekakkadkkvniavtkedsifp 121
                 ++r++e+ ++dpe+ +++  + ++a ++++ ++++++++++ +k ++ kv++   ++d+i++
  AHX11712.1  75 MQRQRESRARDPEKFREYKAKHYSAHRDEILQRRRESRARDPEKFREYKVKYRAAHRDEIIQ 136
                 6777888888*********************9999999976678889****99999999975 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.011
     DUF4449  60 aerakeeaksdpenapniysryldalkkkftkkkekaeekekakkad 106
                 ++r++e+ ++dpe+ + + ++y++a ++++ ++++++++k+   ka+
  AHX11712.1 135 IQRQRESRARDPERFRGYRTKYYSAHRDEIIQRQREQRAKK---KAE 178
                 4677788888*******************999988888843...222 PP

  == domain 3  score: 7.7 bits;  conditional E-value: 0.00098
     DUF4449  60 aerakeeaksdpenapniysryldalkkkftkkkekaeekekakkadkkvniavtkedsifpdiklpg 127
                  +r +e+ ++dpe+ + +  +y++a  +++ +k++++++++ ++ ++ ++++   ++d+i++  + ++
  AHX11712.1 239 LQRRRESRARDPEKFRGYGAKYYSAHHDEIIQKQRESRARDPKRFREYEAKYRAAHHDEILQRQREQR 306
                 4677777778********************9999999996555666999999999*****97765544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (403 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1445  (0.0805957); expected 358.6 (0.02)
Passed bias filter:                      272  (0.015171); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                        20  (0.00111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.76u 0.26s 00:00:01.02 Elapsed: 00:00:00.44
# Mc/sec: 2776.60
//
Query:       AHX11713.1  [L=601]
Description: MAP7 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    9.9e-08   32.4  47.3      0.014   15.7   2.1    7.3  7  RFXA_RFXANK_bdg  Regulatory factor X-associated C-terminal bi
    6.3e-05   22.8  12.7        1.5    8.6   0.1    5.1  4  PPP1R35_C        Protein phosphatase 1 regulatory subunit 35 
  ------ inclusion threshold ------
      0.017   14.9  18.3        4.8    7.1   0.5    5.0  4  DUF896           Bacterial protein of unknown function (DUF89


Domain annotation for each model (and alignments):
>> RFXA_RFXANK_bdg  Regulatory factor X-associated C-terminal binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.3   1.8   2.7e-05      0.16      10      78 ..      40     104 ..      31     107 .. 0.79
   2 !   15.7   2.1   2.4e-06     0.014       5      78 ..     109     178 ..     105     183 .. 0.84
   3 !   12.2   0.7     3e-05      0.18       5      52 ..     183     231 ..     179     237 .. 0.85
   4 !    6.6   1.7    0.0015         9      16      79 ..     225     283 ..     224     302 .. 0.82
   5 ?    3.4   2.7     0.015        91       9      52 ..     291     339 ..     285     359 .. 0.68
   6 ?    3.5   0.5     0.014        87      16      51 ..     363     398 ..     358     404 .. 0.81
   7 !    9.5   1.5    0.0002       1.2      16      78 ..     393     450 ..     391     455 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2.7e-05
  RFXA_RFXANK_bdg  10 tttqsakqRk.pwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrp 78 
                       t+ + k+Rk +   ++ rn+++++Ky   ++D+++++++    ++++kkk e+p+    + ++++G+  
       AHX11713.1  40 STVLAPKRRKlTPEEQRERNRISQAKYYSAHRDEIIQRQR----EQRAKKKAEQPIQG-TSSSSAPGPST 104
                      45566788887778899*********************99....88899999999994.45567777655 PP

  == domain 2  score: 15.7 bits;  conditional E-value: 2.4e-06
  RFXA_RFXANK_bdg   5 egctetttqsakqRk.pwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrp 78 
                      +++  tt+ + k+Rk +   k+ rn+++++Ky   ++D+++++++    ++++kkk e+p+    + ++++G+  
       AHX11713.1 109 TSSGSTTVLAPKRRKlTPEEKRERNRISQAKYYSAHRDEIIQRQR----EQRAKKKAEQPIQ-GTSSSSAPGPST 178
                      66778899999999988899***********************99....8889999999999.445567777765 PP

  == domain 3  score: 12.2 bits;  conditional E-value: 3e-05
  RFXA_RFXANK_bdg   5 egctetttqsakqRk.pwmckkhrnkmykdKykkkksDqalnskkelvk 52 
                      +++  tt+ + k+Rk +   k+ rn+++++Ky+  ++D+++++++e+  
       AHX11713.1 183 TSSGSTTVLAPKRRKlTPEEKRERNRISQAKYRAAHHDEIMQRQRESRA 231
                      66778899999999988899***********************996554 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.0015
  RFXA_RFXANK_bdg  16 kqRkpwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrpa 79 
                      +qR +      + + y++Ky   ++D+++++ +    ++++kkk e+p+    + ++++G+  a
       AHX11713.1 225 RQRESRARDPEKFREYRAKYYSAHHDEIIQRLR----EQRAKKKAEQPIQ-GTSSSSAPGPSTA 283
                      678888888899999****************99....8889999999999.4556677777665 PP

  == domain 5  score: 3.4 bits;  conditional E-value: 0.015
  RFXA_RFXANK_bdg   9 etttqsakqRk..pw...mckkhrnkmykdKykkkksDqalnskkelvk 52 
                       tt+ + k+Rk  p      ++ rn+++++Ky   ++D+++++++e+  
       AHX11713.1 291 STTVLAPKRRKltPEeqrERNRERNRISQAKYYSAHRDEIMQKQRESRA 339
                      5666666666654331112357899*****************9995443 PP

  == domain 6  score: 3.5 bits;  conditional E-value: 0.014
  RFXA_RFXANK_bdg  16 kqRkpwmckkhrnkmykdKykkkksDqalnskkelv 51 
                      ++R +      + + yk+Ky+  ++D++l++ +e+ 
       AHX11713.1 363 RRRESRARDPEKFREYKAKYRAAHRDEILQRRRESR 398
                      566677777889999**************9999654 PP

  == domain 7  score: 9.5 bits;  conditional E-value: 0.0002
  RFXA_RFXANK_bdg  16 kqRkpwmckkhrnkmykdKykkkksDqalnskkelvkarlekkkeeepvsvtkqrtgsvGdrp 78 
                      ++R +      r + yk+Ky   ++D+++++++    ++++kkk e+p+    + ++++G+  
       AHX11713.1 393 RRRESRARDPERFREYKAKYYSAHRDEIIQRQR----EQRAKKKAEQPIQ-GTSSSSAPGPST 450
                      56667777888999*****************99....8889999999999.445567777765 PP

>> PPP1R35_C  Protein phosphatase 1 regulatory subunit 35 C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.9   0.3   0.00086       5.1      68     106 ..      71     109 ..      68     132 .. 0.87
   2 !    6.9   0.4   0.00086       5.1      68     106 ..     145     183 ..     142     211 .. 0.88
   3 !    5.3   0.1    0.0026        16      68     106 ..     249     287 ..     245     299 .. 0.89
   4 !    8.6   0.1   0.00026       1.5      68     107 ..     417     456 ..     414     482 .. 0.76

  Alignments for each domain:
  == domain 1  score: 6.9 bits;  conditional E-value: 0.00086
   PPP1R35_C  68 eeelisqeaqqRlslapreakakpkkeklpePdlldFfd 106
                 ++e+i+++ +qR++++ +++ + ++ +++p+P+ +d+ +
  AHX11713.1  71 RDEIIQRQREQRAKKKAEQPIQGTSSSSAPGPSTADLST 109
                 68999999999999999999999999*******999976 PP

  == domain 2  score: 6.9 bits;  conditional E-value: 0.00086
   PPP1R35_C  68 eeelisqeaqqRlslapreakakpkkeklpePdlldFfd 106
                 ++e+i+++ +qR++++ +++ + ++ +++p+P+ +d+ +
  AHX11713.1 145 RDEIIQRQREQRAKKKAEQPIQGTSSSSAPGPSTADLST 183
                 68999999999999999999999999*******999976 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.0026
   PPP1R35_C  68 eeelisqeaqqRlslapreakakpkkeklpePdlldFfd 106
                  +e+i++  +qR++++ +++ + ++ +++p+P+ +d+ +
  AHX11713.1 249 HDEIIQRLREQRAKKKAEQPIQGTSSSSAPGPSTADLST 287
                 68999999999999999999999999*******999976 PP

  == domain 4  score: 8.6 bits;  conditional E-value: 0.00026
   PPP1R35_C  68 eeelisqeaqqRlslapreakakpkkeklpePdlldFfdP 107
                 ++e+i+++ +qR++++ +++ + ++ +++p+P+ +d+ + 
  AHX11713.1 417 RDEIIQRQREQRAKKKAEQPIQGTSSSSAPGPSTADLSTS 456
                 68999*99999999999999999999**********9874 PP

>> DUF896  Bacterial protein of unknown function (DUF896)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.4   0.6    0.0014       8.3      14      39 ..      46      72 ..      43      78 .. 0.79
   2 ?    7.1   0.5   0.00081       4.8      14      39 ..     120     146 ..     117     152 .. 0.79
   3 ?    6.4   0.4    0.0014       8.3      14      31 ..     194     211 ..     191     226 .. 0.81
   4 ?    4.9   0.4     0.004        24      14      31 ..     298     315 ..     295     332 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.4 bits;  conditional E-value: 0.0014
      DUF896 14 ktegLTeeEkeeqkkLRk.eYlkafra 39
                k ++LT+eE+ e++++ + +Y +a r 
  AHX11713.1 46 KRRKLTPEEQRERNRISQaKYYSAHRD 72
                8899**********9965267776665 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00081
      DUF896  14 ktegLTeeEkeeqkkLRk.eYlkafra 39 
                 k ++LT+eEk e++++ + +Y +a r 
  AHX11713.1 120 KRRKLTPEEKRERNRISQaKYYSAHRD 146
                 8899**********9965267776665 PP

  == domain 3  score: 6.4 bits;  conditional E-value: 0.0014
      DUF896  14 ktegLTeeEkeeqkkLRk 31 
                 k ++LT+eEk e++++ +
  AHX11713.1 194 KRRKLTPEEKRERNRISQ 211
                 8899*********99865 PP

  == domain 4  score: 4.9 bits;  conditional E-value: 0.004
      DUF896  14 ktegLTeeEkeeqkkLRk 31 
                 k ++LT+eE+ e+++ R+
  AHX11713.1 298 KRRKLTPEEQRERNRERN 315
                 8899*********98775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (601 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1457  (0.081265); expected 358.6 (0.02)
Passed bias filter:                      273  (0.0152267); expected 358.6 (0.02)
Passed Vit filter:                        52  (0.00290033); expected 17.9 (0.001)
Passed Fwd filter:                        29  (0.00161749); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 1.03u 0.30s 00:00:01.33 Elapsed: 00:00:00.46
# Mc/sec: 3909.80
//
Query:       AHX11714.1  [L=41]
Description: hypothetical protein NHE_0787 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       127  (0.0070835); expected 358.6 (0.02)
Passed bias filter:                       99  (0.00552178); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 322.26
//
Query:       AHX11715.1  [L=366]
Description: calcineurin-like phosphoesterase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.3e-14   54.4   1.3    4.8e-14   53.3   1.3    1.6  1  Metallophos    Calcineurin-like phosphoesterase
    2.9e-07   30.8   0.0    6.7e-07   29.6   0.0    1.6  1  Metallophos_2  Calcineurin-like phosphoesterase superfamily d
     0.0081   15.2   0.0      0.012   14.6   0.0    1.2  1  PhoD           PhoD-like phosphatase


Domain annotation for each model (and alignments):
>> Metallophos  Calcineurin-like phosphoesterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.3   1.3   8.1e-18   4.8e-14       2     203 ..     107     297 ..     106     298 .. 0.69

  Alignments for each domain:
  == domain 1  score: 53.3 bits;  conditional E-value: 8.1e-18
                  EEEEEESBTB......TTCCTHHHHHHHHHHHHHHHTTESEEEEESTSSSSS.....HHHHHHHHHHHHHHHH...TSEEEEEC-TTSCHHHHHHHHH CS
  Metallophos   2 rilvigDlHl......algggqlddllkllddllreekpdlvllaGDlvdrg.....dlekellellaalvky...pipvylllGNHegfeeellnky 85 
                  ri++igD+++      +  ++  + +++++  +  +  pd+v+++GD+++r      ++++++++++ +  ++   +ip+ l++GNHe    ++ +  
   AHX11715.1 107 RIAIIGDTGCrvksfiSQDCEKNWFFQEIVGLVVGH-SPDMVIHVGDYIYREkgyqdNWDTWTADFFLPAARLldsNIPLLLVRGNHE----DCRRNG 199
                  89*******999988866666666677777666777.**************889***9999999997555555677************....888886 PP

                  HHHHHHHHHHEHHHCEEETSEEEEEETTE...EEEEEEESECEEETHHHHHHHHHHHSCHHHHCCHHHHHH...HHHHTTCSEEEEEESSESSCSSSC CS
  Metallophos  86 gylgifsepwrsdaevfnnlplaslgsgs...lkvlllhGgspellvsldklgslnleleapepgdewlkd...lekrekadwvivlgHsplyrgsgy 177
                    +    +  +++++  + ++ +++ +     ++                               +++l d     + ++++ + +l+H+p+     +
   AHX11715.1 200 NGWFALLGRENKECQDHEQPYAIDINGRRlavIDSTYE---------------------------KNLLTDleeINATTDTKRTWILTHKPII-FRNK 269
                  66666633333333444444444433331221111111...........................3444444445566777778888999999.7777 PP

                  SCCHHHHHHHHHHTT..ESEEEEESSSS CS
  Metallophos 178 lfgdealedllkkyg..vdlvisGHtHv 203
                   + +  + ++ kk +  + l isGH+Hv
   AHX11715.1 270 AHIPVGYIEFAKKLKkeIELFISGHIHV 297
                  77777777775555556**********7 PP

>> Metallophos_2  Calcineurin-like phosphoesterase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.6   0.0   1.1e-10   6.7e-07       3     135 ..     108     303 ..     107     340 .. 0.59

  Alignments for each domain:
  == domain 1  score: 29.6 bits;  conditional E-value: 1.1e-10
  Metallophos_2   3 laiiSDlH...........snldaleavlealkevgvdaiihaGDl.eeeep............e.vleellela....pvlaVrGNnD....... 62 
                    +aii D+            ++ +  ++++  + ++++d++ih+GD+ + e+                 ++l   +    p+l VrGN++       
     AHX11715.1 108 IAIIGDTGcrvksfisqdcEKNWFFQEIVGLVVGHSPDMVIHVGDYiYREKGyqdnwdtwtadfFlPAARL---LdsniPLLLVRGNHEdcrrngn 200
                    5666666666666666666566667788899999***********87444445566666655321233333...25669**********8987755 PP

  Metallophos_2  63 ...eevveedvlreaaelgtdlpeeaelelagekvlliHgdpl...............................gvkdalaellkeaeegsd..vv 122
                              ++re++e++++  +   ++++g+++++i ++                                 +++  + +  ++++ +++  ++
     AHX11715.1 201 gwfA-----LLGRENKECQDHE-QPYAIDINGRRLAVIDSTYEknlltdleeinattdtkrtwilthkpiifrnKAHIPVGYIEFAKKLKKEieLF 290
                    4440.....4444444443322.333333334444444333223334444444444444444444444448*9955555555555544444455** PP

  Metallophos_2 123 vcGHtHvpeveke 135
                    ++GH+Hv++  k 
     AHX11715.1 291 ISGHIHVAQFLKF 303
                    *******965554 PP

>> PhoD  PhoD-like phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0     2e-06     0.012      22      46 ..     141     162 ..     123     178 .. 0.73

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 2e-06
        PhoD  22 eeedlDlvlhlGDyiYeygpgeyas 46 
                  + ++D+v+h+GDyiY ++  +y+ 
  AHX11715.1 141 GH-SPDMVIHVGDYIYREK--GYQD 162
                 34.9************995..3433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (366 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      358  (0.0199677); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.51u 0.26s 00:00:00.77 Elapsed: 00:00:00.44
# Mc/sec: 2473.91
//
Query:       AHX11716.1  [L=426]
Description: tol-Pal system beta propeller repeat protein TolB [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-32  110.1  10.2    2.3e-09   36.9   0.1    6.5  6  PD40             WD40-like Beta Propeller Repeat
    3.4e-09   35.9   0.0     0.0096   14.7   0.0    4.9  4  DPPIV_N          Dipeptidyl peptidase IV (DPP IV) N-terminal 
    3.1e-07   30.5   0.1    8.4e-07   29.1   0.1    1.8  1  TolB_N           TolB amino-terminal domain
    2.8e-06   26.3   0.0     0.0089   14.7   0.1    2.4  2  Pectate_lyase22  Oligogalacturonate lyase
    0.00052   19.8   0.0      0.034   13.9   0.0    2.9  4  Gmad1            Lipoprotein LpqB beta-propeller domain
  ------ inclusion threshold ------
      0.026   14.4   0.0        5.9    6.7   0.0    3.1  3  eIF2A            Eukaryotic translation initiation factor eIF
       0.03   14.6   0.0        2.8    8.3   0.0    3.2  2  ANAPC4_WD40      Anaphase-promoting complex subunit 4 WD40 do
        0.1   13.0   0.0        0.7   10.3   0.0    2.2  2  DUF4467          Domain of unknown function with cystatin-lik
       0.67    9.7   4.4         57    3.5   0.1    4.4  4  Proteasome_A_N   Proteasome subunit A N-terminal signature


Domain annotation for each model (and alignments):
>> PD40  WD40-like Beta Propeller Repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.8   0.0   2.5e-06    0.0049      13      28 ..     193     208 ..     185     216 .. 0.89
   2 !   11.6   0.0   0.00011      0.21      10      23 ..     234     247 ..     227     259 .. 0.83
   3 !   36.9   0.1   1.2e-12   2.3e-09       2      38 .]     270     305 ..     269     305 .. 0.94
   4 !   24.5   0.2     9e-09   1.8e-05       2      36 ..     314     347 ..     313     349 .. 0.92
   5 !   19.0   0.0   4.9e-07   0.00097       3      32 ..     358     389 ..     356     398 .. 0.77
   6 ?    2.1   0.0     0.098     2e+02       3      17 ..     407     421 ..     406     422 .. 0.90

  Alignments for each domain:
  == domain 1  score: 16.8 bits;  conditional E-value: 2.5e-06
                 EEEE-TTSSEEEEEEE CS
        PD40  13 aPsfSPDGkrlaFsSd 28 
                  P+fSPDG+++++ S+
  AHX11716.1 193 TPRFSPDGSKIVYMSY 208
                 6************997 PP

  == domain 2  score: 11.6 bits;  conditional E-value: 0.00011
                 .EEEEEE-TTSSEE CS
        PD40  10 negaPsfSPDGkrl 23 
                    aP+fSPDGk+ 
  AHX11716.1 234 VVSAPRFSPDGKSV 247
                 5579********86 PP

  == domain 3  score: 36.9 bits;  conditional E-value: 1.2e-12
                 EE--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEEEE CS
        PD40   2 krltntpgnegaPsfSPDGkrlaFsSdRgsGkpdIyv 38 
                 k+lt +++++++Ps+SPD +r++F+SdR+ G+p++y+
  AHX11716.1 270 KKLTVHSAINTSPSYSPDQTRIVFTSDRS-GSPQLYT 305
                 6788899**********************.******5 PP

  == domain 4  score: 24.5 bits;  conditional E-value: 9e-09
                 EE--SSSS.EEEEEE-TTSSEEEEEEECT.TCEEE CS
        PD40   2 krltntpgnegaPsfSPDGkrlaFsSdRgsGkpdI 36 
                 kr+ ++ g ++aP +SP G  +aF+  R+  ++ I
  AHX11716.1 314 KRISFGGGSYTAPVWSPRGDLIAFTTVRN-RQFYI 347
                 8999************************9.88887 PP

  == domain 5  score: 19.0 bits;  conditional E-value: 4.9e-07
                 E--SSSS.EEEEEE-TTSSEEEEEEECT...T CS
        PD40   3 rltntpgnegaPsfSPDGkrlaFsSdRg..sG 32 
                 r++ t    ++P++ P+G+ +aF+++     G
  AHX11716.1 358 RILATGHLVEGPTWAPNGRLIAFTREERsvNG 389
                 56666666799**************9765555 PP

  == domain 6  score: 2.1 bits;  conditional E-value: 0.098
                 E--SSSS.EEEEEE- CS
        PD40   3 rltntpgnegaPsfS 17 
                 rl++t  n  +Ps+S
  AHX11716.1 407 RLLPTKHNASDPSWS 421
                 8999999*******9 PP

>> DPPIV_N  Dipeptidyl peptidase IV (DPP IV) N-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0   4.8e-06    0.0096     216     301 ..     128     208 ..      60     211 .. 0.71
   2 !    4.3   0.0    0.0071        14      20      61 ..     210     251 ..     197     254 .. 0.85
   3 !    9.5   0.0   0.00018      0.36     243     302 ..     275     350 ..     250     360 .. 0.68
   4 ?    0.3   0.0      0.11   2.2e+02     107     119 ..     370     382 ..     364     389 .. 0.68

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 4.8e-06
                 ETTTCCEEEEEEEESSS-SSS-S-EEE-TTTSSEEEEEEETTSSEEEEEEESSS-C.EEESS-SSS-EEEEEEEETTTTEEEEEES CS
     DPPIV_N 216 daetgravvkleetsdgWvelhdevhflkrdesgflwisekdGfkHLylfdldgkseikqlTsGeweVtsilavdekrdlvyFtat 301
                   ++++ +v+++  +  + +l+ +v ++   ++++  +se dG k+L+++d dg++  + +T G + V    +++ + +++ + ++
  AHX11716.1 128 SNAQNHRKVAHSIADSIYTKLTGDVGYF---NTSIAHTSEIDGKKRLAIMDQDGAN-LRFITDGRFLV-LTPRFSPDGSKIVYMSY 208
                 23568888888999**************...99***********************.***********.55677777777777765 PP

  == domain 2  score: 4.3 bits;  conditional E-value: 0.0071
                 EETTEEEEEETTTEECEEEETTTT.BSEEEEESSTTEEEEEE CS
     DPPIV_N  20 sytaeyyiydletneveelspgeeklqlakwSPagdklafvr 61 
                 +++++++i+dle+++ + + + ++ ++ +++SP+g++++   
  AHX11716.1 210 KLQGKVFIKDLEKRKDTMVGNFKGVVSAPRFSPDGKSVILAT 251
                 57899********9999999999************9998665 PP

  == domain 3  score: 9.5 bits;  conditional E-value: 0.00018
                 -.........TTTSSEEEEEEETTSSEEEEEEESSS-C.EE.ESS-SSS-E......EEEEEEETTTTEEEEEESS CS
     DPPIV_N 243 l.........krdesgflwisekdGfkHLylfdldgkseik.qlTsGeweV......tsilavdekrdlvyFtatk 302
                           ++d+++++++s+++G  +Ly ++ +g+s+++     G++        ++++a+   r++ +++++ 
  AHX11716.1 275 HsaintspsySPDQTRIVFTSDRSGSPQLYTMNANGASQKRiSFGGGSYTApvwsprGDLIAFTTVRNRQFYIGVM 350
                 233444466669999*******************999966676666666656666677788998888888888875 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.11
                 EE-TTSSEEEEEE CS
     DPPIV_N 107 wWspdgsrlaylr 119
                  W+p+g+ +a++r
  AHX11716.1 370 TWAPNGRLIAFTR 382
                 5777777777766 PP

>> TolB_N  TolB amino-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.1   0.1   4.2e-10   8.4e-07       1     105 [.      20     120 ..      20     121 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.1 bits;  conditional E-value: 4.2e-10
                 BXXEEEESGGGSEEEEE---EESSSS.S-SS-HHHHHHHHHHHTTSEEE--GGG-S---SSGGG--HHHHHTTT-SEEEEEEEE-TTSE.EEEEEEEEE CS
      TolB_N   1 leieItkggaealpiAvvpfksegsaeelaediseviaaDLerSGlFrpldksafpqkpsseaevdfadWkalgadalvtGsvtesgdgrlkvefrLwD 99 
                 l+i+I++g+a+++++  v+  +e+ +   ++ i++++aaDL+ +G  ++ ++++++ ++ +++  +f   ++   ++++  +v+ s+dg+l+v++r +D
  AHX11716.1  20 LKIDINRGNASKIKLILVQCTQEDHN--KGSIIANIVAADLASTGFLDVQPNTEIKCNA-NASISNFGTLRDTD-NLILSLAVSLSEDGKLTVKYRAID 114
                 68******************988877..9****************88888888877654.78888999999876.567777888888899********* PP

                 -SSSTX CS
      TolB_N 100 vvkgke 105
                 +  +k+
  AHX11716.1 115 TSIRKQ 120
                 988777 PP

>> Pectate_lyase22  Oligogalacturonate lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    9.0   0.0   0.00026      0.51     216     270 ..     169     221 ..     155     241 .. 0.80
   2 !   14.7   0.1   4.5e-06    0.0089     328     381 ..     255     307 ..     236     311 .. 0.82

  Alignments for each domain:
  == domain 1  score: 9.0 bits;  conditional E-value: 0.00026
  Pectate_lyase22 216 armwlinedgsnlrkvkehaegescthevwvpdgsalayvsylkgsterviysad 270
                       r+ ++++dg+nlr + +       t   + pdgs ++y+sy k + + +i + +
       AHX11716.1 169 KRLAIMDQDGANLRFITDG-RFLVLT-PRFSPDGSKIVYMSYSKLQGKVFIKDLE 221
                      5888999*******99653.333444.4568**************9999997654 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 4.5e-06
  Pectate_lyase22 328 kkgtqaklakhdtswkvlegdrqvthphpsftpddkqvlftsdvegkpalylak 381
                       +   +++  h+   k l     +    ps++pd+ +++ftsd +g p ly ++
       AHX11716.1 255 ANTDIHRVYLHNNVQKKLTVHSAI-NTSPSYSPDQTRIVFTSDRSGSPQLYTMN 307
                      556667888888888888877766.468***********************765 PP

>> Gmad1  Lipoprotein LpqB beta-propeller domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.4   0.0      0.78   1.6e+03     123     123 ..     200     200 ..     153     274 .. 0.62
   2 !   13.9   0.0   1.7e-05     0.034      25      78 ..     279     334 ..     265     344 .. 0.87
   3 !    6.1   0.0    0.0042       8.4      31      92 ..     329     391 ..     329     407 .. 0.83
   4 ?    0.3   0.0      0.24   4.8e+02      20      73 ..     362     421 ..     357     423 .. 0.72

  Alignments for each domain:
  == domain 1  score: -1.4 bits;  conditional E-value: 0.78
       Gmad1 123 G 123
                 G
  AHX11716.1 200 G 200
                 2 PP

  == domain 2  score: 13.9 bits;  conditional E-value: 1.7e-05
       Gmad1  25 lrsaAvSrdgqqvaavtapdggrtLvvgsyggeasevl..eggsltrpSwdrdgal 78 
                  +s++ S+d +++++ ++ +g+ +L++++ +g+ ++ +   ggs+t+p w++ g+l
  AHX11716.1 279 NTSPSYSPDQTRIVFTSDRSGSPQLYTMNANGASQKRIsfGGGSYTAPVWSPRGDL 334
                 5799*************999********999999888878999*********9987 PP

  == domain 3  score: 6.1 bits;  conditional E-value: 0.0042
       Gmad1  31 SrdgqqvaavtapdggrtLvvg..syggeasevl.eggsltrpSwdrdgalWvvedgaevvravr 92 
                 S++g+ +a+ t    +r+ ++g  +++g  + +l +g+ +  p+w ++g l +  +++++v+ +r
  AHX11716.1 329 SPRGDLIAFTT--VRNRQFYIGvmKPDGSGERILaTGHLVEGPTWAPNGRLIAFTREERSVNGKR 391
                 789999*****..66666666545999999999967888889********999988888887665 PP

  == domain 4  score: 0.3 bits;  conditional E-value: 0.24
       Gmad1  20 egavdlrsaAvSrdgqqvaavt......apdggrtLvvgsyggeasevl.eggsltrpSwd 73 
                  g+  ++ +  +++g+ +a+         +++ ++++ ++  g+ + +l ++++ ++pSw+
  AHX11716.1 362 TGH-LVEGPTWAPNGRLIAFTReersvnGKRSISKIYSIDITGKNERLLpTKHNASDPSWS 421
                 455.667777788888888888777665556666778888888888888677899999997 PP

>> eIF2A  Eukaryotic translation initiation factor eIF2A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.7   0.0    0.0029       5.9     107     163 ..     195     252 ..     191     257 .. 0.85
   2 ?    2.8   0.0     0.048        96      84     129 ..     300     349 ..     251     380 .. 0.60
   3 ?    1.4   0.0      0.12   2.5e+02      13      69 ..     371     422 ..     368     425 .. 0.73

  Alignments for each domain:
  == domain 1  score: 6.7 bits;  conditional E-value: 0.0029
                 EE-TTSSEEEEE-TTSSS-EEEEEETT.TTEEEEEEE-TT--EEEE-TTSSEEEEEE- CS
       eIF2A 107 ffspkgklvllaGfgnlaGeleiwdvk.kkkkiakaeaanatlvewspdgryvlTatt 163
                  fsp g  ++   +  l+G++ i d + +k+++    +   +   +spdg+ v+ at+
  AHX11716.1 195 RFSPDGSKIVYMSYSKLQGKVFIKDLEkRKDTMVGNFKGVVSAPRFSPDGKSVILATS 252
                 69*********************9999555566666666778889******9999887 PP

  == domain 2  score: 2.8 bits;  conditional E-value: 0.048
                 EEEEEECS....CEEEEEEEEES--EEEE-TTSSEEEEE-TTSSS-EEEE CS
       eIF2A  84 kvslfdlk....vkviskleeqkrNtiffspkgklvllaGfgnlaGelei 129
                 + +l+ ++     ++  +++  +  + ++sp+g l+++   +n +  + +
  AHX11716.1 300 SPQLYTMNangaSQKRISFGGGSYTAPVWSPRGDLIAFTTVRNRQFYIGV 349
                 44556555344455566777777777788888888888877776655555 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.12
                 E-TTTTEEEEEEE.E--TT-CEEEEEEEEEESSSTT--EEECCEESSS.EEEEEE-T CS
       eIF2A  13 WnkkGtsllvlvstevdktnksyygetelyliklkkkksevvelkkegpihdvaWsp 69 
                 W  +G  +++  +   +++ +   + +++y i++++k++  ++ k++  + d +Ws 
  AHX11716.1 371 WAPNGRLIAFTRE---ERSVNGKRSISKIYSIDITGKNERLLPTKHN--ASDPSWSD 422
                 6666666666555...4445555556899********9999988777..79999986 PP

>> ANAPC4_WD40  Anaphase-promoting complex subunit 4 WD40 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.3   0.0       0.1   2.1e+02      39      72 ..     233     267 ..     206     282 .. 0.76
   2 ?    8.3   0.0    0.0014       2.8       3      62 ..     328     387 ..     327     406 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.3 bits;  conditional E-value: 0.1
  ANAPC4_WD40  39 sevrsLaWkpdgklLavaysdg.evrlldaesgkv 72 
                  + v++ +++pdgk    a+s+g +  ++ ++  + 
   AHX11716.1 233 GVVSAPRFSPDGKSVILATSNGaNTDIHRVYLHNN 267
                  55777789*************96667777765444 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.0014
  ANAPC4_WD40   3 wcptmDLiAlatedge...llvfRl..ngqrvwtleedkedsevrsLaWkpdgklLavaysdgev 62 
                  w+p  DLiA+ t +++   + v     +g+r+  +     ++ v++  W p+g+l+a+  ++ +v
   AHX11716.1 328 WSPRGDLIAFTTVRNRqfyIGVMKPdgSGERILAT-----GHLVEGPTWAPNGRLIAFTREERSV 387
                  99999999999977653335566653345888887.....999*************998877655 PP

>> DUF4467  Domain of unknown function with cystatin-like fold (DUF4467)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00035       0.7      24      80 ..     167     223 ..     155     233 .. 0.84
   2 ?    0.4   0.0      0.42   8.4e+02      30      80 ..     231     281 ..     218     289 .. 0.74

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00035
     DUF4467  24 ndvevd.ikkedanvyVyedgKlivlaykllknreevtyvaYeikdkkveykrdindk 80 
                  +++   ++++ an +   dg+++vl  +   +  ++ y+ Y + ++kv +k d++++
  AHX11716.1 167 GKKRLAiMDQDGANLRFITDGRFLVLTPRFSPDGSKIVYMSYSKLQGKVFIK-DLEKR 223
                 45666668999*************************************9774.66665 PP

  == domain 2  score: 0.4 bits;  conditional E-value: 0.42
     DUF4467  30 ikkedanvyVyedgKlivlaykllknreevtyvaYeikdkkveykrdindk 80 
                 +k   +  +   dgK ++la     n +  + +  +  +kk   +  in  
  AHX11716.1 231 FKGVVSAPRFSPDGKSVILATSNGANTDIHRVYLHNNVQKKLTVHSAINTS 281
                 55555555666799*****99999999999999999999999988888865 PP

>> Proteasome_A_N  Proteasome subunit A N-terminal signature
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.3      0.11   2.1e+02       8      12 ..     196     200 ..     193     201 .. 0.87
   2 ?    3.5   0.1     0.028        57       7      13 ..     239     245 ..     236     245 .. 0.84
   3 ?   -0.3   0.0      0.46   9.2e+02       7      14 ..     327     334 ..     323     335 .. 0.83
   4 ?    1.8   0.0     0.096   1.9e+02       7      14 ..     370     377 ..     369     378 .. 0.91

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.11
  Proteasome_A_N   8 FSPdG 12 
                     FSPdG
      AHX11716.1 196 FSPDG 200
                     ****9 PP

  == domain 2  score: 3.5 bits;  conditional E-value: 0.028
  Proteasome_A_N   7 tFSPdGR 13 
                      FSPdG+
      AHX11716.1 239 RFSPDGK 245
                     5*****7 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.46
  Proteasome_A_N   7 tFSPdGRL 14 
                     ++SP G L
      AHX11716.1 327 VWSPRGDL 334
                     8***9987 PP

  == domain 4  score: 1.8 bits;  conditional E-value: 0.096
  Proteasome_A_N   7 tFSPdGRL 14 
                     t+ P GRL
      AHX11716.1 370 TWAPNGRL 377
                     9******9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (426 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       606  (0.0338); expected 358.6 (0.02)
Passed bias filter:                      516  (0.0287802); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.62u 0.26s 00:00:00.88 Elapsed: 00:00:00.44
# Mc/sec: 2931.02
//
Query:       AHX11717.1  [L=398]
Description: 5-aminolevulinic acid synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.6e-70  236.3   0.0    6.4e-70  236.1   0.0    1.0  1  Aminotran_1_2    Aminotransferase class I and II
      6e-09   34.9   0.0    9.4e-09   34.3   0.0    1.2  1  Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
     0.0011   18.0   0.0     0.0017   17.4   0.0    1.3  1  Aminotran_5      Aminotransferase class-V
     0.0033   16.8   0.1     0.0045   16.3   0.1    1.3  1  Beta_elim_lyase  Beta-eliminating lyase
  ------ inclusion threshold ------
       0.13   12.7   0.1         28    5.3   0.0    2.7  2  DUF1843          Domain of unknown function (DUF1843)


Domain annotation for each model (and alignments):
>> Aminotran_1_2  Aminotransferase class I and II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.1   0.0   1.8e-73   6.4e-70       3     362 ..      46     388 ..      44     389 .. 0.96

  Alignments for each domain:
  == domain 1  score: 236.1 bits;  conditional E-value: 1.8e-73
                    EEESSSSSTTSTTSSHHHHHHHHHHHH..HHHHHTSTTST-BTTHHHHHHHHHHHHHCTCTTCHTTGGEGEEEESHHHHHHHHHHHHHHHTTT-EE CS
  Aminotran_1_2   3 vinLgsneylgdsgkptlpevakaeke..galaggtlneygpidglpeleealakflgrseklklkreaavvvgsGagaliealifllklnpgdei 96 
                    ++ ++sn+ylg++++ t+ + +k++++  ga+aggt+n++g+++    le+++ak+++        +eaa+ +  G+ a+++ + +l++l+ ++  
     AHX11717.1  46 IVLWCSNDYLGMGQNFTVCDSMKETIDrmGAGAGGTRNISGNNKEVVLLEQEIAKLHH--------KEAALSFVCGYVANLASISTLTSLMEDCIA 133
                    789************6666667777777******************************........999*************************** PP

                    EEEESS-THHHHHHHHTTSEEEEEEBEETTTTEE-HHHHHHHHTTHHCTTETEEEEEEESS-TTT--B--HHHHHHHHHHHHHTTEEEEEEETTTT CS
  Aminotran_1_2  97 lvpdptyasyknilrlsggevvryplyseedfhldlealeealkeapegnkktkvilvesphNPtGtvatleeleklldlakkynlllfvDeaYag 192
                    ++++ +++s++++++ s++e + ++       h+dl++lee+l++ap++    k+i++es+++++G++a+ e +++l   a+ky++l+++De++a+
     AHX11717.1 134 FSDQYNHSSIIEGIKSSRCEKRIFH-------HNDLKHLEELLSQAPQHTY--KIIIFESVYSMDGDIAPIEGICDL---AEKYGALTYIDEVHAV 217
                    *************************.......*******************..************************...**************** PP

                    CBSSSSHTHHH..HGGSTTSTTEEEEEESSSTTSSGGG-EEEEEEEHHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
  Aminotran_1_2 193 fvfgsldavat..ranveeepnllivgslsKafGlaGeRvGyilgnaavvsqlrklsrpflsssllqaavaaalsdallkqseleemrqrlqkrrk 286
                    +++g+++a  +   +++ ++++ +i g+l+Ka+G+ G   Gy++++a++++ +r+ +++f+++++l++++aaa + + ++  + + +r++  ++  
     AHX11717.1 218 GMYGKHGAG-IseELGLTDRID-IIQGTLAKAYGVIG---GYVAAKANIIDVIRSHASGFIFTTALPPVIAAAGRSSIRHLYNSDIERKKQRENVG 308
                    ****98543.235999*****9.**************...**************************************999899999********* PP

                    HHHHHHHHSTEEEECCSCSSEEEEEETHHCHHHHHHHHHHTCTEEEEEGGGGTS...TTEEEEEC.TTS-HHHHHHHHHH CS
  Aminotran_1_2 287 elrdeLaelglkvlasqsgmflltdlsaetakelskkLleevgvyvtpgtsftv...pgrlRitv.Aglteeeleelvea 362
                    +l+  L++ ++k+l+s+++++++  +++e+ k +sk Llee+++ ++ ++++tv   ++rlRit+ + +t++++eelv a
     AHX11717.1 309 KLKILLKQNNIKFLESPTHIVPIIIGNPEQCKLASKRLLEEFKIFIQYINYPTVprgTERLRITPtPQHTDKMMEELVLA 388
                    ******999********************99999999********************9******************9865 PP

>> Cys_Met_Meta_PP  Cys/Met metabolism PLP-dependent enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.3   0.0   2.6e-12   9.4e-09      51     181 ..      88     220 ..      81     228 .. 0.84

  Alignments for each domain:
  == domain 1  score: 34.3 bits;  conditional E-value: 2.6e-12
                      -HHHHHHHHHHHHHHT-SEEEEESSHHHHHHHHHHTTS-TTEEEEEESTSSHHHHHHHHHTHHHTTCE.EEEESTTSHHHH.HHHCCTTEEEEE CS
  Cys_Met_Meta_PP  51 nptrsvleeriaaLeggeaalavssGmaAiaaailallkaGdeivvsddlYggtqrllkkvlkklgie.vkfvdtsdleel.ekaikentklvy 142
                      n  +  le++ia+L++ eaal + +G  A  a+i +l +  ++ ++ +d Y+ ++ +     ++ + + +++ d ++leel  +a ++  k++ 
       AHX11717.1  88 NKEVVLLEQEIAKLHHKEAALSFVCGYVANLASISTLTSLMEDCIAFSDQYNHSSIIEGIKSSRCEKRiFHHNDLKHLEELlSQAPQHTYKIII 181
                      4556789*********************************************998776666666544414566666666651445555779*** PP

                      EESS-TTTT----HHHHHHHHHHTT-EEEEEGTTTHTTT CS
  Cys_Met_Meta_PP 143 lEtptnpllkvvDiekiaklakkagvlvvvDntfaspll 181
                      +E++ +   +++ ie i++la k g+l+ +D + a +++
       AHX11717.1 182 FESVYSMDGDIAPIEGICDLAEKYGALTYIDEVHAVGMY 220
                      *******************************99888765 PP

>> Aminotran_5  Aminotransferase class-V
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.4   0.0   4.7e-07    0.0017     128     181 ..     161     218 ..      92     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.4 bits;  conditional E-value: 4.7e-07
                  EGGGHHHH-....-TTEEEEEEESBETTTTEB--HHHHHHHHHHTT-EEEEE-TTTTT CS
  Aminotran_5 128 dldelekll....nektklvaithvsnvtGtiqpveeigklakkkgalvlvDaaqavg 181
                  dl++le+ll    ++++k++++  v ++ G i p+e i++la k+gal+ +D + avg
   AHX11717.1 161 DLKHLEELLsqapQHTYKIIIFESVYSMDGDIAPIEGICDLAEKYGALTYIDEVHAVG 218
                  55666666644447999*************************************9987 PP

>> Beta_elim_lyase  Beta-eliminating lyase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.3   0.1   1.2e-06    0.0045       9     168 ..      65     213 ..      62     322 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.3 bits;  conditional E-value: 1.2e-06
                      ---HHHHHHH.HCS----CCCT--HHHHHHHHHHHHHTT-SEEEEES-HHHHHHHHHHHH--TTEEEEEETT-HHHHSSTTHHHHCC--EEEEE CS
  Beta_elim_lyase   9 kgteamsdaq.aaamlGdesYgedktvnrLedavaelfgkeaalfvpqGtaAnsillkillqrgeevivtepahihfdetgaiaelagvklrdl 101
                        +++ +d++ a+a    +  g++k+v  Le+++a+l  keaal ++ G  An  ++++l+       + e++  + d     + ++g+k   +
       AHX11717.1  65 DSMKETIDRMgAGAGGTRNISGNNKEVVLLEQEIAKLHHKEAALSFVCGYVANLASISTLT------SLMEDCIAFSDQYNHSSIIEGIKSSRC 152
                      447888899955554444579****************************************......345555445454455555599999999 PP

                      -EBTTTBE-HHHHHHHS--S-TTS-EEEEEEEESSBTTTTTB---HHHHHHHHHHHHHCT-EEEEEE CS
  Beta_elim_lyase 102 knkeaGkmdlekleaaikevgaheekiklisltvTnntagGqvvsleelrevaaiakkygiplhlDg 168
                      +++     dl+ le+++ +  +     k+i+ +     + G + ++e    + ++a+kyg    +D 
       AHX11717.1 153 EKRIFHHNDLKHLEELLSQAPQ--HTYKIIIFESVYS-MDGDIAPIE---GICDLAEKYGALTYIDE 213
                      9999899999999999999777..5566666666555.477776654...55677777777777775 PP

>> DUF1843  Domain of unknown function (DUF1843)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.3   0.1     0.016        56      39      50 ..      90     101 ..      86     103 .. 0.89
   2 ?    5.3   0.0    0.0077        28      14      29 ..     160     175 ..     157     180 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.3 bits;  conditional E-value: 0.016
     DUF1843  39 aleqLkaEIAKl 50 
                 ++ +L++EIAKl
  AHX11717.1  90 EVVLLEQEIAKL 101
                 7899*******8 PP

  == domain 2  score: 5.3 bits;  conditional E-value: 0.0077
     DUF1843  14 GDLakMKalaaqaeqq 29 
                 +DL+++ +l++qa q+
  AHX11717.1 160 NDLKHLEELLSQAPQH 175
                 8************999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (398 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       556  (0.0310112); expected 358.6 (0.02)
Passed bias filter:                      473  (0.0263818); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.50u 0.25s 00:00:00.75 Elapsed: 00:00:00.39
# Mc/sec: 3033.02
//
Query:       AHX11718.1  [L=58]
Description: ribosomal protein S21 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    3.8e-08   32.9   8.4      1e-07   31.6   8.4    1.8  1  Ribosomal_S21  Ribosomal protein S21


Domain annotation for each model (and alignments):
>> Ribosomal_S21  Ribosomal protein S21
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   8.4   5.6e-12     1e-07       4      55 .]       2      50 ..       1      56 [. 0.94

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 5.6e-12
  Ribosomal_S21  4 VkdgenierALkrfkrkveragvirevrrrryyekpsekrkrkkkearrrrr 55
                   V+ g ++e+AL+r+k  ++r+gv +   r+r +ekpsekr r + e  r++r
     AHX11718.1  2 VHHG-DVEQALRRLKQHLSREGVTPG--RKRVFEKPSEKRHRRAVEIKRKIR 50
                   8999.******************997..667***************999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (58 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       999  (0.0557198); expected 358.6 (0.02)
Passed bias filter:                      433  (0.0241508); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 431.61
//
Query:       AHX11719.1  [L=111]
Description: ccmE family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    9.1e-22   77.4   0.0      1e-21   77.3   0.0    1.0  1  CcmE      CcmE


Domain annotation for each model (and alignments):
>> CcmE  CcmE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   5.7e-26     1e-21      25     128 .]       2      99 ..       1      99 [. 0.92

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 5.7e-26
                 XXXXXSSSXXBXTTTTTS--S-TTSEEEEEEEE-TTT-EE-TTSSEEEEEEE-T.-EEEEEEES---TT--TTSEEEEEEEE-TTSEEEECCEEESS-X CS
        CcmE  25 salqenlvyfltpsevlekkaeegrrlrvgGlVkegsvkrdpesleveFvvtdlekelkVeYegilPdlFregqgvvveGrleedgvfeAeevlaKhde 123
                  +l +++++f++ps+++ k ae++ ++r+gG+Vk   ++r pe+   +F ++d +++lkV Y g  P l+reg +vvv G+l+ d+ ++A+++l+Khde
  AHX11719.1   2 FSLGSSISFFYSPSDIA-KLAESNAEIRLGGKVKT--IERFPET--THFIISDDSADLKVIYVGLSPALMREGIDVVVVGKLK-DHIMYAKQILIKHDE 94 
                 578899**********6.56899**********87..9999865..79*****99***************************6.67************* PP

                 XXX.H CS
        CcmE 124 kYmpk 128
                 +Y p+
  AHX11719.1  95 RYYPP 99 
                 **996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (111 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       307  (0.0171231); expected 358.6 (0.02)
Passed bias filter:                      281  (0.0156729); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 891.22
//
Query:       AHX11720.1  [L=542]
Description: metallo-beta-lactamase superfamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-12   47.2   1.5    4.1e-12   46.5   1.5    1.3  1  Lactamase_B     Metallo-beta-lactamase superfamily
    1.5e-11   44.0   0.1    3.6e-10   39.6   0.1    2.5  2  RMMBL           Zn-dependent metallo-hydrolase RNA specificit
    1.6e-07   31.1   0.2    1.6e-07   31.1   0.2    1.7  2  Lactamase_B_2   Beta-lactamase superfamily domain
  ------ inclusion threshold ------
       0.12   12.6   0.0         14    6.0   0.0    2.8  2  Gly_acyl_tr_C   Aralkyl acyl-CoA:amino acid N-acyltransferase
       0.15   11.7   0.0       0.28   10.8   0.0    1.4  1  ssDNA-exonuc_C  Single-strand DNA-specific exonuclease, C ter
       0.67   10.1   2.3        2.2    8.5   0.1    2.7  3  B-block_TFIIIC  B-block binding subunit of TFIIIC


Domain annotation for each model (and alignments):
>> Lactamase_B  Metallo-beta-lactamase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   1.5   1.4e-15   4.1e-12       6     150 ..      19     159 ..      14     183 .. 0.80

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 1.4e-15
                  SEEEEEEETTCEEEES--SCHHHHHHHH......HHHHHTSGGGGEEEEE-SBSSHHHHTTGGGCTTHHCCEETCCEHHHHCCHCHHHHHHHHHCCHH CS
  Lactamase_B   6 vnsyliegdggviLiDtGtsteaaraal......elaalglkpkdvdavilTHlHlDHiGglgglveatdvpvgavaeeapalfmeeaddaasrkgll 97 
                   n+ l    +++i+iD+G + + a++        +   ++   +d+  +i+TH+H DH+G+l++l ++ ++pv+  + +a    +  ++         
   AHX11720.1  19 MNVSLYKYRDKWIMIDCGAGFADADLPGidiivaDVSFIEQRKDDLLGIIITHAHEDHCGALPYLWDKLGAPVYTTQFTANFIVKKIGYN-------- 108
                  58999999*****************999************************************************99999999999944........ PP

                  TTCHCGCCEEEEETTTEECCCTEEEEEHECTT.STSCCEEEEEETTCCEEEECT CS
  Lactamase_B  98 lagvsadkpdvdeeeldgnaggrralyvtggp.ghghghgvveygggkvlftGD 150
                      ++++  v+e +  +n+g+ ++  v  ++ ++  + + ++ ++g v  +GD
   AHX11720.1 109 ---KVHFPIHVVEPGVVLNLGEFVLEFVNLTHsVPEMSAIAIHTEEGVVFHSGD 159
                  ...444555555555555555555444444441555555666667777777777 PP

>> RMMBL  Zn-dependent metallo-hydrolase RNA specificity domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.7   0.0     0.086   2.6e+02      25      60 ..      56      92 ..      54      94 .. 0.73
   2 !   39.6   0.1   1.2e-13   3.6e-10       6      58 ..     353     405 ..     348     409 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.7 bits;  conditional E-value: 0.086
       RMMBL 25 lirklkprn..vilvHGeeeatsalarllkeeegidvf 60
                +i++ k     +i+ H +e+++ al  +l+++ g  v+
  AHX11720.1 56 FIEQRKDDLlgIIITHAHEDHCGAL-PYLWDKLGAPVY 92
                555555555779***********99.444477777766 PP

  == domain 2  score: 39.6 bits;  conditional E-value: 1.2e-13
       RMMBL   6 ar.ieeidfSgHadknellelirklkprnvilvHGeeeatsalarllkeeegid 58 
                 ++  +++++SgH +++el+++ ++lkp  vi+vHGe  ++ ++a+ + e+ g++
  AHX11720.1 353 TErTHTVHVSGHPYRDELKQMYQLLKPNTVIPVHGENLHLYEHAKFA-EKCGVK 405
                 55489**************************************9999.888865 PP

>> Lactamase_B_2  Beta-lactamase superfamily domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.1   0.2   5.2e-11   1.6e-07       2     147 ..      30     164 ..      29     180 .. 0.79
   2 ?   -3.7   0.1       2.3   6.9e+03     175     200 ..     357     386 ..     340     386 .. 0.68

  Alignments for each domain:
  == domain 1  score: 31.1 bits;  conditional E-value: 5.2e-11
                    EEEES--TT...........HHHHHTCGGS--S...SS--..SEEEEE-SS--HHHHGGGGCCCCC--EEEEEEEEHHHHHHCCTTCGHHHCHTTT CS
  Lactamase_B_2   2 riLiDagpd...........lrqqalralqPve...lrdelppidaVllthaHyDHlaglltlrelrpkklplyapkgvlavleanfvylaleeep 83 
                    +i iD+g +           +++        v+   +r++  ++ ++++thaH DH+  l+ l    +  +p+y ++ ++  + +++ y+      
     AHX11720.1  30 WIMIDCGAGfadadlpgidiIVAD-------VSfieQRKD--DLLGIIITHAHEDHCGALPYLWDKLG--APVYTTQFTANFIVKKIGYNKV---- 110
                    99*******555555555543333.......233114556..9**************99999999444..79**999999999999888654.... PP

                    TEEEEEE-TTSEEEECSTTEEEEEEEE-EE--CTCCE-TTTSEEEEEECTTEEEEEESS-S--- CS
  Lactamase_B_2  84 avnvheldwgesfelgdggleitatparhksgrrldrnagdtlGlriegggkrvyyigDtgyip 147
                    + ++h +++g  + lg+  + ++++ + h+ ++        + + +i +++  v+++gD +  +
     AHX11720.1 111 HFPIHVVEPGVVLNLGE--FVLEFVNLTHSVPE--------MSAIAIHTEEGVVFHSGDWKIDD 164
                    466************96..559***********........999999999*********98544 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 2.3
                    HHT---S....TSHHHHCTTSSSSEEEEES CS
  Lactamase_B_2 175 hmgHltp....eeaveaaadlgakrlvliH 200
                    h +H++     +e  ++ + l++ +++++H
     AHX11720.1 357 HTVHVSGhpyrDELKQMYQLLKPNTVIPVH 386
                    555555444557777888888888888888 PP

>> Gly_acyl_tr_C  Aralkyl acyl-CoA:amino acid N-acyltransferase, C-terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    6.0   0.0    0.0047        14      17      38 ..      12      33 ..       4      40 .. 0.84
   2 ?    3.3   0.0     0.032        97      49      78 ..      85     114 ..      67     117 .. 0.88

  Alignments for each domain:
  == domain 1  score: 6.0 bits;  conditional E-value: 0.0047
  Gly_acyl_tr_C 17 dqtgelrmagtlpkYrrqglva 38
                     tge++m  +l kYr +  + 
     AHX11720.1 12 GGTGEIGMNVSLYKYRDKWIMI 33
                   569*************987765 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.032
  Gly_acyl_tr_C  49 ekkgiPvYshvdkenekvqklseslghvei 78 
                    +k+g PvY+   ++n +v+k+ ++  h++i
     AHX11720.1  85 DKLGAPVYTTQFTANFIVKKIGYNKVHFPI 114
                    799******************998877766 PP

>> ssDNA-exonuc_C  Single-strand DNA-specific exonuclease, C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.3e-05      0.28      67     135 ..     330     398 ..     308     402 .. 0.89

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.3e-05
  ssDNA-exonuc_C  67 lPesleqleellekkqperiyllfyqeesayleglPtReqFkklYkflkkqkefdlkkelkaLakhlgw 135
                     +P +++++++++++  + ++ ++ ++++   ++g P R++ k++Y++lk ++ + ++ e   L +h + 
      AHX11720.1 330 IPGNEKRIAKMINRFIAMHVSVITERTHTVHVSGHPYRDELKQMYQLLKPNTVIPVHGENLHLYEHAKF 398
                     5899999999**9999*********************************99999988887777777765 PP

>> B-block_TFIIIC  B-block binding subunit of TFIIIC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.49   1.5e+03       6      20 ..     254     268 ..     251     271 .. 0.88
   2 ?   -1.8   0.1       1.2   3.7e+03      35      50 ..     449     464 ..     446     473 .. 0.77
   3 ?    8.5   0.1   0.00074       2.2      21      54 ..     500     533 ..     498     541 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.49
  B-block_TFIIIC   6 klLelIassRysGit 20 
                      lL++I+++++ G++
      AHX11720.1 254 SLLSVISAAKETGYL 268
                     69***********97 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.2
  B-block_TFIIIC  35 lfyrlksLekkgLIvk 50 
                     l + +k+L++ g I  
      AHX11720.1 449 LIKTRKKLQSAGMILV 464
                     667899****999965 PP

  == domain 3  score: 8.5 bits;  conditional E-value: 0.00074
  B-block_TFIIIC  21 qsdLakeskqdprslfyrlksLekkgLIvkqsii 54 
                      +dL +e + d + +++ +++  ++ LI+k++i+
      AHX11720.1 500 EKDLRSERNVDFKTITKATRKIVRNSLIYKNKIP 533
                     689****************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (542 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      336  (0.0187406); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.53u 0.26s 00:00:00.79 Elapsed: 00:00:00.42
# Mc/sec: 3881.12
//
Query:       AHX11721.1  [L=67]
Description: hypothetical protein NHE_0795 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (67 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       164  (0.00914719); expected 358.6 (0.02)
Passed bias filter:                      147  (0.00819901); expected 358.6 (0.02)
Passed Vit filter:                        14  (0.000780858); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.22s 00:00:00.53 Elapsed: 00:00:00.36
# Mc/sec: 559.48
//
Query:       AHX11722.1  [L=450]
Description: tRNA-i(6)A37 thiotransferase enzyme MiaB [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.2e-30  106.2   0.0    6.2e-30  104.8   0.0    1.7  2  Radical_SAM  Radical SAM superfamily
    1.1e-29  102.3   1.2      2e-29  101.5   1.2    1.4  1  UPF0004      Uncharacterized protein family UPF0004
      0.001   19.0   0.0     0.0024   17.8   0.0    1.7  1  TRAM         TRAM domain
     0.0042   17.2   0.2      0.022   14.9   0.0    2.3  2  TRAM_2       TRAM domain


Domain annotation for each model (and alignments):
>> Radical_SAM  Radical SAM superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.79   3.6e+03      47      70 ..      81     103 ..      43     136 .. 0.52
   2 !  104.8   0.0   1.4e-33   6.2e-30       2     167 .]     163     337 ..     162     337 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.79
                  SEEEEEESSTGGGSTTHHHHHHHH CS
                  xxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  47 vkevilgggepllypdfvellerl 70 
                  +k ++++ g   ++++  e+++r+
   AHX11722.1  81 KKIMTVVAG-CVAQAEGDEIIKRA 103
                  333333322.33333333333333 PP

  == domain 2  score: 104.8 bits;  conditional E-value: 1.4e-33
                  EEESEESS--TTTSCCTTHHHHHHHHHHHHHHHHHHHHHHHHHTTSEEEEEESSTGGGS..........TTHHHHHHHHHHTCCCTEEEEEEECSSCH CS
                  xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..........xxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM   2 vvtrgCnlrCsfCarpetvrregrgrslsveeileevkelkaekgvkevilgggeplly..........pdfvellerlaklavpgiritvetngtlp 89 
                  ++++gC   CsfC +p+   ++g ++s++ve + +e+ +l   +gvke++l+g++++ y           ++ +l+ r+a +  + +ri+++t+++++
   AHX11722.1 163 SIQEGCDKFCSFCVVPY---TRGSEYSRTVEAVYREALAL-TANGVKEITLLGQNVNGYhgsldageytMNLGQLISRIANI-PSLLRIRYTTSHPVD 255
                  6899************9...7*******************.7889**************99966665555555555555555.6*************8 PP

                  G.HHHHHHHHHTT..-SEEEEEEBSSSHHHHHHHHTCTSHHHHHHHHHHHHHHTTSET...EEEEEEEBTTTSHHHHHHHHHHH CS
                  x.xxxxxxxxxxx..xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx...xxxxxxxxxxxxxxxxxxxxxxx RF
  Radical_SAM  90 d.eeklerllelg..vdrvslgleaaddekvlklmnrghtfeevlealeklreagikr...vvdrivglpGendeeleellell 167
                  + +e  e++++    +  ++l++++++d+ vlk+mnr++t + +le +++l++a  ++   ++d+ivg+pGe+d++++++lel+
   AHX11722.1 256 MhDELYEAHAKESklMPFIHLPVQSGSDR-VLKRMNRKYTASTYLEIVQRLKKA-RDDiafSSDFIVGFPGESDDDFQQTLELV 337
                  8**********99****************.************************.5667*9********************986 PP

>> UPF0004  Uncharacterized protein family UPF0004
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.5   1.2   4.5e-33     2e-29       2      98 .]      12     111 ..      11     111 .. 0.93

  Alignments for each domain:
  == domain 1  score: 101.5 bits;  conditional E-value: 4.5e-33
                 EEEE--S-CCCCHHHHHHHHHTTTSSS----SSS--SEEEEEE--SSSSHHHHTHHHHHHHHTTS...T.--EEEEEEHHHHS-HHHHHHH-TTS-EEE CS
     UPF0004   2 vaietlGCqmNevdseelaslLkkegyelvedeeeAdvvlvnTCavrekaekkviqalrelkalk...kpekkvvvlGCmaqrekeellkeepevdlvl 97 
                 ++i+t+GCqmN++dse++ +++ ++g+++ve++e+Ad+v++nTC++reka +k++++l++l+al+   +++   vv+GC+aq+e++e++k++++vd+v+
  AHX11722.1  12 LYIKTYGCQMNVYDSEMIEKIVGQMGFRTVETAEDADLVILNTCHIREKAAEKIYSELGKLRALEkrkQKKIMTVVAGCVAQAEGDEIIKRARNVDIVV 110
                 689**********************************************************999864335566689**********************9 PP

                 - CS
     UPF0004  98 g 98 
                 g
  AHX11722.1 111 G 111
                 8 PP

>> TRAM  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.8   0.0   5.5e-07    0.0024       1      58 [.     389     443 ..     389     447 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.8 bits;  conditional E-value: 5.5e-07
                 XXXXXXEEEEEEEEE-.TTSEEEEEET.TEEEEETT-.-T..TEEEEEEEEEE-SSEEE CS
        TRAM   1 rsyvGstqeVlveglsksegegiGrtdngkvvfvpgd.lpgIGdfVeVkItkvkrqyLr 58 
                 ++++G+t+ Vl+ +++   +++ Grt+++++v+ +++ l   G+ V+ +++++  ++L+
  AHX11722.1 389 QKMIGKTVKVLFDKKN--TDQISGRTEYMQPVYSDDAsL--FGKMVTMEVKDASAFTLK 443
                 689************8..89*************999744..6***********999997 PP

>> TRAM_2  TRAM domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0       2.5   1.1e+04      42      60 ..      31      50 ..      23      50 .. 0.69
   2 !   14.9   0.0   4.9e-06     0.022       1      60 [.     392     443 ..     392     447 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 2.5
                ...T-EEEEEEEEEETTEEE CS
      TRAM_2 42 k.vGdfvkvkItdadeyDLi 60
                k vG++    ++ a++ DL+
  AHX11722.1 31 KiVGQMGFRTVETAEDADLV 50
                34677777778888888885 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 4.9e-06
                 BTSEEEEEEEEEETTEEEEEETTS-TTTS--EEEES---T...T-EEEEEEEEEETTEEE CS
      TRAM_2   1 iGktvevlvdgeeeglyvGRsyadAPEvDgevyvtgaeklskvGdfvkvkItdadeyDLi 60 
                 iGktv+vl d+++ +   GR+++  P     vy ++a+     G++v+ +++da+ + L 
  AHX11722.1 392 IGKTVKVLFDKKNTDQISGRTEYMQP-----VYSDDASL---FGKMVTMEVKDASAFTLK 443
                 9**********99999*******988.....77775433...599999999999998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (450 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       631  (0.0351944); expected 358.6 (0.02)
Passed bias filter:                      469  (0.0261587); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.53u 0.25s 00:00:00.78 Elapsed: 00:00:00.42
# Mc/sec: 3226.75
//
Query:       AHX11723.1  [L=47]
Description: hypothetical protein NHE_0798 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (47 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       328  (0.0182944); expected 358.6 (0.02)
Passed bias filter:                      149  (0.00831056); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.23s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 356.60
//
Query:       AHX11724.1  [L=145]
Description: ribosomal S9/S16 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      1e-43  148.7   0.0    1.2e-43  148.5   0.0    1.0  1  Ribosomal_S9  Ribosomal protein S9/S16


Domain annotation for each model (and alignments):
>> Ribosomal_S9  Ribosomal protein S9/S16
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.5   0.0   6.5e-48   1.2e-43       1     121 []      24     145 .]      24     145 .] 0.98

  Alignments for each domain:
  == domain 1  score: 148.5 bits;  conditional E-value: 6.5e-48
                   EECTTEEEEEEEEESSSEEEETTEE.CCHHSTTSCHHHHHCHHHHHTTTSSSEEEEEEEESS-HHHHHHHHHHHHHHHHHHHHHHHHHHHCTCCCTS CS
  Ribosomal_S9   1 GrrKesvArvwikegkgkilvngks.leeYfkeeaarekvleplkltgllgkfdvfvkvkgGGlsgqaeAirlgiaraLvalekeekkeLkkagllt 96 
                   GrrK++vArvwik+g+g ++vngk+ l +++++++  ++v +pl++ +  gkfdvf+++kgGG+sgqa+A+rlg++raL+++++ +++ Lkk++ll+
    AHX11724.1  24 GRRKTAVARVWIKAGTGLFRVNGKPdLYSHLEHQYLCQDVCSPLRVCDVAGKFDVFATIKGGGVSGQAGALRLGLSRALQNFNPGFREPLKKNSLLV 120
                   9***********************8788889*****************************************************99*********** PP

                   -B--------TTSSCTTB----S-- CS
  Ribosomal_S9  97 rDpRvvErkKtgkkkARkkyqwskR 121
                   rD+R+vErkK+gkkkARk++q+skR
    AHX11724.1 121 RDSRIVERKKYGKKKARKSFQFSKR 145
                   ************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       302  (0.0168442); expected 358.6 (0.02)
Passed bias filter:                      236  (0.013163); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.38
# Mc/sec: 1144.59
//
Query:       AHX11725.1  [L=152]
Description: ribosomal protein L13 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.2e-50  170.1   0.0    2.6e-50  169.9   0.0    1.0  1  Ribosomal_L13  Ribosomal protein L13


Domain annotation for each model (and alignments):
>> Ribosomal_L13  Ribosomal protein L13
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.9   0.0   1.5e-54   2.6e-50       1     125 []      14     139 ..      14     139 .. 0.98

  Alignments for each domain:
  == domain 1  score: 169.9 bits;  conditional E-value: 1.5e-54
                    -EEEEEETTSBHHHHHHHHHHHHHTTTSTT--TTS--S-EEEEEEGGCBB-SSTHHTT-EEEEE-SSTTSEEEEEHHHHH.CCSHHHHHHHHHHCC CS
  Ribosomal_L13   1 kWyviDAegqvlgrlaskiakvLrGkhkptytphvdcGdyvvvinaekvaltgkkleqkvyyrhtgypgglkevtakell.ekkpeeilekaVkgm 95 
                    kW+viDA++ v+grla+ +++vLrGk k  ytph+dcGd+v+++na+kv+++g+k+ +kvyyrhtgypgglk++t ++ll  kkp+e++++aVk+m
     AHX11725.1  14 KWVVIDATDAVVGRLAAFVSTVLRGKTKVAYTPHMDCGDNVIILNASKVKFSGTKMLNKVYYRHTGYPGGLKSTTPRKLLdGKKPCEVVRLAVKRM 109
                    7*****************************************************************************9966899*********** PP

                    S-SSHHHHHHGCTEEEESSSTTSGGGGSCE CS
  Ribosomal_L13  96 LpknklgrrrlkrLkvyageehpheaqkpe 125
                    L  + ++rrr+k+L+vyag+eh+heaq+p+
     AHX11725.1 110 LDDGPMARRRFKNLYVYAGPEHKHEAQNPQ 139
                    ***************************996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (152 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       362  (0.0201908); expected 358.6 (0.02)
Passed bias filter:                      313  (0.0174578); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.26s 00:00:00.63 Elapsed: 00:00:00.40
# Mc/sec: 1133.84
//
Query:       AHX11726.1  [L=202]
Description: colicin V production family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    2.2e-20   73.1   1.7    2.8e-20   72.7   1.7    1.1  1  Colicin_V  Colicin V production protein
     0.0032   17.3   0.0     0.0075   16.2   0.0    1.6  1  DUF3437    Domain of unknown function (DUF3437)


Domain annotation for each model (and alignments):
>> Colicin_V  Colicin V production protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.7   1.7   3.2e-24   2.8e-20      18     139 ..       2     136 ..       1     141 [. 0.90

  Alignments for each domain:
  == domain 1  score: 72.7 bits;  conditional E-value: 3.2e-24
   Colicin_V  18 rrGfvrevlsllgwvvafvvasllypslaellaelilspalaaiiaflllfllvllivsllgallsklvsktglglldrllGaifGllkglllvvllll 116
                 +rG ++e++s + +v++++++++ ++ + e+++   +s  ++  ++ ++lf++++++++ll++++  lvs+ +lg++dr+lG++ G+l+g++ ++l+++
  AHX11726.1   2 LRGSIKEIFSAAVIVISAMITYHNGNIFLEFFNV--SSGPVVTPLSWIALFIISVVVLGLLNSWIMYLVSPIRLGPTDRVLGLLCGALRGVVYCYLIFA 98 
                 79********************************..799************************************************************ PP

   Colicin_V 117 llalvplpkvqe...............wlqnSvlapll 139
                 +l+++ ++ + +               wl++++ +++l
  AHX11726.1  99 VLNIFYYSLNGDeekdleqkpgyylptWLKSAKAYSTL 136
                 *****998773334556666777777788877777765 PP

>> DUF3437  Domain of unknown function (DUF3437)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.2   0.0   8.4e-07    0.0075      20      80 ..     121     179 ..     118     185 .. 0.80

  Alignments for each domain:
  == domain 1  score: 16.2 bits;  conditional E-value: 8.4e-07
     DUF3437  20 ydvPkwlp..evleeLaraardpa.pirktvkktlseFkrthqDtWeedkkkFteeqledledv 80 
                 y +P+wl+  ++ ++L+   ++ +  i  +v   l+++ +t +D+W     kFtee  + ++++
  AHX11726.1 121 YYLPTWLKsaKAYSTLSYLDSSLNaAIPGEVFASLRSYSKTFKDDW-----KFTEEGSDSFTGL 179
                 77899997224678899999999978********************.....7777766666665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (202 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       745  (0.0415528); expected 358.6 (0.02)
Passed bias filter:                      463  (0.0258241); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.38u 0.28s 00:00:00.66 Elapsed: 00:00:00.38
# Mc/sec: 1579.87
//
Query:       AHX11727.1  [L=857]
Description: TRAP transporter, 4TM/12TM fusion family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    5.1e-73  246.3  51.9    1.5e-70  238.2  51.9    2.2  1  DctM          Tripartite ATP-independent periplasmic transpor
    5.2e-44  150.1   0.0      9e-44  149.3   0.0    1.4  1  DUF3394       Domain of unknown function (DUF3394)
     0.0053   15.4   0.1      0.011   14.4   0.1    1.4  1  A-2_8-polyST  Alpha-2,8-polysialyltransferase (POLYST)


Domain annotation for each model (and alignments):
>> DctM  Tripartite ATP-independent periplasmic transporter, DctM component
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  238.2  51.9   2.5e-74   1.5e-70       3     408 ..     138     666 ..     136     671 .. 0.84

  Alignments for each domain:
  == domain 1  score: 238.2 bits;  conditional E-value: 2.5e-74
        DctM   3 sllvllalgvpvaislalasl..lllallgelllgv......pleqilaqrvve.......glssfallaipfFvlaGivlersGlakrlidlaaalvG 86 
                 + ++l+a +++v+ ++++++l  l++  +ge+++         l+ i+ ++ ++       ++++++ +++  +vl+G++le++G++ ++i+l   l+ 
  AHX11727.1 138 ICVLLEAARRTVGSAVVIVVLvsLFYSRFGEIMPDLvvhkdyMLSAIASHQWFStegvfgtAIAVSVDFVFL-YVLFGALLEKTGAGHFFIELSFLLLN 235
                 56899***************9999********7776799998777778888877899888889999999999.************************** PP

        DctM  87 rvrGGlakvsvvgsalfgaiSGsavAnvaavGsitipamkrsGykrefaaaviaasstlgqiiPPslglivfama.vlgvsigdlfaaaiipglllavg 184
                 r+rGG+ak++vv+s l+g+iSGs++An+++vGs+tip+mk+ G+ +e+aaa++ ++++ gqi+PP++g+++f+ma +l++++++++  a++p++l++++
  AHX11727.1 236 RFRGGPAKAAVVSSGLMGMISGSSIANTITVGSLTIPMMKKMGFSPEKAAAIEVSAGINGQIMPPVMGAAAFLMAeYLSIPYIEVVKHAFLPAVLVYIA 334
                 *************************************************************************************************** PP

        DctM 185 lllavaiaakkenlrs.............................................................................ktkael 206
                 ll +v+i+a k n +                                                                              ++   +
  AHX11727.1 335 LLYIVHIEACKLNAPVvvvseggsggissvilrmllafsvialcfsgiyaliegfmvfsglknisgtygplvigglccfiyvallwyqntlknNPSLDK 433
                 **********99999999888888888888888888888888888888888888888888888888888888888888888888888877643344444 PP

        DctM 207 krlgqalkeaipalllpliili.gillgiftpteagavavvyalviallv........yrrltleevaaa........llstakttaavlfilaaagif 288
                   ++  l++++   ++pl+ili  +l+  ++p   + +  ++ l+ +l+         + r+ + ++ ++        ++ + k  ++v+++ aaagi+
  AHX11727.1 434 STVSFKLRTGL-HHFMPLVILIwCLLVEHMSPALSAYWT-ILFLLFELFTkevilgffECRFAFCSLIKSgcmkcidaMIMSSKNMTVVAVATAAAGII 530
                 44555555666.555565555505556667777544444.4445555555677778885555555555557777666666667777899********** PP

        DctM 289 aglltltgvplklselllslsggk.llfLilvnllvlvlGmfldttaaiiilvpilaPaaakl....gidp..ihfgvvivlnlsiglitPPvGlalfv 380
                 +g ++ltgv+lk++ +l s+s+g+ l++L l++ +++vlGm+++tta++ii++++++P++ ++    gid     +++++++++ ++++tPPvGla ++
  AHX11727.1 531 VGSVSLTGVGLKIGGVLDSVSNGNlLVTLFLTAFMCMVLGMGMPTTACYIIVSTLMVPVLLHItkknGIDIplFSIHLFVFYFGLMADVTPPVGLASYA 629
                 ************************999************************9999999875542222666444889*********************** PP

        DctM 381 assia.........kvsveeivkalvPflvvlvvalv 408
                 a++ia         ++++ +i  +l+Pfl+vl++ ++
  AHX11727.1 630 AAAIAggnaimtgvQAFFYNIRTMLLPFLFVLNPQIL 666
                 **************9*****************99876 PP

>> DUF3394  Domain of unknown function (DUF3394)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  149.3   0.0   1.5e-47     9e-44       2     180 ..     677     855 ..     676     856 .. 0.98

  Alignments for each domain:
  == domain 1  score: 149.3 bits;  conditional E-value: 1.5e-47
     DUF3394   2 ilvivvaliaiLlfaAatqgyfltrsrlyEsvlLLlvaftLfrPgffldlisppyeelepselvevveelpkgselrlkvegenlegeeiektvalplg 100
                 i viv+++i+i++++A++qgy+++rs++yEs++L+l++++L++P++f++l+++++++le+++  +++++++++++lr++++++++ g++  ++++++ +
  AHX11727.1 677 IQVIVFSVIGIIAITAGSQGYLIVRSKFYESIILFLTGIALMTPSVFVELVTKEFSNLEMNS--AILSHFNDSKRLRIVLNDKDFFGNPEITKFNIDNK 773
                 89*********************************************************999..8999******************************* PP

     DUF3394 101 eeatgeerLeaaGl.tlleedgkvl.vdevefgspaekagldfdfeivevevpadrppkelvyipAllllalvallQrrrkk 180
                 +++t +e+L+a+G+ t +++d++vl + +v+++  +++++ld+ ++i+e++v++ ++p+++vy ++lll+ +++++Qr+r++
  AHX11727.1 774 TSGTIDEQLRACGIvTDYDHDENVLdILSVSHSPVSRCTKLDSTMKISEIMVSQPQMPRWVVYSVSLLLFSCIFMVQRKRDR 855
                 **************999*****9999******************************************************76 PP

>> A-2_8-polyST  Alpha-2,8-polysialyltransferase (POLYST)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.1   1.8e-06     0.011     244     320 ..     694     770 ..     682     777 .. 0.86

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 1.8e-06
  A-2_8-polyST 244 sqrypisdelyyklivetlnrislriegkifiklhPkemenkyimslfln.ivkinprlvvinekdflieplikltki 320
                   sq y i    +y++i+  l+ i l     +f+ l  ke  n  ++s  l+ +++ ++  +v+n+kdf+ +p i + +i
    AHX11727.1 694 SQGYLIVRSKFYESIILFLTGIALMT-PSVFVELVTKEFSNLEMNSAILShFNDSKRLRIVLNDKDFFGNPEITKFNI 770
                   99********************9975.67************9999866661555555589**********99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (857 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1036  (0.0577835); expected 358.6 (0.02)
Passed bias filter:                      431  (0.0240393); expected 358.6 (0.02)
Passed Vit filter:                        26  (0.00145016); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.74u 0.28s 00:00:01.02 Elapsed: 00:00:00.45
# Mc/sec: 5676.82
//
Query:       AHX11728.1  [L=208]
Description: superoxide dismutase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
      2e-35  121.0   3.4    3.2e-35  120.4   0.1    2.3  3  Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal do
    2.4e-26   92.0   0.5    4.6e-26   91.1   0.5    1.5  1  Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin


Domain annotation for each model (and alignments):
>> Sod_Fe_C  Iron/manganese superoxide dismutases, C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.1   0.0      0.49   4.4e+03      78      94 ..      31      48 ..      25      56 .. 0.74
   2 ?    1.0   0.2     0.054   4.9e+02      67      77 ..      77      87 ..      46      91 .. 0.77
   3 !  120.4   0.1   3.6e-39   3.2e-35       1     101 [.      99     202 ..      99     203 .. 0.94

  Alignments for each domain:
  == domain 1  score: -2.1 bits;  conditional E-value: 0.49
                HHTT-HHHHHHHHGG.GB CS
    Sod_Fe_C 78 dyqnkradYieafwn.vv 94
                +y ++ a Y++++ + +v
  AHX11728.1 31 HYDKHHAGYVNKVNElLV 48
                688889999999877555 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.054
                EEE-SGGGTHH CS
    Sod_Fe_C 67 alDvwehAYyl 77
                a  vw+h +y 
  AHX11728.1 77 AAQVWNHTFYW 87
                4689****997 PP

  == domain 3  score: 120.4 bits;  conditional E-value: 3.6e-39
                 --HHHHHHHHHHHSSHHHHHHHHHHHHHHSSSSEEEEEEEETT.TEEEEEEEETTTBGGGGTTC.EEEEEE-SGGGTHHHHTT-HHHHHHHHGG.GBBH CS
    Sod_Fe_C   1 psgelaeaieedfgslekfkkefkaaalavfgsGwawLvldkk.kkLeivttknqdnplvkeak.plLalDvwehAYyldyqnkradYieafwn.vvnW 96 
                 p+++l+ +i +dfg +e++k++++ aa+++fgsGwawL++dk  ++L++v+t+n+++pl++++  plLa+DvwehAYyldyqn+r+dY+++f+  ++nW
  AHX11728.1  99 PDDRLMLQIVKDFGGMEELKQQLSLAAVTQFGSGWAWLIFDKAsQRLSVVKTSNAETPLTNQNFvPLLAIDVWEHAYYLDYQNRRPDYVATFLAqLINW 197
                 6789999*********************************998689**************86656***************************988**** PP

                 HHHHH CS
    Sod_Fe_C  97 kevee 101
                 +++++
  AHX11728.1 198 DFASA 202
                 *9976 PP

>> Sod_Fe_N  Iron/manganese superoxide dismutases, alpha-hairpin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.1   0.5   5.1e-30   4.6e-26       4      81 ..       9      90 ..       6      91 .. 0.91

  Alignments for each domain:
  == domain 1  score: 91.1 bits;  conditional E-value: 5.1e-30
                ----SS-TTTTTTTS-HHHHHHHHHTHHHHHHHHHHHHHHCHHHHCHCCHHHHHH....HHHHHHHHHHHHHHHHHHHHHTB CS
    Sod_Fe_N  4 LpeLpYaydaLePhisketlelHhdkHhktYvnnlNkalekleeakkkleelvlk....klekalrnnagghvnHslfwknl 81
                LpeLpY+ daLeP is++tl +H+dkHh++Yvn++N++l + +   ++l  ++ +    + ++a++nna++++nH+++w+++
  AHX11728.1  9 LPELPYHKDALEPLISEKTLGFHYDKHHAGYVNKVNELLVESDDVGDTLLCVIRNtwnkQGKEAIFNNAAQVWNHTFYWNSM 90
                9**************************************999999998777766666668899*****************99 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (208 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       500  (0.0278878); expected 358.6 (0.02)
Passed bias filter:                      419  (0.02337); expected 358.6 (0.02)
Passed Vit filter:                        17  (0.000948185); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.25s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1623.63
//
Query:       AHX11729.1  [L=198]
Description: glycoprotease family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.9e-05   22.5   0.0    9.4e-05   22.2   0.0    1.1  1  Peptidase_M22  Glycoprotease family


Domain annotation for each model (and alignments):
>> Peptidase_M22  Glycoprotease family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.0   5.3e-09   9.4e-05      49      98 ..      51     100 ..      34     147 .. 0.78

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 5.3e-09
                    GGEEEEEEEEESS-HHHHHHHHHHHHHHHHHCT--EEEEEHHHHHHHCCH CS
  Peptidase_M22  49 edldaIavtkgPGlftgLrvGvsfAkglalalnkPlvgVnhleahalaar 98 
                    ++++  a+ +gPG++tg+r G+++ +g+++++ k l+g     +++ + r
     AHX11729.1  51 TEINILAINTGPGSYTGVRAGIAVLNGMSIGARKQLIGFDAFTVLLSKFR 100
                    578889********************************988888877766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       503  (0.0280551); expected 358.6 (0.02)
Passed bias filter:                      447  (0.0249317); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 1512.80
//
Query:       AHX11730.1  [L=395]
Description: major Facilitator Superfamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-24   87.0  52.9    1.5e-24   86.6  52.9    1.2  1  MFS_1     Major Facilitator Superfamily


Domain annotation for each model (and alignments):
>> MFS_1  Major Facilitator Superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   86.6  52.9   8.3e-29   1.5e-24       9     350 ..      13     346 ..       5     384 .. 0.83

  Alignments for each domain:
  == domain 1  score: 86.6 bits;  conditional E-value: 8.3e-29
       MFS_1   9 alarsi...lgpalpl.alaedlgispseigllltlyalgaavaslplGrlsdrfGrrrvlllglllfalglllll.fasslwlllvlrvlqGlgagal 102
                 ++++     ++p++    + + + is +++g +++ly++++ ++ +p+G + dr+ +r+v+++g+ll +l+ +++l ++ss++ll+++ +l G +++++
  AHX11730.1  13 FFTYQYilrVLPNIVVdDVIQRFSISSAVVGQVTGLYYVAYTLLHIPIGIMLDRMAPRKVIFVGALLVVLS-MVPLvYTSSVTLLVIGKLLLGGASSVG 110
                 333333123334444445566699***********************************************.55553767777**************** PP

       MFS_1 103 fpagaaliadwfpkeergraigllsagfslGailgpllggllasslgWravfyilaivsllafvlfllllpeepperkrkspkeeekgtgpaplvpawk 201
                 + + + +++  fp e+ ++ +g+    + +Ga+ g    g++++ +gW  +f  + iv+l+ +  ++l++p++ +++k ++ ke             ++
  AHX11730.1 111 VLGLLRVVRSSFPAEKFSLIFGISIFIALIGAMYGGQPLGYCIHTFGWYTTFTTILIVGLVIAFSAYLFIPDKCSTSKAPPVKET------------LS 197
                 ***********************************666677888******************88878888888888888766666............66 PP

       MFS_1 202 allkdpvlwillialllfffgfsg...lltllplylqevl.glsglllaglllallalvgailallagrlsdrlgrrrrlllallllllaalglallav 296
                 +l++ +  w l+i+l+++ ++  +   +  + + ++  v+ g+ g+ +ag+l++l+ l+ a++a+l+g +  r+gr  ++l a+++l+++ + l++++ 
  AHX11730.1 198 ELFSLR-RW-LVISLIGGLMVGPLqgfADGWATKFFSVVYpGI-GASMAGFLPSLILLGLAFGAPLLGLITVRFGRYYTILTACSFLMFVGFQLMFTGQ 293
                 677666.46.666666665555557778888888866666344.58***************************************************** PP

       MFS_1 297 tssavllllvlvliGfglgfvfpsllalasdlappeeagtasglfn.tagslgga 350
                   s  +l ++lv++G +++ ++++++ las+++p + +gta++ +n ++ ++g +
  AHX11730.1 294 V-SLNFLFVILVVVGAASS-YQTLVIHLASSMVPDRCMGTAAACANmIIMAFGYF 346
                 *.44444446666666555.7*************************455556665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (395 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       909  (0.0507); expected 358.6 (0.02)
Passed bias filter:                      295  (0.0164538); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.55u 0.26s 00:00:00.81 Elapsed: 00:00:00.44
# Mc/sec: 2702.88
//
Query:       AHX11731.1  [L=236]
Description: class II Aldolase and Adducin N-terminal domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.4e-39  135.2   0.1    2.9e-39  135.0   0.1    1.1  1  Aldolase_II  Class II Aldolase and Adducin N-terminal domain


Domain annotation for each model (and alignments):
>> Aldolase_II  Class II Aldolase and Adducin N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  135.0   0.1   1.6e-43   2.9e-39       1     186 []       8     188 ..       8     188 .. 0.91

  Alignments for each domain:
  == domain 1  score: 135.0 bits;  conditional E-value: 1.6e-43
                  HHHHHHHHHHHHTTSSCTTBCEEEEEETSTTEEEEEBTSS-GGGHTGGGEEEEETTSCEEEECECSSSTB-.TTHHHHHHHHHH-TT-SEEEEE--HH CS
  Aldolase_II   1 eelaeasrllarrglvegtgGniSvrvpeedsflitpsgvdfeeltaedlvvvdldsgevvegkekggkps.setplHlaiykarpdaravvHtHspa 97 
                  +el  a+ ++a  ++++ t+ +i++r +++d f+i ++g+ f++ t +dl++v+ld ge++egke  ++ +  ++ +H  iyk r+d++a+ H+H++a
   AHX11731.1   8 QELLHAYLIIAYMRMDDLTYTHITARPKNADFFYILRFGKLFARATIQDLIKVSLD-GEILEGKE--HTYNkTAYIIHGSIYKTRKDVNAIYHLHTHA 102
                  68999*********************76677777*********************9.****9955..4556699************************ PP

                  HHHHHTCCSTSCHCCSSHHHHC.HSSSEEEEES-SSTTCHHH.....HHHHHHHHHHS-SEEEETTTEEEEEESSHHHHHHHHHHHHHHHHHHH CS
  Aldolase_II  98 avalsalagkeglppltqeaaklllgdevpvipyaapgteel.....gealaealkedakavllrnHGlltvGetleeAvalaetleeaaeiql 186
                   +a+s +  k gl pl+q+a+ ++  +++++ +y+      l     ge+la++l+ ++ka+l+r+HGllt+G++l+eA++++  le+a++iq+
   AHX11731.1 103 SIAVSVM--KCGLLPLSQFAMPFF--ENIAYHEYTSLL---LnassqGESLAKDLG-SKKAMLMRSHGLLTCGNNLKEAFFYIRFLEQACKIQV 188
                  *****77..9************77..88***7777733...234477********8.889********************************96 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (236 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       384  (0.0214178); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.21s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1893.04
//
Query:       AHX11732.1  [L=389]
Description: aminotransferase class-III family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    2.3e-96  323.0   0.1    3.2e-96  322.5   0.1    1.2  1  Aminotran_3  Aminotransferase class-III
  ------ inclusion threshold ------
      0.079   12.5   0.1       0.29   10.8   0.0    2.0  2  Rsa3         Ribosome-assembly protein 3


Domain annotation for each model (and alignments):
>> Aminotran_3  Aminotransferase class-III
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  322.5   0.1  3.6e-100   3.2e-96       7     404 ..       9     385 ..       6     387 .. 0.96

  Alignments for each domain:
  == domain 1  score: 322.5 bits;  conditional E-value: 3.6e-100
                  --SCEEEEEEEBTEEEETTS-EEEESSHHHHTTTT-BT-HHHHHHHHHHHTT-S---TTTCEEHHHHHHHHHHHHHCT-..SEEEEESSHHHHHHHHH CS
  Aminotran_3   7 dnlllvitkaeGvyltdvdgkrylDlvssiavvnlGhahPkvvkavkeqaaklshvsfgaltnepalklaekllklapkgldkvflansGseAvetAl 104
                  +++++ i  a+Gv l d  gk+ylDl+s+ia vn+Gh++++++  +++q+  l+h+s ++++ne ++++ae l++++    +k+f++ sG eA+e+A+
   AHX11732.1   9 HKFPITIAHAKGVHLFDTLGKKYLDLTSGIATVNFGHCNEHIASKISQQLYRLWHCS-NLFSNELQEQAAERLVNATSF-GEKIFFCSSGLEAIEAAV 104
                  466799***************************************************.***************888776.59**************** PP

                  HHHHHHHHHTSHCTT-EEEEETTT---SSHHHHHHSS--TTTTTTCTTB-TSEEEE-TTBGGGTB-HHHHHHHHHHHHHHHHCHTCCCEEEEEE-SCE CS
  Aminotran_3 105 KlarkyarekkatektkiiafkgafHGrtlgalsvtgskkkyktlfgpflpevvrlkypdeevlkeneeeeaalleelealekkkkdevaAvivEpiq 202
                  K++r+y +e+++t kt+ii++k++fHGr  + +s++g  +  +++f p+l ++++++++d                    l  + +  +aAvi+E iq
   AHX11732.1 105 KFIRRYFHETGHTGKTEIITLKNGFHGRSITGISAGGT-EAARRGFAPLLEGFTQVEAND-----------------TDVLHTAVSHRTAAVILELIQ 184
                  **************************************.9*******************9.................44566788899********** PP

                  TTTTSEB--CCHHHHHHHHHHHHT-EEEEE-TTTTTTTTSSSSGGGGCTS--SEEEE-GGGGTTSS-EEEEEEHHHHTTS-TTSB--TTTT-HHHHHH CS
  Aminotran_3 203 gegGvvvaspeflaklrelckkhdvllivDEvqtGfGrTGklfAlehagvspDlmtlaKaltgGlplsavlataevmqalapgshgsTfgGnplacav 300
                  +egGv   ++e++++l el +k + ll +DE+qtGfGr Gklf +e++ v+pDl+t aK++++G+p+   +++++++  l    hg+T++Gn la+a+
   AHX11732.1 185 SEGGVHEITQEYVNELNELREKFNFLLCFDEIQTGFGRIGKLFHYENLRVEPDLLTCAKGMGNGFPVGGCIVNQKIAANLPFATHGGTYSGNSLAMAA 282
                  ************************************************************************************************** PP

                  HHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHCTT-.TTEEEEEEETTEEEEEEBCCCETTCHHHHHHHHHCTEE-EEETT.TEEEE---TT--HHHHH CS
  Aminotran_3 301 alavleiieeekllenaqelgaalkegLeelqkky.evikevRgkGlmiaielkeeaevkekeilkkakekGvlilsaGd.nvirllppliitdeeid 396
                  ++ +l++++ ekl ++++ +++++ e L+ ++k   e+i e+Rg+Gl+i++el  + +  ++++++k ++ Gv i  + + +v+r+lppliit+e++d
   AHX11732.1 283 VNGALDLLN-EKLFKHVESMSSYFMESLHCMAKLVpEQIIEIRGRGLLIGVELATHID--SWDFMNKCLKSGVAITRTSKpQVLRILPPLIITKEDVD 377
                  ******885.7899*******************999*******************999..68***********99888777***************** PP

                  HHHHHHHH CS
  Aminotran_3 397 elleilkk 404
                   ++e l k
   AHX11732.1 378 FAIEVLYK 385
                  ***98865 PP

>> Rsa3  Ribosome-assembly protein 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   3.2e-05      0.29       8      26 ..     191     209 ..     189     210 .. 0.89
   2 ?   -3.5   0.0      0.93   8.4e+03      36      44 ..     346     354 ..     346     354 .. 0.84

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 3.2e-05
        Rsa3   8 llteeFgdDLDelRkapdF 26 
                 ++t+e+ ++L+elR++ +F
  AHX11732.1 191 EITQEYVNELNELREKFNF 209
                 68************99777 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 0.93
        Rsa3  36 daLkqGtnl 44 
                 ++Lk+G+++
  AHX11732.1 346 KCLKSGVAI 354
                 69****976 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (389 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       524  (0.0292264); expected 358.6 (0.02)
Passed bias filter:                      494  (0.0275531); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.48u 0.25s 00:00:00.73 Elapsed: 00:00:00.39
# Mc/sec: 2984.79
//
Query:       AHX11733.1  [L=161]
Description: peptidyl-prolyl cis-trans isomerase F [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      4e-49  166.9   0.1    4.4e-49  166.8   0.1    1.0  1  Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans iso


Domain annotation for each model (and alignments):
>> Pro_isomerase  Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  166.8   0.1   2.4e-53   4.4e-49       8     158 .]       7     159 ..       1     159 [. 0.86

  Alignments for each domain:
  == domain 1  score: 166.8 bits;  conditional E-value: 2.4e-53
  Pro_isomerase   8 s....kGrivieLfadkaPktvenFlklvkeg....fYdgttFhRvikgfmvqgGdptgktsageqekkggesiraipdEitsklkh.krGalama 94 
                    s    +G+i ieL+ad aPkt enFlkl+ +g     Y+g++FhR+i+ fm+qgGd+tg++ +g  +   +     ++dE+ +klkh  +G+++ma
     AHX11733.1   7 SggemLGEIDIELAADIAPKTSENFLKLC-TGekgfGYKGSIFHRIIPSFMIQGGDFTGGNGTGGYS-IYDH--GVFADEN-FKLKHtGPGVVSMA 97 
                    344668***********************.5668899*********************995533322.2222..4799***.8999999******* PP

  Pro_isomerase  95 rtgkepnsagsqFfItlkeaphldgkytvFGkVveGmdvvekiekvetdeerpkknvkivsaev 158
                    ++g  pn++gsqFfIt+  +p+ldgk++vFGkV++Gm vv+kie+  ++   p+k +ki++++v
     AHX11733.1  98 NRG--PNTNGSQFFITTVSTPWLDGKHVVFGKVIQGMSVVNKIESYGSETGVPSKVIKIEDCRV 159
                    *98..8***************************************7666679***9*****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (161 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       297  (0.0165653); expected 358.6 (0.02)
Passed bias filter:                      260  (0.0145016); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1260.07
//
Query:       AHX11734.1  [L=240]
Description: phosphoribosylaminoimidazolesuccinocarboxamide synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    4.3e-61  206.7   0.1    4.8e-61  206.6   0.1    1.0  1  SAICAR_synt  SAICAR synthetase


Domain annotation for each model (and alignments):
>> SAICAR_synt  SAICAR synthetase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  206.6   0.1   2.7e-65   4.8e-61       1     251 [.       6     232 ..       6     233 .. 0.96

  Alignments for each domain:
  == domain 1  score: 206.6 bits;  conditional E-value: 2.7e-65
                  EEEE-SSEEEEE-.SSTTEEEEEEESEEEECCCTEEEEETTHHHHHHHHHHHHHHHHHH..--BSEEEE.....-SSSEEEEE-EEEESEEEEEEEE- CS
  SAICAR_synt   1 llyeGKvrdvYel.edddklllvakDrisAfdvvlkeeipgKGkvltqlsafwfeklek..ipnhliksldpeqlegrsmlvkklkmlpvEvvvRgyl 95 
                  +lyeGK++ +++  ++++ +  ++kD+i+A +  ++  ipgKG++++ +saf++++l++  i++h+ik      l+ +++lvkk++++p+EvvvR+++
   AHX11734.1   6 KLYEGKAKILFSFpDNPNLVTQHFKDDITANNNEKRAVIPGKGVINNYISAFFMQNLQNigIRTHFIKV-----LNMKEQLVKKAELIPFEVVVRNIV 98 
                  68***********777799***************************************558******66.....99********************** PP

                  -HHH.......HH....HH..T--TT-EEEEEEEEEEE--CCCT.S-EE-HHHHH.HTT..-HHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEEEEEE CS
  SAICAR_synt  96 tGslwkeykksgkvcgirlpeglkegeklpepiftpstKaeegehDeniseeevvealg..teeeaeeieelalavyekaaelaaergiilvDtKlEF 191
                  +G l       +k    rl  g++eg  l++p++++++K+++++ D+++++++++ +++  ++ e+eei+ +a ++++ ++ ++++ gi+lvD KlEF
   AHX11734.1  99 AGGL-------AK----RL--GMEEGIILESPLIEMYLKNDKLG-DPMVTDDHII-TFNwlRQFEIEEIKIMAWRINDFLSGALSSAGITLVDLKLEF 181
                  ****.......88....99..**********************9.**********.77889999********************************** PP

                  EEETTTTEEEEES--.STTTEEEEETTT.....GGGB-STHHHHTT-STHHHHHHHHHHH CS
  SAICAR_synt 192 GldeedgelvLaDevltpDssRfwdaetyeegkeqeslDKqfvRdwleeveekwkekler 251
                  G++  d++++L+De+ +pD++Rfwd+et      +e++DK+++R++++ v++ +ke+++r
   AHX11734.1 182 GFH--DDQIILIDEI-SPDTCRFWDSET------KEKMDKDRFRRDMGGVSKYYKEVAKR 232
                  **9..79********.************......9****************999999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (240 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      404  (0.0225333); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.40
# Mc/sec: 1787.34
//
Query:       AHX11735.1  [L=198]
Description: riboflavin synthase, alpha subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    7.7e-43  144.4   1.0    3.3e-22   78.3   0.2    2.1  2  Lum_binding  Lumazine binding domain


Domain annotation for each model (and alignments):
>> Lum_binding  Lumazine binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   65.2   0.0   2.2e-22   3.9e-18       2      86 ..       4      85 ..       3      86 .. 0.91
   2 !   78.3   0.2   1.8e-26   3.3e-22       1      87 []      99     183 ..      99     183 .. 0.97

  Alignments for each domain:
  == domain 1  score: 65.2 bits;  conditional E-value: 2.2e-22
                 S--SEEEEEEEEE.ECGCTTEETEESGGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEEEEEE CS
  Lum_binding  2 GiVeevgtvesiekeekledltielpelakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkVNlEr 86
                 Gi+e+vg ++++  +++   l +++pel+ ++v+ G+s+a+nG+cLTV+  +v ++++++ ++peT+++t++++ k+g+++NlE+
   AHX11735.1  4 GIIEAVGAITKLLIKDNQIFLVVNAPELKAKVVP-GSSVACNGACLTVT--SVMDSSLEFYLSPETFQKTNFRTFKEGSRINLET 85
                 9***********5455678888889999999998.55***********8..7999*****************************7 PP

  == domain 2  score: 78.3 bits;  conditional E-value: 1.8e-26
                  -S--SEEEEEEEEE.ECGCTTEETEES.GGGGG..TTT-EEEETTEEEEEEEEEE.SSEEEEEEEHHHHHHSSGGG--TTSEEEEEEE CS
  Lum_binding   1 tGiVeevgtvesiekeekledltielp.elakylvekGdsiavnGvcLTVvteeveeeeftvdvipeTlerttlgelkvgdkVNlEra 87 
                  +G+V+++ ++++i+++++++ +t++l+ e+++y++ kG s++++G++LTV+   v++++f+v++ip+T+++t ++  ++gd+VN+E +
   AHX11735.1  99 QGHVDTTTKITDIQQSGESHMITFALTkEISPYIAYKG-SVCIDGTSLTVN--GVSDDSFSVNIIPYTWSNTIFRYNEIGDEVNVESD 183
                  8************999999999999989**********.***********9..89*******************************76 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      386  (0.0215294); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.24s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1445.74
//
Query:       AHX11736.1  [L=265]
Description: prolipoprotein diacylglyceryl transferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.5e-68  229.4  10.6      4e-68  229.3  10.6    1.0  1  LGT       Prolipoprotein diacylglyceryl transferase


Domain annotation for each model (and alignments):
>> LGT  Prolipoprotein diacylglyceryl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  229.3  10.6   2.2e-72     4e-68       1     241 [.      13     254 ..      13     255 .. 0.92

  Alignments for each domain:
  == domain 1  score: 229.3 bits;  conditional E-value: 2.2e-72
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxx RF
         LGT   1 pvafsigpleirwYgllialgfllavllakrrakkeglkeekdkvddlliyavilgii.GaRlgyvlfY....ylsnpleilkiwegGlaihGgligvl 94 
                 p afs+gp++++wY++++++g++  +++++r+      + ++  +d++++y++ lg+i G+Rlgy+lfY    y+++ple l++w+gG+++hGgligvl
  AHX11736.1  13 PDAFSLGPFSVKWYAIAYVIGIVYTYFFLARHSGL---ESKE--LDSFFCYGT-LGVIlGGRLGYILFYnleyYVTHPLETLMVWNGGMSFHGGLIGVL 105
                 679***********************999877665...4545..9********.9*999********99888788************************ PP

                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxx RF
         LGT  95 lalllyakkkklsflkvlDivapvvalgqaigRlGNfingelyGkptdlpwglvfkkaeelplprhPtqlYes.lenlllflilllllskkkkkkkkdg 192
                 l+++l++++    f+++ D++a+++ lg ++gR++Nfin el G++t+++wg+vf++ +++p  rhPtqlYe+ +e+lllf+++ +ll  ++  k+ +g
  AHX11736.1 106 LGIFLFSRRYSRAFFSLSDLCACTASLGICLGRIANFINAELCGRATQHSWGVVFPNSDGIP--RHPTQLYEAmSEGLLLFIVMQVLLFGTSI-KRSSG 201
                 *******8889***************************************************..********************998765444.4669* PP

                 xxxxxxxxxxxxxxxxxxxxx.xxx...xxxxxxxxxxxxxxxxxxxxxxxxx RF
         LGT 193 evfglylilyglgRffiEflR.tds...lllgslrmgqllsiplvlagialli 241
                  ++g++++lyg++R+++E +R +d     ++ s++mgq+ls+pl+l gi++++
  AHX11736.1 202 MLSGIWITLYGFARIVMENFRePDPqigYFFSSITMGQILSLPLILSGIMIIL 254
                 *********************99954544459*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (265 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       643  (0.0358637); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 2044.43
//
Query:       AHX11737.1  [L=309]
Description: cytochrome oxidase assembly family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
      3e-92  309.2  13.0    3.4e-92  309.0  13.0    1.0  1  COX15-CtaA  Cytochrome oxidase assembly protein


Domain annotation for each model (and alignments):
>> COX15-CtaA  Cytochrome oxidase assembly protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  309.0  13.0   1.9e-96   3.4e-92      14     323 ..       1     300 [.       1     301 [. 0.96

  Alignments for each domain:
  == domain 1  score: 309.0 bits;  conditional E-value: 1.9e-96
  COX15-CtaA  14 vvvlGgltRltdsGlsitdWppctGalppltdeeweaefekyketpeykkl.agmtlaefkaiawiEwiHRllgrllGllilvpllyflakkrisrelk 111
                 +v++Gg+tRlt+sGlsit+W+p+tG++pplt+e+w  efekyk+tpeyk+   ++++ efk+i+++E++HRl+grl+Gl++++ +lyf  k+r+s++  
  AHX11737.1   1 MVFIGGFTRLTESGLSITEWKPITGIVPPLTQEDWLVEFEKYKNTPEYKLRyFDISYVEFKFIYLVEYVHRLVGRLTGLVFIAGFLYFRYKGRLSEASC 99 
                 8************************************************************************************************** PP

  COX15-CtaA 112 kllllllllvglQGllGwwmVksgLsekprvspyrlaaHLllaflllalllwlalrllakeaesaeeeaaakklrllallllallllqialGalvagld 210
                  +l+l+lll+ +QG++Gw+mVksgL ++p+vs+yrla+HL++a +l++ll++ +l + +        ++++ ++ ++  ++++ll+ q++lG+lvagl+
  AHX11737.1 100 VRLVLVLLLGTAQGFIGWYMVKSGLIDVPAVSHYRLALHLGCASALFMLLVYEFLPVTQI-------RSSTFGWSVTGGIAITLLCGQVLLGGLVAGLR 191
                 ********************************************************9988.......578999************************** PP

  COX15-CtaA 211 AglayntfplmggelipdklplceldwrnlfenpatvqfaHRllAilvllvllllailllrkarspklarlavllaallllQvalGistvllavplsla 309
                 Agl+yntfplm+ge++p+  +l++    + f++p+ vqf HR+ ++lv +++ l++i  ++ +    +     ll++l+l+Q+++G++t++++vp+++a
  AHX11737.1 192 AGLVYNTFPLMNGEFLPA--ELLRRTGLEWFSDPVCVQFLHRMNGFLVSFMVFLAWIGSCFCSW--SMFMRVSLLMCLVLAQMFFGVLTLVFQVPVDIA 286
                 ******************..66689999*************************99888888855..55556667799********************** PP

  COX15-CtaA 310 vaHqlgaallllal 323
                 ++Hql+a+lll + 
  AHX11737.1 287 LVHQLMAFLLLGVS 300
                 ***********886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (309 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       821  (0.0457917); expected 358.6 (0.02)
Passed bias filter:                      297  (0.0165653); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.40
# Mc/sec: 2302.48
//
Query:       AHX11738.1  [L=37]
Description: hypothetical protein NHE_0816 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (37 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       200  (0.0111551); expected 358.6 (0.02)
Passed bias filter:                      152  (0.00847788); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.23s 00:00:00.54 Elapsed: 00:00:00.38
# Mc/sec: 295.21
//
Query:       AHX11739.1  [L=38]
Description: hypothetical protein NHE_0817 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (38 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       205  (0.011434); expected 358.6 (0.02)
Passed bias filter:                      194  (0.0108205); expected 358.6 (0.02)
Passed Vit filter:                         5  (0.000278878); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 304.34
//
Query:       AHX11740.1  [L=39]
Description: hypothetical protein NHE_0818 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       237  (0.0132188); expected 358.6 (0.02)
Passed bias filter:                      165  (0.00920297); expected 358.6 (0.02)
Passed Vit filter:                         7  (0.000390429); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.35
# Mc/sec: 335.59
//
Query:       AHX11741.1  [L=1049]
Description: trbL/VirB6 plasmid conjugal transfer family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-19   70.9  21.7    1.3e-19   70.9  21.7    1.8  2  TrbL      TrbL/VirB6 plasmid conjugal transfer protein


Domain annotation for each model (and alignments):
>> TrbL  TrbL/VirB6 plasmid conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   70.9  21.7   7.1e-24   1.3e-19       1     183 [.     296     488 ..     296     508 .. 0.87
   2 ?   -2.6   0.4      0.21   3.8e+03     164     191 ..     601     628 ..     597     640 .. 0.73

  Alignments for each domain:
  == domain 1  score: 70.9 bits;  conditional E-value: 7.1e-24
        TrbL   1 ltiyiilygyaialgaieepiaelvkrllklgliaalatn..wggyativvdsfaglpeaaggallssagsstsp.....tldqlgldvadklleqass 92 
                 +++ i+l+g++ +lg +e p +el+ ++l +++i+ l+    w+ + ++++ +f +  +++ + ++s +g s +p        +  ++++ ++l ++++
  AHX11741.1 296 IVLVIVLMGLKFLLGMSEHPASELLVKVLQMAIILQLISPssWDFFYNNLFRLFIDGLNEVIAVVNSHTGGSYQPdqpfaF-LDRTVNTLFEVLVSTKV 393
                 699**********************************65444**************7777778888888888877886743.33356666666656665 PP

        TrbL  93 ls....ffsniggilagllawlgvlllflvaavvlllakialalllalgpifIafllFkaTrdlFenWlgqvlsyalllvllavivglgsglfas 183
                  +       +++++l++++++++ ++l+++a+vv+++a+++l +l++l pi+ + +lF++ +  F+nW+ q ls++++ ++++ +v+l s+++++
  AHX11741.1 394 RAillaYPLGVFWWLILFFVLVIYVILVAYAFVVYMTALVGLSVLIVLMPILFLGMLFGQLKHTFDNWFTQALSFCFQAIMIFTLVSLFSAMVKD 488
                 556889999********************************************************************************999873 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 0.21
        TrbL 164 alllvllavivglgsglfasalaalgad 191
                 +++l+llavi+  + +l++s+ aal + 
  AHX11741.1 601 VFILLLLAVIMYHMRDLVQSVGAALVGA 628
                 6788888888888888888888888777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1049 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1315  (0.0733449); expected 358.6 (0.02)
Passed bias filter:                      631  (0.0351944); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.82u 0.30s 00:00:01.11 Elapsed: 00:00:00.44
# Mc/sec: 7132.74
//
Query:       AHX11742.1  [L=1243]
Description: cagA exotoxin family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.7e-25   88.9  29.6    1.3e-24   87.1  24.5    2.2  2  TrbL      TrbL/VirB6 plasmid conjugal transfer protein
    5.5e-07   29.7   2.9        6.5    6.6   0.0    4.4  4  CagA      CagA exotoxin


Domain annotation for each model (and alignments):
>> TrbL  TrbL/VirB6 plasmid conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   87.1  24.5   1.5e-28   1.3e-24       1     185 [.     635     829 ..     635     844 .. 0.82
   2 !    4.4   0.2     0.003        27      13      82 ..     876     948 ..     873     966 .. 0.69

  Alignments for each domain:
  == domain 1  score: 87.1 bits;  conditional E-value: 1.5e-28
        TrbL   1 ltiyiilygyaialgaieepiaelvkrllklgliaalatn..wggyativvdsfaglpeaaggallssagsstsp..tldql....gldvadklleqas 91 
                 +++y+i yg+  +lg i++p +++v+r+ k+++i+ l+    w+ + ++++++f +  +++   ++++ +   +p  t+  l    g+ ++++ + ++ 
  AHX11742.1 635 IVLYLITYGLSFLLGIIRDPRSDVVMRVAKIAFILLLVSDysWHFFGETIFNLFINSSNELIYYFTGNLSGKYAPdnTFEFLdrtaGVILTNQFWLRML 733
                 79***********************************765559***********999988877777777766656654444455588888888888888 PP

        TrbL  92 slsffsniggilagllawlgvlllflvaavvl..llakialalllalgpifIafllFkaTrdlFenWlgqvlsyalllvllavivglgsglfasal 185
                  l  +   g+ ++++++w + l++ +++ +++  l+ +ia  ll++l+p+fIafllF++T++lFe+Wl++++s+al +++++  ++l+ +++ +al
  AHX11742.1 734 ALFLAGPAGWLVMAIILWGVFLFFSCIIEAMIvyLMILIATGLLFLLAPLFIAFLLFQRTKPLFEGWLKMLISFALRPIFIFGTLALLNAIMMAAL 829
                 888555555566666666666666677655553377888888*********************************************999987766 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.003
        TrbL  13 algaieepiaelvkrllklgliaalatnwggyativvdsfag.lpeaaggallssagsstsp...tldqlgldv 82 
                 ++g  ++ ++ l    + +++++ +a   + + + ++ds+ + +++++ g ++s++g s+s+   +  q +l+v
  AHX11742.1 876 VTGEARTHFMGLPLSFIVVIVFLLVAHAMKSFLK-ITDSMVDmITNTMMGYTGSAGGGSPSDaghQAYQAMLSV 948
                 5677888888888888888899999888888888.555555557777777777777776666555444443333 PP

>> CagA  CagA exotoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.0   0.00077       6.9      23      51 ..    1047    1074 ..    1039    1079 .. 0.83
   2 !    6.6   0.0   0.00075       6.8      23      51 ..    1094    1121 ..    1085    1126 .. 0.83
   3 !    6.6   0.0   0.00075       6.8      23      51 ..    1141    1168 ..    1132    1173 .. 0.83
   4 !    6.6   0.0   0.00073       6.5      23      51 ..    1188    1215 ..    1179    1222 .. 0.83

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.00077
                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        CagA   23 lknstepiyakvnkkktgqvaspeepiyt 51  
                       epiya v+k ktg+    e+piy 
  AHX11742.1 1047 AEGQEEPIYATVDKPKTGEG-MVENPIYE 1074
                  556789************85.56899995 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.00075
                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        CagA   23 lknstepiyakvnkkktgqvaspeepiyt 51  
                       epiya v+k ktg+    e+piy 
  AHX11742.1 1094 AEGQEEPIYATVDKPKTGEG-MVENPIYE 1121
                  556789************85.56899995 PP

  == domain 3  score: 6.6 bits;  conditional E-value: 0.00075
                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        CagA   23 lknstepiyakvnkkktgqvaspeepiyt 51  
                       epiya v+k ktg+    e+piy 
  AHX11742.1 1141 AEGQEEPIYATVDKPKTGEG-MVENPIYE 1168
                  556789************85.56899995 PP

  == domain 4  score: 6.6 bits;  conditional E-value: 0.00073
                  XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
        CagA   23 lknstepiyakvnkkktgqvaspeepiyt 51  
                       epiya v+k ktg+    e+piy 
  AHX11742.1 1188 AEGQEEPIYATVDKPKTGEG-MVENPIYE 1215
                  556789************85.56899995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (1243 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       724  (0.0403815); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.80u 0.26s 00:00:01.06 Elapsed: 00:00:00.45
# Mc/sec: 8293.79
//
Query:       AHX11743.1  [L=821]
Description: trbL/VirB6 plasmid conjugal transfer family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.3e-25   89.6  27.4    2.3e-25   89.6  27.4    1.8  2  TrbL      TrbL/VirB6 plasmid conjugal transfer protein


Domain annotation for each model (and alignments):
>> TrbL  TrbL/VirB6 plasmid conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   89.6  27.4   1.3e-29   2.3e-25       1     188 [.     495     687 ..     495     716 .. 0.86
   2 ?   -2.0   0.5      0.14   2.5e+03      99     120 ..     735     756 ..     712     770 .. 0.52

  Alignments for each domain:
  == domain 1  score: 89.6 bits;  conditional E-value: 1.3e-29
        TrbL   1 ltiyiilygyaialgaieepiaelvkrllklgliaal..atnwggyativvdsfaglpeaaggallssagsstsptldqlgldvadklleqassls... 94 
                 +++y+++yg+a ++g +++p a+l+ +l+klg++a+l   ++w+ +++ ++ +f +  +++ + +++ ++  +   ld +    +++ + ++ +++   
  AHX11743.1 495 IVLYMTVYGLAFLFGLVKTPQADLIVFLVKLGIVAVLfgPNSWKFFNEHLFALFVEGSSQLINYVSGDDSGVDLAFLDRV----LSP-FGSQRNWArif 588
                 79***********************************77778**************888888888887754432234444....333.33333333366 PP

        TrbL  95 .....ffsniggilagllawlgvlllflvaavvlllakialalllalgpifIafllFkaTrdlFenWlgqvlsyalllvllavivglgsglfasalaal 188
                       + +i++++++++ +++++ +++ +++ ++++ +++a+ll+l+pifI +++Fk+T+ +F+nW+++++++++++v+++++++l+s+++ +++aal
  AHX11743.1 589 sflfsGGLGILYFVFIIVGLILIVKAMFTIIIAYFMSIVMVAILLCLAPIFISMIFFKRTKAIFDNWIKNLAQVSITPVITFAAFALLSEVALGIVAAL 687
                 666888899*********************************************************************************999888876 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 0.14
        TrbL  99 iggilagllawlgvlllflvaa 120
                 +g +l++ ++++  ++++++  
  AHX11743.1 735 VGIGLVIAFLVISNAIMAFASH 756
                 3334444444444444444433 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (821 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1326  (0.0739584); expected 358.6 (0.02)
Passed bias filter:                      589  (0.0328518); expected 358.6 (0.02)
Passed Vit filter:                        68  (0.00379274); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.82u 0.29s 00:00:01.10 Elapsed: 00:00:00.47
# Mc/sec: 5263.39
//
Query:       AHX11744.1  [L=848]
Description: trbL/VirB6 plasmid conjugal transfer family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    5.5e-15   55.7  22.4    5.5e-15   55.7  22.4    4.3  4  TrbL      TrbL/VirB6 plasmid conjugal transfer protein


Domain annotation for each model (and alignments):
>> TrbL  TrbL/VirB6 plasmid conjugal transfer protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   5.5      0.02   3.7e+02     108     139 ..      59      90 ..      47     106 .. 0.67
   2 !    5.8   1.1   0.00058        10       1      44 [.     377     418 ..     377     464 .. 0.70
   3 !   55.7  22.4   3.1e-19   5.5e-15      74     185 ..     545     667 ..     532     678 .. 0.80
   4 ?    1.0   0.6     0.017   3.1e+02      22      87 ..     742     806 ..     725     826 .. 0.60

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.02
        TrbL 108 awlgvlllflvaavvlllakialalllalgpi 139
                 ++l++l++ +v++ +ll+   +l +++alg+i
  AHX11744.1  59 LALIGLIAGVVGGMILLIGSSGLMIVVALGMI 90 
                 45666666666666666666666666666666 PP

  == domain 2  score: 5.8 bits;  conditional E-value: 0.00058
        TrbL   1 ltiyiilygyaialgaieepiaelvkrllklgliaalatnwggy 44 
                 l++ ++l+g+++++g ++  i+e+++ ++k+++ia++   ++g 
  AHX11744.1 377 LVLAVLLFGFKLLTGGVG-GIQEWTILVMKIAAIAYFTI-GDGM 418
                 6899***********965.6889999**********933.3333 PP

  == domain 3  score: 55.7 bits;  conditional E-value: 3.1e-19
        TrbL  74 tldqlgldvadklleqassls...........ffsniggilagllawlgvlllflvaavvlllakialalllalgpifIafllFkaTrdlFenWlgqvl 161
                  l++ + ++++ +++++++             f+ +++ +l++ll ++++ll++l +  +++la ial++l+++ pifI++llF+ T+++Fe+Wl+ v+
  AHX11744.1 545 GLADAATSMTAGAISAMGGGIfivpvlvlallFAGQVVIALLVLLYVILILLIILWITHLFILAIIALTILILFSPIFIPMLLFQVTKPFFEGWLKEVM 643
                 4555545555555555555555666666777677788888888888888888888888899************************************** PP

        TrbL 162 syalllvllavivglgsglfasal 185
                 +y+l++++l+ +++l++++f++++
  AHX11744.1 644 AYSLYPIVLFGFLALVFSVFDKLY 667
                 *********************854 PP

  == domain 4  score: 1.0 bits;  conditional E-value: 0.017
        TrbL  22 aelvkrllklgliaalatnw.ggyativvdsfaglpeaaggallssagsstsptldqlgldvadkll 87 
                 + l ++l +++l ++l   + g +     +++ ++ ++++  +++++++++  +l+++ l++a+ + 
  AHX11744.1 742 SALWIKLGMMALMLFLFFHFlGILGGLAAELVGNFRADLSRHVSNPQATAR--KLAAVSLNAAKGAT 806
                 444455555555555555542444445667777788888888888887777..77777666655544 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (848 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1402  (0.0781973); expected 358.6 (0.02)
Passed bias filter:                      616  (0.0343577); expected 358.6 (0.02)
Passed Vit filter:                        67  (0.00373696); expected 17.9 (0.001)
Passed Fwd filter:                        14  (0.000780858); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.80u 0.30s 00:00:01.10 Elapsed: 00:00:00.45
# Mc/sec: 5616.73
//
Query:       AHX11745.1  [L=801]
Description: type IV secretion/conjugal transfer ATPase, VirB4 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.5e-56  191.0   0.4    1.4e-55  188.6   0.0    2.4  3  CagE_TrbE_VirB  CagE, TrbE, VirB family, component of type IV
    1.8e-09   37.0   0.0     0.0018   17.2   0.0    2.5  2  AAA_10          AAA-like domain
    2.2e-06   28.3   2.0    0.00014   22.4   0.0    3.1  3  AAA_23          AAA domain
    0.00032   20.1   0.0    0.00068   19.1   0.0    1.5  1  FtsK_SpoIIIE    FtsK/SpoIIIE family
    0.00065   20.0   0.0      0.021   15.1   0.0    2.6  2  AAA_22          AAA domain
     0.0086   15.8   0.0      0.023   14.4   0.0    1.7  1  AAA_29          P-loop containing region of AAA domain
     0.0092   14.9   0.0      0.023   13.6   0.0    1.6  2  TrwB_AAD_bind   Type IV secretion-system coupling protein DNA
     0.0099   16.4   0.0      0.063   13.8   0.0    2.3  2  ABC_tran        ABC transporter
  ------ inclusion threshold ------
      0.018   15.5   0.0       0.17   12.3   0.0    2.4  2  AAA_16          AAA ATPase domain
       0.02   14.9   0.0       0.13   12.2   0.0    2.2  2  ResIII          Type III restriction enzyme, res subunit
      0.026   13.6   1.0      0.039   13.0   0.0    1.7  2  T2SSE           Type II/IV secretion system protein
       0.03   13.9   0.0      0.061   12.8   0.0    1.5  1  AAA_7           P-loop containing dynein motor region
      0.031   14.4   0.1       0.28   11.2   0.0    2.2  2  DUF87           Helicase HerA, central domain
      0.039   14.0   0.4         15    5.6   0.0    2.9  3  AAA_14          AAA domain
      0.051   13.3   0.1        2.6    7.8   0.0    2.7  3  DEAD            DEAD/DEAH box helicase
      0.094   13.1   0.5        2.8    8.4   0.0    3.0  3  AAA             ATPase family associated with various cellula
       0.12   12.1   0.0       0.29   10.8   0.0    1.6  1  AAA_24          AAA domain
       0.15   11.6   0.0       0.39   10.3   0.0    1.6  1  cobW            CobW/HypB/UreG, nucleotide-binding domain


Domain annotation for each model (and alignments):
>> CagE_TrbE_VirB  CagE, TrbE, VirB family, component of type IV transporter system
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.6   0.0       1.2   1.2e+03     108     155 ..     144     191 ..     137     195 .. 0.86
   2 !  188.6   0.0   1.4e-58   1.4e-55       3     206 .]     191     394 ..     189     394 .. 0.98
   3 ?   -2.0   0.0       3.2   3.2e+03      84     106 ..     717     739 ..     682     756 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.6 bits;  conditional E-value: 1.2
  CagE_TrbE_VirB 108 alsklkkkqsrllsiedkaksqiteledlidevasgdvalGayhlslv 155
                      l+ l +k +r+ s e k++   ++ e+l+++++  ++ l ++ +sl+
      AHX11745.1 144 FLNDLYRKITRKDSKEGKIADLKVAHEELEEMTNKLLISLRNNSPSLL 191
                     5566777889999999999*******************9999999986 PP

  == domain 2  score: 188.6 bits;  conditional E-value: 1.4e-58
  CagE_TrbE_VirB   3 Lsereerellfselleflnflin.Gene.pvklpsgsmlldeliatskvpfgkdkfiirtakdekfasilsikeYpeetrsslldsllsldieli 95 
                     L+  + +++ +se++ fl+ + n G  e  + lp g   +de++ +++++fg + ++i t+  +++a+i+s+keY+++t++++ld++l+ ++e i
      AHX11745.1 191 LGLKKVKGVMCSEVFTFLSKIANcGIVEsDLILPTG--RIDESLVAHRMYFGRKSIEIVTPSGSRYAGIVSLKEYGQNTSAGMLDAFLQIPYEVI 283
                     56666789*****************9999*******..99****99************************************************* PP

  CagE_TrbE_VirB  96 itesfskiskqkalsklkkkqsrllsiedkaksqiteledlidevasgdvalGayhlslvlfaedkekLdkavseatkllnakGivavketigme 190
                     it++f+++++q+a++k++ +qsr+l+++dka+sq++e++ ++d + sg +a+G++hl++++ +++++ L++ +s ++++l + G+ av+e+i++e
      AHX11745.1 284 ITQTFQFVNRQVAINKMQVQQSRMLQTQDKAVSQVVEISRALDDAMSGRIAFGLHHLTILCCEKTEKGLENVLSLVESELTNTGVYAVREKINLE 378
                     *********************************************************************************************** PP

  CagE_TrbE_VirB 191 paFfsqlPgnirlnvR 206
                     paF++qlPgn++++vR
      AHX11745.1 379 PAFWAQLPGNFDYIVR 394
                     **************99 PP

  == domain 3  score: -2.0 bits;  conditional E-value: 3.2
  CagE_TrbE_VirB  84 ldsllsldieliitesfskiskq 106
                     +++++ ++ e++++++++++++ 
      AHX11745.1 717 RSVFMLSEREYALIKNTDPATRF 739
                     56777777777777777777764 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.0   1.8e-06    0.0018      22      90 ..     447     523 ..     442     563 .. 0.76
   2 !   16.9   0.0   2.3e-06    0.0023     243     295 ..     645     697 ..     630     704 .. 0.91

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 1.8e-06
      AAA_10  22 sasliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfketl........peiakkinvvtLdseeenegvL 90 
                  ++liiG++G GK vl ++l  + + +  ++++ D+ +  e f ++l        p     +n ++Ld   en+  L
  AHX11745.1 447 GHTLIIGPTGSGKTVLLNFLCAQSMKFRPRMFFFDKDRGAEIFIRALggiytviePRTRAYFNPLQLDDTPENRTFL 523
                 699************************************999*9999777555544466669999999888888766 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 2.3e-06
      AAA_10 243 vvifDEawiftssaeGkkllkelvRiGRsynaavylvtqsadDvlkeelknni 295
                 ++i+DEaw++ + +  +  +k+ ++  R+ n++v+++tqs++D++k+ +++ +
  AHX11745.1 645 MIILDEAWALIDNSVFAPTIKDWLKVLRKLNTFVVFATQSVEDASKSAISDTL 697
                 689******************************************99877655 PP

>> AAA_23  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.1      0.19   1.9e+02      73     130 ..     130     185 ..      89     207 .. 0.66
   2 ?    1.0   0.0      0.53   5.3e+02     111     146 ..     281     316 ..     240     363 .. 0.78
   3 !   22.4   0.0   1.4e-07   0.00014      15      41 ..     439     468 ..     429     533 .. 0.88

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.19
      AAA_23  73 ayveltfenkdgrytrsiererelskkkgkttkkaklelleideleqfisellgskki 130
                  y+++  +n++++  +++ +   ++  k ++  k +  ++ ++ele+++++ll s  +
  AHX11745.1 130 LYISIVRRNDKKI--EFLNDLYRKITRKDSKEGKIADLKVAHEELEEMTNKLLISLRN 185
                 3555556665553..3444433344444445555577788888998888887665554 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.53
      AAA_23 111 lleideleqfisellgskkiilnlilflgqerfeef 146
                 ++ i+++ qf+++++ ++k + +++ +l+ ++++  
  AHX11745.1 281 EVIITQTFQFVNRQVAINKMQVQQSRMLQTQDKAVS 316
                 455688999999999999999999999999997433 PP

  == domain 3  score: 22.4 bits;  conditional E-value: 1.4e-07
      AAA_23  15 idF...skgltlItGpNGaGKTTildAikl 41 
                 ++F   + g tlI+Gp+G+GKT +l++++ 
  AHX11745.1 439 FNFhskDVGHTLIIGPTGSGKTVLLNFLCA 468
                 677765569*******************96 PP

>> FtsK_SpoIIIE  FtsK/SpoIIIE family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.0   6.8e-07   0.00068      23      59 ..     429     466 ..     417     474 .. 0.86

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 6.8e-07
                   EEETTS-EEEEEGGGS-..SEEEE--TTSSHHHHHHHH CS
  FtsK_SpoIIIE  23 gkeisgnplvldlkkma.shllvaGatgsGKStalntL 59 
                   +   sg p++++  +   +h+l++G tgsGK++ ln L
    AHX11745.1 429 FDTTSGTPFYFNFHSKDvGHTLIIGPTGSGKTVLLNFL 466
                   445599999999999889*****************977 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.1   0.0   2.1e-05     0.021       6      28 ..     447     469 ..     442     490 .. 0.87
   2 ?    1.6   0.0      0.31   3.1e+02      86     131 ..     639     683 ..     616     691 .. 0.63

  Alignments for each domain:
  == domain 1  score: 15.1 bits;  conditional E-value: 2.1e-05
      AAA_22   6 gilvvtGesGtGKTtllrrlleq 28 
                 g+++++G++G+GKT+ll+ l  q
  AHX11745.1 447 GHTLIIGPTGSGKTVLLNFLCAQ 469
                 899**************998766 PP

  == domain 2  score: 1.6 bits;  conditional E-value: 0.31
      AAA_22  86 lrarav.ielliiDEaqhlr.seealeeLrsllnlsrkgvqliLvGtp 131
                 l+     ++++i+DEa  l+ +     +++++l++ rk+ +++++ t+
  AHX11745.1 639 LD---GaPSMIILDEAWALIdNSVFAPTIKDWLKVLRKLNTFVVFATQ 683
                 33...24569********887444444555555554445455555554 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.4   0.0   2.3e-05     0.023      22      39 ..     446     463 ..     437     473 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.4 bits;  conditional E-value: 2.3e-05
      AAA_29  22 kgatlltGpsGsGKSTll 39 
                  g tl++Gp+GsGK+ ll
  AHX11745.1 446 VGHTLIIGPTGSGKTVLL 463
                 248************998 PP

>> TrwB_AAD_bind  Type IV secretion-system coupling protein DNA-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.6   0.0   2.3e-05     0.023      12      51 ..     443     482 ..     434     489 .. 0.89
   2 ?   -3.5   0.0       3.8   3.8e+03     261     298 ..     664     698 ..     658     714 .. 0.55

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 2.3e-05
  TrwB_AAD_bind  12 eretqhilivGttGsGKtqalekllrairargdraivlDl 51 
                    ++++ h+li+G tGsGKt+ l+ l ++  +   r+  +D+
     AHX11745.1 443 SKDVGHTLIIGPTGSGKTVLLNFLCAQSMKFRPRMFFFDK 482
                    67789*******************9999999999988886 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 3.8
  TrwB_AAD_bind 261 lksllaegRkfGgavvlglqsiaqlrevYGedaaqsil 298
                    +k+ l+ +Rk    vv + qs++   +   ++ +++++
     AHX11745.1 664 IKDWLKVLRKLNTFVVFATQSVEDASK---SAISDTLV 698
                    555555555555555555555443332...33344444 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   13.8   0.0   6.3e-05     0.063      13      35 ..     448     470 ..     439     483 .. 0.85
   2 ?   -1.5   0.0       3.3   3.3e+03     122     136 ..     638     652 ..     634     653 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 6.3e-05
                 EEEEEESTTSSHHHHHHHHTTSS CS
                 xxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran  13 kvaivGenGaGKStLlkllagll 35 
                  + i+G++G+GK+ Ll+ l+ ++
  AHX11745.1 448 HTLIIGPTGSGKTVLLNFLCAQS 470
                 678****************9876 PP

  == domain 2  score: -1.5 bits;  conditional E-value: 3.3
                 HHHHTSSEEEEESTT CS
                 xxxxxxxxxxxxxxx RF
    ABC_tran 122 allkkpkllllDEpt 136
                 +l  +p++++lDE+ 
  AHX11745.1 638 SLDGAPSMIILDEAW 652
                 566789*******85 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0       1.4   1.4e+03      66     125 ..     269     339 ..     246     359 .. 0.60
   2 ?   12.3   0.0   0.00017      0.17      23      46 ..     445     468 ..     438     570 .. 0.70

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 1.4
      AAA_16  66 a........ipysa.laqalareellrqlldeaesaeleawrekleeala....avpelagaeasrllellkr 125
                 a        ipy + ++q++ +  + rq++ ++ + ++++  ++ ++a++    ++++l++a + r++  l +
  AHX11745.1 269 AgmldaflqIPYEViITQTF-Q-FVNRQVAINKMQVQQSRMLQTQDKAVSqvveISRALDDAMSGRIAFGLHH 339
                 34555556699977688888.4.56666666655556666666666666622224444444444555544444 PP

  == domain 2  score: 12.3 bits;  conditional E-value: 0.00017
      AAA_16  23 rpelvllsGesGvGKsslvrellr 46 
                 + + +l++G+ G+GK+ l++ l  
  AHX11745.1 445 DVGHTLIIGPTGSGKTVLLNFLCA 468
                 55789**************88775 PP

>> ResIII  Type III restriction enzyme, res subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   0.00013      0.13      20      57 ..     442     477 ..     419     484 .. 0.82
   2 ?   -1.1   0.0       1.7   1.7e+03     131     163 ..     641     680 ..     635     683 .. 0.77

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                 ...TTSEEEEEESTTSTHHHHHHHHHHHH-S.....-E CS
      ResIII  20 kskrdkrglikmaTGtGKTlvaaklierllkkgkeekf 57 
                 +sk+  + li  +TG+GKT+++  l+++ +k ++  ++
  AHX11745.1 442 HSKDVGHTLIIGPTGSGKTVLLNFLCAQSMKFRP--RM 477
                 44666799**************999999999866..33 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 1.7
                 TT-SEEEEETGGGTTS........TTTHHHHHT---SEEE CS
      ResIII 131 drfdviiiDEaHrlgak.......kswreilekfkeavll 163
                 ++  +ii DEa  l ++       k w ++l+k++ +v++
  AHX11745.1 641 GAPSMIILDEAWALIDNsvfaptiKDWLKVLRKLNTFVVF 680
                 55679******99999866665555999999888877765 PP

>> T2SSE  Type II/IV secretion system protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.3       2.7   2.7e+03      92     123 ..     289     320 ..     283     325 .. 0.77
   2 ?   13.0   0.0   3.9e-05     0.039     131     151 ..     448     468 ..     431     478 .. 0.86

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 2.7
       T2SSE  92 alviRkksakeltlddlgaeealkekiaevlr 123
                 ++v R+ + +++++++ ++ +++++++++v++
  AHX11745.1 289 QFVNRQVAINKMQVQQSRMLQTQDKAVSQVVE 320
                 57778888888899999999998888888776 PP

  == domain 2  score: 13.0 bits;  conditional E-value: 3.9e-05
       T2SSE 131 lilvsGgTgsGKttllyallk 151
                   l+ G+TgsGKt+ll+ l +
  AHX11745.1 448 HTLIIGPTGSGKTVLLNFLCA 468
                 56899***********98765 PP

>> AAA_7  P-loop containing dynein motor region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.8   0.0   6.1e-05     0.061      23      57 ..     436     470 ..     425     511 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.8 bits;  conditional E-value: 6.1e-05
       AAA_7  23 syllelllknkkpvllvGptGtGKtviikdllkkl 57 
                  + ++ + k   ++l++GptG+GKtv+++ l+ + 
  AHX11745.1 436 PFYFNFHSKDVGHTLIIGPTGSGKTVLLNFLCAQS 470
                 467788888999***************99855443 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.3   0.1      0.62   6.2e+02     164     209 ..     124     166 ..      34     183 .. 0.74
   2 ?   11.2   0.0   0.00028      0.28      24      49 ..     447     472 ..     427     490 .. 0.75

  Alignments for each domain:
  == domain 1  score: 0.3 bits;  conditional E-value: 0.62
       DUF87 164 aiarlldkledllrkggsfsnsstdliallleklekegkitiidls 209
                 ++   +  ++ + r+ +++ ++ +dl++++ +k +kegki+ +  +
  AHX11745.1 124 SMFVNELYISIVRRNDKKI-EFLNDLYRKITRKDSKEGKIADL--K 166
                 4444444455555555666.99999999998888888877654..3 PP

  == domain 2  score: 11.2 bits;  conditional E-value: 0.00028
       DUF87  24 rHlAilgsTGsGKSntvavLleelle 49 
                  H++i+g TGsGK+ +   L+++ ++
  AHX11745.1 447 GHTLIIGPTGSGKTVLLNFLCAQSMK 472
                 5*****************99998774 PP

>> AAA_14  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1       6.6   6.5e+03      33      61 ..     129     157 ..     119     163 .. 0.70
   2 ?    5.6   0.0     0.015        15       6      39 ..     450     483 ..     447     542 .. 0.77
   3 ?    5.3   0.0     0.019        19      67     118 ..     645     702 ..     613     727 .. 0.79

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 6.6
      AAA_14  33 ilyinldderdkkladpekllelileklk 61 
                  lyi++ + +dkk++  ++l++ i +k +
  AHX11745.1 129 ELYISIVRRNDKKIEFLNDLYRKITRKDS 157
                 47888888888888877677777777643 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.015
      AAA_14   6 vitGaRrvGKTtllkqlikellvkkesilyinld 39 
                 +i G+  +GKT+ll+ l  +++  + ++++++ d
  AHX11745.1 450 LIIGPTGSGKTVLLNFLCAQSMKFRPRMFFFDKD 483
                 799***********99888877334455555544 PP

  == domain 3  score: 5.3 bits;  conditional E-value: 0.019
      AAA_14  67 ylflDEiqev.......pewekalkslvdegknldvivtGSnskllskeiatslagrva 118
                 +++lDE+  +       p+++++lk l + +  + v++t S     ++ i+++l+ ++a
  AHX11745.1 645 MIILDEAWALidnsvfaPTIKDWLKVLRKLN-TFVVFATQSVEDASKSAISDTLVQQTA 702
                 4555555555555555599999999999988.899***************999988766 PP

>> DEAD  DEAD/DEAH box helicase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1         5     5e+03      82     113 ..     299     330 ..     271     343 .. 0.56
   2 ?    7.8   0.0    0.0026       2.6      15      39 ..     447     471 ..     440     564 .. 0.71
   3 ?    2.4   0.0      0.11   1.1e+02     122     169 ..     642     683 ..     620     691 .. 0.72

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 5
                 ETTSSHHHHHHHHHTTCSEEEEEHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  82 iggvaardqlskldngvdivvgtpgrlddlls 113
                   +v++++ l++ d+ v  vv     ldd +s
  AHX11745.1 299 KMQVQQSRMLQTQDKAVSQVVEISRALDDAMS 330
                 22445555555556667777777777777664 PP

  == domain 2  score: 7.8 bits;  conditional E-value: 0.0026
                 CEEEEEESTTSSHHHHHHHHHHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD  15 gdvlvaaeTGsGKTlaflipvlqiv 39 
                 g+ l+ ++TGsGKT    + + q++
  AHX11745.1 447 GHTLIIGPTGSGKTVLLNFLCAQSM 471
                 567899********99888888877 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.11
                 E.EEEEEETHHHHHHT.TTHHHHHHHHHHSHHHCTTSTTTSEEEEEESSB CS
                 x.xxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        DEAD 122 v.rflVlDEadrlldq.gfsdfinrilnqlpqitcdgklqrqvivlSATl 169
                   ++++lDEa  l d+  f ++i+  l+ l+      kl+  + v+ AT 
  AHX11745.1 642 ApSMIILDEAWALIDNsVFAPTIKDWLKVLR------KLN--TFVVFATQ 683
                 4489***********9899999999999884......333..55555555 PP

>> AAA  ATPase family associated with various cellular activities (AAA)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0       0.8     8e+02      59     110 ..     122     169 ..      82     187 .. 0.74
   2 ?    8.4   0.0    0.0028       2.8       2      22 ..     450     470 ..     449     504 .. 0.82
   3 ?   -0.3   0.0       1.4   1.4e+03      58     113 ..     642     686 ..     629     703 .. 0.66

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.8
                 SEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEES CS
         AAA  59 psilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatn 110
                  + +f+ E++  + +r    ++++ + +n L++++ + ++ke+k+  + +++
  AHX11745.1 122 NKSMFVNELYISIVRR----NDKKIEFLNDLYRKITRKDSKEGKIADLKVAH 169
                 3568889998877777....79999999999999999999877766555555 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0028
                 EEESSTTSSHHHHHHHHHHHH CS
         AAA   2 llyGppGtGKTllakavakel 22 
                 l++Gp G GKT l + ++ ++
  AHX11745.1 450 LIIGPTGSGKTVLLNFLCAQS 470
                 899************999874 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 1.4
                 TSEEEEEETGGGHHHHHTTCCCHHHHHHHHHHHHHHHHTTTSSSTEEEEEEESSGG CS
         AAA  58 kpsilfiDEidalaksrsgseseeeervvnqLlteldgvkkkeskvivigatnrpd 113
                 +ps +++DE+ al+ ++           ++++   l+ ++k   +++v+ at++++
  AHX11745.1 642 APSMIILDEAWALIDNS---------VFAPTIKDWLKVLRKL--NTFVVFATQSVE 686
                 58999999999998888.........5555555555555554..346666666644 PP

>> AAA_24  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   0.00029      0.29       6      35 ..     450     486 ..     448     495 .. 0.93

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00029
      AAA_24   6 liyGpsgiGKTtlakel.......gpkplfidtekGl 35 
                 li+Gp g+GKT l++ l        p+ +f+d ++G+
  AHX11745.1 450 LIIGPTGSGKTVLLNFLcaqsmkfRPRMFFFDKDRGA 486
                 89***********999999999*************97 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.3   0.0   0.00039      0.39       3      24 ..     449     470 ..     448     477 .. 0.85

  Alignments for each domain:
  == domain 1  score: 10.3 bits;  conditional E-value: 0.00039
                 EEEEESTTCCHHHHHHHHHCT- CS
        cobW   3 tvltGflGsGKTtLlnhllenr 24 
                 t++ G+ GsGKT Lln l++++
  AHX11745.1 449 TLIIGPTGSGKTVLLNFLCAQS 470
                 6899************999665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (801 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       783  (0.0436723); expected 358.6 (0.02)
Passed bias filter:                      586  (0.0326845); expected 358.6 (0.02)
Passed Vit filter:                        96  (0.00535445); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.77u 0.26s 00:00:01.03 Elapsed: 00:00:00.44
# Mc/sec: 5487.05
//
Query:       AHX11746.1  [L=46]
Description: putative type IV secretion system protein VirB3 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-06   28.1   0.0    1.9e-06   28.0   0.0    1.0  1  VirB3     Type IV secretory pathway, VirB3-like protein


Domain annotation for each model (and alignments):
>> VirB3  Type IV secretory pathway, VirB3-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.0   0.0     1e-10   1.9e-06      46      83 ..       1      38 [.       1      39 [. 0.96

  Alignments for each domain:
  == domain 1  score: 28.0 bits;  conditional E-value: 1e-10
       VirB3 46 lvplhlvlrliakrDpqmfrvlllrlktrlrlrnrrfw 83
                ++++h+++++i+ ++p +++++l+r +++++++nr+++
  AHX11746.1  1 MPVIHGIGYAICFNEPLFLELFLVRNQKCMKCKNRAYH 38
                589*********************************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (46 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       615  (0.034302); expected 358.6 (0.02)
Passed bias filter:                      355  (0.0198003); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.22s 00:00:00.54 Elapsed: 00:00:00.36
# Mc/sec: 379.39
//
Query:       AHX11747.1  [L=588]
Description: ABC transporter family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.7e-34  117.0   0.1    1.5e-33  116.2   0.1    1.4  1  ABC_tran      ABC transporter
    5.3e-26   91.9  15.5    6.9e-26   91.5  15.5    1.1  1  ABC_membrane  ABC transporter transmembrane region
      2e-06   27.4   3.8    0.00011   21.8   0.2    2.3  2  SMC_N         RecF/RecN/SMC N terminal domain
     0.0017   18.5   0.1      0.012   15.7   0.0    2.1  2  DUF87         Helicase HerA, central domain
     0.0029   17.3   0.4      0.007   16.1   0.4    1.6  1  AAA_29        P-loop containing region of AAA domain
     0.0072   16.2   0.0      0.022   14.7   0.0    1.8  1  RsgA_GTPase   RsgA GTPase
  ------ inclusion threshold ------
       0.01   14.8   0.1      0.066   12.1   0.0    1.9  2  AAA_10        AAA-like domain
      0.017   15.4   1.2       0.18   12.1   1.2    2.2  1  AAA_22        AAA domain
      0.017   14.9   0.5       0.03   14.0   0.5    1.4  1  AAA_15        AAA ATPase domain
      0.021   14.2   0.4        2.9    7.3   0.0    2.5  3  TniB          Bacterial TniB protein
      0.025   13.8   0.3        1.7    7.7   0.1    2.2  2  NB-ARC        NB-ARC domain
      0.032   14.3   0.1       0.14   12.2   0.1    2.0  1  CbiA          CobQ/CobB/MinD/ParA nucleotide binding domain
      0.045   14.3   0.0       0.12   12.9   0.0    1.7  2  AAA_18        AAA domain
      0.049   13.7   1.6       0.19   11.8   0.4    2.2  2  DUF4528       Domain of unknown function (DUF4528)
      0.056   12.6   0.1      0.085   12.0   0.1    1.3  1  G-alpha       G-protein alpha subunit
       0.16   12.3   0.1       0.35   11.2   0.1    1.6  1  AAA_16        AAA ATPase domain


Domain annotation for each model (and alignments):
>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  116.2   0.1   1.4e-36   1.5e-33       1     136 [.     359     509 ..     359     510 .. 0.90

  Alignments for each domain:
  == domain 1  score: 116.2 bits;  conditional E-value: 1.4e-36
                 EEEEEEEEETTSEEEEEESTTSSHHHHHHHHTTSS--SEEEEEETTCEGGGB-HHHCCHCEEEE-SS--S-TTSBHHHH.................HHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.................xxx RF
    ABC_tran   1 lknvslklkegekvaivGenGaGKStLlkllagllkpteGeilldgkdlkeqeleslrkeigvlpqepqlfpeltvren.................esd 82 
                 lk++s+ +++g+++aivG++G+GKSt+ kll gl++p +G+il+d++d+++ ++e ++k igv+pq+ +lf+++ + +n                 ++ 
  AHX11747.1 359 LKDLSFRIEKGKTLAIVGKSGSGKSTISKLLFGLYTPSKGRILIDDQDIQYLRKETFQKYIGVVPQDITLFNDT-IFNNiayanpgnatlddvikvAKL 456
                 799***********************************************************************.99999**99999877777555555 PP

                 TCHHHHHHHSTTGGTTCBGESTTSGGS-HHHHHHHHHHHHHHH.TSSEEEEESTT CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxx RF
    ABC_tran  83 eeiekalsklglkelkdtvvksspssLSgGqkqrvalarallk.kpkllllDEpt 136
                 + i++++ + ++++  +t+v++++ +LSgG+kqrva+ar+llk ++k+l++DE++
  AHX11747.1 457 ASIHDLVMSTEDQY--QTIVGERGLKLSGGEKQRVAIARMLLKeNAKILIFDEAS 509
                 55666666666665..99999999****************996379*******96 PP

>> ABC_membrane  ABC transporter transmembrane region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   91.5  15.5   6.2e-29   6.9e-26       1     273 [.      23     297 ..      23     298 .. 0.94

  Alignments for each domain:
  == domain 1  score: 91.5 bits;  conditional E-value: 6.2e-29
                   HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSS...TCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSTHHHHHH CS
  ABC_membrane   1 liliillailagvlsplfplvlgrildtlldk...gdpetealnvysllllllglaqfilallqsyllnvtgerlskrlrrklfkkilrqpmsffdt 94 
                   +il+++++ l++v+s l+p++++ +++  ++    ++     +++++l ++++ +++ il+ +++ ++  + ++ +++l  ++f ++ ++ ++f+ +
    AHX11747.1  23 FILAFFFLCLSKVASGLVPFFYKFLFEAASKIdgiNTVGP--VVLLILGYTGVRFLSQILNEIKEVFFVLVEQNSVRALALEAFSHLQSMGLKFHVS 117
                   5899*************************99966677777..******************************************************* PP

                   SCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHSHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTH CS
  ABC_membrane  95 nsvGellsrltndvsklrdglgeklglffqslltfvgglivmfylgwkltlv.llailpliilvsaviakilkklkkkeqkavakassvaeEslsgi 190
                   ++ Ge++    + +  ++++l +  + ++  +l ++ ++++++++ ++  +v l+++l+++++ ++vi+++ + + kk++ a +++s  a +sl ++
    AHX11747.1 118 KKIGEISKITERGTKAIETFLRFLTFSILPTFLEMIFVCALVLIFYPYYYCVsLTVTLLCYCIYTVVITQWRTGYVKKMKVADNQSSHRAMDSLVNY 214
                   ******999999*****************9999999888888886666655516678899************************************* PP

                   HHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSTHHHHHHHHHHHHHHHHH CS
  ABC_membrane 191 rtVkafgreeyflekfekaleeakkagikkaianglligitqllgllsyalalwfGttlvisgelsvgdlvvflslfailfga 273
                   +tVk+f+++ y+++ +   l+++   +i+  ++ ++l++ + l++ l  +++ +  ++ ++sg+ s+gd+  +++++ +l  +
    AHX11747.1 215 ETVKYFNNQCYEVSCYSALLKDYSDLAIRNKRYLSILNIGQGLIIALGLVVINLAVVFDILSGAASLGDFALVNAYLLQLYVP 297
                   *****************************************************************************999876 PP

>> SMC_N  RecF/RecN/SMC N terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.5   0.5    0.0046       5.1      26      42 ..     371     387 ..     359     398 .. 0.79
   2 !   21.8   0.2   9.6e-08   0.00011     135     210 ..     467     551 ..     392     558 .. 0.79

  Alignments for each domain:
  == domain 1  score: 6.5 bits;  conditional E-value: 0.0046
                 EEEEEESTTSSHHHHHH CS
                 xxxxxxxxxxxxxxxxx RF
       SMC_N  26 ftaivGpNGSGKsnlld 42 
                   aivG+ GSGKs +  
  AHX11747.1 371 TLAIVGKSGSGKSTISK 387
                 458**********9865 PP

  == domain 2  score: 21.8 bits;  conditional E-value: 9.6e-08
                 T............CS-HHHHHHHHHHHHHHHHCCS--SEEEECTTTTTS-HHHHHHHHHHHHHHCTTSEEEEE-SSHHHCCC-SCEEE CS
                 x............xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
       SMC_N 135 e............lLSgGektLvalaLlfAiqkvkpaplyllDeidaaLDeknvkkvaellkeksknaQfivislreemlekadklvg 210
                 e             LSgGek+ va+a ++     + a + ++De  + LD k  + + e +++   n+  ++i++r  ++  ad+++ 
  AHX11747.1 467 EdqyqtivgerglKLSGGEKQRVAIARML---LKENAKILIFDEASSSLDGKTEAVIKESIEKIGRNCTSLIIAHRLSTVVYADEIII 551
                 04555555555557***********9774...56678899****************************************99999875 PP

>> DUF87  Helicase HerA, central domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.7   0.0   1.1e-05     0.012      25      60 ..     371     405 ..     361     473 .. 0.82
   2 ?   -0.0   0.0      0.68   7.7e+02      44      59 ..     491     506 ..     487     510 .. 0.79

  Alignments for each domain:
  == domain 1  score: 15.7 bits;  conditional E-value: 1.1e-05
       DUF87  25 HlAilgsTGsGKSntvavLleellekkgatililDp 60 
                  lAi+g++GsGKS+  ++L   l+   +++ili D 
  AHX11747.1 371 TLAIVGKSGSGKSTISKLL-FGLYTPSKGRILIDDQ 405
                 58***********887765.5677466778888665 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.68
       DUF87  44 leellekkgatililD 59 
                 ++++l k +a+ili+D
  AHX11747.1 491 IARMLLKENAKILIFD 506
                 3445559********9 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.4   6.3e-06     0.007      16      38 ..     363     385 ..     358     398 .. 0.82

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 6.3e-06
      AAA_29  16 tieidlkg.atlltGpsGsGKSTl 38 
                 +++i+ kg +  ++G+sGsGKST+
  AHX11747.1 363 SFRIE-KGkTLAIVGKSGSGKSTI 385
                 56676.455899***********8 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.7   0.0     2e-05     0.022      90     120 ..     359     390 ..     320     406 .. 0.83

  Alignments for each domain:
  == domain 1  score: 14.7 bits;  conditional E-value: 2e-05
                  HHHHHHHCTT.SEEEEECSTTSSHHHHHHHHC CS
  RsgA_GTPase  90 leelkellkd.ktsvlvGqSGvGKStLinall 120
                  l++l+ ++++ kt ++vG+SG GKSt+ + l 
   AHX11747.1 359 LKDLSFRIEKgKTLAIVGKSGSGKSTISKLLF 390
                  67888999888***************998876 PP

>> AAA_10  AAA-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0   5.9e-05     0.066      23      67 ..     371     414 ..     361     438 .. 0.77
   2 ?    0.0   0.0      0.28   3.2e+02     238     274 ..     497     533 ..     489     543 .. 0.82

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 5.9e-05
      AAA_10  23 asliiGdlGnGKSvlakllvlyisllggkaliiDpkkerekfket 67 
                   +i+G+ G GKS ++kll+   +  +g++li D   + +  ket
  AHX11747.1 371 TLAIVGKSGSGKSTISKLLFGLYTPSKGRILIDDQDIQ-YLRKET 414
                 459**************************997665433.444444 PP

  == domain 2  score: 0.0 bits;  conditional E-value: 0.28
      AAA_10 238 kkefkvvifDEawiftssaeGkkllkelvRiGRsyna 274
                 k+  k+ ifDEa +  + +  + + +++ +iGR    
  AHX11747.1 497 KENAKILIFDEASSSLDGKTEAVIKESIEKIGRNCTS 533
                 6778999*****9988888888999999999998765 PP

>> AAA_22  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   1.2   0.00016      0.18       4     104 ..     368     513 ..     365     545 .. 0.60

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 0.00016
      AAA_22   4 tagilvvtGesGtGKTtllrrlleqldeeakaee.........erpevv.fvtlpsstsskdllrellralglelka...................... 70 
                 + + l+++G sG+GK+t  + l+  ++  +             + +e++ ++   ++ + + +   +++++   + +                      
  AHX11747.1 368 KGKTLAIVGKSGSGKSTISKLLFGLYTPSKGRILiddqdiqylR-KETFqKYIGVVPQDITLFNDTIFNNIAYANPGnatlddvikvaklasihdlvms 465
                 567899****************9998644333337777777742.333335555555555555555555555444444555555555555555555555 PP

      AAA_22  71 ..............erlsseellealeqalraravielliiDEaqh.lr 104
                               +    e  + a+++ l +  + ++li DEa   l+
  AHX11747.1 466 tedqyqtivgerglKLSGGEKQRVAIARMLLKENA-KILIFDEASSsLD 513
                 55555555555555444455555566666666666.6777777766665 PP

>> AAA_15  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.5   2.7e-05      0.03      21      83 ..     366     425 ..     359     544 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 2.7e-05
      AAA_15  21 lsee.ltvliGkNnsGKSsilealdlFlnnkekknkkvikiekedleifeniseskdikIdvef 83 
                 +++  +  ++Gk +sGKS+i ++l  + + +    k  i i+++d+++ +++ + k i +  + 
  AHX11747.1 366 IEKGkTLAIVGKSGSGKSTISKLLFGLYTPS----KGRILIDDQDIQYLRKETFQKYIGVVPQD 425
                 33333779****************9999988....999**********9999999988766655 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.5   0.0       5.1   5.7e+03      85     116 ..      74     108 ..      69     141 .. 0.55
   2 ?    4.4   0.0      0.02        22      36      53 ..     370     387 ..     357     400 .. 0.83
   3 ?    7.3   0.0    0.0026       2.9     106     138 ..     486     518 ..     470     537 .. 0.84

  Alignments for each domain:
  == domain 1  score: -3.5 bits;  conditional E-value: 5.1
        TniB  85 rlyaaiLealgaplkara...rvskleqqvlrllr 116
                 r+ ++iL+++++ +       +v +l  ++ + l+
  AHX11747.1  74 RFLSQILNEIKEVFFVLVeqnSVRALALEAFSHLQ 108
                 67777777777665433300033333333344444 PP

  == domain 2  score: 4.4 bits;  conditional E-value: 0.02
        TniB  36 pnlllvGdsnnGKtmive 53 
                 + l +vG+s  GK++i +
  AHX11747.1 370 KTLAIVGKSGSGKSTISK 387
                 6899***********987 PP

  == domain 3  score: 7.3 bits;  conditional E-value: 0.0026
        TniB 106 kleqqvlrllrelkvrvLiiDEihnllagsark 138
                 k++ ++ r+l + ++++Li+DE  + l g+ ++
  AHX11747.1 486 KQRVAIARMLLKENAKILIFDEASSSLDGKTEA 518
                 667778899999***************998765 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0016       1.7      21      38 ..     370     387 ..     357     394 .. 0.80
   2 ?    3.9   0.0     0.023        26     109     195 ..     447     532 ..     445     538 .. 0.80

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0016
                 EEEEEEESTTSSHHHHHH CS
      NB-ARC  21 lvvalvGmgGvGKttlak 38 
                   +a+vG+ G+GK+t++k
  AHX11747.1 370 KTLAIVGKSGSGKSTISK 387
                 5799************87 PP

  == domain 2  score: 3.9 bits;  conditional E-value: 0.023
                 EEEE-SHHHH.....HHHHCHTTSEEEEEESBCCCCCCS-S-EEEEEESS--HHHHHHHHHHCCTS-GGCHH..CHHHHHHHHHHCT CS
      NB-ARC 109 lDDVweeedwdkigvvlparenrlrvllTTRdeevanavsatsekievelLekdeawellenkvfekkleekesleevakeivekck 195
                 lDDV +  ++ +i   + + e + + ++  R  ++++  ++    i   lL+++    ++ +     + +++ +++e  ++i ++c 
  AHX11747.1 447 LDDVIKVAKLASIHDLVMSTEDQYQTIVGERGLKLSGGEKQ-RVAIARMLLKENAKILIFDEASSSLDGKTEAVIKESIEKIGRNCT 532
                 9*************99999****************999999.666666666666666666666666666666668888787777775 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   0.00013      0.14       5      43 ..     375     413 ..     372     553 .. 0.68

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 0.00013
                 ESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCC CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        CbiA   5 stkGGvGKTtlaanLaralarrglrVllvDaDpqannla 43 
                  +k+G+GK+t++  L  +    + r+l  D D q    +
  AHX11747.1 375 VGKSGSGKSTISKLLFGLYTPSKGRILIDDQDIQYLRKE 413
                 58*************************999999965555 PP

>> AAA_18  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   0.00011      0.12       2      68 ..     373     438 ..     372     468 .. 0.67
   2 ?   -2.8   0.0       7.6   8.5e+03      52      89 ..     511     546 ..     479     569 .. 0.58

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 0.00011
      AAA_18   2 lltGtpGvGKttlakeL..skrlgf....gvnlrdvakenglllevdpealdeskrldedkldklldaleens 68 
                 ++ G++G+GK+t++k L       +    g++l+d     +l+ e +++      ++ +d +  + +++++++
  AHX11747.1 373 AIVGKSGSGKSTISKLLfgL----YtpskGRILIDDQDIQYLRKETFQK---YIGVVPQDITLFNDTIFNNIA 438
                 589**************440....1444567777766666666666666...566666666666666666664 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 7.6
      AAA_18  52 ldedkldklldaleenssaleegknlvidghlaelese 89 
                   ++k+++++++  e +   +++ +l+i  +l+  +++
  AHX11747.1 511 SLDGKTEAVIKESIEKIG--RNCTSLIIAHRLSTVVYA 546
                 333444444444444443..566666666665555544 PP

>> DUF4528  Domain of unknown function (DUF4528)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.4   0.00017      0.19      16     106 ..     184     273 ..     171     290 .. 0.84
   2 ?    0.1   0.0      0.68   7.6e+02      71     113 ..     426     468 ..     399     474 .. 0.77

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00017
     DUF4528  16 kePpWtsyfvkyksvkndqfglshfnwkvdganyhilrtgcfPfikyhctkrpvqdlsledklfkvlkvinlGiPt.layGlaalllirate 106
                    +W + +vk  +v+++q ++  ++  v+ +  + +   c+    y    + + dl++ +k    l ++n+G    +a Gl  + l+ + +
  AHX11747.1 184 VITQWRTGYVKKMKVADNQSSHRAMDSLVNYETVKYFNNQCYEVSCYSALLKDYSDLAIRNKR--YLSILNIGQGLiIALGLVVINLAVVFD 273
                 567899999*********************99999**************************95..588889887651567888777766555 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.68
     DUF4528  71 dlsledklfkvlkvinlGiPtlayGlaallliratetvktskg 113
                    ++d++f+ +   n G  tl   +    l++ ++ v  ++ 
  AHX11747.1 426 ITLFNDTIFNNIAYANPGNATLDDVIKVAKLASIHDLVMSTED 468
                 3347999***************999999999999999987665 PP

>> G-alpha  G-protein alpha subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.1   7.6e-05     0.085      25      66 ..     371     417 ..     358     534 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 7.6e-05
                 EEEEEESTTSSHHHHHHHHHHHCS--.....--HHHHHCCHHHHHHH CS
     G-alpha  25 kllllGqseSGKsTilkqlkllykkg.....fseeelatwraviqln 66 
                 +l ++G+s+SGKsTi k l  ly+++     +++++++++r+  +++
  AHX11747.1 371 TLAIVGKSGSGKSTISKLLFGLYTPSkgrilIDDQDIQYLRKETFQK 417
                 6899*******************999899996666666644433332 PP

>> AAA_16  AAA ATPase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.1   0.00031      0.35      22      63 ..     369     409 ..     358     508 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 0.00031
      AAA_16  22 grpelvllsGesGvGKsslvrellralekdg.giflrgkcdql 63 
                 g    + ++G sG+GKs++ + l+  ++ ++  i++  +  q+
  AHX11747.1 369 G--KTLAIVGKSGSGKSTISKLLFGLYTPSKgRILIDDQDIQY 409
                 3..6799****************98877775233355554444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (588 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       884  (0.0493056); expected 358.6 (0.02)
Passed bias filter:                      481  (0.026828); expected 358.6 (0.02)
Passed Vit filter:                        97  (0.00541023); expected 17.9 (0.001)
Passed Fwd filter:                        16  (0.000892409); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              16  [number of targets reported over threshold]
# CPU time: 0.69u 0.30s 00:00:00.99 Elapsed: 00:00:00.47
# Mc/sec: 3734.39
//
Query:       AHX11748.1  [L=370]
Description: patatin-like phospholipase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.6e-29  102.1   0.2      1e-28  100.9   0.2    1.6  1  Patatin       Patatin-like phospholipase
  ------ inclusion threshold ------
      0.074   13.3   0.1       0.47   10.7   0.0    2.2  2  Orthopox_F14  Orthopoxvirus F14 protein
       0.14   11.6   0.0       0.25   10.8   0.0    1.3  1  DNA_gyraseB   DNA gyrase B


Domain annotation for each model (and alignments):
>> Patatin  Patatin-like phospholipase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  100.9   0.2   1.7e-32     1e-28       1     203 [.       6     190 ..       6     191 .. 0.95

  Alignments for each domain:
  == domain 1  score: 100.9 bits;  conditional E-value: 1.7e-32
     Patatin   1 LvlsGGGsrgafslgalkaL.kkelgerfdiisGtSaGAiialllalgrdpaalvddlrnlllnkifdrdllirelaanlaarlsgllgkgglfdaeal 98 
                 Lv++GGG++ ++s+gal+++ + +++ +++  +G+SaGA++all+a+ +d  ++++++ n+ l    dr+        ++ a++ ++++  g +++e+l
  AHX11748.1   6 LVFKGGGAKIFYSVGALEEIaERGILNDVERTAGVSAGAVLALLVAMDMDINEIKEFFLNFSLTEELDRF--------DDIAETERFFNHYGRYTGENL 96 
                 8******************8799***********************************************........********************* PP

     Patatin  99 rellrkvladktlkrlsarlgklpllkslftanqavpaittataatastanranglytedddddvdladavraSsafPglfppvsl.dgelyvDGGils 196
                  + l+++l++k  +  ++  ++              +   ++ ++ +    +   +++  d+++ ++a++vraSs+ P++f pv+  +gel+vDGG+l+
  AHX11748.1  97 LSQLKALLEAKYGNPDITFQEMH------------DLGCKDVYIFVTDVISQQLVQFSWLDTPNYSVASVVRASSSYPFYFVPVDGpNGELFVDGGLLD 183
                 *****999888888888888888............666788999999*************************************997899********* PP

     Patatin 197 NvPilaa 203
                 N+P+ ++
  AHX11748.1 184 NYPLWIF 190
                 ***9887 PP

>> Orthopox_F14  Orthopoxvirus F14 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.5   0.0      0.26   1.6e+03      21      33 ..      47      60 ..      41      79 .. 0.73
   2 ?   10.7   0.0   7.9e-05      0.47       7      31 ..     288     313 ..     282     322 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.5 bits;  conditional E-value: 0.26
  Orthopox_F14 21 sqlstsdtdi.eid 33
                  + l ++d+di ei 
    AHX11748.1 47 ALLVAMDMDInEIK 60
                  55677888883444 PP

  == domain 2  score: 10.7 bits;  conditional E-value: 7.9e-05
  Orthopox_F14   7 seGleistdl.nsiisqlstsdtdie 31 
                      ++istd+ ns   q+st d+d++
    AHX11748.1 288 EGEISISTDFvNSTGRQQSTFDLDVD 313
                   44589****8799999******9986 PP

>> DNA_gyraseB  DNA gyrase B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   4.2e-05      0.25      76     143 ..      75     141 ..      69     158 .. 0.90

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 4.2e-05
  DNA_gyraseB  76 lneyakkkkllkkkeekisgediregltavvsvkipepqFeGQTKekLgnsevksivekvvseeleaf 143
                  ++++a++++++++   +++ge+++++l a ++ k  +p  + Q  + Lg ++v  +v++v+s++l +f
   AHX11748.1  75 FDDIAETERFFNHYG-RYTGENLLSQLKALLEAKYGNPDITFQEMHDLGCKDVYIFVTDVISQQLVQF 141
                  67899999**99999.************************************************9764 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (370 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       366  (0.0204139); expected 358.6 (0.02)
Passed bias filter:                      331  (0.0184617); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.21s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2720.90
//
Query:       AHX11749.1  [L=275]
Description: hypothetical protein NHE_0827 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
       0.22   10.3   1.7        2.9    6.6   0.1    2.0  2  DUF2207   Predicted membrane protein (DUF2207)
       0.54    8.8   0.0       0.54    8.8   0.0    2.4  3  MFS_2     MFS/sugar transport protein
       0.75   10.0   2.1        3.4    7.9   0.7    2.3  2  DUF2749   Protein of unknown function (DUF2749)
        2.7    8.9   5.0         54    4.8   0.0    3.2  4  EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
        4.3    6.9  14.7         22    4.6   0.5    2.6  3  SUR7      SUR7/PalI family


Domain annotation for each model (and alignments):
>> DUF2207  Predicted membrane protein (DUF2207)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.1    0.0063        23     384     429 ..      16     109 ..       3     141 .. 0.70
   2 ?    6.6   0.1    0.0008       2.9     376     435 ..     129     237 ..     120     246 .. 0.75

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.0063
     DUF2207 384 salglgliilglilillallllvll...................................................lvfllilllillliaiivlll 429
                 s+ + g ++++++ +++al l   +                                                   + ++++++ i l++++i  ++
  AHX11749.1  16 SLMSSGMFLCLVLTLTVALTL---MkefsnvdklskfvlkyledlyrsqpsnpaalllygnrnlliesirishdklIKWCALIMAIALVAMVISSAC 109
                 333344444444444444444...2455999999999999999999999999999999999999999999999998666666666666666665443 PP

  == domain 2  score: 6.6 bits;  conditional E-value: 0.0008
     DUF2207 376 gkkklkklsalglgliilglilillallllvll..................................................lvfllilllillliai 424
                 ++kk+k+ +++g++l++ + +  ll+l l++++                                                  +  +li++l++ ++++
  AHX11749.1 129 PRKKRKTAHLAGFMLGFSIGVT-LLSLSLFTPFlivrernlgnilclafdasgfdrnplaevakkilketfkneviienttneIHKYLIIILVISIVSV 226
                 4566666666666655444333.3333344444568999999999999999999999999999999999999999999999999999999999999999 PP

     DUF2207 425 ivlllfsrllg 435
                 + l+ +s+ll 
  AHX11749.1 227 LSLVALSILLH 237
                 98888877665 PP

>> MFS_2  MFS/sugar transport protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.2   0.3      0.62   2.2e+03     401     420 ..      18      37 ..      11      44 .. 0.52
   2 ?    3.0   0.4    0.0083        30     316     379 ..      94     159 ..      88     169 .. 0.71
   3 ?    8.8   0.0   0.00015      0.54     159     213 ..     203     253 ..     193     257 .. 0.81

  Alignments for each domain:
  == domain 1  score: -3.2 bits;  conditional E-value: 0.62
       MFS_2 401 lrllyavlpavlllvallll 420
                 +++ +++  +++l+val l+
  AHX11749.1  18 MSSGMFLCLVLTLTVALTLM 37 
                 44444444444444444444 PP

  == domain 2  score: 3.0 bits;  conditional E-value: 0.0083
       MFS_2 316 lflvllviagfgvgvaallpwsmladvvDygelktGkrregv..ffavlsfisklatgiglgvsgl 379
                 l ++++++a+++  +++++++  ++  +   e  t+++++ +  ++++ + +s  +t ++l++++ 
  AHX11749.1  94 LIMAIALVAMVISSACGMVAHVCYTRKIQCKECHTPRKKRKTahLAGFMLGFSIGVTLLSLSLFTP 159
                 556677777777788899999999999999999998877777545555555666666666666654 PP

  == domain 3  score: 8.8 bits;  conditional E-value: 0.00015
       MFS_2 159 lilgglkserkgylifaliialLmllgviivvlgtkervemrkkekteqkeklsl 213
                 +i+++ ++e + yli++l+i+++++l+ +++++  ++r++   +++t+ +++ +l
  AHX11749.1 203 IIENT-TNEIHKYLIIILVISIVSVLSLVALSILLHSRES---ASETAPASPAPL 253
                 45555.9999**************************9955...466666666655 PP

>> DUF2749  Protein of unknown function (DUF2749)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.7   0.0      0.17   5.9e+02      10      20 ..      95     105 ..      91     134 .. 0.61
   2 ?    7.9   0.7   0.00094       3.4       5      34 ..     215     245 ..     211     257 .. 0.76

  Alignments for each domain:
  == domain 1  score: 0.7 bits;  conditional E-value: 0.17
     DUF2749  10 viavaagagti 20 
                 ++a+a++a  i
  AHX11749.1  95 IMAIALVAMVI 105
                 33333333222 PP

  == domain 2  score: 7.9 bits;  conditional E-value: 0.00094
     DUF2749   5 ilIvlvia.vaagagtilwlvvqpragtsgs 34 
                  +I+lvi  v++ +  +l +++++r ++s +
  AHX11749.1 215 LIIILVISiVSVLSLVALSILLHSRESASET 245
                 68899998899**************554422 PP

>> EphA2_TM  Ephrin type-A receptor 2 transmembrane domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.0      0.55     2e+03       8      25 ..      22      38 ..      15      64 .. 0.57
   2 ?    3.8   0.8      0.03   1.1e+02       1      35 [.      95     129 ..      92     147 .. 0.60
   3 ?   -2.6   0.0         3   1.1e+04       6      26 ..     146     166 ..     140     170 .. 0.57
   4 ?    4.8   0.0     0.015        54       2      32 ..     216     246 ..     215     269 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.55
    EphA2_TM  8 glvllvilvilvlvlvrr 25
                 +++lv++++++l l+ +
  AHX11749.1 22 MFLCLVLTLTVALTLM-K 38
                2333333333333333.3 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.03
    EphA2_TM   1 iiaaavaglvllvilvilvlvlvrrrsknrkqksd 35 
                 i+a+a++++v+  +  +++ v++ r+ ++++ ++ 
  AHX11749.1  95 IMAIALVAMVISSACGMVAHVCYTRKIQCKECHTP 129
                 45566666666666666666666555555554443 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 3
    EphA2_TM   6 vaglvllvilvilvlvlvrrr 26 
                  +g+ ll + + + +++vr+r
  AHX11749.1 146 SIGVTLLSLSLFTPFLIVRER 166
                 455555555555566666555 PP

  == domain 4  score: 4.8 bits;  conditional E-value: 0.015
    EphA2_TM   2 iaaavaglvllvilvilvlvlvrrrsknrkq 32 
                 i+++v+ +v +++lv+l ++l +r s ++++
  AHX11749.1 216 IIILVISIVSVLSLVALSILLHSRESASETA 246
                 6777888888888899999988887776655 PP

>> SUR7  SUR7/PalI family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.7   0.2      0.53   1.9e+03     159     167 ..      23      31 ..       7      55 .. 0.53
   2 ?    4.6  10.6    0.0063        23     102     162 ..      82     229 ..      56     236 .. 0.66
   3 ?    4.6   0.5    0.0062        22      87     138 ..     194     238 ..     173     273 .. 0.64

  Alignments for each domain:
  == domain 1  score: -1.7 bits;  conditional E-value: 0.53
        SUR7 159 flatllaal 167
                 fl+++l+  
  AHX11749.1  23 FLCLVLTLT 31 
                 111111111 PP

  == domain 2  score: 4.6 bits;  conditional E-value: 0.0063
        SUR7 102 rktlsklnnltkalfilhiialvlsfislvvgllai.c............................................................. 138
                 r +++k   l+k+   ++ ialv+++is  +g++a+ c                                                             
  AHX11749.1  82 RISHDK---LIKWCALIMAIALVAMVISSACGMVAHvCytrkiqckechtprkkrktahlagfmlgfsigvtllslslftpflivrernlgnilclafd 177
                 555555...89*************************669999999999666666666666666666666666666666666666666666666666666 PP

        SUR7 139 ............................vspdnsrllsflnlllsvlsflat 162
                                              + ++   ++++ l++s++s+l++
  AHX11749.1 178 asgfdrnplaevakkilketfkneviieNTTNEIHKYLIIILVISIVSVLSL 229
                 6666655555555555555555555544222222235555555555555555 PP

  == domain 3  score: 4.6 bits;  conditional E-value: 0.0062
        SUR7  87 lnsesngkvdlPsnlrktlsklnnltkalfilhiialvlsfislvv.gllaic 138
                 l+ + +++v + +n+++ ++k+       +i++++  + s++slv  ++l ++
  AHX11749.1 194 LKETFKNEV-IIENTTNEIHKY-------LIIILVISIVSVLSLVAlSILLHS 238
                 344444333.667777777774.......555555555566655553555554 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (275 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1163  (0.064867); expected 358.6 (0.02)
Passed bias filter:                      574  (0.0320152); expected 358.6 (0.02)
Passed Vit filter:                        73  (0.00407162); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.51u 0.27s 00:00:00.78 Elapsed: 00:00:00.40
# Mc/sec: 2060.08
//
Query:       AHX11750.1  [L=324]
Description: alpha/beta hydrolase fold family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.2e-15   56.1   0.1    2.7e-14   53.4   0.1    1.9  1  Abhydrolase_1  alpha/beta hydrolase fold
    5.8e-11   42.1   0.0    9.3e-11   41.4   0.0    1.2  1  Hydrolase_4    Serine aminopeptidase, S33
    1.7e-09   38.7   0.0    2.5e-09   38.0   0.0    1.4  1  Abhydrolase_6  Alpha/beta hydrolase family
    0.00011   21.8   0.0    0.00017   21.2   0.0    1.2  1  DUF676         Putative serine esterase (DUF676)
    0.00057   19.0   0.0    0.00077   18.6   0.0    1.3  1  DUF1057        Alpha/beta hydrolase of unknown function (DUF1
     0.0054   15.9   0.0        1.7    7.6   0.0    2.3  2  TcA_TcB_BD     Tc toxin complex TcA C-terminal TcB-binding do
  ------ inclusion threshold ------
      0.014   14.7   0.1      0.023   13.9   0.1    1.3  1  Acyl_transf_2  Acyl transferase
      0.029   13.7   0.0        1.3    8.3   0.0    2.5  3  DUF915         Alpha/beta hydrolase of unknown function (DUF9
      0.041   13.5   0.4       0.13   11.9   0.4    1.8  1  Esterase       Putative esterase
        0.1   12.9   0.1        2.6    8.4   0.0    2.2  2  DUF5413        Family of unknown function (DUF5413)
       0.17   11.4   0.0        2.6    7.6   0.1    2.4  2  DLH            Dienelactone hydrolase family


Domain annotation for each model (and alignments):
>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.4   0.1   1.7e-17   2.7e-14       2     256 ..      70     309 ..      69     310 .. 0.82

  Alignments for each domain:
  == domain 1  score: 53.4 bits;  conditional E-value: 1.7e-17
                    EEEEE-STTTCGGGGTTGHHHHHHHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTTSSEEEEEETHHHHHHHHHHHHHGGG CS
  Abhydrolase_1   2 vlvilhGlpgssdvwaerglapaLakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgddkltlvGhSmGGmialayaaeyper 97 
                    +++++hG   + + +    la +L k+gf+vi+lD++G g+Ss   ++    y+  ++  ++  + ++l++ ++ lvG SmGG i++++aa+ p +
     AHX11750.1  70 PIICIHGVNRNKHDFDY--LAAGLVKNGFRVIALDMLGRGESSYMDRE---LYTYQTYKVIMLEFIERLNLSRFSLVGTSMGGIISMMVAADMPGY 160
                    89***************..***********************988874...444444888888********************************* PP

                    EEEEEEESECSSCCHHHHHHHHHHHHHHCHHCHHHHHHHHHHHHHHHHCCSCHHHHHHHHHHHHHHHCHHHCCHH.HHHHHCHHHHHHHHHHHHHH CS
  Abhydrolase_1  98 Vkalvllgaidpaaslieaqrqqaksfpdffdgyaadcarnpagplladelaaleqrhrlvdalkfpdkskrfps.sgsdnasslatgalksieqw 192
                    +  l+  +          +++ ++ ++ +++  y + +    a  +l    + l+++ + +  +  +++++r ++ ++  n+    + ++k + + 
     AHX11750.1 161 IGTLIINDI------GPYTDKSAMLTLSKYLCMYPEFEHLAEAEKFLRVLFKPLNLSEEEHWQHMINSSMRRKENgKYVLNFDPEIFRGHKEKITG 250
                    *********......99*******************999999999999999999999775444444666666555233333333333344444444 PP

                    HHCCHHHHHHHHHCTHHHHSEEEEEEETTCSSSCHHHHHHHHHCHTSEEEEEEETCSSSHHHHS CS
  Abhydrolase_1 193 pttdsaklllrlrelknvlaptlvisgtsDplvppkaledlaqllpkkrlvvisdagHlafleg 256
                    + +++   + ++++    ++p+lv+ g+  ++ + + l ++ ql p+++++ +++ gH   l+g
     AHX11750.1 251 SRDLWKV-WESIDN----SIPILVLRGELSRMLSKETLIQMVQLRPNASYIEYPGIGHAPSLFG 309
                    4444433.333333....35**************************************988876 PP

>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.4   0.0   5.7e-14   9.3e-11       7     233 ..      71     304 ..      67     310 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.4 bits;  conditional E-value: 5.7e-14
  Hydrolase_4   7 vvlvHGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpelplfllGhSmGGliallyllrypdkvagl 104
                  ++ +HG++     ++ la+ L+++Gf v+alD  G G+s     ++  +++y   + +f+e    + + +++ l+G SmGG+i++ ++++ p  +  l
   AHX11750.1  71 IICIHGVNRNKHDFDYLAAGLVKNGFRVIALDMLGRGESSYMDRELYTYQTYKVIMLEFIE----RLNLSRFSLVGTSMGGIISMMVAADMPGYIGTL 164
                  7889***********************************6555555555555554555554....55577899********************89899 PP

  Hydrolase_4 105 il..saPalkikakl.......kappllkl..llkllgkllpklqvsnnlkadslsrdpevvaayeadplv.hgkitv.rlllelldamkrleeraak 189
                  i+  ++P  +  a+l        +p++ +l  + k+l  l++ l +  + + ++    ++ +++ e+ ++v  +++ + r   e +++  +l++  ++
   AHX11750.1 165 IIndIGPYTDKSAMLtlskylcMYPEFEHLaeAEKFLRVLFKPLNL--SEEEHWQHMINSSMRRKENGKYVlNFDPEIfRGHKEKITGSRDLWKVWES 260
                  9866688888887776666665233333335578999999999999..4577777777777777777777777777653788899************9 PP

  Hydrolase_4 190 it..lPllllhGeaDkvvdpeasrelyerlgskdktlklypglyHe 233
                  i+  +P+l+l Ge  +  ++e   ++++  +  + ++  ypg  H 
   AHX11750.1 261 IDnsIPILVLRGELSRMLSKETLIQMVQLRP--NASYIEYPGIGHA 304
                  9999*********999999888888887777..7999999999996 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.0   0.0   1.6e-12   2.5e-09       1     209 [.      71     305 ..      71     319 .. 0.53

  Alignments for each domain:
  == domain 1  score: 38.0 bits;  conditional E-value: 1.6e-12
                    EEEE--GC.....GCHHHH.HHHHCCTCEEEEE--TTSTS-GGCS--HHHCHHH....HHHHCCTT..TTSEEEEEETCHHHHHHHHHHCC....E CS
  Abhydrolase_6   1 vlllHGagssassWlvapL.aallaagvhvlapDlpGhGrsdpppldledladl....aalldelaagggpvvlvGHSlGGalalaaapla..lvv 89 
                    ++++HG   +++++    L a l   g++v+a+D  G G+s+ ++ +l  ++++    ++++++l  +  ++ lvG S+GG++++++a+      +
     AHX11750.1  71 IICIHGVNRNKHDFD--YLaAGLVKNGFRVIALDMLGRGESSYMDRELYTYQTYkvimLEFIERL--NLSRFSLVGTSMGGIISMMVAADMpgY-I 161
                    799***777799996..67466667779***********99888877777677764477777777..59999**************33333665.4 PP

                    E.EEES-..----TTTS----TTHHHHHHTT-CCCCHCCH..S-HSCCCCHHH..CCCCHCHCCCGHH................HHCCHHC....H CS
  Abhydrolase_6  90 g.vlldppptalpagllaaalelllallallrllawlsre..plprlfladed..adaawrarlarla................allaglg....l 160
                    g ++++    ++p ++ +a l+l + l     + + l+++  +l+  +++++   ++++w+ +                         +       
     AHX11750.1 162 GtLIIND---IGPYTDKSAMLTLSKYLCMYPEF-EHLAEAekFLR-VLFKPLNlsEEEHWQHMINSSMrrkengkyvlnfdpeiFRGHKEKitgsR 252
                    4488888...55555533333333322221111.11111111122.22222221112222222222222222222222111111222211122112 PP

                    TTCCHHTT-TTGC..EEE.CTT-C.HHHHCHHCCCH.STTEEETCE...SSS-H CS
  Abhydrolase_6 161 lpaaawadlpvpl..lvl.ggeDp.lvprllerlla.qagarlpvvlpgaGHlp 209
                      +  w+ +  ++  lvl g+  + l +++l ++ + ++ a + +++pg GH+p
     AHX11750.1 253 DLWKVWESIDNSIpiLVLrGELSRmLSKETLIQMVQlRPNASY-IEYPGIGHAP 305
                    2244555555555656666777774444555555556777777.8888888854 PP

>> DUF676  Putative serine esterase (DUF676)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.2   0.0     1e-07   0.00017       8      98 ..      71     155 ..      64     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 21.2 bits;  conditional E-value: 1e-07
      DUF676   8 vVlvHGlqgnsaDlelikeqlekikeklpeekieflmsennesktfkgidvlgerlaeevl.evvkkkkdknkkiSfvghSlGgliaraaia 98 
                 ++++HG++ n+ D+ ++++ l+k     +  +++ l   +  + ++ + ++ ++++ + ++ e++++ + +  + S+vg S+Gg+i+ ++ a
  AHX11750.1  71 IICIHGVNRNKHDFDYLAAGLVK-----NGFRVIALDMLGRGESSYMDRELYTYQTYKVIMlEFIERLNLS--RFSLVGTSMGGIISMMVAA 155
                 89*********************.....4558888888899999**************9973666666666..***********99877665 PP

>> DUF1057  Alpha/beta hydrolase of unknown function (DUF1057)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.6   0.0   4.7e-07   0.00077      24     143 ..      58     176 ..      41     222 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.6 bits;  conditional E-value: 4.7e-07
     DUF1057  24 vYeDslasgsplGtvvalhGsPGshnDfkYirskleelkiRligvnyPGfefvtgylgqkytnaeRnsyskalleelelkgklillghsRGcenaLqla 122
                 vY D  +  s l  ++ +hG      Df Y+   l ++  R+i+++  G    +    + yt +  +  +  ++e+l+l+ +  l+g s G+  ++++a
  AHX11750.1  58 VYLDW-NRNSKLSPIICIHGVNRNKHDFDYLAAGLVKNGFRVIALDMLGRGESSYMDRELYTYQTYKVIMLEFIERLNLS-RFSLVGTSMGGIISMMVA 154
                 66664.566788899***********************************9999888999***999999999****9996.899*************99 PP

     DUF1057 123 vtl.eahGlvlinptGlrvhkg 143
                 + +   +G  +in  G  + k+
  AHX11750.1 155 ADMpGYIGTLIINDIGPYTDKS 176
                 9993579*******99777665 PP

>> TcA_TcB_BD  Tc toxin complex TcA C-terminal TcB-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.6   0.0    0.0011       1.7     139     171 ..      12      44 ..       4      56 .. 0.90
   2 !    5.9   0.0    0.0035       5.8     111     246 ..     108     239 ..      82     256 .. 0.76

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
  TcA_TcB_BD 139 lkLretgkcefelpEvlFdldypghylRriksV 171
                 +kL ++  c+ +l+E  Fdld  g  +R   sV
  AHX11750.1  12 AKLTHHNCCKCKLDELFFDLDTSGAQNRMTSSV 44 
                 689999**********************98887 PP

  == domain 2  score: 5.9 bits;  conditional E-value: 0.0035
  TcA_TcB_BD 111 eaaylernkreleitktiSLrqldplallkLretgkcefelpEvlFdldypghylRriksVsltipcvvgpytsvnatLtllsskvrvkadikavkyle 209
                 e++y++r+  +++  k i L+ ++ l+l ++   g+    +  ++   d pg            i   +gpyt+ +a Ltl +  +++ +  ++   +e
  AHX11750.1 108 ESSYMDRELYTYQTYKVIMLEFIERLNLSRFSLVGTSMGGIISMMVAADMPGYIG-------TLIINDIGPYTDKSAMLTLSKYLCMYPE-FEHLAEAE 198
                 6777777777777777777777777777777777777777777777777777533.......2233468***********9987776665.44444444 PP

  TcA_TcB_BD 210 k....eedderlvtdliaiqsialSsgqndsGlFelnfrde 246
                 k      +  +l ++++ ++ i  S  ++++G + lnf+ e
  AHX11750.1 199 KflrvLFKPLNLSEEEHWQHMINSSMRRKENGKYVLNFDPE 239
                 444448889999999999999****************9876 PP

>> Acyl_transf_2  Acyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   1.4e-05     0.023      29     122 ..      67     157 ..      60     183 .. 0.79

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 1.4e-05
                    -S-EEEEE-TT-GGGGGGHHHHHHHHTTT--EEEE---B-------------HHHHHHHHHHHHHHHHHTT---EEEEEETTHHHHHHHHTTTS CS
  Acyl_transf_2  29 rnntiviasgfarrmdhfaglaeylsengfhvirydslnhvglssgeidefsmsvgkkslltvidwlkekkinnigliasslsariayevvaei 122
                    +   i+   g  r    f  la  l +ngf+vi  d l     s  + + ++  + k  +l  i+ l   ++ +  l+ +s+   i+  v+a++
     AHX11750.1  67 KLSPIICIHGVNRNKHDFDYLAAGLVKNGFRVIALDMLGRGESSYMDRELYTYQTYKVIMLEFIERL---NLSRFSLVGTSMGGIISMMVAADM 157
                    556688899*****************************98777777777788888887776666665...556666777777777776666665 PP

>> DUF915  Alpha/beta hydrolase of unknown function (DUF915)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.5   0.0     0.046        76       7      35 ..      64      92 ..      62     103 .. 0.84
   2 ?    8.3   0.0   0.00082       1.3      88     118 ..     121     151 ..     113     157 .. 0.87
   3 ?   -3.9   0.0       4.2   6.8e+03     169     194 ..     250     274 ..     243     277 .. 0.71

  Alignments for each domain:
  == domain 1  score: 2.5 bits;  conditional E-value: 0.046
      DUF915  7 ekkkeiPtifihGyggtaeslnemvkqle 35
                 ++k  P+i ihG + +++ ++ +++ l 
  AHX11750.1 64 RNSKLSPIICIHGVNRNKHDFDYLAAGLV 92
                578999*************9999888775 PP

  == domain 2  score: 8.3 bits;  conditional E-value: 0.00082
      DUF915  88 wlkkvlseLkkkYnikkfnavGhSmGglalt 118
                   k ++ e  ++ n+ +f +vG SmGg+  +
  AHX11750.1 121 TYKVIMLEFIERLNLSRFSLVGTSMGGIISM 151
                 5688999********************9765 PP

  == domain 3  score: -3.9 bits;  conditional E-value: 4.2
      DUF915 169 aykkllknqkkkipkdlevlniaGdl 194
                  +++l k   + i++++ +l + G+l
  AHX11750.1 250 GSRDLWKV-WESIDNSIPILVLRGEL 274
                 55666666.47889999999999886 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.4   8.1e-05      0.13     117     138 ..     138     159 ..      48     166 .. 0.92

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 8.1e-05
                 EEEEEETHHHHHHHHHHHCSTT CS
    Esterase 117 ravaGqSmGGlgALilalkhpd 138
                  +++G SmGG +++++a++ p+
  AHX11750.1 138 FSLVGTSMGGIISMMVAADMPG 159
                 589***************9996 PP

>> DUF5413  Family of unknown function (DUF5413)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.1   0.1      0.14   2.2e+02       7      30 ..     138     161 ..     134     164 .. 0.90
   2 ?    8.4   0.0    0.0016       2.6       5      51 ..     164     210 ..     162     213 .. 0.93

  Alignments for each domain:
  == domain 1  score: 2.1 bits;  conditional E-value: 0.14
     DUF5413   7 faaigplvggfllllattyqsgyw 30 
                 f+++g ++gg++ +++++   gy 
  AHX11750.1 138 FSLVGTSMGGIISMMVAADMPGYI 161
                 899**************9999995 PP

  == domain 2  score: 8.4 bits;  conditional E-value: 0.0016
     DUF5413   5 lifaaigplvggfllllattyqsgywdetnlaevaklfkvlfktlqy 51 
                 li+  igp      +l ++ y + y +   lae +k+++vlfk l+ 
  AHX11750.1 164 LIINDIGPYTDKSAMLTLSKYLCMYPEFEHLAEAEKFLRVLFKPLNL 210
                 68889*************************************99876 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   0.1    0.0016       2.6      15     119 ..      70     157 ..      58     167 .. 0.61
   2 ?   -2.8   0.0       2.2   3.7e+03     145     188 ..     265     304 ..     259     305 .. 0.66

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0016
         DLH  15 vvvviqeifGvndnikdiserlaeeGYvalaPdlYarqaldpndeaeaaraldelvskvaeekvlddlkaavaylksvpevstkkvgvvGfCmGGalal 113
                  ++ i+ +  ++++++  ++ l+++G+ ++a d++ r++   +++  ++++++    kv +          +++++  +    +++ +vG  mGG +++
  AHX11750.1  70 PIICIHGVNRNKHDFDYLAAGLVKNGFRVIALDMLGRGE---SSYM-DRELYTYQTYKVIM----------LEFIERLN---LSRFSLVGTSMGGIISM 151
                 566666555555777788999999999999999999999...2332.33333223333312..........23333333...45666777777777777 PP

         DLH 114 llaaev 119
                  +aa  
  AHX11750.1 152 MVAADM 157
                 777766 PP

  == domain 2  score: -2.8 bits;  conditional E-value: 2.2
         DLH 145 apilalfgeeDefipadevekleealkaanvdlelkvYpgagHa 188
                  pil+l ge   +  +++   l + + +  +++    Ypg gHa
  AHX11750.1 265 IPILVLRGELSRMLSKET---LIQMV-QLRPNASYIEYPGIGHA 304
                 677777777777777764...44433.45566677778888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (324 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       577  (0.0321825); expected 358.6 (0.02)
Passed bias filter:                      478  (0.0266607); expected 358.6 (0.02)
Passed Vit filter:                        44  (0.00245412); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.54u 0.24s 00:00:00.78 Elapsed: 00:00:00.41
# Mc/sec: 2387.51
//
Query:       AHX11751.1  [L=260]
Description: outer membrane beta-barrel domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      8e-06   26.1   4.8    1.1e-05   25.6   4.8    1.3  1  OMP_b-brl  Outer membrane protein beta-barrel domain


Domain annotation for each model (and alignments):
>> OMP_b-brl  Outer membrane protein beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.6   4.8   6.4e-10   1.1e-05       3     140 ..       9     178 ..       6     212 .. 0.76

  Alignments for each domain:
  == domain 1  score: 25.6 bits;  conditional E-value: 6.4e-10
   OMP_b-brl   3 llllaalsaaaaa....assfggfyvggglglskvkvdgvgsds.....................g.fgfgvgagyefnd.nvgvegglsysgdkdysg 74 
                 ll+l+++  +a a    + + +gfy+ gg+g+    + gv++ +                     +  +f+v ag  +    + veg ++y+++ ++s+
  AHX11751.1   9 LLSLLLFLSPAEAlfgiN-ANTGFYISGGYGALMSGKAGVDNAAtyanqaaqkfrsvskdhllheDlKNFNVAAGFSILGfSLDVEGLYGYLESAKTSK 106
                 444555555544477743.449********9884444444443355678899999********98459**********8779*********77766666 PP

   OMP_b-brl  75 s.......gktdikinllsvpvnagyafnlsds..vlpyggaGlgytkvevdvsgngasdsdtdfglglgaGvey 140
                 +       +++  ++++ ++ + +  ++ +s+   ++py+g+G+g + v++ + ++   dsd++ g+ l+  +++
  AHX11751.1 107 NgtlklklPEKVGDQEFSYFLGFVNANLEFSGAalLNPYVGLGIGTGTVTFAIENK---DSDRRYGFPLATQIKA 178
                 667999987778888898999999999999999999*********99999988755...7777766665544443 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (260 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       432  (0.024095); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.44u 0.22s 00:00:00.66 Elapsed: 00:00:00.39
# Mc/sec: 2013.01
//
Query:       AHX11752.1  [L=315]
Description: hypothetical protein NHE_0830 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       326  (0.0181828); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        15  (0.000836633); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 2291.94
//
Query:       AHX11753.1  [L=230]
Description: outer membrane beta-barrel domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.2e-09   38.0   5.5    5.4e-08   32.6   5.5    2.0  1  Surface_Ag_2  Surface antigen
    2.4e-07   31.1   5.6    3.7e-07   30.4   5.6    1.4  1  OMP_b-brl     Outer membrane protein beta-barrel domain


Domain annotation for each model (and alignments):
>> Surface_Ag_2  Surface antigen
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.6   5.5     6e-12   5.4e-08      56     222 ..      58     210 ..       3     222 .. 0.75

  Alignments for each domain:
  == domain 1  score: 32.6 bits;  conditional E-value: 6e-12
  Surface_Ag_2  56 sakeykikfkknlltafeGaiGYsldgaRvelEvsYerfdvknegnaiksdakkiaaltkdagalaraeekavvlkveaitsiSlmlNacYDilteg 152
                    ++++k +++++ +++++ a+GY+ +g+RvelE+s  + d k+         +ki  +++          +a  +k  +   +  ml + YD++ ++
    AHX11753.1  58 DTSKFKPEYESS-FIGGSAALGYYFGGMRVELEGSMYNVDSKKG--------SKIPETKQ---------PDAPAIKYGGACFMGGMLSVNYDVALTD 136
                   456677788776.**********************999988732........23333322.........345669999******************9 PP

  Surface_Ag_2 153 ipvvPYvcaGvGadfvs..vvea...inpKfayrgklGlsYaitpeislfaGafyhkvlgnefdeiplskistlt 222
                     ++PY ++G G + vs  ++++   +   ++ + k G+s    + +  +aG  +  + ++ + +++l ++++l+
    AHX11753.1 137 Y-ISPYFGVGFGLSRVSlkLDDDalsTAYHMSSQLKGGVSITGLAAVVPYAGYKFTYMNDKGYSKVALANSTELA 210
                   6.9**************863333111334566677*****999999999***99999999999999998887765 PP

>> OMP_b-brl  Outer membrane protein beta-barrel domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   30.4   5.6   4.2e-11   3.7e-07       4     157 ..      11     193 ..       8     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 30.4 bits;  conditional E-value: 4.2e-11
   OMP_b-brl   4 lllaalsaaaaa.assf....ggfyvggglglskvkv........dgvgsds......gf.gfgvgagyefnd.nvgvegglsysgdkdysgs...... 75 
                 +l+++l++a+++ a++       fy+++g++++k++         +g++s+       +f g+ + +gy+f+  +v +eg++   +  +++gs      
  AHX11753.1  11 ALAGVLCLASTSdAQDAledaDIFYAKVGYNATKMQPvewtkarvSGDTSKFkpeyesSFiGGSAALGYYFGGmRVELEGSMYNVD--SKKGSkipetk 107
                 55555554433332222233489**********9999889998886665555678875544889999****754777777777633..33333333343 PP

   OMP_b-brl  76 ..gktdikinlls..........vpvnagyafnlsdsvlpyggaGlgytkvevdvsgngasdsdtdfglglgaGveyaladnwslkaeYrytdl 157
                   +         +           ++ + y++ l d+++py+g+G+g ++v ++ +++ a ++  + + +l  Gv +     +   a+Y+ t +
  AHX11753.1 108 qpD-------APAikyggacfmgGMLSVNYDVALTDYISPYFGVGFGLSRVSLKLDDD-ALSTAYHMSSQLKGGVSITGLAAVVPYAGYKFTYM 193
                 331.......222333445653344448888999999**********99999998888.78888888888888887766555555666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       317  (0.0176809); expected 358.6 (0.02)
Passed bias filter:                      288  (0.0160634); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.25s 00:00:00.69 Elapsed: 00:00:00.42
# Mc/sec: 1641.47
//
Query:       AHX11754.1  [L=107]
Description: preprotein translocase, SecG subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model      Description
    ------- ------ -----    ------- ------ -----   ---- --  --------   -----------
    3.2e-11   43.1  11.8      5e-11   42.5  11.8    1.3  1  SecG        Preprotein translocase SecG subunit
  ------ inclusion threshold ------
      0.031   14.2   0.8      0.064   13.1   0.7    1.5  1  DUF5134     Domain of unknown function (DUF5134)
       0.79   10.2   2.5        6.3    7.3   0.1    2.2  2  ATP-synt_8  ATP synthase protein 8
        3.5    7.5   7.1       0.99    9.3   3.1    1.9  2  ODV-E18     Occlusion-derived virus envelope protein ODV-E18
        4.7    7.2  10.3        4.7    7.2   0.6    2.1  2  DUF4389     Domain of unknown function (DUF4389)


Domain annotation for each model (and alignments):
>> SecG  Preprotein translocase SecG subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.5  11.8   1.4e-14     5e-11       1      68 [.       3      68 ..       3      70 .. 0.86

  Alignments for each domain:
  == domain 1  score: 42.5 bits;  conditional E-value: 1.4e-14
                HHHHHHHHHHHHHHHHHHHCHHCCSCCHHTT...SS-SS--SSCCCHHCCHHHHHHHHHHHHHHHHHH CS
        SecG  1 illillvivsilLillvLlQsgkgaglsgafgggasdslfgsrgaekfLtkiTvilavlFfvlslvla 68
                +l++l+++v++lL+llvL+Q++ ++ ++gaf+++  + + +  g+ ++  kiT++l ++Ff+++++l+
  AHX11754.1  3 FLIVLQFVVAVLLVLLVLFQNSGSS-VTGAFASK-HGGMSTVGGVSGLAAKITWVLLFVFFLNTVLLG 68
                79******************88765.55899443.23466889***********************97 PP

>> DUF5134  Domain of unknown function (DUF5134)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.7   1.8e-05     0.064      83     123 ..      25      71 ..       7      99 .. 0.65

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 1.8e-05
     DUF5134  83 aggghsghaaagasmpgg......vplvtgvlavyFaaaalvwlarl 123
                 +++ +++ a+++  m+++       + +t+vl+++F + +++ ++  
  AHX11754.1  25 GSSVTGAFASKHGGMSTVggvsglAAKITWVLLFVFFLNTVLLGRLN 71 
                 33344444444444444366888899****************99533 PP

>> ATP-synt_8  ATP synthase protein 8
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.8   0.5     0.047   1.7e+02      13      30 ..      10      27 ..       2      35 .. 0.77
   2 ?    7.3   0.1    0.0018       6.3       7      32 ..      52      76 ..      50      90 .. 0.77

  Alignments for each domain:
  == domain 1  score: 2.8 bits;  conditional E-value: 0.047
  ATP-synt_8 13 illmwltLfiliqlklls 30
                +++++l+L++l+q   +s
  AHX11754.1 10 VVAVLLVLLVLFQNSGSS 27
                567889999999876555 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0018
  ATP-synt_8  7 stWltiillmwltLfiliqlkllsft 32
                +tW++++++++ t+ +l  l+++s +
  AHX11754.1 52 ITWVLLFVFFLNTV-LLGRLNFSSNV 76
                79*99998887775.67888877755 PP

>> ODV-E18  Occlusion-derived virus envelope protein ODV-E18
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.3   3.1   0.00028      0.99      26      56 ..       2      36 ..       1      52 [. 0.58
   2 ?    0.3   0.2      0.18   6.5e+02      37      51 ..      55      69 ..      38      98 .. 0.58

  Alignments for each domain:
  == domain 1  score: 9.3 bits;  conditional E-value: 0.00028
     ODV-E18 26 llltil..vvlviiillvllvqsss..tGsdssss 56
                l+l +l  vv v+++llvl+ +s s  tG+ +s  
  AHX11754.1  2 LFLIVLqfVVAVLLVLLVLFQNSGSsvTGAFASKH 36
                45555522566677777777776442245544444 PP

  == domain 2  score: 0.3 bits;  conditional E-value: 0.18
     ODV-E18 37 iillvllvqssstGs 51
                ++l+v+++++   G 
  AHX11754.1 55 VLLFVFFLNTVLLGR 69
                334444444444443 PP

>> DUF4389  Domain of unknown function (DUF4389)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.5   3.4    0.0092        33      13      31 ..       2      20 ..       1      30 [. 0.68
   2 ?    7.2   0.6    0.0013       4.7      17      43 ..      45      71 ..      39      77 .. 0.89

  Alignments for each domain:
  == domain 1  score: 4.5 bits;  conditional E-value: 0.0092
     DUF4389 13 lfaivlslaslvlwvvvvv 31
                lf+ivl+++  vl+v++v+
  AHX11754.1  2 LFLIVLQFVVAVLLVLLVL 20
                6777777766666665554 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0013
     DUF4389 17 vlslaslvlwvvvvvqflivLvtgrpn 43
                v +la  ++wv+++v fl ++++gr n
  AHX11754.1 45 VSGLAAKITWVLLFVFFLNTVLLGRLN 71
                78899999*************999987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (107 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       826  (0.0460706); expected 358.6 (0.02)
Passed bias filter:                      425  (0.0237046); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 814.46
//
Query:       AHX11755.1  [L=518]
Description: CTP synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   1.1e-101  339.6   0.2   1.4e-101  339.2   0.2    1.2  1  CTP_synth_N    CTP synthase N-terminus
    5.5e-50  169.8   0.0    9.2e-50  169.1   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    5.9e-05   22.9   1.0       0.28   10.9   0.0    3.1  3  Peptidase_C26  Peptidase C26


Domain annotation for each model (and alignments):
>> CTP_synth_N  CTP synthase N-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  339.2   0.2  2.4e-105  1.4e-101      27     263 ..       2     237 ..       1     239 [. 0.97

  Alignments for each domain:
  == domain 1  score: 339.2 bits;  conditional E-value: 2.4e-105
                  HCTT--EEEEEEE-SSSSSSTT--CCCC--EEE-TT--EEETHHHHHHHHHT----GGGEEEHHHHHHHHHHHHHTTTTTT----CCCHHHHHHHHHH CS
  CTP_synth_N  27 ksrglkvtlikiDPYlnvdagtlsplehGEvfvlddGaetDlDlGnYeRfldikltkennittGkiyksviekerrGdylGktvqviphvtdeikeri 124
                  +s++lkv + k+DPYlnvd+gt+spl+hGEvfv+ddGae+DlDlG+YeRf++i++t+ +++t+G+iy ++ie+errGdylG+tvqviphvt+ ik+ i
   AHX11755.1   2 QSMNLKVCIRKMDPYLNVDPGTMSPLQHGEVFVTDDGAESDLDLGHYERFTGINCTRYDSVTAGRIYMNLIERERRGDYLGATVQVIPHVTNLIKDFI 99 
                  7899********************************************************************************************** PP

                  HHHH.HCT-SEEEEEE-S-TTSGGGHHHHHHHHHHHHHH-TTTEEEEEEEE--B-TTTSSB-HHHHHHHHHHHHHHT---SEEEEEESS.---HHHHH CS
  CTP_synth_N 125 ekvakkveadvviveigGtvgdieslpfleairqlklelgkenvllihvtlvpvlkaagelktkptqhsvkelrslGiqpdiivcrsek.eleeevke 221
                  +  a+  e dv+++eigGtvgdie++pf+eairq+++e+gkenv++ih+tl p+l+++gelktkptqhsvk+l++lGiqpd+i+cr++   ++ + k+
   AHX11755.1 100 YYRAN--EYDVILCEIGGTVGDIEGQPFFEAIRQVAYEIGKENVVYIHLTLAPYLHSSGELKTKPTQHSVKTLNALGIQPDFIICRTQGiCMSPSDKR 195
                  *9998..9*******************************************************************************962578899** PP

                  HHHHHCT--GGGEEEEE--S-GGGHHHHHHHCTHHHHHHHHT CS
  CTP_synth_N 222 kialfcnvekeavisvkdvesiyevpllleeqglaelilekl 263
                  kialfcnv++ +vi+++dv+++y++p+++++q+l+++i + l
   AHX11755.1 196 KIALFCNVKEGNVIEAQDVSNVYQIPVIYKNQELDKKISKLL 237
                  **************************************9987 PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  169.1   0.0   1.5e-53   9.2e-50       2     189 ..     277     509 ..     276     510 .. 0.89

  Alignments for each domain:
  == domain 1  score: 169.1 bits;  conditional E-value: 1.5e-53
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTTTTTHHHHHHHHCTSTS-EEEETHHHHHHHHHTTTEEE....... CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspgvegkieaikearenkiPiLGICLGmQllaiefgrkvv....... 93 
                 l D+y s++ +l++a+++lgv+v v    a  e+  ++l+++d+il++gG+g  g+egk++a+++ar n+iP+LGICLG+Q+++ief+r+v        
  AHX11755.1 277 LCDAYISINAALKDAGYALGVDVSVQILCARTENL-SILSGFDAILIPGGFGLEGIEGKLAAANYARINNIPFLGICLGFQIAVIEFARNVLglkdass 374
                 78******************999888888766666.479**************************************************5555555555 PP

                 ..........................EEECEEEEEEEEEEEETTT........CGGTTTTSEEEEEEEEEEEEESG...CHHHTTEEEEEEEETTEEEE CS
      GATase  94 ..........................kekekehhggtmrlgddet........allyglknevierhrHryevnpk...elepaglevtakseddeelm 155
                                           k+++ ++ ggtmrlg++ +        + +y++ +++ erhrHryevnp+   +le++g+ +++ s+ ++ + 
  AHX11755.1 375 vefspeckdpvicfmhewktlegsveKRERSSQIGGTMRLGKYTCmlmegskaRSIYKDAESISERHRHRYEVNPSyltQLEERGMFFSGYSSMGKDIP 473
                 5566666666666666666666666688889**********************99******************************************** PP

                 EEEEETT.T.EEEESSBTTSTTSTTHHHHHHHHHHH CS
      GATase 156 eiiekkn.p.fvgvQFHPEststpegpellfnflik 189
                 e+ e+++ p f gvQFHPE++s+  +p++lf +l++
  AHX11755.1 474 EVLELREhPwFLGVQFHPEFRSSVFNPHPLFCSLLE 509
                 *******9***********************98876 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.1   0.0      0.11   6.4e+02      35      67 ..     293     325 ..     273     332 .. 0.82
   2 !    8.6   0.1   0.00023       1.4      99     119 ..     339     359 ..     329     367 .. 0.79
   3 !   10.9   0.0   4.7e-05      0.28     195     216 .]     472     492 ..     421     492 .. 0.89

  Alignments for each domain:
  == domain 1  score: -0.1 bits;  conditional E-value: 0.11
  Peptidase_C26  35 kagglpvllpieedeedvkaildkldgllltGg 67 
                     a g+ v + i   +++  +il+ +d++l++Gg
     AHX11755.1 293 YALGVDVSVQILCARTENLSILSGFDAILIPGG 325
                    5678899999999999999*************9 PP

  == domain 2  score: 8.6 bits;  conditional E-value: 0.00023
  Peptidase_C26  99 raalergvPilgiCrGlqlln 119
                    + a  +++P lgiC+G+q+  
     AHX11755.1 339 NYARINNIPFLGICLGFQIAV 359
                    4555679***********865 PP

  == domain 3  score: 10.9 bits;  conditional E-value: 4.7e-05
  Peptidase_C26 195 viEaieseeakafvlgvQwHPE 216
                    + E +e++e++ ++lgvQ+HPE
     AHX11755.1 472 IPEVLELREHP-WFLGVQFHPE 492
                    56899999988.9********9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (518 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       555  (0.0309554); expected 358.6 (0.02)
Passed bias filter:                      510  (0.0284455); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.55u 0.29s 00:00:00.84 Elapsed: 00:00:00.43
# Mc/sec: 3600.63
//
Query:       AHX11756.1  [L=730]
Description: hypothetical protein NHE_0836 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    0.00096   19.2   0.0     0.0048   16.9   0.0    2.1  2  Y_phosphatase3  Tyrosine phosphatase family
     0.0079   15.9   0.3       0.09   12.4   0.0    2.2  2  DUF5314         Family of unknown function (DUF5314)


Domain annotation for each model (and alignments):
>> Y_phosphatase3  Tyrosine phosphatase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.8   0.0      0.29   2.6e+03      66     105 ..     280     323 ..     266     338 .. 0.59
   2 !   16.9   0.0   5.4e-07    0.0048      94     142 ..     477     529 ..     428     536 .. 0.79

  Alignments for each domain:
  == domain 1  score: -1.8 bits;  conditional E-value: 0.29
  Y_phosphatase3  66 ap..legaryvhlpve..eaaeeekeeeeaeetlaelYrelles 105
                     +p  l+++++ +  ++  +++ ++k++e+ ee  ++ Y++l+++
      AHX11756.1 280 NPagLDTITVLNSYIHsaALSGTQKDKETREEVAQRNYKQLCTR 323
                     44332222333333323223677777888888888888888775 PP

  == domain 2  score: 16.9 bits;  conditional E-value: 5.4e-07
  Y_phosphatase3  94 tlaelYrellesakkayrkvfealad.ee...pvlfHCtaGKDRTGvlaalll 142
                      +++ +r+ +++++++++ ++++l + ++    + + C +GKDRTG  ++l  
      AHX11756.1 477 IITAPFRRQPRNKNARIAGMLTTLWNkTQpdrCLAVSCKSGKDRTGYESMLAD 529
                     44455566666999************644799999***********9999865 PP

>> DUF5314  Family of unknown function (DUF5314)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.4   0.0     1e-05      0.09      53     136 ..     100     182 ..      89     189 .. 0.87
   2 ?    0.7   0.0     0.039   3.5e+02      81     118 ..     383     421 ..     369     427 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 1e-05
     DUF5314  53 d.issirveagltdaqkksvlstldtaLiklIlksvskevkikieeyfqnhkkkketslelLe.yLkskYgrkkvsstaeifselq 136
                 d ++s + e++ ++a+   v+  l++  i+ I++ +  e ++ +e y++ h+     ++ +L+  L ++Y+ + ++s+ +i++  +
  AHX11756.1 100 DiVKSLPPEYKTSSAKADVVITQLNKSAIRCIQTAITLEHEESCERYLKRHN---GEVIGVLRnVLPQRYSINEIQSLLRIAEGYT 182
                 56889999******************************************99...78899996379999*9999999988877655 PP

  == domain 2  score: 0.7 bits;  conditional E-value: 0.039
     DUF5314  81 klIlksvskevkikieeyfqnhkkkketsl.elLeyLks 118
                  + ++++ k  k+  + y++nh  +++ +l +l++yL +
  AHX11756.1 383 CISKNTIKKSCKAVFSGYISNHLLEEKEGLqDLVKYLTK 421
                 4446899999*************7777776369999965 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (730 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       497  (0.0277205); expected 358.6 (0.02)
Passed bias filter:                      405  (0.0225891); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.58u 0.28s 00:00:00.86 Elapsed: 00:00:00.42
# Mc/sec: 5181.38
//
Query:       AHX11757.1  [L=145]
Description: nusB family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-12   46.7   0.1    4.2e-12   46.5   0.1    1.1  1  NusB      NusB family
  ------ inclusion threshold ------
      0.018   14.8   0.0       0.13   12.1   0.0    2.0  2  DUF1450   Protein of unknown function (DUF1450)


Domain annotation for each model (and alignments):
>> NusB  NusB family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.5   0.1   4.7e-16   4.2e-12       3     133 ..       8     135 ..       6     136 .. 0.87

  Alignments for each domain:
  == domain 1  score: 46.5 bits;  conditional E-value: 4.7e-16
                 HHHHHHHHHHHHHHH-S-HHHHHHHHHHHT-.......--HHHHHHHHHHHHHHHHTHHHHHHHHHH.TTTT--GGGS-HHHHHHHHHHHHHHTTS-SS CS
        NusB   3 aRelalqalyqveinkedeeekeailqealnklleeedldeedkafltelvkgvlrnleelDeliek.llknwplerlskvdraiLrlavyellylddv 100
                 aR l +++ y+  ++   + +++ +l++al+ l++ + + + d  +l+ l++ ++ nle   ++ie+ l+++w+++r++   ++iLr+a+ el  +   
  AHX11757.1   8 ARLLSVEVCYSSYFS---DLDQNVLLKKALD-LHDVSYMRKYDPTLLDPLLELCFSNLELDAQVIERfLSEDWNINRIDNLKLSILRVAISELRLTGLE 102
                 566666666666222...4556667777777.7888899999999999999999***9999999***999**************************999 PP

                 HHHHHHH.HHHHHHHHS-HHHHHHHHHHHHHHH CS
        NusB 101 PakvaineavelakkygdeksakFvNgVLrkva 133
                  ++ +i+e+v l + +   + ++F+N++L+k+a
  AHX11757.1 103 QKNLVIDEYVTLSRLFLPMQDSNFINAILDKLA 135
                 ******************************985 PP

>> DUF1450  Protein of unknown function (DUF1450)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.0     0.081   7.2e+02       5      18 ..      13      26 ..      11      41 .. 0.76
   2 ?   12.1   0.0   1.4e-05      0.13       2      33 ..      51      82 ..      50      88 .. 0.88

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.081
     DUF1450  5 vEfCvsnlasgtqe 18
                vE+C s+  s  ++
  AHX11757.1 13 VEVCYSSYFSDLDQ 26
                89999998887764 PP

  == domain 2  score: 12.1 bits;  conditional E-value: 1.4e-05
     DUF1450  2 kpivEfCvsnlasgtqevleklekdpdvdvie 33
                +p++E+C snl   +q +++ l +d +++ i+
  AHX11757.1 51 DPLLELCFSNLELDAQVIERFLSEDWNINRID 82
                79*********************999988766 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (145 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       345  (0.0192426); expected 358.6 (0.02)
Passed bias filter:                      285  (0.015896); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.41u 0.23s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1098.79
//
Query:       AHX11758.1  [L=198]
Description: septum formation protein Maf [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.6e-43  148.5   0.0    1.8e-43  148.3   0.0    1.0  1  Maf            Maf-like protein
  ------ inclusion threshold ------
       0.11   12.7   0.1       0.54   10.5   0.0    2.1  2  Anth_synt_I_N  Anthranilate synthase component I, N terminal 


Domain annotation for each model (and alignments):
>> Maf  Maf-like protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  148.3   0.0     2e-47   1.8e-43       2     165 ..       5     186 ..       4     187 .. 0.94

  Alignments for each domain:
  == domain 1  score: 148.3 bits;  conditional E-value: 2e-47
                 EEEE---HHHHHHHHCT-.E..EEE------.......HHHHHHHHHHHHHHHHH.....TCEEEEEEEEEE...CE---SSHHHHHHHHHHHTTSEEE CS
         Maf   2 liLASaSprRkelLeqlg.f..evvpsdvde.......aeelvlrlAeaKaeava.....alvigaDtvvvl...ilgKPkdeeealemLkklsgrthe 82 
                 +iL+S+S+ R ++L+ lg f  +vv++++de       +  +v+r+A +Ka ++      + +i+aDtv+ +   il K+ ++++ + +L++lsgr+h+
  AHX11758.1   5 FILGSSSKHRLQILSVLGlFpkSVVSPEIDEspkkkeiPLSYVKRMALEKALKLReayplENIITADTVASCgrrILPKALSDSDVRCCLEMLSGRKHR 103
                 79****************96789***********999*888***********9999999966*********98877*********************** PP

                 EEEEEEEEE.EEE..EEEEEEEEEE----HHHHHHHHHCTSGCCSTTS--TTCGGGGGCEEEECS-HHHHHT--HHHHHHHHCC CS
         Maf  83 vvTgvavlk.ekevksfvettevtfkelsdeeieaYvatgepldkAGaygiqgllglalverieGsysnVvGLPlaellelLke 165
                 ++T++++++ ++ev + v+ t ++fk+lsdee++ Y+ ++e ++kAG+y iqg+ + ++v +++Gsy+nVvGLP  e+++lLk+
  AHX11758.1 104 LYTSICLVTsSGEVRQRVTMTVLKFKRLSDEEVDFYLTSKEGIGKAGGYSIQGI-AQSFVISMQGSYFNVVGLPAYEVVSLLKS 186
                 *******999667888899999*******************************8.888************************96 PP

>> Anth_synt_I_N  Anthranilate synthase component I, N terminal region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.0   0.0      0.21   1.9e+03      19      45 ..       5      30 ..       2      64 .. 0.68
   2 ?   10.5   0.0   6.1e-05      0.54       9      55 ..     128     174 ..     122     197 .. 0.81

  Alignments for each domain:
  == domain 1  score: -1.0 bits;  conditional E-value: 0.21
  Anth_synt_I_N 19 flLeSaeneggegrySfigldpflelk 45
                   f+L S++ +++    S++gl p+ ++ 
     AHX11758.1  5 FILGSSS-KHRLQILSVLGLFPKSVVS 30
                   7777875.5555888888888865544 PP

  == domain 2  score: 10.5 bits;  conditional E-value: 6.1e-05
  Anth_synt_I_N   9 ylklaeeehkflLeSaeneggegrySfigldpflelkskngeveveg 55 
                    + +l++ee  f L S e+ g+ g yS+ g++++ ++  +++ ++v g
     AHX11758.1 128 FKRLSDEEVDFYLTSKEGIGKAGGYSIQGIAQSFVISMQGSYFNVVG 174
                    67999999************************999888887777776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (198 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       386  (0.0215294); expected 358.6 (0.02)
Passed bias filter:                      335  (0.0186848); expected 358.6 (0.02)
Passed Vit filter:                         9  (0.00050198); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 1629.44
//
Query:       AHX11759.1  [L=93]
Description: translation initiation factor IF-1 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.7e-17   62.3   1.0    3.2e-17   62.1   1.0    1.1  1  eIF-1a    Translation initiation factor 1A / IF-1
     0.0058   16.5   0.2     0.0089   15.9   0.1    1.5  1  DUF1125   Protein of unknown function (DUF1125)


Domain annotation for each model (and alignments):
>> eIF-1a  Translation initiation factor 1A / IF-1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   62.1   1.0   3.6e-21   3.2e-17       3      64 .]       9      71 ..       7      71 .. 0.96

  Alignments for each domain:
  == domain 1  score: 62.1 bits;  conditional E-value: 3.6e-21
                EEEEEEEEETTTEEEEEE.SSSSBEEEEE-HHHH.CT----TT-EEEEEE-.TT-TTEEEEES- CS
      eIF-1a  3 vigkViealgnnlfrVelpdngkevlaeipgkfR.nkiwikrGdyVlVels.pydltkGrIvyr 64
                +ig Vie+l +  frV+l +ngke+la+ +gk+R +ki+i   d+V+V +s +yd ++G Iv+r
  AHX11759.1  9 FIGEVIEVLRGPEFRVRL-ENGKEILAHSCGKMRrKKIKIILSDKVVVAMSlHYDTNRGIIVER 71
                89****************.59******************************999999*****87 PP

>> DUF1125  Protein of unknown function (DUF1125)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.1   9.9e-07    0.0089      14      37 ..      24      48 ..      16      66 .. 0.88

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 9.9e-07
     DUF1125 14 vqfecGndieafscGflyr.kikii 37
                v++e G +i a scG + r kikii
  AHX11759.1 24 VRLENGKEILAHSCGKMRRkKIKII 48
                889************9988469999 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (93 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       411  (0.0229238); expected 358.6 (0.02)
Passed bias filter:                      345  (0.0192426); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.21s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 768.97
//
Query:       AHX11760.1  [L=176]
Description: ahpC/TSA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    7.7e-16   58.1   0.0    1.5e-15   57.2   0.0    1.5  1  AhpC-TSA       AhpC/TSA family
    6.3e-10   39.0   0.0    7.5e-10   38.7   0.0    1.1  1  Redoxin        Redoxin
     0.0027   18.2   0.1     0.0042   17.5   0.1    1.2  1  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.097   13.0   0.1       0.16   12.3   0.1    1.2  1  Thioredoxin_8  Thioredoxin-like


Domain annotation for each model (and alignments):
>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   57.2   0.0   3.4e-19   1.5e-15       1     110 [.      11     135 ..      11     145 .. 0.86

  Alignments for each domain:
  == domain 1  score: 57.2 bits;  conditional E-value: 3.4e-19
                 TTSB----EEESTTCEEEECHHHTT.SEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCH........HHHHHHHH-H.SSEEEE-T CS
    AhpC-TSA   1 vgdkapdfelknadgetvslsdykg.kpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspe........shkkfiekeslnfpllsDe 90 
                 +g +ap+f+    +g  +sls ++g + ++++f+++ +cp+ ++ + +l + ++ ++++g+ vi++ +++          ++ +f++ +++ fp++ D 
  AHX11760.1  11 IGSAAPQFSIA-FNGSVYSLSSIAGsSGTLVMFICN-HCPYVKEIITNLVEDVKLMQANGIGVIAIMPNDFIaypedspeKMIEFARSNNFSFPYVPDV 107
                 799*******8.6689*******99999********.*****************************98765456667777******************* PP

                 TSHHHHHTT-EETT........TTECSC CS
    AhpC-TSA  91 egkvakaygvlkee........kglalr 110
                 +++va++y+++ ++         +l++r
  AHX11760.1 108 NQEVARKYDAVCTPdffgfndkLELQYR 135
                 ***********55555555555445555 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.7   0.0   1.7e-13   7.5e-10       3     138 ..      12     143 ..      10     153 .. 0.86

  Alignments for each domain:
  == domain 1  score: 38.7 bits;  conditional E-value: 1.7e-13
                 TSBB---ECCEETTCEEEEEHHHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHHHHHCSTTTEEEEEESSSHH........HHHHHHHTT-TSEEEE-T CS
     Redoxin   3 gdkaPdftlplaatdgnsvslsefkgkkvvvnfvpgafcPtCsaehpyleklaellkekgvdvvavvadndaf........vkefwgkeglkfpvlsDg 93 
                 g++aP f+   +a +g+ +sls+ +g +  ++ + +++cP+ ++ +  l +  +l  ++g+ v+a++ ++           + ef+ +++ +fp++ D 
  AHX11760.1  12 GSAAPQFS---IAFNGSVYSLSSIAGSSGTLVMFICNHCPYVKEIITNLVEDVKLMQANGIGVIAIMPNDFIAypedspekMIEFARSNNFSFPYVPDV 107
                 8899****...679*****************************9888999999*************55543333444458999**************** PP

                 TSHHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEEEEEESSSCHT CS
     Redoxin  94 saaftkalGlrleedaseglrtpryavidedgkvvylevepepet 138
                 ++++++++++          +tp ++ ++++  + y+++  ++et
  AHX11760.1 108 NQEVARKYDAV---------CTPDFFGFNDKLELQYRGQFMDKET 143
                 *********88.........9********9999999988777654 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.5   0.1   9.4e-07    0.0042       7      99 ..      37     137 ..      33     143 .. 0.84

  Alignments for each domain:
  == domain 1  score: 17.5 bits;  conditional E-value: 9.4e-07
  Thioredoxin_2   7 pvlvvftdpdCpyCkklkkelkel......ddvtvrvllfp.....lkpsfepkavaiwcakekkkafkd.ieenvelarkygvrgtPtivfldgk 90 
                     +lv+f  ++Cpy k + ++l e+      +++ v+ +++p     + +++ +k++++ ++++ +  f    + n+e+arky+   tP+++ ++ k
     AHX11760.1  37 GTLVMFICNHCPYVKEIITNLVEDvklmqaNGIGVI-AIMPndfiaYPEDSPEKMIEFARSNNFS--FPYvPDVNQEVARKYDAVCTPDFFGFNDK 129
                    589**********99999988888899998888888.77788**999999999***999999997..4445588*****************77777 PP

  Thioredoxin_2  91 eivarlpGy 99 
                       ++++G 
     AHX11760.1 130 -LELQYRGQ 137
                    .45577775 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.1   3.5e-05      0.16       4      87 ..      38     124 ..      36     130 .. 0.86

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 3.5e-05
                    EEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-.......SS-HHHHHHHGGGS-TTSEE.EE-TT-HHHHTT-S--TT-SEEE CS
  Thioredoxin_8   4 vlLyfgaswcppckaftpklkelyeklkkkkkveivyvsl.......dkkeeefekylkknkkpwlsvpfddkkrnklkkkynvkaiPtlv 87 
                    +l++f  ++cp  k+++ +l e  + ++ ++++ ++++           + e+++++ ++n     s+p+  + ++++++ky+  + P ++
     AHX11760.1  38 TLVMFICNHCPYVKEIITNLVEDVKLMQ-ANGIGVIAIMPndfiaypEDSPEKMIEFARSN---NFSFPYVPDVNQEVARKYDAVCTPDFF 124
                    6899999999999999999999999998.79*******99888888745579999999999...77789998889********99888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       389  (0.0216967); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.40
# Mc/sec: 1329.39
//
Query:       AHX11761.1  [L=574]
Description: proton antiporter-2 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    6.7e-62  209.5  56.0    9.4e-62  209.0  56.0    1.1  1  Na_H_Exchanger   Sodium/hydrogen exchanger family
    1.5e-23   83.2   0.5    3.6e-23   82.0   0.5    1.7  1  TrkA_N           TrkA-N domain
    4.2e-05   23.2   0.1    8.3e-05   22.2   0.1    1.5  1  UDPG_MGDP_dh_N   UDP-glucose/GDP-mannose dehydrogenase family
     0.0017   18.7   0.7     0.0049   17.2   0.7    1.9  1  Gp_dh_N          Glyceraldehyde 3-phosphate dehydrogenase, NA
     0.0052   16.9   0.1      0.013   15.6   0.1    1.6  1  AdoHcyase_NAD    S-adenosyl-L-homocysteine hydrolase, NAD bin
     0.0073   15.7   0.0      0.013   14.9   0.0    1.4  1  2-Hacid_dh_C     D-isomer specific 2-hydroxyacid dehydrogenas
  ------ inclusion threshold ------
      0.028   15.1   0.1      0.066   13.9   0.1    1.6  1  PglD_N           PglD N-terminal domain
      0.069   13.4   0.1       0.14   12.4   0.1    1.5  1  Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding doma
       0.14   12.6   0.2       0.28   11.7   0.2    1.5  1  NAD_binding_7    Putative NAD(P)-binding
       0.73   10.3   5.5        3.8    8.1   0.7    3.3  2  DUF4179          Domain of unknown function (DUF4179)


Domain annotation for each model (and alignments):
>> Na_H_Exchanger  Sodium/hydrogen exchanger family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  209.0  56.0   5.2e-65   9.4e-62       2     379 ..      12     376 ..      11     378 .. 0.96

  Alignments for each domain:
  == domain 1  score: 209.0 bits;  conditional E-value: 5.2e-65
                     HHHHHHHHHHHHHHHHTTSXHHHHHHHHHHHHTTTTTS.....HHHCHCCHHHHCHHCCHHHHCTCGCCTGCCTHHHHHHHHHHHHHHHHHHHHH CS
  Na_H_Exchanger   2 vllillallvgllarrlklpeivgliiaGlllGpsglgliepseedlevlselglilllFlaGleldlrelrknlksilllallgvlitvvliGl 96 
                     ++l+++a+l+  l+ +l++++i+g+ +aG  +G +g++++e s +  ev++e+g+++llFl+Glel l++++++++ ++ l++l+v++t+++i +
      AHX11761.1  12 IALLSTAILIVSLFLKLNISPILGYFVAGAAIGTHGFKIVEFS-SAMEVFAEFGIVFLLFLIGLELTLDRIMSMRRHVFGLGTLQVIVTAAVIVF 105
                     5677777777778*****************************9.*************************************************** PP

                     HHH.HHTXTTCHHHHHHHHHHHTSSXHHHHHHHC.CCCTSTCCCCCCHHHHHHHHHHHCCCCCHHHHHHTX..XXXXTSSSTSXHHHHHHHHHHH CS
  Na_H_Exchanger  97 llylllilgiplleallfgailsatdpvvvlailkeegrvperlgtlllgesvlnDavavvllavllalak..eeaggetslllllliflvvavg 189
                     ++++   +gi+ ++++++g +++++++++vl++l+e g  ++++g+l +++++++D ++v+ll+++  l +  +++      ++l+++ +v++++
      AHX11761.1 106 ICRM---FGINSSASIIIGCAFALSSTAIVLQVLQETGMKSNQVGRLSIAVLLMQDFTVVPLLVFVALLGNnaPQNLLLPITMSLIKAGIVLLGI 197
                     ***8...799*******************************************************888887999999999999999999999999 PP

                     HHHHHHHHHHHHHHHHHHSCTHHHHHHHHHHHHHHHHHHHHHTSXXXHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHHHHHSXHH CS
  Na_H_Exchanger 190 glllglvigwllrlitrftdddrelevllvlllallaallaellgvsgilgaflaGlvlseyefsnklseklesfreglfnplfFvlvGlsldlk 284
                     +++++l++  +++ i  +  +++el+++ +ll++l+aa+++e+l +s+++gaf+aGl+l+e+e+++++++ + +f  +l+++lfF+ vG+s+dl 
      AHX11761.1 198 FIVGRLLLRPFFKMIAST--KSSELFIATTLLIVLGAAYITEKLELSMAMGAFVAGLLLAETEYRHEVEQVIFPFK-SLLLGLFFMTVGMSIDLR 289
                     999999999999999999..9*******************************************************.9***************** PP

                     HHHXXHHHHHHHHHHHHHHHTHHHHHHHHHTTTXSSXHHHHHHCCCCSS.BHHHHHHHHHHHHHHXHHHHTTSSTTTCSTSXHHHHHHHHHHHHH CS
  Na_H_Exchanger 285 vlnnhlsvlilvllilvaillgrilavflllrllglslrealiigfgglqrgavalalaalgpalgllarelyallivvvlftvlvqGlslkpll 379
                     +l   ++++ l+ +i +a++l ++  + +l++l+g+ +  a+ +g++++q  ++al+l+ l ++  +l+++l ++l+ +v +++      ++pl+
      AHX11761.1 290 IL---IENIDLITGIALALMLLKASIIIALAKLFGFKTGPAINAGLLLAQGSEFALILFKLETSMTVLDTHLANVLVSAVTMSMA-----FTPLF 376
                     **...9******************************************************************************9.....77775 PP

>> TrkA_N  TrkA-N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.0   0.5     2e-26   3.6e-23       1     114 [.     414     527 ..     414     529 .. 0.98

  Alignments for each domain:
  == domain 1  score: 82.0 bits;  conditional E-value: 2e-26
                 EEEES-SHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHTTSEEEES-TTSHHHHHHTTGGGESEEEE-SSSHHHHHHHHHHHHHHTSSSEEEEEESSG CS
      TrkA_N   1 iiiiGlGrvGrslaeeLseggkdvvvidkdeerveelreeglevvvgdatdeevLeeagiekadaviaatgddeanilavllakelnpkkkiiaraqdp 99 
                 +ii+G+GrvG+ +a+ Lse++ ++++id d ++v+++++eg++++ g+  + ++Le++ +++a++v+  +++  +n  a++ ++e++p+++i+ar++d 
  AHX11761.1 414 VIIAGFGRVGKMVARMLSEEQVNYIIIDIDSKVVDKAQREGFPIFRGNINKLATLEAIAVDRASTVVLSMQNEVTNKKAIKFINEHFPHATIVARVSDF 512
                 79*****************8867**************************************************************************** PP

                 GGHHHHHHHTTSEEE CS
      TrkA_N 100 ehaellkklgadvvi 114
                 ++++ lkklga++ +
  AHX11761.1 513 SDIKTLKKLGAHKLV 527
                 ***********9986 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.2   0.1   4.6e-08   8.3e-05       3      57 ..     414     468 ..     412     515 .. 0.81

  Alignments for each domain:
  == domain 1  score: 22.2 bits;  conditional E-value: 4.6e-08
                     EEEE--STTHHHHHHHHHHCTSEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHH CS
  UDPG_MGDP_dh_N   3 isviGlGYvGlvtaavlaeighevigvDideekvdklnsgkipiyepgLeelvkk 57 
                     + + G G vG + a +l+e +++ i++Did++ vdk +++ +pi+  ++++l + 
      AHX11761.1 414 VIIAGFGRVGKMVARMLSEEQVNYIIIDIDSKVVDKAQREGFPIFRGNINKLATL 468
                     7789*****************************************9998887653 PP

>> Gp_dh_N  Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.7   2.7e-06    0.0049       2      36 ..     413     449 ..     412     504 .. 0.87

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.7e-06
                 EEEEESTSHHHHHHHHHHHHHT.TCEEEEEE-.TS-H CS
     Gp_dh_N   2 kvainGfGRIGrlvlralleek.elevvaind.ltdl 36 
                 +v i GfGR+G++v+r+l ee+ +  ++ i + ++d 
  AHX11761.1 413 HVIIAGFGRVGKMVARMLSEEQvNYIIIDIDSkVVDK 449
                 589****************887788899998755665 PP

>> AdoHcyase_NAD  S-adenosyl-L-homocysteine hydrolase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.6   0.1   7.1e-06     0.013      24      80 ..     412     470 ..     396     530 .. 0.69

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 7.1e-06
                    SEEEEE--SHHHHHHHHHHHHCT-EEEEE-S-HHHHHHHHCTT-EE--..HHHCTTT-S CS
  AdoHcyase_NAD  24 kvavvaGyGdvGkGcaaslkglGarvivtevdPicalqaameGfevvt..leevvkkad 80 
                      +++aG+G vGk  a+ l +     i+ ++d     +a  eGf + +  ++++++   
     AHX11761.1 412 NHVIIAGFGRVGKMVARMLSEEQVNYIIIDIDSKVVDKAQREGFPIFRgnINKLATLEA 470
                    5689****************************************886422333333333 PP

>> 2-Hacid_dh_C  D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.9   0.0   7.3e-06     0.013      37      80 ..     412     455 ..     383     491 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.9 bits;  conditional E-value: 7.3e-06
                   SEEEEES-SHHHHHHHHHHHHTT-EEEEESSSHHHHHCHHHHTC CS
  2-Hacid_dh_C  37 ktvGiiGlGrIGqavakrlkafgmkviaydrskkkeeeeeelgv 80 
                     v i G+Gr+G+ va++l++ +++ i++d   k  ++++++g+
    AHX11761.1 412 NHVIIAGFGRVGKMVARMLSEEQVNYIIIDIDSKVVDKAQREGF 455
                   5788**************************99998887776665 PP

>> PglD_N  PglD N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.9   0.1   3.7e-05     0.066       2      55 ..     414     469 ..     413     480 .. 0.86

  Alignments for each domain:
  == domain 1  score: 13.9 bits;  conditional E-value: 3.7e-05
      PglD_N   2 ivIiGaGGhgkvvadiieangeyeiigflDdnk..ktevegypvlgkaiellksls 55 
                 ++I G G  gk+va+++  ++   ii+ +D++   k + eg+p+  + i +l+ l+
  AHX11761.1 414 VIIAGFGRVGKMVARMLSEEQVNYIIIDIDSKVvdKAQREGFPIFRGNINKLATLE 469
                 79******************99999999999953267899*****99999888874 PP

>> Sacchrp_dh_NADP  Saccharopine dehydrogenase NADP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.1     8e-05      0.14       1      88 [.     414     495 ..     414     503 .. 0.70

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 8e-05
                      EEEE--SHHHHHHHHHHHCTCCT-GEEEEEESSHHHHHHHHCHHTTTCEEEEE--TTTHHHHHHHHHTTS..SEEEE-SSGGGHHHHHHH CS
  Sacchrp_dh_NADP   1 vliiGaGsvGqavaellarhfdvdaeitvadrskeklealaakalgvrfeaialdaenyeavLaallkeg..dlvvnlsppissldvlka 88 
                      v+i G+G+vG+ va++l++++ v  + +++d + + ++++    +++ f +   ++++ +  L+a+  ++  ++v+++   + + + +k+
       AHX11761.1 414 VIIAGFGRVGKMVARMLSEEQ-V--NYIIIDIDSKVVDKA----QREGFPIFRGNINKLAT-LEAIAVDRasTVVLSMQNEVTNKKAIKF 495
                      7899***************97.5..799999998886666....55666666666666666.6666333335666666666666666665 PP

>> NAD_binding_7  Putative NAD(P)-binding
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.2   0.00015      0.28       7      80 ..     411     494 ..     407     516 .. 0.71

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 0.00015
  NAD_binding_7   7 gkkvlvvGgGevAarkvrklleagakvtvvapevkeeleelvk.laeeel...ekd...........legadlviaatddrelneriae 80 
                    + +v+++G G+v+   +r l e++ + ++++ ++     + v+ +++e +   +++           +++a +v+  ++++  n++  +
     AHX11761.1 411 DNHVIIAGFGRVGKMVARMLSEEQVNYIIIDIDS-----KVVDkAQREGFpifRGNinklatleaiaVDRASTVVLSMQNEVTNKKAIK 494
                    579*********************9999999993.....22321333333222222233344445568889999999999999988665 PP

>> DUF4179  Domain of unknown function (DUF4179)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.9   0.3     0.087   1.6e+02       9      20 ..      96     119 ..      84     150 .. 0.63
   2 ?    8.1   0.7    0.0021       3.8      14      67 ..     360     412 ..     298     419 .. 0.86

  Alignments for each domain:
  == domain 1  score: 2.9 bits;  conditional E-value: 0.087
                 XXXXXXXXXXX............X CS
     DUF4179   9 vaaaaaalvll............l 20 
                 v+++aa++v++            +
  AHX11761.1  96 VIVTAAVIVFIcrmfginssasiI 119
                 678888888886655555333332 PP

  == domain 2  score: 8.1 bits;  conditional E-value: 0.0021
                 XXXXXXXXXXXXXXXXXXXXX.--SS-HHHHT--SS-HHHHSEEEEEEEEETTE CS
     DUF4179  14 aalvllllssrllspalAsalnpvigslfeklsdskgeqeyvkpvnksaednGi 67 
                  +lv ++ +s+  +p ++s+  ++i + +e+ +++ +e e+ + ++ s++d + 
  AHX11761.1 360 NVLVSAVTMSMAFTPLFSSIG-SIIANKLEAPDKKIEEAELIQLMRASVTDIDN 412
                 3445557889***********.*****9999999999************99665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (574 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       890  (0.0496402); expected 358.6 (0.02)
Passed bias filter:                      367  (0.0204696); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                        10  (0.000557756); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              10  [number of targets reported over threshold]
# CPU time: 0.58u 0.26s 00:00:00.84 Elapsed: 00:00:00.42
# Mc/sec: 4068.64
//
Query:       AHX11762.1  [L=519]
Description: GMP synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.9e-39  132.3   0.0    1.2e-38  131.1   0.0    1.7  1  GMP_synt_C     GMP synthase C terminal domain
    1.1e-27   97.1   0.0    1.8e-27   96.3   0.0    1.4  1  GATase         Glutamine amidotransferase class-I
    5.6e-09   36.1   0.0    2.1e-08   34.2   0.0    2.0  1  Peptidase_C26  Peptidase C26
    1.8e-05   24.0   0.0     0.0048   16.0   0.0    2.3  2  NAD_synthase   NAD synthase
     0.0063   15.4   0.0       0.01   14.6   0.0    1.3  1  tRNA_Me_trans  tRNA methyl transferase
      0.007   16.0   0.0      0.014   15.0   0.0    1.4  1  ThiI           Thiamine biosynthesis protein (ThiI)
  ------ inclusion threshold ------
      0.016   14.8   0.0       0.04   13.5   0.0    1.7  1  GATase_3       CobB/CobQ-like glutamine amidotransferase doma
      0.035   13.9   0.0      0.063   13.0   0.0    1.4  1  ATP_bind_3     PP-loop family


Domain annotation for each model (and alignments):
>> GMP_synt_C  GMP synthase C terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   5.2e-42   1.2e-38       2      92 .]     419     518 ..     418     518 .. 0.98

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 5.2e-42
                 CCCTTT-GGGSSEEEEEEEEEEE----------EEEEEEEEE---------B----H.........HHHHHHHHHHHHHSTT---EEEE---TTTS-S- CS
  GMP_synt_C   2 elkkaglykkiwQafavllpvksvGvmgdkRtyeyvvalRaveseDamtadvaelpy.........evLekissrivnevkgvnrvvyditskPpatiE 91 
                 ++++ gly+kiwQaf+vllp++svGvmgdkR+y+yv+a+Rav+s+D+mta+++ ++          e+L++i+++i n+vk+v+r+vyditskPpatiE
  AHX11762.1 419 TMRRYGLYSKIWQAFTVLLPIRSVGVMGDKRSYNYVCAVRAVTSRDGMTASAYPFESdssdkilflEFLNEIATKIPNQVKEVSRIVYDITSKPPATIE 517
                 68899***************************************************999**************************************** PP

                 - CS
  GMP_synt_C  92 w 92 
                 w
  AHX11762.1 518 W 518
                 * PP

>> GATase  Glutamine amidotransferase class-I
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   96.3   0.0   8.1e-31   1.8e-27       2     188 ..       7     188 ..       6     190 .. 0.86

  Alignments for each domain:
  == domain 1  score: 96.3 bits;  conditional E-value: 8.1e-31
                 EEESSTSTHHHHHHHHHHTT-EEEEEETTSHHHHHHHTHHSTSEEEEEEESSCTT.TTTHHHHHHHHCT....STS-EEEETHHHHHHHHHTTTEEEEE CS
      GATase   2 liDnydsvtenlvhalvelgvkvevvpidasaeeilellknpdgilvsgGpgspg.vegkieaikeare....nkiPiLGICLGmQllaiefgrkvvke 95 
                 +iD ++++t+ ++++l+e++++ +++  +          + ++gi++sg   s   + +  ++++e+++     ++P+LGIC+G Ql+ + fg+ vv+ 
  AHX11762.1   7 IIDLGSQFTQLIARKLRENKCYSQIYSPEGFVFS-----SAMKGIILSGSHKSIDeYVHYRDLVSEILDvnsrYGVPVLGICYGKQLISDFFGARVVSG 100
                 79*************************8854333.....579***********9995555556666655555699**********************99 PP

                 ECEEEEEEEEEEEETTTCGGTTTTSEEEEEEEEEEEEESGCHHHTTEEEEEEEETTEEEEEEEEETTTEEEESSBTTSTTSTTHHHHHHHHHH CS
      GATase  96 kekehhggtmrlgddetallyglknevierhrHryevnpkelepaglevtakseddeelmeiiekknpfvgvQFHPEststpegpellfnfli 188
                 +++e+ +++ +++ ++    + ++++++++++H+++v     +p+g++ +a++ +d+e++ i +++++++g+QFHPE++++++g+ ll+nf i
  AHX11762.1 101 EKREYGKAELQITGESLITENIKERSFTVWMSHGDTVAT---VPDGFRGIART-EDCEFAVIANDQKKLYGFQFHPEVSHSENGEILLRNF-I 188
                 99***********9665444455689************8...***********.56788888888889***************99999998.4 PP

>> Peptidase_C26  Peptidase C26
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.2   0.0   9.3e-12   2.1e-08      80     216 .]      52     173 ..      42     173 .. 0.83

  Alignments for each domain:
  == domain 1  score: 34.2 bits;  conditional E-value: 9.3e-12
  Peptidase_C26  80 sekeeeadpeRdalelaLiraalergvPilgiCrGlqllnvalGGtlyqdieeqsgltdhreheqsaashavkvekgsllaellgseeievnslHh 175
                    +++ +e+   Rd ++ +L     + gvP+lgiC G ql+   +G ++++  +            ++  + +++++ +sl+ e ++++++ v   H 
     AHX11762.1  52 HKSIDEYVHYRDLVSEIL-DVNSRYGVPVLGICYGKQLISDFFGARVVSGEK------------REYGKAELQITGESLITENIKERSFTVWMSHG 134
                    566777888888887655.4556889*************8888866554333............3445789************************* PP

  Peptidase_C26 176 qaikelaeelrveAvaeDgviEaieseeakafvlgvQwHPE 216
                     ++ ++ +++r +A++eD   E+  + ++++ ++g Q+HPE
     AHX11762.1 135 DTVATVPDGFRGIARTEDC--EFAVIANDQKKLYGFQFHPE 173
                    *****************95..66666666778********9 PP

>> NAD_synthase  NAD synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.0   0.0   2.2e-06    0.0048      10      48 ..     208     245 ..     203     281 .. 0.82
   2 !    5.6   0.0    0.0034       7.6     148     178 ..     358     388 ..     353     421 .. 0.88

  Alignments for each domain:
  == domain 1  score: 16.0 bits;  conditional E-value: 2.2e-06
                   HHHHHHCTTSEEEEEE-SSHHHHHHHHHHHHHHTCGEEE CS
  NAD_synthase  10 keyvkkagakgvvlGlSGGvDSslvaalavkalgkenvl 48 
                   ++ +++ g + v+  +SGGvDS+++a++  +a+g+   +
    AHX11762.1 208 RQIIQSVGESHVLAAVSGGVDSTVAAKFMYEAIGSR-LH 245
                   6788999999***********************764.44 PP

  == domain 2  score: 5.6 bits;  conditional E-value: 0.0034
                   BETTTTS-HHHHHHHHHHTT--HHHHCS--B CS
  NAD_synthase 148 lapiaellKtevkeLakelnvPervlkkpPs 178
                   l+p   l+K ev+++ ++++v e +l ++Ps
    AHX11762.1 358 LEPFRLLFKDEVRAIGRNMGVDETILMRHPS 388
                   578999************************9 PP

>> tRNA_Me_trans  tRNA methyl transferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   4.6e-06      0.01       2      74 ..     218     282 ..     217     288 .. 0.70

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 4.6e-06
  tRNA_Me_trans   2 kvvvalSgGVDSsvaaallkeqgyevigvflklweeedeegkeccaeedlkdaervaeklgiplevvdfekey 74 
                    +v++a+SgGVDS+vaa  + e     ig  l+++  +     +   ++++ ++++    lgiplev++ ++++
     AHX11762.1 218 HVLAAVSGGVDSTVAAKFMYE----AIGSRLHCIFVDT----GLLRKNEVDEVKKSFFLLGIPLEVISASHQF 282
                    799*************98854....5555555555511....2445667777777777777777777777776 PP

>> ThiI  Thiamine biosynthesis protein (ThiI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.0     6e-06     0.014       4      48 ..     217     262 ..     214     269 .. 0.80

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 6e-06
        ThiI   4 gkvlaLlSgGiDSpVaaylll.kRGcrvvlvhlknepgtseeaiek 48 
                  +vla +SgG+DS Vaa  +    G r ++++++  +  ++e+ e+
  AHX11762.1 217 SHVLAAVSGGVDSTVAAKFMYeAIGSRLHCIFVDTGLLRKNEVDEV 262
                 579************996555167********99888777776665 PP

>> GATase_3  CobB/CobQ-like glutamine amidotransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.5   0.0   1.8e-05      0.04      26     110 ..      29     115 ..       8     211 .. 0.68

  Alignments for each domain:
  == domain 1  score: 13.5 bits;  conditional E-value: 1.8e-05
    GATase_3  26 rvrfvplkdeslgedadlvilpGgkdtiqdlallresgldeaikeaaeaggpvlgiCGGlqmL....Geeiedpegvegeageveglgl 110
                   +++p ++  + + +  +il G+ + i++  + r+  + e +   +++g+pvlgiC G q+     G +++  e+ e  + e++ +g 
  AHX11762.1  29 SQIYSP-EGFVFSSAMKGIILSGSHKSIDEYVHYRD-LVSEILDVNSRYGVPVLGICYGKQLIsdffGARVVSGEKREYGKAELQITGE 115
                 555555.55556677899**********99888888.899999999***************8622225666666666666666665554 PP

>> ATP_bind_3  PP-loop family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   2.8e-05     0.063       1      61 [.     218     273 ..     218     308 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 2.8e-05
                 EEEEE--SCHHHHHHHHHHHHHCTTTTTEEEEEEEE-SSSTCHHHHHHHHHHHHHHTT-EE CS
  ATP_bind_3   1 kvlvAvSgGlDSmaLllllaklkkklgiklvaihvdhglreeskeeaelvkelckklnikl 61 
                 +vl+AvSgG+DS++  +++++     g++l +i vd gl  +  +e + vk+    l+i+l
  AHX11762.1 218 HVLAAVSGGVDSTVAAKFMYEA---IGSRLHCIFVDTGLLRK--NEVDEVKKSFFLLGIPL 273
                 5899***********9999998...56789999999887543..33444555555555555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (519 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       484  (0.0269954); expected 358.6 (0.02)
Passed bias filter:                      459  (0.025601); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.58u 0.25s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3689.28
//
Query:       AHX11763.1  [L=252]
Description: cobQ/CobB/MinD/ParA nucleotide binding domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.8e-76  255.2   0.1    7.1e-76  254.9   0.1    1.0  1  ParA         NUBPL iron-transfer P-loop NTPase
    7.1e-15   55.2   0.0    9.4e-15   54.8   0.0    1.2  1  CbiA         CobQ/CobB/MinD/ParA nucleotide binding domain
    5.5e-10   39.4   0.2      2e-08   34.4   0.2    2.2  1  AAA_31       AAA domain
    6.6e-07   28.9   0.0    9.4e-07   28.4   0.0    1.3  1  MipZ         ATPase MipZ
    4.3e-06   26.1   1.4     0.0007   18.9   0.1    2.9  3  ArsA_ATPase  Anion-transporting ATPase
    0.00011   22.1   0.9     0.0087   15.9   0.0    2.2  2  AAA_26       AAA domain
    0.00034   20.1   0.0      0.017   14.6   0.0    2.1  2  Fer4_NifH    4Fe-4S iron sulfur cluster binding proteins, Nif
     0.0056   16.0   0.0      0.016   14.5   0.0    1.7  2  VirC1        VirC1 protein
  ------ inclusion threshold ------
      0.019   14.5   0.1      0.036   13.6   0.1    1.4  1  AAA_25       AAA domain


Domain annotation for each model (and alignments):
>> ParA  NUBPL iron-transfer P-loop NTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  254.9   0.1   3.6e-79   7.1e-76       1     245 [.       7     245 ..       7     246 .. 0.94

  Alignments for each domain:
  == domain 1  score: 254.9 bits;  conditional E-value: 3.6e-79
        ParA   1 kvkkviavlSgKGGVGKStvavnlAlaLakkglkvgllDaDiyGpsiprllgveeekpeqsekkliPveakgikvmSigfllesedeavvwrGpmkska 99 
                 +v+k ++v+SgKGGVGKSt+a nlA+ La++  +vgl+DaDi+Gps+  +lg++ +  +++++kliP+e+ g+k +S+g +++  d++++wrGpm+sk+
  AHX11763.1   7 NVSKLLLVASGKGGVGKSTIALNLAVLLAQR-SRVGLIDADIHGPSLSFMLGADVRVSMSETEKLIPLEKFGLKYISMGAMVD-ADAPIIWRGPMLSKI 103
                 58899*********************99876.69********************9877777889******************9.*************** PP

        ParA 100 ikqllkdvewgelDyLiiDlPPGtgDeqltvaqklplagaviVttpqevaladvkkaiemfkkvkvkvlGvveNmsgfvcpkcgekteifgkgggekla 198
                 ++++l ++ w+elDyLi+D+PPGtgD+++t+++++  +g+++Vtt q+val+dv +a +mf+k+ ++vlG+veNms++    +gek+ i +k +++++a
  AHX11763.1 104 LHNFLLNTLWNELDYLIVDTPPGTGDVHITLCNEFYPDGVILVTTAQKVALKDVARANAMFRKLGAPVLGIVENMSYMDSI-TGEKYIIGEKRNVTEFA 201
                 *****************************************************************************9887.68888888999****** PP

        ParA 199 eelgvpllgeipldpeireasdegkplvlkepeseaakaleeiaekv 245
                 +++++ +lg++p+ ++i++++d+  p vl+    e+a++++ i+e++
  AHX11763.1 202 SSVSMLVLGRVPFISQISHSGDSAVPPVLD---PEIASIYNPIVEQI 245
                 *************************99977...47778888887776 PP

>> CbiA  CobQ/CobB/MinD/ParA nucleotide binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.8   0.0   4.7e-18   9.4e-15       1     117 [.      12     217 ..      12     228 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.8 bits;  conditional E-value: 4.7e-18
                 EEEEESSTTSSHHHHHHHHHHHHHHTT--EEEEEEEESSCCCCHHTTEB-HHHH............................................. CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx............................................. RF
        CbiA   1 iaiastkGGvGKTtlaanLaralarrglrVllvDaDpqannlaileglendiep............................................. 54 
                 +++as+kGGvGK+t+a+nLa++la+ + rV l+DaD  +++l+   g   ++                                               
  AHX11763.1  12 LLVASGKGGVGKSTIALNLAVLLAQ-RSRVGLIDADIHGPSLSFMLGADVRVSMsetekliplekfglkyismgamvdadapiiwrgpmlskilhnfll 109
                 589**********************.*****************7666666666699999**************************************** PP

                 ..............................................CCHCCCHHHHHHCHCHHHH..EEEEEEEEESS...-TTCHHHHHHHHHHC... CS
                 ..............................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx... RF
        CbiA  55 ..............................................dlkrllellealgkkkalllkiagvvlnrvdgeneetllkealeelkqry... 104
                                                               d+ r   ++++lg +      ++g+v n+   +  +   ++ +  +k+     
  AHX11763.1 110 ntlwneldylivdtppgtgdvhitlcnefypdgvilvttaqkvalkDVARANAMFRKLGAP------VLGIVENMSYMD--SITGEKYIIGEKRNVtef 200
                 *******************************************999999999999999987......899998886655..333333333333333344 PP

                 ....TS-EEEEEE--CC CS
                 ....xxxxxxxxxxxxx RF
        CbiA 105 ....gvpvlgviprdea 117
                      + vlg +p+ ++
  AHX11763.1 201 assvSMLVLGRVPFISQ 217
                 44446666666666555 PP

>> AAA_31  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   34.4   0.2   9.9e-12     2e-08       2     159 ..      10     159 ..       9     171 .. 0.70

  Alignments for each domain:
  == domain 1  score: 34.4 bits;  conditional E-value: 9.9e-12
      AAA_31   2 kvIaianqKGGvGKTTtsvnlaaalaklgkkvLlvDlDpQa.nattglgiekneiektlyevlieeknikeaiiktkvenldlipssidLaeaeielve 99 
                 k + +a  KGGvGK+T ++nla+ la++  +v l+D+D  + ++++ lg    ++  ++       ++++++i  +k+   ++  s   +++a+  ++ 
  AHX11763.1  10 KLLLVASGKGGVGKSTIALNLAVLLAQR-SRVGLIDADIHGpSLSFMLGA---DVRVSM-------SETEKLIPLEKFGLKYI--SMGAMVDADAPIIW 95 
                 66678999*****************987.69*******998356777774...333333.......44556665444433444..45556666666654 PP

      AAA_31 100 lekk..eeilkellekvkdeYDyiiiDcpPsLgll..tenaLvasdsviipvqaeayaleGleq 159
                       +  ++ ll+++ +e Dy i+D+pP  g +  t    +  d vi ++ a++ al+ +++
  AHX11763.1  96 RGPMlsKILHNFLLNTLWNELDYLIVDTPPGTGDVhiTLCNEFYPDGVILVTTAQKVALKDVAR 159
                 444331555577889***************9885411333445689999999999999988766 PP

>> MipZ  ATPase MipZ
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.4   0.0   4.7e-10   9.4e-07       3     110 ..      12     127 ..      10     155 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.4 bits;  conditional E-value: 4.7e-10
                 EEE--SSTTSSHHHHHHHHHHHHHTTT--EEEEE--TTT-HHHHHHHH..HHHHHHHHT.------EEE-SSS-HHHHTTS-.....HHHHHHHHHHHH CS
        MipZ   3 ivlgnekGGsGksttavhvavaLlkkGarvaaidldlrqrtlarylen..raataerkg.lsLplpealalseaeeaeveee.....eeaevaeleelv 93 
                 + ++  kGG Gkst+a+ +av L+++  rv+ id d+   +l+  l+   r+ + e ++ + L+      +s +++ +++ +        +    + l+
  AHX11763.1  12 LLVASGKGGVGKSTIALNLAVLLAQR-SRVGLIDADIHGPSLSFMLGAdvRVSMSETEKlIPLEKFGLKYISMGAMVDADAPiiwrgPMLSKILHNFLL 109
                 678999**************977665.79*********9999988865227666665542456655555555555555444400000444444445567 PP

                 HHHHHH-SEEEEE--.SS CS
        MipZ  94 adleaeldfividtP.Gs 110
                 + l +eld++++dtP G+
  AHX11763.1 110 NTLWNELDYLIVDTPpGT 127
                 788999********7244 PP

>> ArsA_ATPase  Anion-transporting ATPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.1   3.5e-07    0.0007       4      30 ..      13      39 ..      10      67 .. 0.83
   2 ?    0.6   0.1      0.13   2.6e+02     123     136 ..     114     128 ..     101     134 .. 0.79
   3 ?    4.1   0.0     0.011        22     209     246 ..     143     181 ..     133     203 .. 0.85

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.5e-07
                 EEEEESTTSSHHHHHHHHHHHHHHTTS CS
  ArsA_ATPase  4 ilvgGKGGVGKttvsaatavklsekgk 30
                 ++ +GKGGVGK+t++  +av l++  +
   AHX11763.1 13 LVASGKGGVGKSTIALNLAVLLAQRSR 39
                 5679******************99764 PP

  == domain 2  score: 0.6 bits;  conditional E-value: 0.13
                  SSSSEEEEESBS.CC CS
  ArsA_ATPase 123 eeydvvvlDtaP.TG 136
                  +e d++++Dt+P TG
   AHX11763.1 114 NELDYLIVDTPPgTG 128
                  789********9556 PP

  == domain 3  score: 4.1 bits;  conditional E-value: 0.011
                  EEEEEESSHHHHHHHHHHHHHHHHTT-EEEEEEEEE.E- CS
  ArsA_ATPase 209 frlVvipEklslkEteRaikeLkkygikvdavivNk.ll 246
                  ++lV+++ k++lk+  Ra + + k+g  v  ++ N  ++
   AHX11763.1 143 VILVTTAQKVALKDVARANAMFRKLGAPVLGIVENMsYM 181
                  789*************************99999997444 PP

>> AAA_26  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    4.9   0.3      0.01        21       3      32 ..      12      40 ..      10      43 .. 0.81
   2 !   15.9   0.0   4.4e-06    0.0087     131     195 ..     143     219 ..     101     221 .. 0.88

  Alignments for each domain:
  == domain 1  score: 4.9 bits;  conditional E-value: 0.01
      AAA_26  3 ifvtgtdtgvGKTvvslgLvralkrkgvkv 32
                ++v++   gvGK++++l L+  l ++ ++v
  AHX11763.1 12 LLVASGKGGVGKSTIALNLAVLL-AQRSRV 40
                78999999************888.555555 PP

  == domain 2  score: 15.9 bits;  conditional E-value: 4.4e-06
      AAA_26 131 vilVargglgtinqllltiealrqknvrvlGvilNkvrnp....e........nvetlekksgipvlGvvPylpdle 195
                 vilV+++++ ++++++ + +++r+ + +vlG++ N    +    e        nv+++ ++ ++ vlG+vP +++++
  AHX11763.1 143 VILVTTAQKVALKDVARANAMFRKLGAPVLGIVENMSYMDsitgEkyiigekrNVTEFASSVSMLVLGRVPFISQIS 219
                 8**********************************944444555155555566*******************99875 PP

>> Fer4_NifH  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.6   0.0   8.4e-06     0.017       6      54 ..      16      63 ..      12      85 .. 0.83
   2 ?    3.8   0.0     0.016        33     180     217 ..     184     221 ..     109     247 .. 0.76

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 8.4e-06
   Fer4_NifH  6 yGkGGiGksttsqnlsaalaemgkkvlivGCDPkaDstrlllggkaqet 54
                 GkGG+Gkst + nl+  la++  +v ++  D    s +++lg+ +  +
  AHX11763.1 16 SGKGGVGKSTIALNLAVLLAQRS-RVGLIDADIHGPSLSFMLGADVRVS 63
                59*************99999875.7888889998888888888776655 PP

  == domain 2  score: 3.8 bits;  conditional E-value: 0.016
   Fer4_NifH 180 iinsrkvddereliekfaeelgtkvlevvPrdeivrka 217
                 i+ ++ +  e+  +++fa+++++ vl  vP   ++ ++
  AHX11763.1 184 ITGEKYIIGEKRNVTEFASSVSMLVLGRVPFISQISHS 221
                 444566777888999***************99999876 PP

>> VirC1  VirC1 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.5   0.0   8.2e-06     0.016       2      43 ..      10      50 ..       9      63 .. 0.85
   2 ?   -1.8   0.0      0.75   1.5e+03     189     224 ..     128     163 ..     125     167 .. 0.80

  Alignments for each domain:
  == domain 1  score: 14.5 bits;  conditional E-value: 8.2e-06
       VirC1  2 klitfcslkGGaGkttalmglcsalasdgkrvalfeadenrP 43
                kl+ ++s kGG Gk+t  + l     +++ rv+l +ad   P
  AHX11763.1 10 KLLLVASGKGGVGKSTIALNLAVL-LAQRSRVGLIDADIHGP 50
                68999***********99998665.556789******97665 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 0.75
       VirC1 189 Gmlhltlenlsaapsmrlilrnlraaledlavlakl 224
                 G +h+tl n        l+++  ++al+d+a+  ++
  AHX11763.1 128 GDVHITLCNEFYPDGVILVTTAQKVALKDVARANAM 163
                 668899988888888899999999999999887665 PP

>> AAA_25  AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.6   0.1   1.8e-05     0.036      36      59 ..      13      36 ..       7      50 .. 0.85

  Alignments for each domain:
  == domain 1  score: 13.6 bits;  conditional E-value: 1.8e-05
      AAA_25 36 allaGapgtGKttlaldlalavat 59
                 +  G +g+GK+t+al+la+ +a+
  AHX11763.1 13 LVASGKGGVGKSTIALNLAVLLAQ 36
                56689**************99886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (252 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       373  (0.0208043); expected 358.6 (0.02)
Passed bias filter:                      364  (0.0203023); expected 358.6 (0.02)
Passed Vit filter:                        58  (0.00323498); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.45u 0.25s 00:00:00.70 Elapsed: 00:00:00.40
# Mc/sec: 1904.51
//
Query:       AHX11764.1  [L=200]
Description: ompA family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.8e-13   50.0   0.1    3.4e-12   46.6   0.1    2.0  1  OmpA      OmpA family


Domain annotation for each model (and alignments):
>> OmpA  OmpA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.1   1.9e-16   3.4e-12       2      94 ..      59     188 ..      58     189 .. 0.76

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.9e-16
                 B-TTS--B-GGGHHHHH.....HHHHHHH.S-S--EEEEE---S---HHHHHHHHHHHHHHHHHHHHHTTSSGG......................... CS
        OmpA   2 FapgsseLtpkaksald.....kiaellk.kpeqkitveGhtdaagseernweLSqkRAeaVanylqnegvpps......................... 69 
                 F+++sse+ p+a+  +d      +a  +k  pe k+ v+Gh+d++g++e+n +L ++RA+a ++yl ++ + +s                         
  AHX11764.1  59 FEFDSSEVLPEAMALIDehirdCVAMRMKdDPEVKVLVTGHADKRGTQEYNLALGSRRANATKSYLLKSLLNQSgasveastatevssgevtegtavqs 157
                 9****************655443334444677777*********************************9999996666666666666666666666666 PP

                 ......GEEEEE-TT--------------EE CS
        OmpA  70 ......risvsgyGaerpitanntaekkarn 94 
                       r+ +++ G+ + +++++t+e++++n
  AHX11764.1 158 etnlseRFCLNSKGKAELVDEGETEEAHSKN 188
                 6666666666666666666666666666666 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (200 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       596  (0.0332422); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        25  (0.00139439); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.21s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1638.52
//
Query:       AHX11765.1  [L=232]
Description: hypothetical protein NHE_0845 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.2e-05   25.9   0.1    3.6e-05   24.3   0.0    1.8  2  TPR_16    Tetratricopeptide repeat
    0.00024   21.5   1.9       0.75   10.6   0.0    3.7  4  TPR_6     Tetratricopeptide repeat
      0.002   18.3   3.8        1.5    9.1   1.4    2.9  3  ANAPC3    Anaphase-promoting complex, cyclosome, subunit 3
     0.0037   17.7   0.5        4.1    8.0   0.0    3.3  3  TPR_19    Tetratricopeptide repeat
     0.0052   16.9   3.2      0.027   14.7   1.2    2.7  2  TPR_8     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.014   15.1   0.1      0.031   14.0   0.1    1.5  2  YfiO      Outer membrane lipoprotein
      0.026   14.6   3.1       0.45   10.8   0.5    3.2  3  TPR_2     Tetratricopeptide repeat
       0.16   12.9   0.1        5.6    8.1   0.0    2.8  3  TPR_14    Tetratricopeptide repeat
       0.52   10.2   3.8       0.32   10.9   0.6    2.2  2  TPR_1     Tetratricopeptide repeat


Domain annotation for each model (and alignments):
>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.3   0.0   1.8e-08   3.6e-05       1      53 [.     109     161 ..     109     174 .. 0.95
   2 ?   -1.7   0.0       2.4   4.8e+03      20      38 ..     202     217 ..     201     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 24.3 bits;  conditional E-value: 1.8e-08
      TPR_16   1 lalaraalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeA 53 
                 + +a++++++ +  +A+a+l  +++r+p+s +    ++llgd+++  +++++A
  AHX11765.1 109 YRHALLLIKQSKKKEAEAQLSGFIERFPESNLLDNIYYLLGDLYFSEKNYKLA 161
                 789************************************************98 PP

  == domain 2  score: -1.7 bits;  conditional E-value: 2.4
      TPR_16  20 leaalkrdpssPdaaeAll 38 
                 l++al  +   Pd+a+ ++
  AHX11765.1 202 LHRALNEF---PDNAAIRM 217
                 57888899...99999886 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.4   0.0         9   1.8e+04      21      28 ..      38      45 ..      34      47 .. 0.62
   2 !   10.6   0.0   0.00038      0.75       4      33 .]     109     138 ..     108     138 .. 0.97
   3 ?    2.9   0.1      0.11   2.1e+02       3      19 ..     145     161 ..     144     172 .. 0.85
   4 ?    5.3   0.0     0.018        36       9      33 .]     188     212 ..     181     212 .. 0.73

  Alignments for each domain:
  == domain 1  score: -3.4 bits;  conditional E-value: 9
                HHHHHHHH CS
       TPR_6 21 ealerlik 28
                + le+l++
  AHX11765.1 38 AKLEKLLQ 45
                55677766 PP

  == domain 2  score: 10.6 bits;  conditional E-value: 0.00038
                 HHHHHHHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   4 yklalsyrklgdtdkAlealerlikeYPdS 33 
                 y+ al+++k+ ++ +A + l  +i+++P+S
  AHX11765.1 109 YRHALLLIKQSKKKEAEAQLSGFIERFPES 138
                 999******99*****************98 PP

  == domain 3  score: 2.9 bits;  conditional E-value: 0.11
                 HHHHHHHHHHHHHHHHH CS
       TPR_6   3 lyklalsyrklgdtdkA 19 
                 +y+l+ +y++ +++  A
  AHX11765.1 145 YYLLGDLYFSEKNYKLA 161
                 79*******98898855 PP

  == domain 4  score: 5.3 bits;  conditional E-value: 0.018
                 HHHHHHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   9 syrklgdtdkAlealerlikeYPdS 33 
                 s+r  +++  A+ +l r ++e+Pd+
  AHX11765.1 188 SLRLIKEYGHACSILHRALNEFPDN 212
                 555545666699***********95 PP

>> ANAPC3  Anaphase-promoting complex, cyclosome, subunit 3
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.3   0.0    0.0013       2.7      19      49 ..     101     131 ..      93     139 .. 0.80
   2 !    9.1   1.4   0.00077       1.5      22      79 ..     140     202 ..     133     205 .. 0.63
   3 ?    0.7   0.0      0.31   6.1e+02      32      60 ..     188     217 ..     177     221 .. 0.82

  Alignments for each domain:
  == domain 1  score: 8.3 bits;  conditional E-value: 0.0013
                 HH--HHHHHHHHHHHHHTT-HHHHHHHHHCT CS
      ANAPC3  19 etespedayllAlclylngqykrAyellrka 49 
                 e+  +ed+y +Al l ++++ k+A   l+ +
  AHX11765.1 101 EPSEEEDSYRHALLLIKQSKKKEAEAQLSGF 131
                 5677889999999999999999998887765 PP

  == domain 2  score: 9.1 bits;  conditional E-value: 0.00077
                 -HHHHHHH.HHHHHHTT-HHHHHHHHHCT.SHHHC-H..HHHHHHHHHHHHT.T-HHHHHHHH CS
      ANAPC3  22 spedayll.AlclylngqykrAyellrka.klnsksl..gcrylfAqcllkL.kkyeeAiaaL 79 
                  ++++y+l +  +++ ++yk A   + k+ ++n+k      ++++A  +l L k+y  A ++L
  AHX11765.1 140 LLDNIYYLlGDLYFSEKNYKLASLNFLKSyRSNKKGSktPLALVKAIKSLRLiKEYGHACSIL 202
                 556666644*************75544444666666523445555544455556666666655 PP

  == domain 3  score: 0.7 bits;  conditional E-value: 0.31
                 HHHHTT-HHHHHHHHHCT.SHHHC-HHHHH CS
      ANAPC3  32 clylngqykrAyellrka.klnskslgcry 60 
                 +l l ++y  A+ +l++a ++ + + ++r+
  AHX11765.1 188 SLRLIKEYGHACSILHRAlNEFPDNAAIRM 217
                 5677789999******99888888887776 PP

>> TPR_19  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.6   0.0     0.049        98      29      57 ..     109     137 ..     101     142 .. 0.82
   2 ?    3.3   0.1      0.06   1.2e+02      25      44 ..     142     161 ..     115     163 .. 0.70
   3 !    8.0   0.0    0.0021       4.1       7      31 ..     195     219 ..     193     220 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.6 bits;  conditional E-value: 0.049
      TPR_19  29 llLAeallalgqldeAealLdalpeedpd 57 
                 ++ A +l+++   +eAea L+   e +p 
  AHX11765.1 109 YRHALLLIKQSKKKEAEAQLSGFIERFPE 137
                 677899************99876666665 PP

  == domain 2  score: 3.3 bits;  conditional E-value: 0.06
      TPR_19  25 aearllLAeallalgqldeA 44 
                 +++ +lL +++++ ++++ A
  AHX11765.1 142 DNIYYLLGDLYFSEKNYKLA 161
                 67889999999999999877 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.0021
      TPR_19   7 yaeAlalleqalqedpknaearllL 31 
                 y  A ++l +al e p+na++r++L
  AHX11765.1 195 YGHACSILHRALNEFPDNAAIRMQL 219
                 778899****************986 PP

>> TPR_8  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.0   0.0      0.32   6.4e+02       5      23 ..     109     127 ..     108     137 .. 0.78
   2 !   14.7   1.2   1.3e-05     0.027       3      32 ..     144     173 ..     142     174 .. 0.89

  Alignments for each domain:
  == domain 1  score: 1.0 bits;  conditional E-value: 0.32
                 HHHHHHHHHTT-HHHHHHH CS
       TPR_8   5 ynlgsiylklgdyeeAkey 23 
                 y+ +++++k+ +++eA++ 
  AHX11765.1 109 YRHALLLIKQSKKKEAEAQ 127
                 6678888888888888875 PP

  == domain 2  score: 14.7 bits;  conditional E-value: 1.3e-05
                 HHHHHHHHHHHTT-HHHHHHHHHHHHHHHH CS
       TPR_8   3 ayynlgsiylklgdyeeAkeyyekaleldp 32 
                 +yy+lg++y++ ++y+ A   + k  + ++
  AHX11765.1 144 IYYLLGDLYFSEKNYKLASLNFLKSYRSNK 173
                 8*****************999999887765 PP

>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.0   0.1   1.6e-05     0.031      16      97 ..     116     160 ..     103     198 .. 0.58
   2 ?   -2.0   0.0       1.3   2.5e+03      19      37 ..     193     211 ..     177     221 .. 0.71

  Alignments for each domain:
  == domain 1  score: 14.0 bits;  conditional E-value: 1.6e-05
                 HHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTTHHHHHHHHHHHHHHHHSHSC CS
        YfiO  16 lqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPthknvdyvlYlrglsalaqarell 97 
                 +                                     k++   ea+a++  F++ +P+++  d ++Yl+g+ ++++ +  l
  AHX11765.1 116 I-------------------------------------KQSKKKEAEAQLSGFIERFPESNLLDNIYYLLGDLYFSEKNYKL 160
                 4.....................................45555566666666666666666666666666664444333222 PP

  == domain 2  score: -2.0 bits;  conditional E-value: 1.3
                 T-HHHHHHHHHHHHHHSTT CS
        YfiO  19 gdyaeAikklealdsryPf 37 
                 ++y++A + l+ + + +P 
  AHX11765.1 193 KEYGHACSILHRALNEFPD 211
                 5677777777777777775 PP

>> TPR_2  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.0       1.2   2.3e+03       8      24 ..     112     128 ..     108     137 .. 0.76
   2 ?   10.8   0.5   0.00023      0.45       3      29 ..     144     170 ..     143     174 .. 0.87
   3 ?    2.2   0.0      0.12   2.4e+02      13      34 .]     191     212 ..     187     212 .. 0.85

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 1.2
       TPR_2   8 GlayyklgdyeeAleaf 24 
                 +l+++k+ + +eA++ +
  AHX11765.1 112 ALLLIKQSKKKEAEAQL 128
                 56788888899998765 PP

  == domain 2  score: 10.8 bits;  conditional E-value: 0.00023
       TPR_2   3 alynlGlayyklgdyeeAleafekAle 29 
                 ++y lG++y+  ++y+ A   f k+ +
  AHX11765.1 144 IYYLLGDLYFSEKNYKLASLNFLKSYR 170
                 69****************999988766 PP

  == domain 3  score: 2.2 bits;  conditional E-value: 0.12
       TPR_2  13 klgdyeeAleafekAleldPnn 34 
                   ++y  A   + +Al   P+n
  AHX11765.1 191 LIKEYGHACSILHRALNEFPDN 212
                 56889999999*********97 PP

>> TPR_14  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.4   0.0       0.4   7.9e+02      10      34 ..     114     138 ..     109     151 .. 0.72
   2 ?   -1.4   0.0         3   5.9e+03       3      18 ..     144     159 ..     142     162 .. 0.80
   3 ?    8.1   0.0    0.0028       5.6      12      41 ..     190     219 ..     179     219 .. 0.80

  Alignments for each domain:
  == domain 1  score: 1.4 bits;  conditional E-value: 0.4
      TPR_14  10 allalGdpdeAiallrralalaPdd 34 
                 +l  + + +eA+a l   ++++P++
  AHX11765.1 114 LLIKQSKKKEAEAQLSGFIERFPES 138
                 5666677789************986 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 3
      TPR_14   3 allalaeallalGdpd 18 
                  +++l+++++   +++
  AHX11765.1 144 IYYLLGDLYFSEKNYK 159
                 6899999999988876 PP

  == domain 3  score: 8.1 bits;  conditional E-value: 0.0028
      TPR_14  12 lalGdpdeAiallrralalaPddaeawlll 41 
                 +   ++  A  +l+ral  +Pd+a+++++l
  AHX11765.1 190 RLIKEYGHACSILHRALNEFPDNAAIRMQL 219
                 555678889999**************9986 PP

>> TPR_1  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.5   0.1       1.3   2.6e+03       8      21 ..     112     125 ..     109     127 .. 0.83
   2 ?   10.9   0.6   0.00016      0.32       3      21 ..     144     162 ..     143     168 .. 0.86

  Alignments for each domain:
  == domain 1  score: -1.5 bits;  conditional E-value: 1.3
                 HHHHHHTT-HHHHH CS
       TPR_1   8 GnayfklgkydeAl 21 
                 ++++ k+ k +eA+
  AHX11765.1 112 ALLLIKQSKKKEAE 125
                 67889999999997 PP

  == domain 2  score: 10.9 bits;  conditional E-value: 0.00016
                 HHHHHHHHHHHTT-HHHHH CS
       TPR_1   3 alynlGnayfklgkydeAl 21 
                 ++y lG +yf+ ++y+ A 
  AHX11765.1 144 IYYLLGDLYFSEKNYKLAS 162
                 7***************995 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (232 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       681  (0.0379832); expected 358.6 (0.02)
Passed bias filter:                      441  (0.024597); expected 358.6 (0.02)
Passed Vit filter:                        45  (0.0025099); expected 17.9 (0.001)
Passed Fwd filter:                         9  (0.00050198); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               9  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.41
# Mc/sec: 1688.01
//
Query:       AHX11766.1  [L=433]
Description: 2,3-bisphosphoglycerate-independent phosphoglycerate mutase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    8.9e-58  195.3   0.1    1.8e-57  194.3   0.1    1.5  1  iPGM_N           BPG-independent PGAM N-terminus (iPGM_N)
    1.3e-55  188.5   0.3    1.5e-55  188.3   0.3    1.0  1  Metalloenzyme    Metalloenzyme superfamily
    1.2e-09   38.3   0.2    4.5e-07   29.8   0.0    2.2  2  Phosphodiest     Type I phosphodiesterase / nucleotide pyroph
    0.00068   19.8   0.1     0.0015   18.7   0.1    1.6  1  PglZ             PglZ domain
  ------ inclusion threshold ------
      0.016   14.6   0.0       0.03   13.7   0.0    1.5  1  DegV             Uncharacterised protein, DegV family COG1307
      0.029   13.3   0.1      0.064   12.2   0.1    1.5  1  Alk_phosphatase  Alkaline phosphatase
      0.085   12.6   0.0       0.22   11.3   0.0    1.7  1  Methyltransf_31  Methyltransferase domain


Domain annotation for each model (and alignments):
>> iPGM_N  BPG-independent PGAM N-terminus (iPGM_N)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  194.3   0.1   6.9e-61   1.8e-57      12     213 ..      33     219 ..      24     221 .. 0.87

  Alignments for each domain:
  == domain 1  score: 194.3 bits;  conditional E-value: 6.9e-61
                 G-HHHHHHHHHHHHCTSEEEEEEE-SS--SS--CHHHHHHHHHHHHTT-SEEEEEEEE-SSSSTTT-HHHHHHHHHHHHHHCT--EEEEEEEHHHHT-- CS
      iPGM_N  12 enealkeaiekakkngkalHllGLlSdGgVHShidhllallelakeegvkkvvvhaflDGRDtapksaleyleeleeklkelgvgkiasvsGRyyaMDR 110
                 +++ l+++ + +  +gka+H++GLlSdGgVHShidh+ ++++  +++g+ kv +haflDGRDt+pksal+y+++          ++ia++sGRyy MDR
  AHX11766.1  33 QDKSLNSFAAGL--SGKACHVVGLLSDGGVHSHIDHIDKIADYLESKGI-KVHIHAFLDGRDTPPKSALRYIKNE---------KNIATLSGRYYGMDR 119
                 555555554444..479********************************.*********************9853.........37************* PP

                 SS-HHHHHHHHHHHCCSSSEE.ECTTHHHHHHHHHHTT--GGG---EEE...TCCGGS--TT-EEEE----CCCCHHHHHHHH.STTHHCC.--TT-EE CS
      iPGM_N 111 dkrwervekaydalvkgeges.kaesaveaieesyakgetDefveptviaeegkkegtikdgDaviffNFRaDRareltralt.dkefkefekakklkl 207
                 dk+w+r+++ay+a+++ e+ +   ++++eai+++ya+++tDefv++ vi    + ++  +dgDa++++NFR+DRar++t+ l  +++f +  k+k  k+
  AHX11766.1 120 DKNWDRTQEAYQAITDPEKIKnVFKTPTEAITHYYAQNITDEFVPASVI----DGYTGARDGDALFIANFRPDRARQITSELLgKTNFCGR-KIKFSKI 213
                 ***************88655524558***********************....67899*********************999845456666.478889* PP

                 EESS-S CS
      iPGM_N 208 vtmteY 213
                 +tm +Y
  AHX11766.1 214 MTMSQY 219
                 *****9 PP

>> Metalloenzyme  Metalloenzyme superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  188.3   0.3   5.8e-59   1.5e-55      57     248 .]       1     420 [.       1     420 [. 0.98

  Alignments for each domain:
  == domain 1  score: 188.3 bits;  conditional E-value: 5.8e-59
                    ---HHHHHHHH..................................................................................... CS
                    xxxxxxxxxxx..................................................................................... RF
  Metalloenzyme  57 mgnsevgHlel..................................................................................... 67 
                    mgnse+gHl++                                                                                     
     AHX11766.1   1 MGNSEIGHLTIgsgriiyhdlvhinkkledieqdkslnsfaaglsgkachvvgllsdggvhshidhidkiadyleskgikvhihafldgrdtppks 96 
                    89********************************************************************************************** PP

                    ................................................................................................ CS
                    ................................................................................................ RF
  Metalloenzyme  68 ................................................................................................ 67 
                                                                                                                    
     AHX11766.1  97 alryiknekniatlsgryygmdrdknwdrtqeayqaitdpekiknvfktpteaithyyaqnitdefvpasvidgytgardgdalfianfrpdrarq 192
                    ************************************************************************************************ PP

                    ........................................................HHHHTT-----EEEEEEEE-S---SSHHHHHT--EEEE-- CS
                    ........................................................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Metalloenzyme  68 ........................................................lrisetvkfahvtffwnggrsgyfnpleereeipsdtvit 107
                                                                            l+i+e +k+ahv +f+nggr+++f++ eer+ + s  v t
     AHX11766.1 193 itsellgktnfcgrkikfskimtmsqyfeeplptfvprmeisntlseiishmgmhqLKIAESEKYAHVSYFFNGGRETSFPN-EERILVDSLRVKT 287
                    ********************************************************99************************.************* PP

                    SHHSTT--HHHHHHHHHHHH.CC.-SEEEEEE-HHHHHHHTT-HHHHHHHHHHHHHHHHHHHTTS-TTTEEEEEE-SSB--TTTSS.........- CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
  Metalloenzyme 108 fdlqpemkavevaekaldailsgkfdlvvvniknaDmvGHtgdleatiaaieaaDeavkeildaieqvdgilvvtADHgnaedmvkrdk.qplTsH 202
                    +d +p+m a e++ k+++ai+s kfd++vvn++naDmvGHtg++ atiaa+e++D +++e+ +  + ++  ++vtADHgnae+m ++ +  + T+H
     AHX11766.1 288 YDTAPQMGALEITGKLVEAIKSRKFDFIVVNYANADMVGHTGNMPATIAAVETLDDCLGELYKCTSTEGYEMIVTADHGNAESMYNQRTkLANTAH 383
                    ************************************************************************************875543789*** PP

                    ----EEEEEESTT----S--SSHHHHTT-TTEEEEGGGHHHHHHHH CS
                    xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
  Metalloenzyme 203 tlepVPilivgkglapdkvkegakfrekggLanvaatllnllglea 248
                    t++ VP++++++++++         +++g L+n+a+t+l+llg+++
     AHX11766.1 384 TTNLVPFIVLSDRVKQ---------VKNGRLSNIAGTVLTLLGIKK 420
                    ************9886.........5799*************9985 PP

>> Phosphodiest  Type I phosphodiesterase / nucleotide pyrophosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    6.6   0.1    0.0019       4.9     205     254 ..      34      98 ..      22     181 .. 0.67
   2 !   29.8   0.0   1.8e-10   4.5e-07     170     250 ..     303     383 ..     251     410 .. 0.82

  Alignments for each domain:
  == domain 1  score: 6.6 bits;  conditional E-value: 0.0019
                   HHHHHHHHHHHHHTTGTTTEEEEEEES---.EEEHTTSEEEGGGTSTGGH...................G CS
  Phosphodiest 205 DkaigdLlealderglsaetniilvSDHGm.advsddkvielndlleekg...................l 254
                   Dk ++ + ++l  +   a+  + l+SD G+ +++  d+ ++++d+le kg                   l
    AHX11766.1  34 DKSLNSFAAGLSGK---ACHVVGLLSDGGVhSHI--DHIDKIADYLESKGikvhihafldgrdtppksaL 98 
                   88888888888877...8999********83566..99************99955444444444333322 PP

  == domain 2  score: 29.8 bits;  conditional E-value: 1.8e-10
                   T......SSESEEEEEECCCHHHHHHH-TTSHHHHHHHHHHHHHHHHHHHHHHHTTGTTTEEEEEEES---EEEHTTSEEEGGGTST CS
  Phosphodiest 170 l......ekpdlllvyleetDtvgHkfGpdspevedalrrvDkaigdLlealderglsaetniilvSDHGmadvsddkvielndlle 250
                   l      +k d+++v++ + D vgH  G + p++ +a++++D+++g+L++    +     + +i+++DHG a+  +++ ++l++ ++
    AHX11766.1 303 LveaiksRKFDFIVVNYANADMVGH-TG-NMPATIAAVETLDDCLGELYKCTSTE----GYEMIVTADHGNAESMYNQRTKLANTAH 383
                   2333445899***************.54.9***********************99....9**********99987555555555444 PP

>> PglZ  PglZ domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.1   5.8e-07    0.0015      71     169 ..     266     367 ..     233     375 .. 0.69

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 5.8e-07
        PglZ  71 eesseglenrekilekkl....glavkaddllelkkderre.llkdkevvyivhnkvDalgdkasteqksfeaveeslkelkelvkslleengykvllt 164
                 + ++  + n e il   l     + + +   le+ ++ + +   ++++ +++   + D++g+ +  + ++ +ave+    l el k    e gy++++t
  AHX11766.1 266 GGRETSFPNEERILVDSLrvktYDTAPQMGALEITGKLVEAiKSRKFDFIVVNYANADMVGH-TGNMPATIAAVETLDDCLGELYKCTSTE-GYEMIVT 362
                 555556666666666555443322222222233333333334567778888888899*****.7778888888877666888998888888.******* PP

        PglZ 165 aDHGf 169
                 aDHG+
  AHX11766.1 363 ADHGN 367
                 ****7 PP

>> DegV  Uncharacterised protein, DegV family COG1307
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   1.2e-05      0.03     145     196 ..     376     429 ..     357     433 .] 0.76

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 1.2e-05
                 HHHHHHHHTEEE..EEEES-THHHHHHTCCHHHHHHHCCCCTSEEEEEEETTEE CS
        DegV 145 kkleeikektkl..yfvvddLdyLvkgGRiskaaallgslLkikpilkvedgel 196
                 +kl++++  t+l  ++v++d    vk+GR+s++a+++ +lL ik   ++e+g +
  AHX11766.1 376 TKLANTAHTTNLvpFIVLSDRVKQVKNGRLSNIAGTVLTLLGIKKPTELEEGLV 429
                 555555555544337888888999*******************97777776655 PP

>> Alk_phosphatase  Alkaline phosphatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.1   2.5e-05     0.064     254     323 ..     314     382 ..     290     402 .. 0.83

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 2.5e-05
                      EEEEEETCHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHCHHCTTEEEEEEESSEESEEEESTTSTT..TT CS
  Alk_phosphatase 254 FLlVEGsrIDhaaHendavgalsEvvefdeAvkaalefakkeketlvvvTaDHshvfsfggyttrgesvl 323
                      F++V  ++ D  +H ++    +  v  +d+ + +  + ++  +   ++vTaDH  + s+    t+ ++++
       AHX11766.1 314 FIVVNYANADMVGHTGNMPATIAAVETLDDCLGELYKCTS-TEGYEMIVTADHGNAESMYNQRTKLANTA 382
                      899999**********************************.55556789******999987777744444 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   8.7e-05      0.22      70     120 ..     307     376 ..     294     415 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 8.7e-05
  Methyltransf_31  70 ledekfDlilsn..............evlnaladpdkileeiervlkpggilliedpr.....llaelpa 120
                      ++ +kfD+i+ n              ++++a+  +d++l+e+ +  +++g+ +i +++      +++++ 
       AHX11766.1 307 IKSRKFDFIVVNyanadmvghtgnmpATIAAVETLDDCLGELYKCTSTEGYEMIVTADhgnaeSMYNQRT 376
                      4559********99999999999998888**********************9999999444333333332 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (433 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       502  (0.0279993); expected 358.6 (0.02)
Passed bias filter:                      435  (0.0242624); expected 358.6 (0.02)
Passed Vit filter:                        50  (0.00278878); expected 17.9 (0.001)
Passed Fwd filter:                         7  (0.000390429); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               7  [number of targets reported over threshold]
# CPU time: 0.52u 0.22s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 3309.35
//
Query:       AHX11767.1  [L=250]
Description: alpha/beta hydrolase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    8.9e-09   35.0   0.0    3.3e-08   33.1   0.0    1.7  2  Hydrolase_4    Serine aminopeptidase, S33
    4.4e-08   33.0   0.0    5.7e-08   32.7   0.0    1.2  1  Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
    0.00012   21.8   0.1    0.00028   20.6   0.0    1.5  2  Abhydrolase_1  alpha/beta hydrolase fold
  ------ inclusion threshold ------
      0.015   14.9   0.0      0.022   14.3   0.0    1.2  1  DLH            Dienelactone hydrolase family
      0.061   13.9   0.0      0.067   13.8   0.0    1.2  1  Abhydrolase_6  Alpha/beta hydrolase family
      0.075   12.5   0.0       0.62    9.5   0.0    2.1  2  Peptidase_S9   Prolyl oligopeptidase family
        0.1   12.4   0.0       0.15   11.9   0.0    1.2  1  Abhydrolase_5  Alpha/beta hydrolase family
       0.13   11.9   0.0       0.18   11.4   0.0    1.2  1  Esterase       Putative esterase


Domain annotation for each model (and alignments):
>> Hydrolase_4  Serine aminopeptidase, S33
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.0   1.5e-11   3.3e-08      11     115 ..      40     142 ..      39     158 .. 0.89
   2 ?   -0.4   0.0      0.26   5.8e+02     192     209 ..     151     168 ..     146     191 .. 0.78

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 1.5e-11
  Hydrolase_4  11 HGlaehsgryaelaeaLaaqGfavyalDhrGhGrsegkrghvpsfddyvdDlaafvekvkeehpel.plfllGhSmGGliallyllrypdkvaglils 107
                  HG +   + ++ +   ++++G a++ +++rG G s g+     + +d+++D++a++e +++ +p    + + G S G+ ++l+++ r+p+ ++g++ +
   AHX11767.1  40 HGGTMRNKVVKTIYSCFTKRGLATLRMNYRGVGYSSGQVS--VRDEDLIKDANAAIEWLQSCYPLVsSFWVAGFSYGAWLSLNLVMRRPE-ISGFVAV 134
                  77777777788888899******************88877..67799******************9788899******************.******* PP

  Hydrolase_4 108 aPalkika 115
                  a+ lki+ 
   AHX11767.1 135 ASPLKIHD 142
                  **999984 PP

  == domain 2  score: -0.4 bits;  conditional E-value: 0.26
  Hydrolase_4 192 lPllllhGeaDkvvdpea 209
                  +  l+++G++D+++d  +
   AHX11767.1 151 VSGLMIQGDQDQLCDIPE 168
                  556999*******99765 PP

>> Peptidase_S15  X-Pro dipeptidyl-peptidase (S15 family)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.7   0.0   2.6e-11   5.7e-08      52     130 ..      46     132 ..      18     164 .. 0.80

  Alignments for each domain:
  == domain 1  score: 32.7 bits;  conditional E-value: 2.6e-11
                    H.........HHHTT-EEEEEE-TTSTTS-S---TTTTTHHHHHHHHHHHHHHCTTEEEEEEEEEECHHHHHHHHHCTT--TTEEEEE CS
  Peptidase_S15  52 v.........fvarGYavVvqdvrGtggSeGeftvgdsdeaedgadvidWlakqpwsnGkVgmtGiSYlGttqllaaatgvpalkaiv 130
                    +         f +rG a +  + rG g+S G++ v d+d ++d+ ++i+Wl+       +  + G+SY+++++l + +++++ +   v
     AHX11767.1  46 NkvvktiyscFTKRGLATLRMNYRGVGYSSGQVSVRDEDLIKDANAAIEWLQSCYPLVSSFWVAGFSYGAWLSLNLVMRRPE-ISGFV 132
                    03345566679******************************************96666788999**********99996655.33333 PP

>> Abhydrolase_1  alpha/beta hydrolase fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.6   0.0   1.2e-07   0.00028      25     111 ..      56     144 ..      40     156 .. 0.80
   2 ?   -2.3   0.0       1.2   2.8e+03     215     239 ..     154     178 ..     149     188 .. 0.78

  Alignments for each domain:
  == domain 1  score: 20.6 bits;  conditional E-value: 1.2e-07
                    HHHTTSEEEEEEETTSTTSSSTTTGB.CHHSHHHHHHHHHHHHHHCTT.SSEEEEEETHHHHHHHHHHHHHGGGEEEEEEESE...CSSCC CS
  Abhydrolase_1  25 LakdgfdvillDlrGvgySspapacinddygtasvaddldrildalgd.dkltlvGhSmGGmialayaaeyperVkalvllga...idpaa 111
                    + k+g  ++ ++ rGvgySs   + +++d   +  ++ +++++  +++  ++++ G+S+G  ++l++  + pe ++++v++++   i++++
     AHX11767.1  56 FTKRGLATLRMNYRGVGYSSGQVSVRDEDLIKD-ANAAIEWLQSCYPLvSSFWVAGFSYGAWLSLNLVMRRPE-ISGFVAVASplkIHDFS 144
                    45568888999************9777777774.8888889999999725566*******************9.********966655544 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 1.2
                    EEEEETTCSSSCHHHHHHHHHCHTS CS
  Abhydrolase_1 215 lvisgtsDplvppkaledlaqllpk 239
                    l+i+g++D+l ++ +l +l++ +++
     AHX11767.1 154 LMIQGDQDQLCDIPELLRLTSPISQ 178
                    7899*****9999777777766666 PP

>> DLH  Dienelactone hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   9.8e-06     0.022      74     181 ..      81     187 ..      72     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 9.8e-06
         DLH  74 aeekvlddlkaavaylksvpevstkkvgvvGfCmGGalalllaaevpevdaavafYGlspekeleeaakikapilalfgeeDefipadevekleealka 172
                  +e++ +d++aa+++l+s+    ++ + v Gf  G++l+l+l  + pe+ + va       ++ +      +  l++ g++D+  +  e+ +l++ +++
  AHX11767.1  81 RDEDLIKDANAAIEWLQSCY-PLVSSFWVAGFSYGAWLSLNLVMRRPEISGFVAVASPLKIHDFSFLSPCTVSGLMIQGDQDQLCDIPELLRLTSPISQ 178
                 4678888899*********9.7889*********************99999888765455555566666666667777888888888888777777777 PP

         DLH 173 anvdlelkv 181
                 +  +++++ 
  AHX11767.1 179 RLGKFRVEF 187
                 666666665 PP

>> Abhydrolase_6  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     3e-05     0.067      27      98 ..      61     146 ..      17     242 .. 0.62

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 3e-05
                    CEEEEE--TTST........S-GGCS--HHHCHHHHHHHCCTT..TTSE....EEEEETCHHHHHHHHHHCC...EE.EEES-.........- CS
  Abhydrolase_6  27 vhvlapDlpGhG........rsdpppldledladlaalldelaagggpv....vlvGHSlGGalalaaapla.lvvg.vlldppp.......t 98 
                     ++l + ++G G        r+     dl  + d  a+++ l + + p     ++ G S+G++l+l +++    ++g v++++p        +
     AHX11767.1  61 LATLRMNYRGVGyssgqvsvRD----EDL--IKDANAAIEWLQS-CYPLvssfWVAGFSYGAWLSLNLVMRRpEISGfVAVASPLkihdfsfL 146
                    4556677777773222222222....222..3333444444443.22223445**********999966666687889999995433333220 PP

>> Peptidase_S9  Prolyl oligopeptidase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.5   0.0   0.00028      0.62       8      93 ..      54     133 ..      47     143 .. 0.76
   2 ?    0.5   0.0      0.15   3.4e+02     145     182 ..     152     189 ..     139     216 .. 0.73

  Alignments for each domain:
  == domain 1  score: 9.5 bits;  conditional E-value: 0.00028
                   HHHHCCT-EEEEE--TTSSTTHCHHHHTTSGGGGHHHHHHHHHHHHHHHHTT.S--GGGEEEEEETHHHHHHHHHHHH-GGG-SEEE CS
  Peptidase_S9   8 qlladrGyvvvvanirGsggyGeafhdagkrklgqnefdDfiaaaealakeg.yvdserlaitGgSyGGyltgaalnqrpdlFkaav 93 
                   + +++rG + + +n+rG g+ + +          +  ++D  aa+e+l + + +   +   + G SyG +l++ ++++rp++ + ++
    AHX11767.1  54 SCFTKRGLATLRMNYRGVGYSSGQVSV-----RDEDLIKDANAAIEWLQSCYpL--VSSFWVAGFSYGAWLSLNLVMRRPEISGFVA 133
                   567788888888888888855544443.....4567799999*****9666555..58899****************9999855544 PP

  == domain 2  score: 0.5 bits;  conditional E-value: 0.15
                   EEEEEEETT-SSS-THHHHHHHHHHH--S-SEEEEEET CS
  Peptidase_S9 145 plLlihGlaDdrvppaealklvaaLqkkgknvlllifp 182
                   + L+i+G++D+ + + e l+l +   ++  ++++    
    AHX11767.1 152 SGLMIQGDQDQLCDIPELLRLTSPISQRLGKFRVEFIE 189
                   5699***********99999988777555555555555 PP

>> Abhydrolase_5  Alpha/beta hydrolase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   6.5e-05      0.15      51     147 ..      98     197 ..      72     201 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 6.5e-05
  Abhydrolase_5  51 keapklekfvvgGhslGGvvasrfaaeeekiegvvflasYPekdelselskk...vlsivgteDgvlnvkslekakkflpkdtkvvsieGgnhagf 143
                    + +p +  f v+G s G  ++ +++ +  +i g v +as  +  ++s ls      l i g++D++ ++ +l +    +++      +e    a+f
     AHX11767.1  98 SCYPLVSSFWVAGFSYGAWLSLNLVMRRPEISGFVAVASPLKIHDFSFLSPCtvsGLMIQGDQDQLCDIPELLRLTSPISQRLGKFRVEFIENADF 193
                    45788999*******************************88866677665541116779*******999998888888887777777777777777 PP

  Abhydrolase_5 144 GsYG 147
                     + G
     AHX11767.1 194 RMSG 197
                    6666 PP

>> Esterase  Putative esterase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   8.2e-05      0.18     105     149 ..      95     138 ..      90     161 .. 0.91

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 8.2e-05
                 HHHHHCSEECCCEEEEEETHHHHHHHHHHHCSTTTCCEEEEES-- CS
    Esterase 105 lldanfrtapdgravaGqSmGGlgALilalkhpdrFgsvssfSpi 149
                 +l++ ++  ++   vaG+S G+  +L+l +++p+  g+v++ Sp+
  AHX11767.1  95 WLQSCYPLVSS-FWVAGFSYGAWLSLNLVMRRPEISGFVAVASPL 138
                 77777777777.88*****************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (250 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       336  (0.0187406); expected 358.6 (0.02)
Passed bias filter:                      326  (0.0181828); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 1811.92
//
Query:       AHX11768.1  [L=502]
Description: methionine--tRNA ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   4.4e-107  358.2   0.9    6.5e-65  219.4   0.0    2.2  2  tRNA-synt_1g  tRNA synthetases class I (M)
    1.8e-23   82.7   3.3    1.9e-11   43.0   0.5    3.9  3  tRNA-synt_1   tRNA synthetases class I (I, L, M and V)
    1.6e-11   44.1   0.0    4.1e-06   26.4   0.1    2.6  3  tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
    0.00038   20.4   1.1    0.00075   19.5   0.1    2.0  2  Anticodon_1   Anticodon-binding domain of tRNA
  ------ inclusion threshold ------
      0.054   12.4   0.0        4.3    6.1   0.0    2.2  2  tRNA-synt_1f  tRNA synthetases class I (K)


Domain annotation for each model (and alignments):
>> tRNA-synt_1g  tRNA synthetases class I (M)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  138.5   0.2   6.8e-44   2.4e-40       1     135 [.       3     137 ..       3     143 .. 0.98
   2 !  219.4   0.0   1.8e-68   6.5e-65     163     391 .]     136     360 ..     133     360 .. 0.93

  Alignments for each domain:
  == domain 1  score: 138.5 bits;  conditional E-value: 6.8e-44
                   EEEEE--B--SS---HHHHHHHHHHHHHHHHHHHTT-EEEEEEEE---SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT---SEEEETTSHHHH CS
  tRNA-synt_1g   1 vlvttalpYangklHlGhllevisaDifaRykrlrgeevlfvcgtDehGtpielkAekegvtpeelvekvheeikelfkklnisfdkygrttseehk 97 
                   ++vtt+++Y+n+++H+Gh+++ ++aDi+aR  r+ g+evlf +gtDehG++++ +A+k +++ +++v++++ +++el + ++ +f++++rtt+ +hk
    AHX11768.1   3 YYVTTPVYYVNDVPHIGHAYSSLIADIIARSLRMAGHEVLFTTGTDEHGQKVQNTARKLNISEKNFVDRISLRFRELCEVMQYQFSDFIRTTEARHK 99 
                   69*********************************************************************************************** PP

                   HHHHHHHHHHHHTT-EEEEEEEEEEETTTTEEE-GGG- CS
  tRNA-synt_1g  98 elvqeifkklkekgliyekeieqlycpkderflpdryv 135
                   e+v+++++kl +++liy +e++++y+++de f+++ ++
    AHX11768.1 100 EAVKNVWNKLWQNELIYLGEYSGWYSERDECFYAETEL 137
                   *********************************99875 PP

  == domain 2  score: 219.4 bits;  conditional E-value: 1.8e-68
                   ..............EEE.EEEEEE-GGGGHHHHHHHH.HH-TT.SHHHHHHHH.HHHHT----EE-E.SS-SSS-EETTECCEEE-HHHHHHHHHHH CS
  tRNA-synt_1g 163 elinpksaisgskpevketehlffklskfekklkewieeeeke.leenvkkivkewlkegLkdlais.rdldwGipvPgaekkvlYVWldAligYis 257
                   el++ k+       +vk + ++ff+ls++++kl+++++e+e+   ++n  + ++++l+ g++dl+is ++++wGi vP+++++++YVWldAl +Yi+
    AHX11768.1 136 ELQDDKAPTGAPVTWVK-EASYFFRLSQLSEKLRKFYKENESFiRPRNRFNEALSFLEMGINDLSISrTKVEWGIAVPNDPSHTIYVWLDALTNYIT 231
                   66666666666667777.9******************77766588888999999*************6689************************** PP

                   TTTTT-...TTSGGGG.G--S......EEEEEGGGHHHHHTHHHHHHHHTT----S-EEEE--EEE--------------HHHHHHHH-HHHHHHHH CS
  tRNA-synt_1g 258 atkelakkkgeeekwkeyWakdkevelvhfigkdiikFHtifwPaillgaelklpkkvvaheyltvegkKlSkSrgvvvkakealerldadllRYyl 354
                   ++++     + ++k++e+W   ++ +++h++gkdi++FH i+wPa+l+g +lk+p+ + ah+++t +g+K+SkS g+ +++ e++ ++ +d +RY+l
    AHX11768.1 232 SLGYPD--ISPDSKYSEFW---ENGHVIHIVGKDILRFHGIYWPAFLMGVGLKVPDIILAHGWWTNNGQKISKSLGNTIDPFELVSEFGVDSVRYFL 323
                   ****97..66689******...4699*********************************************************************** PP

                   HHHS-TTS-EEE-HHHHHHHHHHHCCCHHHHHHHHH. CS
  tRNA-synt_1g 355 aaeapekkDldfswedfvervNseLadklgnlvnRvl 391
                   ++e    +D +fs + + +r+NseLa+++gnl++R+l
    AHX11768.1 324 IREVTIGNDGSFSKALLKDRINSELANNIGNLLQRTL 360
                   ***********************************85 PP

>> tRNA-synt_1  tRNA synthetases class I (I, L, M and V)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.0   0.5   5.2e-15   1.9e-11      25     118 ..       3      94 ..       1     144 [. 0.81
   2 ?    2.4   0.0      0.01        36     368     432 ..     144     212 ..     140     217 .. 0.85
   3 !   33.7   0.0   3.3e-12   1.2e-08     489     599 ..     221     333 ..     214     336 .. 0.67

  Alignments for each domain:
  == domain 1  score: 43.0 bits;  conditional E-value: 5.2e-15
  tRNA-synt_1  25 filvdgPPyvtGslHiGhalaktlkdivirykrmkGkevlyvpGwDhaGlaieakvekklgakekkerkklgreefrekvrewkaeyaeeirkq 118
                  + ++ +  yv+  +HiGha+ + + di+ r+ rm G+evl+++G+D +G  ++ +  +kl ++ek+ +  ++  +fre +  ++ ++++ ir +
   AHX11768.1   3 YYVTTPVYYVNDVPHIGHAYSSLIADIIARSLRMAGHEVLFTTGTDEHGQKVQNT-ARKLNISEKNFVDRISL-RFRELCEVMQYQFSDFIRTT 94 
                  667778889*****************************************99976.57788888765555554.68888877777777777655 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.01
  tRNA-synt_1 368 skkpiiyrateqWfvrvkeladaalkave..kvqfvpkskekryaswle.niqdWciSRqrw.WGhrip 432
                  +++p+      ++f r+++l +++ k  +  +  + p  + ++  s+le  i+d  iSR ++ WG  +p
   AHX11768.1 144 TGAPVTWVKEASYFFRLSQLSEKLRKFYKenESFIRPRNRFNEALSFLEmGINDLSISRTKVeWGIAVP 212
                  567888899999***********99998876677789998888889887479*******8755**9887 PP

  == domain 3  score: 33.7 bits;  conditional E-value: 3.3e-12
  tRNA-synt_1 489 vWFsSgswpfstlgypee.dteelkkffpad..mlleGlDiirgWvarlillslaltgsePfkevlvhglvrdeeGrKmSKslgNvidpldvikkyga 583
                  vW +     +++lgyp+    +++++f+     + + G Di+r+       + + +  ++P   +l hg  + ++G+K+SKslgN+idp +++++ g+
   AHX11768.1 221 VWLDALTNYITSLGYPDIsPDSKYSEFWENGhvIHIVGKDILRFHGIYWPAFLMGVGLKVP-DIILAHGWWT-NNGQKISKSLGNTIDPFELVSEFGV 316
                  6777666667777777662334455555443113345777777754443333333334455.5688888765.68*********************** PP

  tRNA-synt_1 584 dalRltli.lsdvgrdi 599
                  d++R++li + + g+d 
   AHX11768.1 317 DSVRYFLIrEVTIGNDG 333
                  ********777777775 PP

>> tRNA-synt_1e  tRNA synthetases class I (C) catalytic domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.4   0.1   1.1e-09   4.1e-06      19     143 ..      12     136 ..       1     148 [. 0.79
   2 !   14.9   0.0   3.6e-06     0.013     241     282 ..     284     325 ..     254     345 .. 0.88
   3 ?   -1.8   0.0      0.44   1.6e+03      98     140 ..     364     406 ..     331     432 .. 0.61

  Alignments for each domain:
  == domain 1  score: 26.4 bits;  conditional E-value: 1.1e-09
                   TTS--BHHHHHHHHHHHHHHHHHHHTT-EEEEEEEBB--SHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHTT----SB-.-BGGGGHHHHHHHHHH CS
  tRNA-synt_1e  19 vydashlGhaRslvafDilrrilqalgYdvqfvqnvtDidDkiikrareeeksvkelaekfieefkkdleaLnvlkptle.prvsekvdeiielvek 114
                   v d  h+Gha s ++ Di++r l+++g++v f     +   k+ + ar+ + s k++++++   f +  e ++ + +++  +  + + +++ ++ +k
    AHX11768.1  12 VNDVPHIGHAYSSLIADIIARSLRMAGHEVLFTTGTDEHGQKVQNTARKLNISEKNFVDRISLRFRELCEVMQYQFSDFIrTTEARHKEAVKNVWNK 108
                   6799******************************999999*************99999999999999999999887765413344455667777788 PP

                   HHHTTSEEE-TTS-EEE-GGG-TTTTTTT CS
  tRNA-synt_1e 115 liekgyaYavsdgdvyfdvskkeeYgkls 143
                   l ++   Y  +     ++ +++  Y++ +
    AHX11768.1 109 LWQNELIYLGE-YSGWYSERDECFYAETE 136
                   88888888877.44455555566666655 PP

  == domain 2  score: 14.9 bits;  conditional E-value: 3.6e-06
                   EEEE--EEETTBE--TTTT---BHHHHHTTS-HHHHHHHHHS CS
  tRNA-synt_1e 241 flhnghlkiegekmsksLknfitikdvlkkfdprqlRlllls 282
                    l +g+ + +g+k+sksL+n i   +++ +f    +R++l+ 
    AHX11768.1 284 ILAHGWWTNNGQKISKSLGNTIDPFELVSEFGVDSVRYFLIR 325
                   567899999******************************975 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.44
                   --BGGGGHHHHHHHHHHHHHTTSEEE-TTS-EEE-GGG-TTTT CS
  tRNA-synt_1e  98 eprvsekvdeiielvekliekgyaYavsdgdvyfdvskkeeYg 140
                     +   +v+e+ +l ++l+e +y+ a++    +++ s +++  
    AHX11768.1 364 VKQCGSRVPEVPKLSNRLLELSYSLASDYKANMLKLSLNDSLE 406
                   3455667888888888888888877777655555555444444 PP

>> Anticodon_1  Anticodon-binding domain of tRNA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.4   0.1       1.1   4.1e+03      88     138 ..     109     169 ..     105     176 .. 0.44
   2 !   19.5   0.1   2.1e-07   0.00075       6      89 ..     383     464 ..     379     489 .. 0.84

  Alignments for each domain:
  == domain 1  score: -2.4 bits;  conditional E-value: 1.1
  Anticodon_1  88 lwqr.............eeeelgkkesimlaewpekaeel.ekele.....eeevellkeivkairklrs 138
                  lwq+             e       +++++ae + +++++ +          +e +++ ++ ++ +klr+
   AHX11768.1 109 LWQNeliylgeysgwysE------RDECFYAETELQDDKApT---GapvtwVKEASYFFRLSQLSEKLRK 169
                  666666666653333321......234444443332111111...0122223344555666666666665 PP

  == domain 2  score: 19.5 bits;  conditional E-value: 2.1e-07
  Anticodon_1   6 selnklvkevteayeeyrfnkaasalyeffwndlcdwylelvkprlysesaedkraaqevllevletllrllaPfmPfitEelw 89 
                     ++l++++++++ ++++n+ + ++ ++   + ++ y+  ++p+  ++++e+ +++ +++le+l+ + + l+Pf+P  +  + 
   AHX11768.1 383 ELSYSLASDYKANMLKLSLNDSLEKIIHL--ATQANEYISQSEPWKLKNEPEKLHEILYTMLEALRIIGIALQPFIPGSAKAML 464
                  556789999*******************8..55579**********999985558899*******************7777666 PP

>> tRNA-synt_1f  tRNA synthetases class I (K)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.9   0.0    0.0058        21      37      69 ..      16      48 ..      10      71 .. 0.88
   2 ?    6.1   0.0    0.0012       4.3     277     310 ..     292     325 ..     283     339 .. 0.90

  Alignments for each domain:
  == domain 1  score: 3.9 bits;  conditional E-value: 0.0058
  tRNA-synt_1f 37 iHiGnlrevltadlvaralrkrgeevrlilisD 69
                  +HiG +   l ad++ar+lr  g+ev + +  D
    AHX11768.1 16 PHIGHAYSSLIADIIARSLRMAGHEVLFTTGTD 48
                  8***********************987766666 PP

  == domain 2  score: 6.1 bits;  conditional E-value: 0.0012
  tRNA-synt_1f 277 kggekmssSkGnvltledwlevaepevlrflilr 310
                   ++g+k+s+S Gn + + ++++    +++r++++r
    AHX11768.1 292 NNGQKISKSLGNTIDPFELVSEFGVDSVRYFLIR 325
                   5678***************************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (502 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       707  (0.0394333); expected 358.6 (0.02)
Passed bias filter:                      578  (0.0322383); expected 358.6 (0.02)
Passed Vit filter:                        51  (0.00284455); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.59u 0.27s 00:00:00.86 Elapsed: 00:00:00.44
# Mc/sec: 3395.37
//
Query:       AHX11769.1  [L=103]
Description: thioredoxin [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    6.2e-24   84.0   0.0    6.7e-24   83.9   0.0    1.0  1  Thioredoxin    Thioredoxin
    2.9e-09   37.3   0.0    4.2e-09   36.8   0.0    1.3  1  Thioredoxin_2  Thioredoxin-like domain
    4.1e-07   29.8   0.0    4.5e-07   29.7   0.0    1.1  1  Thioredoxin_9  Thioredoxin
    4.9e-07   30.0   0.0      1e-05   25.7   0.0    2.1  2  Thioredoxin_8  Thioredoxin-like
    7.3e-07   29.2   0.0    8.4e-07   29.0   0.0    1.1  1  TraF           F plasmid transfer operon protein
    5.6e-05   23.0   0.0    5.6e-05   23.0   0.0    1.2  1  AhpC-TSA       AhpC/TSA family
     0.0009   19.0   0.0     0.0011   18.7   0.0    1.1  1  DUF3088        Protein of unknown function (DUF3088)
  ------ inclusion threshold ------
      0.015   15.5   0.0      0.019   15.2   0.0    1.3  1  Glutaredoxin   Glutaredoxin
      0.025   14.3   0.1      0.049   13.4   0.0    1.5  2  Redoxin        Redoxin
      0.032   14.2   0.0      0.046   13.7   0.0    1.2  1  HyaE           Hydrogenase-1 expression protein HyaE
      0.038   14.2   0.1      0.084   13.1   0.1    1.5  1  Thioredoxin_7  Thioredoxin-like
        0.1   12.7   0.0       0.14   12.2   0.0    1.2  1  Thioredoxin_3  Thioredoxin domain


Domain annotation for each model (and alignments):
>> Thioredoxin  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.9   0.0   4.5e-27   6.7e-24       8     102 ..       5      99 ..       1     100 [. 0.93

  Alignments for each domain:
  == domain 1  score: 83.9 bits;  conditional E-value: 4.5e-27
                  HHHHHHHTTTSSEEEEEEE-TTSHHHHCHHHHHHHHHHHCTTTSEEEEEETTT.SHHHHHHTT-SSSSEEEEEETTEEEEEEESS-HHHHHHHHHH CS
  Thioredoxin   8 enFeeevakekklvlveFyApwCghCkalaPeleklaeelkdkvklakvdvde.nedlakkyevegiPtlklfkngkevkkyegarekeklaaflk 102
                  e+F ++v++++ lvl++F+A+wCg+Ck++ P+l++++e    +v ++kv++d  ++ la + +v+++Ptl+lfk+gk  ++ +g  + ++++++++
   AHX11769.1   5 EDFSKQVSDAHGLVLLDFWAEWCGPCKQMIPVLQAFSEVSP-HVSVYKVNIDGpKQALAIENGVRAVPTLILFKDGKMLDRKVGMLSLSQIKEWVA 99 
                  78********************************9988777.*********9626789**********************************9986 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   36.8   0.0   2.8e-12   4.2e-09       5     108 ..      15      97 ..      11      98 .. 0.90

  Alignments for each domain:
  == domain 1  score: 36.8 bits;  conditional E-value: 2.8e-12
  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkkelkelddvtvrvllfplkpsfepkavaiwcakekkkafkdieenvelarkygvrgtPtiv.fldgkeivarlpGy 99 
                    +  vl++f++++C+ Ck++  +l+  ++v         +p+++ + v+i++ k+             la + gvr++Pt++ f dgk +++r +G+
     AHX11769.1  15 HGLVLLDFWAEWCGPCKQMIPVLQAFSEV---------SPHVSVYKVNIDGPKQA------------LAIENGVRAVPTLIlFKDGK-MLDRKVGM 88 
                    6679*******************999555.........999************97............999*********66699***.******** PP

  Thioredoxin_2 100 vpaeeleal 108
                    ++  +++++
     AHX11769.1  89 LSLSQIKEW 97 
                    *99998876 PP

>> Thioredoxin_9  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.7   0.0     3e-10   4.5e-07      48     107 ..      22      79 ..       2      98 .. 0.85

  Alignments for each domain:
  == domain 1  score: 29.7 bits;  conditional E-value: 3e-10
                    E--TT-HHHHHHHHHHHHHHHH-TTEEEEEE-HHHHHHHTTTTTT-SS--SSEEEEE-TT CS
  Thioredoxin_9  48 ltedwCgDaavnvPvlakiaelnpnievkillrdenlelmdqyltngaraiPtliildee 107
                    + ++wCg + +++Pvl++++e +p ++v  +  d  ++ +    +ng ra+Ptli+++++
     AHX11769.1  22 FWAEWCGPCKQMIPVLQAFSEVSPHVSVYKVNIDGPKQALA--IENGVRAVPTLILFKDG 79 
                    5689******************************9999988..569*********99765 PP

>> Thioredoxin_8  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.7   0.0   6.9e-09     1e-05       3      45 ..      17      56 ..      16      64 .. 0.86
   2 ?    3.7   0.0     0.051        76      69      90 ..      56      77 ..      46      81 .. 0.77

  Alignments for each domain:
  == domain 1  score: 25.7 bits;  conditional E-value: 6.9e-09
                   EEEEEE--SSSHHHHHHHHHHHHHHHHHHHTTSEEEEEEE-SS CS
  Thioredoxin_8  3 vvlLyfgaswcppckaftpklkelyeklkkkkkveivyvsldk 45
                   +vlL f+a+wc pck+++p l++++e       v +  v++d 
     AHX11769.1 17 LVLLDFWAEWCGPCKQMIPVLQAFSEVSP---HVSVYKVNIDG 56
                   69***********************9985...77777777775 PP

  == domain 2  score: 3.7 bits;  conditional E-value: 0.051
                   T-HHHHTT-S--TT-SEEEEE- CS
  Thioredoxin_8 69 kkrnklkkkynvkaiPtlvvld 90
                   + +++l+ + +v a+Ptl++ +
     AHX11769.1 56 GPKQALAIENGVRAVPTLILFK 77
                   45889999999******99976 PP

>> TraF  F plasmid transfer operon protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   5.6e-10   8.4e-07     125     221 ..       9      96 ..       2      99 .. 0.86

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 5.6e-10
        TraF 125 kklakeygLlf..Fyrgkcpyceaqapilqafadky.glevraVsvdgrplpelpnarvdkgqaarlgvkrtPalvlvdpksqkvvpvaaGllsldele 220
                 k++++ +gL++  F ++ c+ c++++p+lqaf +   + +v  V++dg     l+          + gv+ +P+l+l++    k+    +G+lsl++++
  AHX11769.1   9 KQVSDAHGLVLldFWAEWCGPCKQMIPVLQAFSEVSpHVSVYKVNIDGPKQ-ALAI---------ENGVRAVPTLILFKDG--KMLDRKVGMLSLSQIK 95 
                 6788888887756899*****************9877**********9644.5677.........88***********998..7777789*******99 PP

        TraF 221 e 221
                 e
  AHX11769.1  96 E 96 
                 7 PP

>> AhpC-TSA  AhpC/TSA family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.0   0.0   3.8e-08   5.6e-05      18      75 ..       9      62 ..       1      97 [. 0.83

  Alignments for each domain:
  == domain 1  score: 23.0 bits;  conditional E-value: 3.8e-08
                EECHHHTTSEEEEEEESTST-CCHHHHHHHHHHCHHHCCCTTEEEEEEESSSCHHHHH CS
    AhpC-TSA 18 vslsdykgkpvvlffypkdwcpvCttelpalaklyeefkergvevigvsvdspeshkk 75
                +++sd  g  v+l f+++ wc +C++ +p l++  e      v v+ v++d p++  +
  AHX11769.1  9 KQVSDAHG-LVLLDFWAE-WCGPCKQMIPVLQAFSEVSP--HVSVYKVNIDGPKQALA 62
                57789999.*********.************99887666..89999999999997655 PP

>> DUF3088  Protein of unknown function (DUF3088)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.5e-07    0.0011      22      77 ..      26      79 ..      22      96 .. 0.88

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.5e-07
     DUF3088 22 yCpdcaaleGllasfPalaekldvervdfarPRkavvallgeenqslPvLvLadga 77
                 C+ c ++  +l+ f ++  ++ v +v+++ P++a+  ++++  + +P+L+L ++ 
  AHX11769.1 26 WCGPCKQMIPVLQAFSEVSPHVSVYKVNIDGPKQAL--AIENGVRAVPTLILFKDG 79
                7*********************************99..69999********98775 PP

>> Glutaredoxin  Glutaredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.2   0.0   1.3e-05     0.019       6      54 ..      24      74 ..       7      82 .. 0.77

  Alignments for each domain:
  == domain 1  score: 15.2 bits;  conditional E-value: 1.3e-05
                  STSSHHHHHHHHHHHHTT...GGEEEEEGCCSHHHHHHHHHHHTSSSSSEEE CS
  Glutaredoxin  6 kptCpyCkkakrlLkelg...vkfeeidvdkdeeireelkelsgvrtvPqvf 54
                    +C+ Ck+++ +L+ +      + ++ v+ d   +++l   +gvr+vP++ 
    AHX11769.1 24 AEWCGPCKQMIPVLQAFSevsPHVSVYKVNID-GPKQALAIENGVRAVPTLI 74
                  489***********999985533677777776.4577777777******987 PP

>> Redoxin  Redoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.4   0.0   3.3e-05     0.049      24      56 ..      12      42 ..       3      61 .. 0.79
   2 ?   -1.8   0.0       1.5   2.3e+03      96     128 ..      60      82 ..      48      93 .. 0.54

  Alignments for each domain:
  == domain 1  score: 13.4 bits;  conditional E-value: 3.3e-05
                HHHTTSEEEEEEESTTT-HHHHHTHHHHHTHHH CS
     Redoxin 24 sefkgkkvvvnfvpgafcPtCsaehpyleklae 56
                s+  g  v++ f++  +c++C++ +p l+ ++e
  AHX11769.1 12 SDAHGL-VLLDFWAE-WCGPCKQMIPVLQAFSE 42
                554444.599*****.*******9998888876 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.5
                 HHHHHTT-TTEEE.GGGEEE-EEEEEEETTEEE CS
     Redoxin  96 aftkalGlrleedaseglrtpryavidedgkvv 128
                 a++ + G+          r+  + ++ +dgk  
  AHX11769.1  60 ALAIENGV----------RAVPTLILFKDGKML 82 
                 44444443..........333334444555555 PP

>> HyaE  Hydrogenase-1 expression protein HyaE
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.0   3.1e-05     0.046      54     105 ..      37      97 ..      30      99 .. 0.67

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 3.1e-05
                 HCT-TTS-EEEEEE...THHHHHHHHHCCT-TSSSEEEEEETTEEE....E..EEESSSTH CS
        HyaE  54 lkaFpnalraavva...dreqeealaerfgvlktPsllflrdgeyl....g..vlakirdW 105
                 l+aF +++  + v     ++ ++ala + gv+ +P+l++++dg++l    g  +l++i++W
  AHX11769.1  37 LQAFSEVSPHVSVYkvnIDGPKQALAIENGVRAVPTLILFKDGKMLdrkvGmlSLSQIKEW 97 
                 56677776665544122367789********************986222232234566666 PP

>> Thioredoxin_7  Thioredoxin-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.1   0.1   5.6e-05     0.084      20      81 ..      18      76 ..      10      78 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.1 bits;  conditional E-value: 5.6e-05
                   EEEEE--TT-HHHHHHHHHHHH-HHHHH.HHHT-EEEEESS--S-GGG.-TT-..--SSEEEEE CS
  Thioredoxin_7 20 vlvffgaswcftCqalerdflsdeevkaalaekfvllrvdvterdanilelde..qgvPvvafl 81
                   vl++f a+wc++C+ +  ++    e    ++ ++ + +v+++  ++ + ++++  + vP+++++
     AHX11769.1 18 VLLDFWAEWCGPCKQMIPVLQAFSE----VSPHVSVYKVNIDGPKQAL-AIENgvRAVPTLILF 76
                   89************99877665555....5569999999999999988.656644669999887 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0   9.7e-05      0.14      10      75 ..      27      98 ..      22      99 .. 0.75

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9.7e-05
                   STTCHHHHHHHHHHCHCC.TCECEEECC.TTHHHH.HHCT-SSSSEEEC..TTCE..EEESS---CCHHHHHH CS
  Thioredoxin_3 10 CakCpklekavkeaaaek.gikaevekv.tdfeei.ekygVmsvPalvi..dgkv..vvsGkvpseeeirkll 75
                   C  C+++  ++++  + +  +++  +++    + +  ++gV++vP+l++  dgk+  + +G + s  +i++++
     AHX11769.1 27 CGPCKQMIPVLQAFSEVSpHVSVYKVNIdGPKQALaIENGVRAVPTLILfkDGKMldRKVG-MLSLSQIKEWV 98
                   8999999999998888885588855555155555599**********55348998555788.88888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (103 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       419  (0.02337); expected 358.6 (0.02)
Passed bias filter:                      398  (0.0221987); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                        12  (0.000669307); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              12  [number of targets reported over threshold]
# CPU time: 0.36u 0.23s 00:00:00.59 Elapsed: 00:00:00.37
# Mc/sec: 826.02
//
Query:       AHX11770.1  [L=122]
Description: ribosomal protein L19 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-33  113.4   0.2    5.5e-33  113.2   0.2    1.0  1  Ribosomal_L19  Ribosomal protein L19


Domain annotation for each model (and alignments):
>> Ribosomal_L19  Ribosomal protein L19
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  113.2   0.2   3.1e-37   5.5e-33      13     110 ..      19     116 ..       4     117 .. 0.92

  Alignments for each domain:
  == domain 1  score: 113.2 bits;  conditional E-value: 3.1e-37
  Ribosomal_L19  13 kdlpefkvGdtvkVkvkikegkkeRiqafeGvviarkgkgisetftvRki.segvgvervfplhspkiekievvrrgkvrrakLyYLrelkgkaar 107
                    +++pef++G +++V+++++ g+  R+q+f+G++ia+++kg++++ft+Rk+ +++v ver+f l+ p+i++i+v r+gkvrrakLyY+r l gka+r
     AHX11770.1  19 REYPEFRSGYAMSVEFYVQ-GTSGRTQVFKGLCIAKSNKGVHSSFTLRKLsVHDVYVERTFCLYWPSIKSISVERKGKVRRAKLYYIRALAGKATR 113
                    589**************97.79***************************956899***************************************** PP

  Ribosomal_L19 108 ike 110
                    i++
     AHX11770.1 114 IRK 116
                    *86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (122 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       333  (0.0185733); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.23s 00:00:00.61 Elapsed: 00:00:00.39
# Mc/sec: 939.26
//
Query:       AHX11771.1  [L=216]
Description: tRNA (guanine(37)-N(1))-methyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    5.4e-44  150.2   0.0    5.9e-44  150.1   0.0    1.0  1  tRNA_m1G_MT  tRNA (Guanine-1)-methyltransferase


Domain annotation for each model (and alignments):
>> tRNA_m1G_MT  tRNA (Guanine-1)-methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  150.1   0.0   3.3e-48   5.9e-44       6     192 ..      20     208 ..      15     211 .. 0.93

  Alignments for each domain:
  == domain 1  score: 150.1 bits;  conditional E-value: 3.3e-48
                  HHHHHHHHHHHHHHHHHHHCSSCEEEEEEETSSHHHHHHHHHHHCCGH.HC.GG-TTEEEESSCGGHHHHCCCHHHCGGGEEEEETTTSSBECCGGTT CS
  tRNA_m1G_MT   6 ekelvslevqllrdytanrrntvddelygggagmvlkaepelealesv.nt.ekwkvilltptGkkftqelaeeLsekeklvylcgdyegvdervddd 101
                   ++  slev+  r+++++ r  vdd++yggg+gmv+ +   ++ale++ ++ e  ++++l+p G kft ++       e+++++cg+ egvd+r+ d 
   AHX11771.1  20 SRGCWSLEVVPIRRFATKTR--VDDTPYGGGPGMVMRPDVLGDALEYAlSVrEVNRRVFLSPRGPKFTHKSIAGFVDAESVLLVCGRFEGVDQRFLDY 115
                  57888999********9988..************************99865577899***************************************** PP

                  SSE.EEEEESSSSTTCSTTHHHHHHHHHHHHTTTC..EEB-S-CCC...CHCTS..CTTSEHHTEHHHHHHHHHCCCTTTHHHHHHHHHHHSC CS
  tRNA_m1G_MT 102 kvd.eysIGdfVlkggekgalvlidavkrllaGvl.ntaslpedsfsnrllekpnytrpltlrglkVpeiLlsgnhakienWrlkealertvp 192
                  +   e s+Gd+Vl+gge++a++++d+ +r+++Gvl n++sl+ +s     le+++ytrp ++rgl Vpe+Llsg+h ki++Wr   a   t  
   AHX11771.1 116 YNFeELSVGDYVLSGGEIAAMAVMDSCVRQIPGVLgNAKSLECESLTSSSLEHDHYTRPSAWRGLMVPEVLLSGDHRKIGEWRASSAGHITRR 208
                  9669******************************************************************************98877665555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (216 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       146  (0.00814323); expected 358.6 (0.02)
Passed bias filter:                      144  (0.00803168); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.37
# Mc/sec: 1748.38
//
Query:       AHX11772.1  [L=82]
Description: ribosomal protein L27 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    9.8e-38  128.0   2.2    1.1e-37  127.9   2.2    1.0  1  Ribosomal_L27  Ribosomal L27 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L27  Ribosomal L27 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  127.9   2.2     6e-42   1.1e-37       1      79 []       2      81 ..       2      81 .. 0.97

  Alignments for each domain:
  == domain 1  score: 127.9 bits;  conditional E-value: 6e-42
  Ribosomal_L27  1 AhkkagGstkngrdskgkrlGvKkfggqlvkagnIivrQrgtkfhpGenvgiGkdhtlfAlvdGvVkfe.kkkkrkyvsv 79
                   A+kkagGs++ngrds gkrlGvKkfg + v++gnIivrQrgtkfhpG+nvgiG+dhtlfAl++GvV+f+   + r++v+v
     AHX11772.1  2 ATKKAGGSSSNGRDSIGKRLGVKKFGSESVIPGNIIVRQRGTKFHPGKNVGIGRDHTLFALKSGVVSFSvGLNGRHFVHV 81
                   89*******************************************************************75789999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (82 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       197  (0.0109878); expected 358.6 (0.02)
Passed bias filter:                      163  (0.00909142); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.31u 0.21s 00:00:00.52 Elapsed: 00:00:00.33
# Mc/sec: 733.42
//
Query:       AHX11773.1  [L=99]
Description: ribosomal protein L21 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-26   90.9   7.7      6e-26   90.7   7.7    1.1  1  Ribosomal_L21p  Ribosomal prokaryotic L21 protein


Domain annotation for each model (and alignments):
>> Ribosomal_L21p  Ribosomal prokaryotic L21 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   90.7   7.7   3.3e-30     6e-26       1     101 []       1      97 [.       1      97 [. 0.91

  Alignments for each domain:
  == domain 1  score: 90.7 bits;  conditional E-value: 3.3e-30
                     XEEEEECSTEEEEESSSEEEEEESSSSSTTCEEEESSEEE....EE..ECTSSSESSTCEEEEEEEEEE---EEEEEEETTTTEEEEEEE--EEE CS
  Ribosomal_L21p   1 myAiietgGkqykVeegdvlkvekleaevgdkveldkVllvgskdd.vkvGaplvegakVeaevvehgkgkkiivfkkkrrknyrrkqghRqkyt 94 
                     m A++e g+kqy V+ g+v+kvek+ ae g+++e+++V +v ++++  ++G+      +V+aev++  ++kk+++fkk+rrkn+rrk+ghRq++t
      AHX11773.1   1 MLAVVEQGNKQYLVKRGQVIKVEKIVAELGQEIEMSSVKYVLDEKSkSIFGS-----GTVRAEVISMERDKKLVIFKKRRRKNSRRKNGHRQSVT 90 
                     89************************************99655544255554.....5779********************************** PP

                     EEEEEEE CS
  Ribosomal_L21p  95 klrItkI 101
                     +lrI++I
      AHX11773.1  91 VLRIKDI 97 
                     *****98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (99 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       976  (0.0544369); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.33u 0.22s 00:00:00.55 Elapsed: 00:00:00.35
# Mc/sec: 859.05
//
Query:       AHX11774.1  [L=56]
Description: hypothetical protein NHE_0854 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (56 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       438  (0.0244297); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 492.84
//
Query:       AHX11775.1  [L=196]
Description: recombination protein RecR [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    7.6e-21   74.4   0.1    1.3e-20   73.7   0.1    1.4  1  Toprim_4  Toprim domain
    1.1e-11   44.1   1.3    2.2e-11   43.1   1.3    1.6  1  RecR      RecR protein
    2.2e-05   24.6   0.1    3.9e-05   23.8   0.1    1.4  1  Toprim    Toprim domain
  ------ inclusion threshold ------
      0.036   14.7   0.2       0.17   12.5   0.1    2.1  2  HHH_5     Helix-hairpin-helix domain
      0.045   13.6   0.0       0.14   12.1   0.0    1.9  1  HHH       Helix-hairpin-helix motif


Domain annotation for each model (and alignments):
>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.7   0.1   3.5e-24   1.3e-20       2      88 ..      79     168 ..      78     169 .. 0.94

  Alignments for each domain:
  == domain 1  score: 73.7 bits;  conditional E-value: 3.5e-24
    Toprim_4   2 eiiiVEgyaDvlaleka.giknvvavlggalspldgirpeklktenlve..aekkvkevilaldgDaeGeataerlaellleegvkvtrl 88 
                  ++iVE  +D++a+e+a   ++ ++vl gals  +gi pe+l +e+l+e   e  vke+i+a++++ eG++ta+++++l+++  vk ++l
  AHX11775.1  79 ILCIVEEITDLWAIERAgVHNGKYHVLNGALSVINGITPESLQIESLREkvVETGVKELIIATNSTIEGQTTAQYIVDLFKNVPVKLSFL 168
                 79***************888999****************************9999***********************887888887776 PP

>> RecR  RecR protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   43.1   1.3   6.2e-15   2.2e-11       3      40 .]      39      76 ..      37      76 .. 0.96

  Alignments for each domain:
  == domain 1  score: 43.1 bits;  conditional E-value: 6.2e-15
                HHHHHHHHHHHHH-EE-TTT--EESSSS-CCCCSTTSE CS
        RecR  3 eeLaeaLqeakekvrhCsrCgnlteedlCaICsdprRD 40
                 ++++a+q + +++r C+ Cgnl    +C+IC+++rRD
  AHX11775.1 39 LKFIDAMQVLYDTIRSCESCGNLESVSPCSICTNDRRD 76
                689**********************************9 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   23.8   0.1   1.1e-08   3.9e-05       2      88 ..      80     159 ..      79     169 .. 0.87

  Alignments for each domain:
  == domain 1  score: 23.8 bits;  conditional E-value: 1.1e-08
                 EEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHH..HHHSEEEEECSSSHHHHHHHHHHHHHHT CS
      Toprim   2 lvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkela..kradeiilatDpDreGeaiawellevlk 88 
                 l+ivE  +d  +i++a g  ++++  + G +  +          i ++  ++++l+e      ++e+i+at+   eG+++a ++++++k
  AHX11775.1  80 LCIVEEITDLWAIERA-GVHNGKYHVLNGALSVING--------ITPESLQIESLREKVveTGVKELIIATNSTIEGQTTAQYIVDLFK 159
                 8***************.8777777777777776666........8899999*******9999999********************8887 PP

>> HHH_5  Helix-hairpin-helix domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.5   0.1   4.8e-05      0.17      39      55 ..      13      30 ..       5      32 .. 0.83
   2 ?   -1.1   0.0      0.85     3e+03       7      13 ..     112     118 ..     107     139 .. 0.64

  Alignments for each domain:
  == domain 1  score: 12.5 bits;  conditional E-value: 4.8e-05
                T.STTS-HHHHHHHHHHH CS
       HHH_5 39 k.ipGiGkktAeriilel 55
                + +pG+G+k A+ri+l l
  AHX11775.1 13 EnLPGLGPKSARRIVLHL 30
                448***********9976 PP

  == domain 2  score: -1.1 bits;  conditional E-value: 0.85
                 STT--HH CS
       HHH_5   7 vsGiGpk 13 
                 ++Gi p+
  AHX11775.1 112 INGITPE 118
                 5555554 PP

>> HHH  Helix-hairpin-helix motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.1   0.0     4e-05      0.14      15      29 ..      14      28 ..       4      29 .. 0.88

  Alignments for each domain:
  == domain 1  score: 12.1 bits;  conditional E-value: 4e-05
                TSTT-SHHHHHHHHH CS
         HHH 15 alPGVGpktAeaIls 29
                 lPG Gpk A++I  
  AHX11775.1 14 NLPGLGPKSARRIVL 28
                59***********75 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (196 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       592  (0.0330191); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1432.59
//
Query:       AHX11776.1  [L=227]
Description: DSBA-like thioredoxin domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.9e-31  107.6   0.0    8.1e-31  107.4   0.0    1.0  1  Thioredoxin_4   Thioredoxin
    3.9e-08   33.3   0.0      0.006   16.4   0.0    2.1  2  DSBA            DSBA-like thioredoxin domain
  ------ inclusion threshold ------
      0.011   15.6   0.0      0.023   14.6   0.0    1.4  1  Thioredoxin_12  Thioredoxin-like domain
       0.14   12.2   0.0          5    7.2   0.0    2.3  2  Thioredoxin_3   Thioredoxin domain


Domain annotation for each model (and alignments):
>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.4   0.0   1.8e-34   8.1e-31       2     165 ..      46     221 ..      45     222 .. 0.88

  Alignments for each domain:
  == domain 1  score: 107.4 bits;  conditional E-value: 1.8e-34
                    SSSSEEES-TT-SEEEEEEE-TT-HHHHHHHHHHH.HHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--T..T.HHHHHHHHHHHHTHHH CS
  Thioredoxin_4   2 tetdiviGnpdApvtvieyedlrCphCakfeeeve.klleeyidtGkvkfiirdfpldkekeslkaamaarcagee..s.peaflaikallysqqe 93 
                    +++d++iG++dApvtvi y++++C hC++ +ee+  +l e y+++Gkv +i+r+fpld  +  ++a+++++c+ +   s + +fl+i+ +l++  +
     AHX11776.1  46 LPKDHAIGSTDAPVTVIDYSSFSCTHCKTAFEELIrPLHESYVKQGKVLLIMRHFPLDYLS--FSASVFLECYRQHveSdNDKFLNITGVLFDIGA 139
                    5899*************************7777665***********************96..**********998763599************** PP

                    HTTS-HHHHH...............H..HHHHTS-------HHHHHHHHHHH.HHHT--SS-EEEETTEEE-TT--HHHHHHHHT CS
  Thioredoxin_4  94 ewaeslkelaae..........aldk..dekfeacleeekldalveaeskea.kkagiestPtfiingekveepqtyeelkalid 165
                    e++++ ++l +           +  +  +++f++c+++ +++++v   +  a k+++i +tP ++inge+++++ +++ ++  i+
     AHX11776.1 140 EARNK-EDLTSRldkiildsglS--EsvRKEFSSCMNDLDVKNEVLHSKLFAiKQLEIAGTPVLYINGERYTGKFNFSNFSDRIE 221
                    ****9.66554345666664433..2569****************88888888************************99998876 PP

>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.0   0.1   3.5e-06     0.016       1      40 [.      60     103 ..      60     108 .. 0.92
   2 !   16.4   0.0   1.3e-06     0.006     118     192 ..     143     220 ..     120     221 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.0 bits;  conditional E-value: 3.5e-06
                 EEEEEEBTTBHHHHHHHHHHHHHHHHC....CTEEEEEEE-SSS CS
        DSBA   1 tvdeffDvlCPyCylgkerleklaars....pdvkvvlrpfela 40 
                 tv+ ++++ C +C++++e+l + ++ s     +v + +r+f+l+
  AHX11776.1  60 TVIDYSSFSCTHCKTAFEELIRPLHESyvkqGKVLLIMRHFPLD 103
                 6788*********************999*9666*********97 PP

  == domain 2  score: 16.4 bits;  conditional E-value: 1.3e-06
                 S-TSSHHHHHHHHHHTTS.HHH...HHHHHTSHHHHHHHHHHHH.HHHHTT-SSSSEEEETTCEEEESSSSHHHHHHHH CS
        DSBA 118 qaitddqellevaekaGldaee...ldealeseavkeavrenta.aaqslgvtGvPtvvvdgkrmvfGadrldtladal 192
                  + + ++ l+++  + Gl+ +    +   +++ +vk++v  +   a ++l + G+P  +++g+   +G  ++ ++ d++
  AHX11776.1 143 NKEDLTSRLDKIILDSGLSESVrkeFSSCMNDLDVKNEVLHSKLfAIKQLEIAGTPVLYINGE-RYTGKFNFSNFSDRI 220
                 4445556699999999996543233888999999999987776615679**************.9*********99987 PP

>> Thioredoxin_12  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.6   0.0     5e-06     0.023     132     185 ..      45     101 ..      32     105 .. 0.75

  Alignments for each domain:
  == domain 1  score: 14.6 bits;  conditional E-value: 5e-06
                     --TT---BS....--SEEEEEEE--SSTTSHHHHHHHHHHH.....HHTSEEEEEEE-- CS
  Thioredoxin_12 132 llpfDhvypgskeasspvaILYgdlgskefkefhkkLkela.....kegkvkYvlRhvp 185
                      lp Dh + gs++ +  ++I Y +++++++k++++ L +       k+gkv  ++Rh+p
      AHX11776.1  45 SLPKDHAI-GSTD-APVTVIDYSSFSCTHCKTAFEELIRPLhesyvKQGKVLLIMRHFP 101
                     6899****.6655.5555888*****98766555555443333349***********98 PP

>> Thioredoxin_3  Thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.032   1.4e+02       8      22 ..      67      82 ..      58     100 .. 0.74
   2 ?    7.2   0.0    0.0011         5      20      58 ..     168     205 ..     160     214 .. 0.70

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.032
                   SSSTTCH.HHHHHHHH CS
  Thioredoxin_3  8 pgCakCp.klekavke 22
                    +C++C+ ++e++++ 
     AHX11776.1 67 FSCTHCKtAFEELIRP 82
                   47*****888887765 PP

  == domain 2  score: 7.2 bits;  conditional E-value: 0.0011
                    HHHHCHCCTCECEEECCTTHHHHHHCT-SSSSEEECTTC CS
  Thioredoxin_3  20 vkeaaaekgikaevekvtdfeeiekygVmsvPalvidgk 58 
                    + ++++++++k ev + + f  i++ ++  +P l+i+g+
     AHX11776.1 168 FSSCMNDLDVKNEVLHSKLF-AIKQLEIAGTPVLYINGE 205
                    55555555666666655554.5899************98 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (227 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       553  (0.0308439); expected 358.6 (0.02)
Passed bias filter:                      491  (0.0273858); expected 358.6 (0.02)
Passed Vit filter:                        48  (0.00267723); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.24s 00:00:00.64 Elapsed: 00:00:00.38
# Mc/sec: 1788.68
//
Query:       AHX11777.1  [L=72]
Description: hypothetical protein NHE_0857 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (72 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       251  (0.0139997); expected 358.6 (0.02)
Passed bias filter:                      205  (0.011434); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.26s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 535.58
//
Query:       AHX11778.1  [L=257]
Description: DSBA-like thioredoxin domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    2.6e-14   53.4   0.0    5.3e-12   45.9   0.0    2.3  1  DSBA           DSBA-like thioredoxin domain
    7.9e-10   39.1   0.2    5.2e-09   36.5   0.0    2.2  2  Thioredoxin_4  Thioredoxin
     0.0016   18.8   0.3       0.21   12.1   0.0    2.6  3  Thioredoxin_2  Thioredoxin-like domain
  ------ inclusion threshold ------
      0.039   14.1   0.1       0.15   12.2   0.0    1.8  2  CaMKII_AD      Calcium/calmodulin dependent protein kinase II
      0.092   12.3   0.0       0.17   11.5   0.0    1.4  1  DUF3153        Protein of unknown function (DUF3153)
        3.4    7.5  12.2        3.3    7.6   8.7    2.7  2  ScsC_N         Copper resistance protein ScsC N-terminal doma


Domain annotation for each model (and alignments):
>> DSBA  DSBA-like thioredoxin domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   45.9   0.0   1.8e-15   5.3e-12       1     186 [.     101     248 ..     101     254 .. 0.91

  Alignments for each domain:
  == domain 1  score: 45.9 bits;  conditional E-value: 1.8e-15
                 EEEEEEBTTBHHHHHHHHHHHHHHHHCCTEEEEEEE-SSSCHHHHCT.S.GGGSHHHHHHHHHHHHHHHHHHT....GGSSHHHHHHHHHHHHHHHHHH CS
        DSBA   1 tvdeffDvlCPyCylgkerleklaarspdvkvvlrpfelagakkasgnvgpselpeklkylledlkrlaeaegiplrfpkdklknstraarlllaagae 99 
                 tv+e fD  C+yC+++++ l ++ + +p+++  lr +++ g                                       + + ++++   + l  +++
  AHX11778.1 101 TVVELFDASCGYCKIASQMLVRAMNDYPNANYILRNLPILGR--------------------------------------NSMVAARYDLGFSLFIREK 161
                 79999*************************************......................................2234667777799999999 PP

                 HGHHHHHHHHHHHHHTSSS-TSSHHHHHHHHHHTTS.HHHHHHHHTS..HHHHHHHHHHHHHHHHTT-SSSSEEEETTCEEEESSSSHH CS
        DSBA 100 glaekvvrelfealwsegqaitddqellevaekaGldaeeldeales..eavkeavrentaaaqslgvtGvPtvvvdgkrmvfGadrld 186
                 gl   ++ e++ +l++   + + ++ +le+++++G++  e++ ++e+  +++ e+++++ ++a +l++ G+P ++vd +  + Ga   +
  AHX11778.1 162 GLSFSKYLEFYLKLMDHSGQYDPEA-ILEMVSSLGFSKGEFQSFFEKnaDKIDEMINKTVELATKLQLDGTPVFIVDEQ-IIQGANETE 248
                 999******************9998.*******************99667789*************************9.999998765 PP

>> Thioredoxin_4  Thioredoxin
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.2   0.1      0.34     1e+03      63      71 ..      54      62 ..      15      89 .. 0.41
   2 !   36.5   0.0   1.7e-12   5.2e-09      11     164 ..      96     253 ..      95     255 .. 0.71

  Alignments for each domain:
  == domain 1  score: -0.2 bits;  conditional E-value: 0.34
                   TTHHHHHHH CS
  Thioredoxin_4 63 slkaamaar 71
                   s+++  + +
     AHX11778.1 54 SVSRYRLTQ 62
                   222222222 PP

  == domain 2  score: 36.5 bits;  conditional E-value: 1.7e-12
                    TT-SEEEEEEE-TT-HHHHHHHHHHHHHHHHHHHTTSEEEEEEE-..---STTTHHHHHHHTT--T....T...HHHHHHHHHHHHTH.HHHTTS- CS
  Thioredoxin_4  11 pdApvtvieyedlrCphCakfeeeveklleeyidtGkvkfiirdfpldkekeslkaamaarcagee....s...peaflaikallysq.qeewaes 98 
                    pdA+ tv+e  d +C +C+  ++ +   +++y    +  +i r++p+ +++ s+ aa +   +       +    ++ +++ +l+    q+++++ 
     AHX11778.1  96 PDAKTTVVELFDASCGYCKIASQMLVRAMNDY---PNANYILRNLPILGRN-SMVAARYDLGFSLFirekGlsfSKYLEFYLKLMDHSgQYDPEAI 187
                    89*********************999******...***********99997.88888765444333111121123455444444433235555555 PP

                    HHHHH........HHHHHTS-------HHHHHHHHHHHHHHT--SS-EEEETTEEE-TT--HHHHHHHH CS
  Thioredoxin_4  99 lkelaae...aldkdekfeacleeekldalveaeskeakkagiestPtfiingekveepqtyeelkali 164
                    l+ + ++   +++ ++ fe+  + +k+d+++ + ++ a+k+++ +tP fi+++++++++++  el++++
     AHX11778.1 188 LEMVSSLgfsKGEFQSFFEK--NADKIDEMINKTVELATKLQLDGTPVFIVDEQIIQGANE-TELREAL 253
                    55555553323333444555..889*******************************96655.4566665 PP

>> Thioredoxin_2  Thioredoxin-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.91   2.7e+03      43      53 ..      64      74 ..      30     101 .. 0.46
   2 ?    4.1   0.0      0.02        61       5      46 ..      98     144 ..      94     150 .. 0.63
   3 !   12.1   0.0     7e-05      0.21      60      99 ..     198     244 ..     164     253 .. 0.68

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.91
  Thioredoxin_2 43 kpsfepkavai 53
                   +++ ++ a++i
     AHX11778.1 64 EKQQQQRAQEI 74
                   22222222222 PP

  == domain 2  score: 4.1 bits;  conditional E-value: 0.02
  Thioredoxin_2   5 gkpvlvvftdpdCpyCkklkk.elkel...ddvtvrvllfp.lkpsf 46 
                     k ++v   d +C+yCk   +  ++ +   ++ + +++  p l++++
     AHX11778.1  98 AKTTVVELFDASCGYCKIASQmLVRAMndyPNANYILRNLPiLGRNS 144
                    5778888889******9666544444432355555555555665555 PP

  == domain 3  score: 12.1 bits;  conditional E-value: 7e-05
  Thioredoxin_2  60 kkafkd............ieenvelarkygvrgtPtivfldgkeivarlpGy 99 
                    k +f+             i+++vela k++++gtP +++ ++      ++G+
     AHX11778.1 198 KGEFQSffeknadkidemINKTVELATKLQLDGTPVFIVDEQI-----IQGA 244
                    4444446666666777799****************99987654.....5555 PP

>> CaMKII_AD  Calcium/calmodulin dependent protein kinase II association domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.3   0.0      0.73   2.2e+03      53      65 ..      62      74 ..      32      95 .. 0.53
   2 ?   12.2   0.0     5e-05      0.15      22      76 ..     170     222 ..     164     227 .. 0.91

  Alignments for each domain:
  == domain 1  score: -1.3 bits;  conditional E-value: 0.73
                GGS...SSSS-SE CS
   CaMKII_AD 53 yfekllakrkkav 65
                 fek   +r +++
  AHX11778.1 62 QFEKQQQQRAQEI 74
                2333333343333 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 5e-05
                 HHHHHHEEEEEEEE-GGGTT-EEESSHHHHGGGS...SSSS-SEEEEEESEEEEE CS
   CaMKII_AD  22 etytklcdpeltvfepevlgnlveglefhrfyfekllakrkkavrttilnkrvrl 76 
                 e y kl+d + + ++pe+  ++v +l f +  f+ ++ k+  ++  ++ nk+v+l
  AHX11778.1 170 EFYLKLMDHS-GQYDPEAILEMVSSLGFSKGEFQSFFEKNADKI-DEMINKTVEL 222
                 6688999999.*********************************.7899999987 PP

>> DUF3153  Protein of unknown function (DUF3153)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.5   0.0   5.6e-05      0.17      17     105 ..      52     156 ..      46     182 .. 0.75

  Alignments for each domain:
  == domain 1  score: 11.5 bits;  conditional E-value: 5.6e-05
     DUF3153  17 lssasgeql.pwqeeleqrlaelggkveerdeeelrltipflngeeleellnrlvsrase.......aaglslpep...............elrlvern 92 
                 l+s s+  l ++ ++ +qr++e++++ ++ ++e + ++ p+ +  +++++  +l+            +                       +l +  rn
  AHX11778.1  52 LESVSRYRLtQFEKQQQQRAQEIRSAITKHKNEIFDFNYPSRKVPDAKTTVVELFDASCGyckiasqM-------LvramndypnanyilrNLPILGRN 143
                 6677888899******************9999999*******************99444444444330.......134445555556666688888888 PP

     DUF3153  93 lllgveqqlsldl 105
                 ++++ +++l   l
  AHX11778.1 144 SMVAARYDLGFSL 156
                 8888888876655 PP

>> ScsC_N  Copper resistance protein ScsC N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.6   8.7    0.0011       3.3       2      28 ..      33      59 ..      32      72 .. 0.77
   2 ?   -2.6   0.1       1.7   5.1e+03      17      26 ..     184     193 ..     183     194 .. 0.77

  Alignments for each domain:
  == domain 1  score: 7.6 bits;  conditional E-value: 0.0011
      ScsC_N  2 kaaiekivrdYLleNPEiLvEAlqaLq 28
                +a+ie iv+ Y+ +NPE ++E++  ++
  AHX11778.1 33 TAQIESIVEKYIEKNPEKILESVSRYR 59
                79***************9999975543 PP

  == domain 2  score: -2.6 bits;  conditional E-value: 1.7
      ScsC_N  17 PEiLvEAlqa 26 
                 PE ++E++  
  AHX11778.1 184 PEAILEMVSS 193
                 8989999876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (257 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1704  (0.0950416); expected 358.6 (0.02)
Passed bias filter:                      948  (0.0528752); expected 358.6 (0.02)
Passed Vit filter:                        88  (0.00490825); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.52u 0.25s 00:00:00.77 Elapsed: 00:00:00.40
# Mc/sec: 1937.29
//
Query:       AHX11779.1  [L=110]
Description: hypothetical protein NHE_0859 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
      0.078   13.1   0.0      0.089   12.9   0.0    1.1  1  rhaM      L-rhamnose mutarotase
       0.18   12.5   0.0       0.27   11.9   0.0    1.4  1  HypF_C    HypF Kae1-like domain


Domain annotation for each model (and alignments):
>> rhaM  L-rhamnose mutarotase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0   9.9e-06     0.089      15      94 ..      22     106 ..      13     110 .] 0.77

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 9.9e-06
        rhaM  15 eYkklH..aevwpevlealke....agirnysIyldeegntLfailevgddeeadaaaaaadpkvqeWwalmaklqeaapsaspak 94 
                 e+  lH  +++ pevl+  k+      + ny  y +++ + L+ +l+++ +e++d+++  +dp++++ ++ +++++e+  ++++++
  AHX11779.1  22 EFTLLHngEDLTPEVLNLHKKdpaaYVLDNYPQY-RDSIEKLVTVLDYDISESQDTKILPDDPEQRKFEKAIKNVLEKLMKDKENN 106
                 5666676667778887766652221456789999.68999********88999**********************99776655554 PP

>> HypF_C  HypF Kae1-like domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0     3e-05      0.27      30      71 ..      16      57 ..       8      77 .. 0.90

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 3e-05
      HypF_C 30 hlGdlenletleayeealeeleklleikpevivcDlhpdyls 71
                  Gdl+++  l++ e+ + e+ +l++ +p+++v D  p+y  
  AHX11779.1 16 ITGDLSEFTLLHNGEDLTPEVLNLHKKDPAAYVLDNYPQYRD 57
                57**************************************86 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (110 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       763  (0.0425568); expected 358.6 (0.02)
Passed bias filter:                      497  (0.0277205); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.35u 0.23s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 907.67
//
Query:       AHX11780.1  [L=333]
Description: putative 85kDa strain-specific antigen [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
  ------ inclusion threshold ------
      0.012   15.6   0.6        7.7    6.5   0.0    3.3  3  DUF2001          Phage tail tube protein
      0.014   15.0   9.1       0.47    9.9   0.6    3.6  3  vATP-synt_AC39   ATP synthase (C/AC39) subunit
      0.014   14.9   0.0         13    5.4   0.0    4.2  5  XAF1_C           XIAP-associated factor 1 C-terminal domain
      0.053   13.2   1.4       0.58    9.8   0.1    3.0  4  TM1506           Domain of unknown function (DUF1893)
        4.6    7.7  12.0    1.6e+02    2.8   0.1    7.0  6  Antimicrobial15  Ocellatin family


Domain annotation for each model (and alignments):
>> DUF2001  Phage tail tube protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.4   0.0      0.17     6e+02      74      98 ..     128     152 ..     124     175 .. 0.84
   2 ?    6.5   0.0    0.0022       7.7      69     107 ..     178     217 ..     172     220 .. 0.89
   3 ?    4.7   0.0     0.008        29      69     100 ..     253     284 ..     249     322 .. 0.92

  Alignments for each domain:
  == domain 1  score: 0.4 bits;  conditional E-value: 0.17
     DUF2001  74 laeyiktGkdprfelivkleDPdav 98 
                 l+++  +G  ++ e++  l+D++av
  AHX11780.1 128 LKDATAAGALKDSEIQGLLKDKTAV 152
                 5678899999************995 PP

  == domain 2  score: 6.5 bits;  conditional E-value: 0.0022
     DUF2001  69 rmrkllaeyiktGkdprfelivkleDPda.vGkervvlkn 107
                 ++++ll+++  +G  ++ e++  l+D++a    er ++++
  AHX11780.1 178 DFQNLLKDQTAAGALKDSEIQGLLKDKTAvDSLERAIVRD 217
                 68999************************77788888876 PP

  == domain 3  score: 4.7 bits;  conditional E-value: 0.008
     DUF2001  69 rmrkllaeyiktGkdprfelivkleDPdavGk 100
                 ++++ll+++  +G  ++ +++  l+D  a+G+
  AHX11780.1 253 DFQNLLKDQTAAGALKDSTIQGLLKDAAAIGA 284
                 68999************************996 PP

>> vATP-synt_AC39  ATP synthase (C/AC39) subunit
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.1   0.2      0.12   4.4e+02     254     254 ..      81      81 ..      18     160 .. 0.64
   2 ?    9.9   0.6   0.00013      0.47      20      65 ..     144     206 ..     127     211 .. 0.75
   3 ?    8.0   0.2   0.00049       1.8      13      62 ..     228     278 ..     225     284 .. 0.82

  Alignments for each domain:
  == domain 1  score: 0.1 bits;  conditional E-value: 0.12
                     G CS
  vATP-synt_AC39 254 a 254
                     +
      AHX11780.1  81 E 81 
                     1 PP

  == domain 2  score: 9.9 bits;  conditional E-value: 0.00013
                     HHTTS.-HH................HHHHHHHTSGGGGG--......SSSHHHHHHHHHHHHH CS
  vATP-synt_AC39  20 nLlqcesle................dvkryLketdYgnfladel.seplsrsdiekalrekla 65 
                      Ll  ++                  +++++Lketd++n l d++ +  l  s+i+ +l++k a
      AHX11780.1 144 GLLKDKTAVdllknaslcgvlknnaEARNLLKETDFQNLLKDQTaAGALKDSEIQGLLKDKTA 206
                     4444444434444444446666666*******************999**********999976 PP

  == domain 3  score: 8.0 bits;  conditional E-value: 0.00049
                     --HHHHHHHTTS.-HHHHHHHHHTSGGGGG--......SSSHHHHHHHHHH CS
  vATP-synt_AC39  13 LteedyenLlqcesledvkryLketdYgnfladel.seplsrsdiekalre 62 
                     L +e ++ Ll+ +  ++++++Lketd++n l d++ +  l  s+i+ +l++
      AHX11780.1 228 LQDEGFSALLRDNVNTEARNLLKETDFQNLLKDQTaAGALKDSTIQGLLKD 278
                     667778888777777899999999999999999998888888888888876 PP

>> XAF1_C  XIAP-associated factor 1 C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0      0.12   4.4e+02       3      26 ..      33      56 ..      31      57 .. 0.64
   2 ?   -0.0   0.0      0.19   6.6e+02       3      19 ..      42      58 ..      40      65 .. 0.82
   3 ?    1.4   0.0     0.068   2.4e+02       2      19 ..      59      76 ..      58      83 .. 0.85
   4 ?    1.4   0.0     0.068   2.4e+02       2      19 ..      77      94 ..      76     101 .. 0.85
   5 ?    5.4   0.0    0.0038        13       8      26 ..     146     164 ..     140     165 .. 0.91

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.12
      XAF1_C  3 rsasaledeaaYDiLrrCsqCgiL 26
                +s+++l+d+ a ++L+     +iL
  AHX11780.1 33 TSSNTLKDTTAAEVLKNTTAGDIL 56
                566777777777777765555554 PP

  == domain 2  score: -0.0 bits;  conditional E-value: 0.19
      XAF1_C  3 rsasaledeaaYDiLrr 19
                ++a++l+++ a DiL+ 
  AHX11780.1 42 TAAEVLKNTTAGDILKN 58
                788999********986 PP

  == domain 3  score: 1.4 bits;  conditional E-value: 0.068
      XAF1_C  2 srsasaledeaaYDiLrr 19
                s++a++l+++ a DiL+ 
  AHX11780.1 59 STAAEVLKNTTAGDILKN 76
                8999************86 PP

  == domain 4  score: 1.4 bits;  conditional E-value: 0.068
      XAF1_C  2 srsasaledeaaYDiLrr 19
                s++a++l+++ a DiL+ 
  AHX11780.1 77 STAAEVLKNTTAGDILKN 94
                8999************86 PP

  == domain 5  score: 5.4 bits;  conditional E-value: 0.0038
      XAF1_C   8 ledeaaYDiLrrCsqCgiL 26 
                 l+d+ a D+L+  s Cg+L
  AHX11780.1 146 LKDKTAVDLLKNASLCGVL 164
                 799**************98 PP

>> TM1506  Domain of unknown function (DUF1893)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.84     3e+03      17      49 ..      13      44 ..       9      65 .. 0.71
   2 ?   -2.2   0.1      0.83     3e+03      29      29 ..      70      70 ..      24     111 .. 0.58
   3 ?    9.8   0.1   0.00016      0.58       2      88 ..     170     255 ..     169     264 .. 0.92
   4 ?    0.7   0.0      0.11   3.9e+02       6      46 ..     267     306 ..     262     310 .. 0.77

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.84
                SSSEEEEE--STTHHHHHHHHH-S-.-TT-EEE CS
      TM1506 17 kedeirtskerGvapllellkeekeflkgalva 49
                ++ ++ t +++ v +ll+  +++++ lk+ ++a
  AHX11780.1 13 NDTNFNTLTDSTVLDLLKHDTSSNT-LKDTTAA 44
                4556777777778888776665554.7776655 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.83
                T CS
      TM1506 29 v 29
                 
  AHX11780.1 70 A 70
                2 PP

  == domain 3  score: 9.8 bits;  conditional E-value: 0.00016
                 HHHHHHHTT-SEEEESSSEEEEE--STTHHHHHHHHH-S-.-TT-EEEEEEE-HHHHHHHHHH--SEEEEEEEEHHHHHHHHHTT-- CS
      TM1506   2 lkklLeeeelslviakedeirtskerGvapllellkeekeflkgalvaDkvvGkaAaaLlvlggvkevYaeviSeaAlelLeeegik 88 
                 +++lL+e+++  +++++      k++ +++ll+  ++ ++ l+ a+v D+   k Aa++l   g +++  + + ++A +lL+e++ +
  AHX11780.1 170 ARNLLKETDFQNLLKDQTAAGALKDSEIQGLLKDKTAVDS-LERAIVRDTLKCKDAAIVLQDEGFSALLRDNVNTEARNLLKETDFQ 255
                 789999******999999999***********99888877.*****************************************98765 PP

  == domain 4  score: 0.7 bits;  conditional E-value: 0.11
                 HHHTT-SEEEESSSEEEEE--STTHHHHHHHHH-S-.-TT- CS
      TM1506   6 LeeeelslviakedeirtskerGvapllellkeekeflkga 46 
                 L++ ++  ++++   i   k++G+++ll+ +++++  l+++
  AHX11780.1 267 LKDSTIQGLLKDAAAIGALKQSGISELLKDTNAKRF-LEDS 306
                 66777777778888999999*******998888765.6665 PP

>> Antimicrobial15  Ocellatin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.4   0.3      0.46   1.6e+03       1       6 [.      25      30 ..      25      31 .. 0.92
   2 ?    1.5   0.0      0.11     4e+02       3       7 ..      54      58 ..      54      62 .. 0.88
   3 ?    1.5   0.0      0.11     4e+02       3       7 ..      72      76 ..      72      80 .. 0.88
   4 ?    1.5   0.0      0.11     4e+02       3       7 ..      90      94 ..      90      98 .. 0.88
   5 ?   -1.1   0.1      0.78   2.8e+03       4      13 ..     100     110 ..      99     111 .. 0.80
   6 ?    2.8   0.1     0.045   1.6e+02       2       8 ..     152     158 ..     151     159 .. 0.90

  Alignments for each domain:
  == domain 1  score: -0.4 bits;  conditional E-value: 0.46
  Antimicrobial15  1 VlDILK 6 
                     VlD LK
       AHX11780.1 25 VLDLLK 30
                     9****9 PP

  == domain 2  score: 1.5 bits;  conditional E-value: 0.11
  Antimicrobial15  3 DILKg 7 
                     DILK+
       AHX11780.1 54 DILKN 58
                     9***9 PP

  == domain 3  score: 1.5 bits;  conditional E-value: 0.11
  Antimicrobial15  3 DILKg 7 
                     DILK+
       AHX11780.1 72 DILKN 76
                     9***9 PP

  == domain 4  score: 1.5 bits;  conditional E-value: 0.11
  Antimicrobial15  3 DILKg 7 
                     DILK+
       AHX11780.1 90 DILKN 94
                     9***9 PP

  == domain 5  score: -1.1 bits;  conditional E-value: 0.78
  Antimicrobial15   4 ILKgA.AKdLl 13 
                      +LK A AK++l
       AHX11780.1 100 VLKDAnAKNVL 110
                      58888799987 PP

  == domain 6  score: 2.8 bits;  conditional E-value: 0.045
  Antimicrobial15   2 lDILKgA 8  
                      +D LK+A
       AHX11780.1 152 VDLLKNA 158
                      8*****9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (333 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       713  (0.039768); expected 358.6 (0.02)
Passed bias filter:                      318  (0.0177366); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.47u 0.22s 00:00:00.69 Elapsed: 00:00:00.40
# Mc/sec: 2510.65
//
Query:       AHX11781.1  [L=126]
Description: hypothetical protein NHE_0861 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   12.8   0.0       0.16   12.2   0.0    1.4  1  SRP54_N   SRP54-type protein, helical bundle domain


Domain annotation for each model (and alignments):
>> SRP54_N  SRP54-type protein, helical bundle domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.0     9e-06      0.16       9      48 ..      49      88 ..      42     103 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 9e-06
                HHHHCCSSCGHHHHHHHHHHHHHHHHHHTT--HHHHHHHH CS
     SRP54_N  9 lkklsgkskideedleealkeleeaLleaDVgvkvvkkli 48
                l ++ g  + ++ ++e+ l+ l ++Ll+ DV+ ++ ++l+
  AHX11781.1 49 LMSIAGMATNSDNTVEDELQALVDILLMPDVNGNTCTSLT 88
                556666667778889999999************9998886 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (126 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      370  (0.020637); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.19s 00:00:00.57 Elapsed: 00:00:00.36
# Mc/sec: 1049.13
//
Query:       AHX11782.1  [L=70]
Description: hypothetical protein NHE_0862 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       548  (0.030565); expected 358.6 (0.02)
Passed bias filter:                      390  (0.0217525); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.23s 00:00:00.56 Elapsed: 00:00:00.36
# Mc/sec: 584.91
//
Query:       AHX11783.1  [L=329]
Description: 50S ribosome-binding GTPase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
      3e-38  129.9   1.3    7.6e-38  128.6   0.5    2.0  2  YchF-GTPase_C  Protein of unknown function (DUF933)
    3.8e-11   43.1   0.0    1.1e-10   41.6   0.0    1.9  1  MMR_HSR1       50S ribosome-binding GTPase
  ------ inclusion threshold ------
      0.044   13.8   0.0       0.13   12.4   0.0    1.8  1  TGS            TGS domain
       0.14   12.2   0.0       0.19   11.7   0.0    1.4  1  PAC2           PAC2 family


Domain annotation for each model (and alignments):
>> YchF-GTPase_C  Protein of unknown function (DUF933)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.2   0.0      0.54   2.4e+03      40      65 ..     104     131 ..     100     148 .. 0.50
   2 !  128.6   0.5   1.7e-41   7.6e-38       1      83 [.     246     328 ..     246     329 .] 0.99

  Alignments for each domain:
  == domain 1  score: -1.2 bits;  conditional E-value: 0.54
  YchF-GTPase_C  40 raevikyedlvel.gs.eaaakeagklr 65 
                     ae+ik+e l +  +s e+++k++++ +
     AHX11783.1 104 DAEIIKMELLLADmQSlENRLKKSKTSK 131
                    5788888544332233344444443333 PP

  == domain 2  score: 128.6 bits;  conditional E-value: 1.7e-41
  YchF-GTPase_C   1 LitffTaGekevraWtikkgttapqaAgviHsDfekgFiraevikyedlvelgseaaakeagklrlegkdyvvqdgDiilfkf 83 
                    Li ffTaGeke+raW+ik+++tapqaAg+iH+Dfek+Fi+ae+i+++d++e+g+e+++k+ gk+r+eg++y+vqdgDii+fk+
     AHX11783.1 246 LIVFFTAGEKEARAWSIKRNSTAPQAAGTIHTDFEKKFIKAETISFSDYIEFGGEQKCKSLGKMRIEGREYIVQDGDIIHFKH 328
                    899******************************************************************************95 PP

>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.0   2.3e-14   1.1e-10      21      87 ..       3      96 ..       1     205 [. 0.82

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 2.3e-14
                TS.TEEESSSTTSSSSEEEEEEEETTEE..................EEEEECGGCSSHHHHHHHHHHHHHHHHC.TSEEEEEEETT........T CS
    MMR_HSR1 21 ge.kaivsdkpgtTrdinegrvklkgke..................ielvDtpGliegaseekglgkaflalee.adlillvvdas........e 87
                ++ +a+++++p++T+++n ++v + + +                  +e+vD++Gl++ga++++glg++fl++++ +d+i++v+++         +
  AHX11783.1  3 KTqAAEAANYPFCTIEPNIAKVPEYD-PrlvqiaeiskaektifsqLEIVDIAGLVQGANQGEGLGNKFLSHIReVDVIIHVLRCFsdddirhvH 96
                543789***************98322.2355555566666666666*********9***************99889*******988544443331 PP

>> TGS  TGS domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.4   0.0   2.8e-05      0.13      12      55 ..     261     323 ..     247     327 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.4 bits;  conditional E-value: 2.8e-05
                 EEETTB-HHHHHHHHSTTHHHHEEEEEECS...................EEEETTSBB-SSEE CS
         TGS  12 dlprgatveDfAykIhrslakkfiyAlVnG...................qrvgldhvLedgdv 55 
                  ++r++t+ ++A  Ih+++ kkfi A                       ++ g ++ ++dgd+
  AHX11783.1 261 SIKRNSTAPQAAGTIHTDFEKKFIKAETISfsdyiefggeqkckslgkmRIEGREYIVQDGDI 323
                 489*********************997666666666666666666665555556666666665 PP

>> PAC2  PAC2 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   4.3e-05      0.19      66     112 ..     164     219 ..     115     299 .. 0.70

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 4.3e-05
                 .SEEEEEEE..E-HSCHHHHHHHHHHHHHHHTTESEEEEEEEEEESS-.......E CS
        PAC2  66 srdllvlqg..repilqyeefakalldwaeelgvkevvvLggldager.......a 112
                 s+++l + +   e il +++f+++++++a+ ++ + vvv +++ a+          
  AHX11783.1 164 SKPMLYVCNveQENILSGNKFSTQIAEFAKTSNMESVVVSAAIEAEIAllesdedR 219
                 3456666667789999999************************9776544333330 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (329 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       935  (0.0521501); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.46u 0.24s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2548.81
//
Query:       AHX11784.1  [L=84]
Description: hypothetical protein NHE_0864 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (84 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       657  (0.0366445); expected 358.6 (0.02)
Passed bias filter:                      376  (0.0209716); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.36u 0.25s 00:00:00.61 Elapsed: 00:00:00.40
# Mc/sec: 623.85
//
Query:       AHX11785.1  [L=41]
Description: hypothetical protein NHE_0866 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (41 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       203  (0.0113224); expected 358.6 (0.02)
Passed bias filter:                      156  (0.00870099); expected 358.6 (0.02)
Passed Vit filter:                        12  (0.000669307); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.22s 00:00:00.56 Elapsed: 00:00:00.39
# Mc/sec: 313.02
//
Query:       AHX11786.1  [L=70]
Description: hypothetical protein NHE_0867 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (70 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       288  (0.0160634); expected 358.6 (0.02)
Passed bias filter:                      216  (0.0120475); expected 358.6 (0.02)
Passed Vit filter:                        11  (0.000613531); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.35u 0.24s 00:00:00.59 Elapsed: 00:00:00.39
# Mc/sec: 536.11
//
Query:       AHX11787.1  [L=449]
Description: peptidase M16 inactive domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    1.1e-21   77.6   0.2    1.3e-19   70.9   0.1    2.6  3  Peptidase_M16_C  Peptidase M16 inactive domain
    1.2e-09   38.3   0.0    2.3e-09   37.4   0.0    1.4  1  Peptidase_M16    Insulinase (Peptidase family M16)


Domain annotation for each model (and alignments):
>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    4.1   0.0    0.0046        41     137     165 ..     107     135 ..      72     149 .. 0.82
   2 !   70.9   0.1   1.5e-23   1.3e-19       2     183 .]     193     369 ..     192     369 .. 0.89
   3 ?   -2.3   0.0      0.44   3.9e+03       5      26 ..     413     434 ..     409     436 .. 0.85

  Alignments for each domain:
  == domain 1  score: 4.1 bits;  conditional E-value: 0.0046
                      SCEEEEEEEEEECTTHHHHHHHHHHHHHH CS
  Peptidase_M16_C 137 dsglfgisatadpenveevvevilkelrk 165
                       s+ ++++++a +en+ ++ve++++ + k
       AHX11787.1 107 ESNSLTVTVSAPKENIRQAVELFCQSVSK 135
                      678899*******************9876 PP

  == domain 2  score: 70.9 bits;  conditional E-value: 1.5e-23
                      H-HHHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSHCSGSCTSSSSSGGGSSEEEEEEEESSSSSEEEEEEEEEECTCTHTT CS
  Peptidase_M16_C   2 ltredlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaskappakptgepltpatlkkppvvlkkldeeqahlslafegpskended 95 
                      +t+ed+++ + + ++   m +a+ G+ + +e+++++++y+ +++ +     + ++  ++ +  +k   v  +++++q+++ ++++g+s+ +de+
       AHX11787.1 193 ITAEDIRKHVVNTFNRISMRVAVLGNTSSDEVKAVLDNYLIEFPLT---VMEVRNLEQP-EFSNKVNCVSIEKNVPQNIILFGQKGLSR-TDEN 281
                      89******************************************87...6666666666.344444446666677**************.**** PP

                      HHHHHHHHHHHHSS.TTSHHHHHHHTTTTSESEEEEEEEEESSCEEEEEEEEEECTTHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHH CS
  Peptidase_M16_C  96 dlalavlntlLggg.mesrLytnlrekeglaysvsafndsyrdsglfgisatadpenveevvevilkelrklkkeglteeeleraknql 183
                       + l+vln++Lgg   es L +++rek+g +y+v+  + +  +  l+gi+ t+   n+ ev + il  l++lk+ gl+ + +e ak+ql
       AHX11787.1 282 FYNLVVLNHILGGSgLESILMREIREKKGYTYGVYTKLYNMGVDLLLGIASTSG-ANAPEVANSILMLLKNLKQSGLDLATVEDAKTQL 369
                      ************988**********************88778777777777666.58******************************97 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.44
                      HHHHHHHHHHSSGGGEEEEEEE CS
  Peptidase_M16_C   5 edlkefykkfYrpenmvlaivG 26 
                      ++l  f+k+f  p+ m ++ vG
       AHX11787.1 413 DSLNLFIKTFLDPKSMLFVNVG 434
                      78899***********999888 PP

>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   37.4   0.0   2.5e-13   2.3e-09      21     128 ..      59     166 ..      56     186 .. 0.85

  Alignments for each domain:
  == domain 1  score: 37.4 bits;  conditional E-value: 2.5e-13
                    -SGGGSCTTTTTHHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEEEEEEEGGGHHHHHHHHHHHHHSBTTSHHHHHHHHHHHHHHH CS
  Peptidase_M16  21 aGSryepkdlnGlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvYyvevlskdlekaldvladvfkaplleesevererkvvekev 116
                    +G +y+ k+  G+++l    +  g +  +s+ ++++l klGg+++   +    + +v+++++++ +a++++++ + +p+l+e+++++ +    +++
     AHX11787.1  59 TGYAYDSKEKLGISNLAVAVLKEGASDISSKDFMKTLGKLGGKISYDLESNSLTVTVSAPKENIRQAVELFCQSVSKPRLDEETLSKVKSMQIAQL 154
                    8999***********************************************************************************555555555 PP

                    HHHCCHHHHHHH CS
  Peptidase_M16 117 eavdaepekvve 128
                    +  +++ + v++
     AHX11787.1 155 KREEDNLSSVAR 166
                    555555544444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       532  (0.0296726); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.52u 0.27s 00:00:00.79 Elapsed: 00:00:00.43
# Mc/sec: 3156.70
//
Query:       AHX11788.1  [L=442]
Description: peptidase M16 inactive domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.7e-21   75.0   0.1    1.1e-20   74.2   0.1    1.4  1  Peptidase_M16    Insulinase (Peptidase family M16)
    5.2e-20   72.2   0.3    1.8e-19   70.5   0.0    1.9  2  Peptidase_M16_C  Peptidase M16 inactive domain


Domain annotation for each model (and alignments):
>> Peptidase_M16  Insulinase (Peptidase family M16)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   74.2   0.1   1.2e-24   1.1e-20       5     143 ..      46     183 ..      42     186 .. 0.89

  Alignments for each domain:
  == domain 1  score: 74.2 bits;  conditional E-value: 1.2e-24
                    EE-TSSSEEEEEEEES-SGGGSCTTTTTHHHHHHHHTTSBBSSSCHHHHHHHHHHTTCEEEEEEESSEEEEEEEEEGGGHHHHHHHHHHHHHSBTT CS
  Peptidase_M16   5 esdppaktsavglvvdaGSryepkdlnGlAHllehmafkgTkkypsnklaeeleklGgslnAttsrentvYyvevlskdlekaldvladvfkapll 100
                    ++d + + ++  l  ++GS+++ k  +G+AH+leh++f ++k+ ++  + +e++kl+  +nA+ts  +tvYy  v +++lek++++ a+ + + ++
     AHX11788.1  46 IRDGTLPIVSHVLLYKVGSANDLKGKSGVAHYLEHLMFRSSKNIQN--ISKEIDKLNSVYNAFTSDYRTVYYELVNKNKLEKVMQLEAERMVNLAI 139
                    5566667788889999*************************99998..************************************************ PP

                    SHHHHHHHHHHHHHH.HHHHCCHHHHHHHHHHHHHHTTTSGGGS CS
  Peptidase_M16 101 eesevererkvveke.veavdaepekvveenlhaaayrekalgr 143
                    ++++ve erk+v++e +  +d++p  ++ e+++aa+yr++++ +
     AHX11788.1 140 TDEAVELERKIVLEErRMRLDNKPLVRLSEEMYAAFYRNDTAWN 183
                    **********6666505567888888899999999999987655 PP

>> Peptidase_M16_C  Peptidase M16 inactive domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.14   1.3e+03     151     178 ..     119     146 ..      55     150 .. 0.72
   2 !   70.5   0.0     2e-23   1.8e-19       1     183 []     193     377 ..     193     377 .. 0.88

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.14
                      THHHHHHHHHHHHHHHHHHTS-HHHHHH CS
  Peptidase_M16_C 151 nveevvevilkelrklkkeglteeeler 178
                      n +++++v+  e +++++  +t+e++e 
       AHX11788.1 119 NKNKLEKVMQLEAERMVNLAITDEAVEL 146
                      4567888888888888888888888875 PP

  == domain 2  score: 70.5 bits;  conditional E-value: 2e-23
                      CH-HHHHHHHHHHHSSGGGEEEEEEESS-HHHHHHHHHHHHTTSTHHSHCSGSCTSSSSSGGGSSEEEEEEEES...SSSSEEEEEEEEEECTC CS
  Peptidase_M16_C   1 sltredlkefykkfYrpenmvlaivGdvdheelvkliekyfgdlkaskappakptgepltpatlkkppvvlkkl...deeqahlslafegpske 91 
                      sl+  d ++ y+k+Y+p+ +vl+i Gd+d ++++ +++ky g +++ k   +k+++  ++ ++    ++ +k l   + e+  l + fe+p++ 
       AHX11788.1 193 SLNQADAQQMYQKYYQPSQAVLVILGDIDINKVKGCVNKYYGVIPNLK--TGKDSSNVVPLEPEHRADITVKMLnsmN-EERNLIYLFEAPNI- 282
                      588999*****************************************9..6666666666666666666555553333.78888889******. PP

                      THTTHHHHHHHHHHHHSSTTSHHHHHHHTTTTSESEEEEEEEEES.SCEEEEEEEEEECT..THHHHHHHHHHHHHHHHHHTS-HHHHHHHHHH CS
  Peptidase_M16_C  92 ndeddlalavlntlLgggmesrLytnlrekeglaysvsafndsyr.dsglfgisatadpe..nveevvevilkelrklkkeglteeeleraknq 182
                      +d+ ++a  v +++L gg  s+L t+l+ +  la +vs + d  +   g+  i +t  +   ++e ++  + + l+++ + g+  e++e ak+ 
       AHX11788.1 283 SDKSHFATLVAAQILAGGKLSVLGTELTHNLRLALDVSVDYDYLTkRKGIVEIVVTPLSPdvKLEVLESSVSRILADVLRSGIANEDIEVAKAM 376
                      ****************************99999*******774447*********99888799999*************************987 PP

                      H CS
  Peptidase_M16_C 183 l 183
                      l
       AHX11788.1 377 L 377
                      5 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (442 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       764  (0.0426125); expected 358.6 (0.02)
Passed bias filter:                      420  (0.0234257); expected 358.6 (0.02)
Passed Vit filter:                        37  (0.0020637); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.50u 0.24s 00:00:00.74 Elapsed: 00:00:00.40
# Mc/sec: 3279.78
//
Query:       AHX11789.1  [L=167]
Description: signal peptidase II [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-30  105.0   7.2    4.5e-30  104.7   7.2    1.2  1  Peptidase_A8  Signal peptidase (SPase) II
  ------ inclusion threshold ------
      0.071   13.6   0.6       0.18   12.3   0.3    1.8  1  TraL          TraL protein


Domain annotation for each model (and alignments):
>> Peptidase_A8  Signal peptidase (SPase) II
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  104.7   7.2     5e-34   4.5e-30       5     138 ..      25     158 ..       8     161 .. 0.85

  Alignments for each domain:
  == domain 1  score: 104.7 bits;  conditional E-value: 5e-34
  Peptidase_A8   5 llllDqltKllvvenlkte..svevipgffkltyveNrgaafglle.sgakrkllillsl.vvilllivlllkkkkkskllrialalilgGalGNli 97 
                    +llD  tK+l    l ++  ++ev+p f++l  v+N+g++fgll+ ++++++++i+l++ +v+++l++ ++k     +l+ +al+l+lgGalGN++
    AHX11789.1  25 TMLLDLYTKYLC-GALVEDivEIEVLP-FLNLVDVRNTGMSFGLLKgFQFSNVFFICLNVpLVVFILLFSCCKC--GVSLEGFALGLVLGGALGNVV 117
                   689*********.45544446777787.****************996555668999999834444454555544..5789***************** PP

  Peptidase_A8  98 DrllygkVvDfldfsleliefpvFNvADvaitvGvilliia 138
                   Dr+ +g+V Df+d+++ ++++p+FN+ADvai++Gv++l++ 
    AHX11789.1 118 DRVAFGAVRDFIDLHVLGWHWPAFNLADVAIFLGVMCLLYR 158
                   *************************************9875 PP

>> TraL  TraL protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.3     2e-05      0.18      20      75 ..      86     142 ..      73     149 .. 0.85

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 2e-05
        TraL  20 ealvillllvvgillgqfviglvlglllvlllrklkkgrgdgfl.lhllYWylpasl 75 
                 +++ ++ +   g+ l+ f +glvlg +l  ++ ++  g  + f+ lh+l W++pa+ 
  AHX11789.1  86 VFILLFSCCKCGVSLEGFALGLVLGGALGNVVDRVAFGAVRDFIdLHVLGWHWPAFN 142
                 56777788899***********************999998887769********875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (167 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       774  (0.0431703); expected 358.6 (0.02)
Passed bias filter:                      432  (0.024095); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.25s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1310.42
//
Query:       AHX11790.1  [L=451]
Description: carboxypeptidase Taq (M32) metallopeptidase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.9e-49  168.8   0.6    2.8e-26   92.3   0.2    2.6  2  Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
  ------ inclusion threshold ------
       0.25   11.6   1.4          2    8.7   0.2    2.8  4  NdhM           Cyanobacterial and plastid NDH-1 subunit M


Domain annotation for each model (and alignments):
>> Peptidase_M32  Carboxypeptidase Taq (M32) metallopeptidase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   73.8   0.0   1.3e-24   1.2e-20       1     310 [.       6     299 ..       6     308 .. 0.87
   2 !   92.3   0.2   3.2e-30   2.8e-26     353     482 ..     321     448 ..     310     449 .. 0.92

  Alignments for each domain:
  == domain 1  score: 73.8 bits;  conditional E-value: 1.3e-24
  Peptidase_M32   1 klkellkkvsalesasallewDketvmpkkgaearaeqlatLselahelltseevaellekleeekeeldekekavveelkreykkakkvpaelve 96 
                    kl+ ++ k+ +l+++ +ll++D +        +++ +q+ tL+e++++ +ts+eva ++++++++++el++++  +   +++   ++k++p +lv+
     AHX11790.1   6 KLERVFTKIDDLQKTLELLDFDVRLHGS--LLDSKVHQIITLKEVIYDVVTSDEVALIIDRIKAKSNELSDWQCVNFGFMQDFCIRKKNIPFDLVK 99 
                    58899*****************998877..77889************************************************************* PP

  Peptidase_M32  97 alakasakaeaaWreareandfalfepsLeevielkreiaell.edlkkspYdaLldeyepgltvekidalFeelkealvpllkkikeskekekkd 191
                    +++++s  +  +++ear+a++f+++++++ +++e++r+ia+l  ++++ ++Y aLl + +  ++ e++++    l  ++ pllk    +k++ +  
     AHX11790.1 100 DFTEKSLACRVSYAEARKARNFEIVKEDFWNLLEVVRTIAALHaKGTDCDKYTALLRANQ--IDPEQLEQ----LCIGVSPLLK----MKVQ-NVG 184
                    ******************************************999***********8754..55566655....5555666632....2332.233 PP

  Peptidase_M32 192 ksflereipeekqrelsrellkalgfdfdrgrldeseHPFttsfsrkDvRittryeednllsslfsvlHEaGHalYeqnlpee.lsktplgggvsl 286
                    + +++ + + +++r   r++++ + f  +  r+d   H    + +++++++  + + + ++ sl+ +    G +lY +nlp + ++ +p+++ +s+
     AHX11790.1 185 ETLSSTSTDRKEMRLNYRRIIEKF-FPKNVVRIDFGDHFHLLG-EKNGIKLIVQEKGEAVIPSLMFL---LGQGLYMKNLPYDkWRAQPICNPTSI 275
                    347788888888888888888887.667779*******77777.99999999998887777777666...5*********9644************ PP

  Peptidase_M32 287 gihEsqSrlyEniigrskeFwevl 310
                    ++  +q +l++ +++ +k F +vl
     AHX11790.1 276 AMYAAQGFLFSHFLFEEKGFAKVL 299
                    ********************9876 PP

  == domain 2  score: 92.3 bits;  conditional E-value: 3.2e-30
  Peptidase_M32 353 lHillRyelEkeliegklsvkdlpeaWnekykeyLgidppddaeGvLQDvHWssgafGYFPtYalGniyaaqlfeamekdlpeleiakgefseikk 448
                     H ++R+ lE+ li+g++s++ ++e++ e    y+ ++  d++  +L   HW  g f Y+P+Y+ G i a+q+f+ m+++ + ++  k  ++++ +
     AHX11790.1 321 THLMIRFSLERSLINGEVSLDGIQELFTEDLSYYFRLN--DQSASILDNHHWFFGEFCYYPSYLKGMIAAGQIFHMMKSENAIYQNGKPMIKKLIT 414
                    7*********************************9765..68888********************************9999444667888****** PP

  Peptidase_M32 449 WLkenihqkGslysseellkkatgeslnaeyyid 482
                    WL++n++ +G++ys +el++k+tge+l+ +++++
     AHX11790.1 415 WLNTNVCANGARYSMDELINKLTGENLDCRFFKK 448
                    *****************************99975 PP

>> NdhM  Cyanobacterial and plastid NDH-1 subunit M
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   0.2   0.00022         2      45      92 ..       5      52 ..       2      57 .. 0.88
   2 ?   -3.2   0.0       1.2     1e+04      11      33 ..     151     174 ..     148     181 .. 0.82
   3 ?   -0.3   0.0      0.14   1.3e+03      78     106 ..     381     409 ..     378     410 .. 0.90
   4 ?   -3.6   0.0       1.5   1.3e+04      50      63 ..     428     441 ..     415     443 .. 0.74

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.00022
        NdhM 45 kkvyekfdelvesyegedlteynlrriGsdlehfirkllqkGeisynl 92
                +k+++ f+++ + ++  +l ++++r  Gs l++ ++++++  e+ y++
  AHX11790.1  5 EKLERVFTKIDDLQKTLELLDFDVRLHGSLLDSKVHQIITLKEVIYDV 52
                67788888888889999**********************999999976 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 1.2
        NdhM  11 faaevennelvese.dkltldvdP 33 
                 ++a ++ n++++++ ++l + v P
  AHX11790.1 151 YTALLRANQIDPEQlEQLCIGVSP 174
                 889999999999887888888877 PP

  == domain 3  score: -0.3 bits;  conditional E-value: 0.14
        NdhM  78 firkllqkGeisynlesrvlnysmGlPrv 106
                 +++ ++ +G+i + ++s    y  G+P +
  AHX11790.1 381 YLKGMIAAGQIFHMMKSENAIYQNGKPMI 409
                 8899*********************9976 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 1.5
        NdhM  50 kfdelvesyegedl 63 
                  +del+++ +ge+l
  AHX11790.1 428 SMDELINKLTGENL 441
                 57889999888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (451 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       523  (0.0291706); expected 358.6 (0.02)
Passed bias filter:                      429  (0.0239277); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.53u 0.22s 00:00:00.75 Elapsed: 00:00:00.38
# Mc/sec: 3562.40
//
Query:       AHX11791.1  [L=51]
Description: hypothetical protein NHE_0872 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (51 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       275  (0.0153383); expected 358.6 (0.02)
Passed bias filter:                      177  (0.00987227); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.21s 00:00:00.51 Elapsed: 00:00:00.33
# Mc/sec: 460.17
//
Query:       AHX11792.1  [L=225]
Description: hypothetical protein NHE_0873 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (225 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       227  (0.0126611); expected 358.6 (0.02)
Passed bias filter:                      204  (0.0113782); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.38u 0.25s 00:00:00.63 Elapsed: 00:00:00.39
# Mc/sec: 1743.03
//
Query:       AHX11793.1  [L=221]
Description: ribonuclease III [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-29  102.2   0.0    3.4e-29  101.6   0.0    1.3  1  Ribonucleas_3_3  Ribonuclease-III-like
    1.4e-20   73.9   0.0      4e-20   72.4   0.0    1.8  2  Ribonuclease_3   Ribonuclease III domain
    2.4e-14   53.8   0.0    3.8e-14   53.1   0.0    1.4  1  dsrm             Double-stranded RNA binding motif
  ------ inclusion threshold ------
       0.01   16.0   0.0      0.025   14.8   0.0    1.7  1  DND1_DSRM        double strand RNA binding domain from DEAD E


Domain annotation for each model (and alignments):
>> Ribonucleas_3_3  Ribonuclease-III-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  101.6   0.0   7.5e-33   3.4e-29       1     124 [.      16     138 ..      16     141 .. 0.94

  Alignments for each domain:
  == domain 1  score: 101.6 bits;  conditional E-value: 7.5e-33
  Ribonucleas_3_3   1 deelleqaltHkSfangrkghNerLefLGdavLklsvseyllekaek.degeltklraslvseeslaeiAkelgLgkvlrlrkgeeetegsgre 93 
                      +++ll + ltH S +   + ++erLefLGdavL+++++++l+e +   +eg+l+++++slv++++la iA++++Lgk+++++  ee  +g+++ 
       AHX11793.1  16 NKTLLIESLTHPSME--VNFSYERLEFLGDAVLDMVIASILYELFPNdPEGSLSNRQSSLVCRDTLAMIARKIDLGKYIFFSSSEELCGGREKV 107
                      68999********76..6679*********************997664899******************************999********** PP

  Ribonucleas_3_3  94 kvladaleAliGAiyldkgaevaqefveeki 124
                      + l +aleAliGAi+ld+g+++a++f++e++
       AHX11793.1 108 SNLENALEALIGAIFLDSGIDTATRFIKEYW 138
                      ***************************9865 PP

>> Ribonuclease_3  Ribonuclease III domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.3   0.0       3.3   1.5e+04      93      99 ..       6      12 ..       4      15 .. 0.79
   2 !   72.4   0.0   8.9e-24     4e-20       1     105 []      36     126 ..      36     126 .. 0.98

  Alignments for each domain:
  == domain 1  score: -3.3 bits;  conditional E-value: 3.3
                    HHHHHHH CS
  Ribonuclease_3 93 vEAliGa 99
                    +EAliG 
      AHX11793.1  6 LEALIGI 12
                    89***96 PP

  == domain 2  score: 72.4 bits;  conditional E-value: 8.9e-24
                     HHHHHHHHHHHHHHHHHHHHHHCTTSSHHHHHHHHHHHTSHHHHHHHHHCTTCHCCHCHH..............HHCCSTTCHCTSHH..HHHHH CS
  Ribonuclease_3   1 erLeflGDavlklaittylfetypdahegrlsklrsklvsnenlarlakklglpkflrasefdpprnwlppgyklsddekedddadkv..ladvv 93 
                     erLeflGDavl+++i + l+e +p++ eg ls+ +s+lv+ ++la +a+k++l k++                  s++e+ + +++kv  l+ ++
      AHX11793.1  36 ERLEFLGDAVLDMVIASILYELFPNDPEGSLSNRQSSLVCRDTLAMIARKIDLGKYIF----------------FSSSEELCGGREKVsnLENAL 114
                     8*********************************************************................999****999999999***** PP

                     HHHHHHHHHHCT CS
  Ribonuclease_3  94 EAliGaiyldsg 105
                     EAliGai+ldsg
      AHX11793.1 115 EALIGAIFLDSG 126
                     **********97 PP

>> dsrm  Double-stranded RNA binding motif
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   53.1   0.0   8.6e-18   3.8e-14       1      67 []     152     217 ..     152     217 .. 0.89

  Alignments for each domain:
  == domain 1  score: 53.1 bits;  conditional E-value: 8.6e-18
                 HHHHHHHHHHHTTSEEEEEEEEEESSTSSSEEEEEEEEETTEEEEEEEESSHHHHHHHHHHHHHHHH CS
        dsrm   1 pKskLqeycqkkgkppnyeyvseegpphslpkFvvtvkvngklygsGvgsnKKeAeqsAAedalekL 67 
                 pKs Lqe++q +g++p++++v+  ++p+++p+F+v+v+v + ++ +++g++KK +e +AA ++++ L
  AHX11793.1 152 PKSILQELLQARGMEPPTYKVIGRTGPDHQPIFEVEVRV-DSKVEKAFGTSKKASEENAARAMIKRL 217
                 8************77777777777777777*********.88888******************9866 PP

>> DND1_DSRM  double strand RNA binding domain from DEAD END PROTEIN 1
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.8   0.0   5.5e-06     0.025       2      47 ..     151     196 ..     150     218 .. 0.78

  Alignments for each domain:
  == domain 1  score: 14.8 bits;  conditional E-value: 5.5e-06
   DND1_DSRM   2 savqlLeelCeknkwgsPvYelhseagpdgkllflYkVvipgiets 47 
                 +++++L+el + +   +P Y++   +gpd+   f + V++ +   +
  AHX11793.1 151 NPKSILQELLQARGMEPPTYKVIGRTGPDHQPIFEVEVRVDSKVEK 196
                 6899**********************************99876555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (221 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       371  (0.0206927); expected 358.6 (0.02)
Passed bias filter:                      362  (0.0201908); expected 358.6 (0.02)
Passed Vit filter:                        24  (0.00133861); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.42u 0.23s 00:00:00.65 Elapsed: 00:00:00.40
# Mc/sec: 1650.17
//
Query:       AHX11794.1  [L=100]
Description: oligomerization domain protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.4e-19   69.1   0.1    3.8e-19   68.9   0.1    1.0  1  RsfS      Ribosomal silencing factor during starvation


Domain annotation for each model (and alignments):
>> RsfS  Ribosomal silencing factor during starvation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.9   0.1   2.1e-23   3.8e-19       3      99 .]       9      99 ..       7      99 .. 0.95

  Alignments for each domain:
  == domain 1  score: 68.9 bits;  conditional E-value: 2.1e-23
                HHHHHHHTT-EEEEEEE-TTTTBSS-SEEEEEEESSHHHHHHHHHHHHHHHHHC.C---EEECBTTS.SEEEEE-SSEEEEEEECCCHHHHHHHHHC CS
        RsfS  3 iaealedkkaedivvidlrekkssladymviatakserhlkalaeelekklkeeaaealsveGlnegddWvlvdlgdvvVhllteeaReeydLEelW 99
                i+e l+++k+ di+v+  r     ++ +m++a+ +s++++k+la+ +++ ++e+ +   + eG+ ++++W+l+d+g+v+Vhl++++ Re+y+ ++lW
  AHX11794.1  9 ILEKLSKHKGDDIKVYGGRG----MTGCMIVASSESHKQVKVLANFIVDLIREH-GFFCKLEGY-DSANWILIDMGEVMVHLFKNDVREYYEVDKLW 99
                7899************9999....899*************************87.668999***.788***************************** PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (100 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       534  (0.0297841); expected 358.6 (0.02)
Passed bias filter:                      471  (0.0262703); expected 358.6 (0.02)
Passed Vit filter:                        35  (0.00195214); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 782.56
//
Query:       AHX11795.1  [L=76]
Description: hypothetical protein NHE_0876 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
     0.0071   16.3   0.0     0.0083   16.1   0.0    1.1  1  FtsL      Cell division protein FtsL


Domain annotation for each model (and alignments):
>> FtsL  Cell division protein FtsL
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.1   0.0   4.6e-07    0.0083      40      90 ..      14      64 ..       4      68 .. 0.89

  Alignments for each domain:
  == domain 1  score: 16.1 bits;  conditional E-value: 4.6e-07
        FtsL 40 lvselekllserdkLeeewrnLlLEestlsahsrvesiAreqLkMkrpspe 90
                l  el++l  +   Le e r L  E + l+  sr+e + ++ L+M++++p 
  AHX11795.1 14 LSGELSSLAMNVAMLELEVRLLEAEFAYLTTSSRIEGLMSRHLRMEHITPG 64
                5668999999999*********************************99875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (76 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       308  (0.0171789); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        16  (0.000892409); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.23s 00:00:00.55 Elapsed: 00:00:00.36
# Mc/sec: 626.15
//
Query:       AHX11796.1  [L=291]
Description: 16S rRNA (cytosine(1402)-N(4))-methyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    2.6e-93  312.9   0.2    4.8e-93  312.0   0.2    1.4  1  Methyltransf_5  MraW methylase family


Domain annotation for each model (and alignments):
>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  312.0   0.2   2.7e-97   4.8e-93       4     309 .]       8     291 .]       6     291 .] 0.97

  Alignments for each domain:
  == domain 1  score: 312.0 bits;  conditional E-value: 2.7e-97
                     X--TTTHHHHHHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---EEEEES-GGGHHHHHHHTTTT-EEEEEE CS
  Methyltransf_5   4 HvpVLlqevvellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekrltlvkgnfkelkealaeanvtkvdgill 98 
                     H+pVLl ev+++l+pk++g+y+DaT+Gagg ++a+L+  +   +++id+D+++ +  ke+ ++f+ r +++++nf+e+++ l +    kvdg+++
      AHX11796.1   8 HKPVLLGEVLKALSPKDGGIYVDATFGAGGYTRAILSSAD-CFVYAIDQDETVEKLFKEVQSDFVGRTEFFNTNFSEMSTLLGDI---KVDGLVF 98 
                     ************************************9864.6899*************************************988...99***** PP

                     E-S--HHHHH-GGG---SSS--BS---S-TTSS--HHHHHHH--HHHHHHHHHHHH--TTHHHHHHHHHHHHHHS---BHHHHHHHHHHHS---- CS
  Methyltransf_5  99 DLGvSslqldkaerGFsfaedapLDmRmdqsaeltAaevlnrlseeeLakilkeygeekfakriakaivekrkkkpiettkelaevikkvvpake 193
                     D+GvS +ql+ ++rGFsf +++pLDmRm ++ +ltA+ ++n++ e+++a+i++++gee+++++ia+aiv++r+k+ i tt+elae++ + +p  +
      AHX11796.1  99 DIGVSTMQLKVPDRGFSFLNEGPLDMRMSNKINLTAETIVNSYTEKRIADIIYQFGEERLSRKIARAIVNSRHKRRIVTTTELAEIVLSCFPRRY 193
                     *****************************************************************************************998765 PP

                     ---..-TTHHHHHHHHHHHHTHHHHHHHHHHHHHHHEEEEEEEEEEESSHHHHHHHHHHHHHTT-------------------EEEEE.E.E--- CS
  Methyltransf_5 194 krkkihpatrvFQAlRIavNdEleeleelleaalellakggrlavisFhSledrivkkvfkeaskkeevPaglpvaseelkaklklitkkpilps 288
                        ki+pat++FQAlRI++N+Ele+l   l+aal +l+ ggr+ v+sFhSledrivk +fk+ +k+                 ++++tkk+++p 
      AHX11796.1 194 Y--KINPATKTFQALRIFINNELEALALGLQAALGMLKVGGRVIVVSFHSLEDRIVKCLFKQVHKN----------------GFNIVTKKVVTPN 270
                     5..89*********************************************************9993................579********** PP

                     HHHHHH-GGGTT-EEEEEEE- CS
  Methyltransf_5 289 eeeikeNprsrsakLrvieki 309
                      ee+k+Np +rsa++rvie+i
      AHX11796.1 271 MEEVKNNPSARSARMRVIERI 291
                     ******************985 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (291 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       573  (0.0319594); expected 358.6 (0.02)
Passed bias filter:                      452  (0.0252106); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.26s 00:00:00.71 Elapsed: 00:00:00.41
# Mc/sec: 2153.14
//
Query:       AHX11797.1  [L=45]
Description: hypothetical protein NHE_0878 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       224  (0.0124937); expected 358.6 (0.02)
Passed bias filter:                      140  (0.00780858); expected 358.6 (0.02)
Passed Vit filter:                         4  (0.000223102); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.34u 0.21s 00:00:00.55 Elapsed: 00:00:00.38
# Mc/sec: 358.26
//
Query:       AHX11798.1  [L=205]
Description: tRNA (guanine-N(7)-)-methyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    4.1e-38  130.6   0.0    5.2e-38  130.2   0.0    1.2  1  Methyltransf_4  Putative methyltransferase
  ------ inclusion threshold ------
       0.15   11.8   0.0       0.21   11.3   0.0    1.2  1  DUF938          Protein of unknown function (DUF938)


Domain annotation for each model (and alignments):
>> Methyltransf_4  Putative methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.2   0.0   5.8e-42   5.2e-38       2     130 ..      41     169 ..      40     196 .. 0.92

  Alignments for each domain:
  == domain 1  score: 130.2 bits;  conditional E-value: 5.8e-42
                     -EEEEEET-TTSHHHHHHHHHSTTSEEEEEES-HHHHHHHHHHHHHCTTSSEEEEES-CCCHHHHCS-TTSEEEEEEES-----SGGGGGGSTTS CS
  Methyltransf_4   2 apvvleiGcGkGeflvalAkknPdknflGiEirvkvvakvlkkiealelkNlrilrgdalkvllelledgslekifilFPDPwfKkrhhKrRllq 96 
                     + +vleiG+G+Ge+l++ A + Pdk f+G E++++++ k+l +i++++l+N+ i   d  ++ll+ l+++ ++ ++ilFPDPw+Kkrh+KrR+++
      AHX11798.1  41 KEIVLEIGFGYGEHLIQRALEAPDKIFIGSEVYENGICKLLGEIKNRGLSNVFIWSLDV-RILLQRLKKQIFNTVYILFPDPWPKKRHNKRRIVN 134
                     6799******************************************************6.*********************************** PP

                     HHHHHHHHHHEEEEEEEEEEESHHHHHHHH.HHHH CS
  Methyltransf_4  97 pellkelarvLkkgGvlelaTDveeyaeem.lkvl 130
                     + +l  l + L+++G+l +aTD ++yae++ ++ +
      AHX11798.1 135 RPFLGLLLENLHPSGELIVATDNKDYAEQIhCTAM 169
                     ****************************9823444 PP

>> DUF938  Protein of unknown function (DUF938)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.3   0.0   2.3e-05      0.21      26      77 ..      40      92 ..      29     114 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.3 bits;  conditional E-value: 2.3e-05
      DUF938 26 te.rvLEiasGtGqHAvffApalpnlkwqpsdqdeelresiaawadelalsnl 77
                ++  vLEi+ G G+H +  A + p   ++ s++ e+    +   +++ +lsn+
  AHX11798.1 40 NKeIVLEIGFGYGEHLIQRALEAPDKIFIGSEVYENGICKLLGEIKNRGLSNV 92
                33379***************************998877777778888888887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       421  (0.0234815); expected 358.6 (0.02)
Passed bias filter:                      403  (0.0224776); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1645.33
//
Query:       AHX11799.1  [L=235]
Description: outer membrane assembly lipoYfiO family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.3e-36  124.6   0.7    5.3e-36  124.3   0.7    1.0  1  YfiO      Outer membrane lipoprotein
    8.9e-15   55.1   0.6    3.6e-12   46.6   0.2    2.7  2  TPR_18    Tetratricopeptide repeat
    9.7e-09   35.3   0.3      0.073   13.7   0.0    4.6  4  TPR_6     Tetratricopeptide repeat
  ------ inclusion threshold ------
      0.072   12.3   0.2      0.094   12.0   0.2    1.2  1  MPS2      Monopolar spindle protein 2
      0.086   13.5   0.1        5.6    7.7   0.1    3.0  4  TPR_16    Tetratricopeptide repeat
       0.31   11.6   2.4       0.57   10.8   2.4    1.5  1  LPAM_1    Prokaryotic membrane lipoprotein lipid attachment s


Domain annotation for each model (and alignments):
>> YfiO  Outer membrane lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  124.3   0.7   1.8e-39   5.3e-36       4     194 ..      38     225 ..      35     231 .. 0.97

  Alignments for each domain:
  == domain 1  score: 124.3 bits;  conditional E-value: 1.8e-39
                 -HHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-SSSTTHHHHHHHHHHHHHHHHSHSCTTTS- CS
        YfiO   4 taselYekgqealqkgdyaeAikklealdsryPfspyaeqaqldliyAyykdadyaealasaerFlrlyPthknvdyvlYlrglsalaqarellrskrd 102
                 ++  +Y+ +++al++g+ +  +  + +l +  Pfsp  e+a+       y  +d+a+a+ sa++++ +yP  k+ dy+l ++g +++   r++      
  AHX11799.1  38 SELSVYNDAVSALKQGKLKISKALFRELSDVSPFSPLGEKAKCFYTELLYDGKDFAAAAGSADEYILNYPVGKDLDYMLSIKGNAYFRMLRNF---ANS 133
                 56678****************************************************************************************...999 PP

                 THHHHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-HHHHHHHHHHHHHHSTTSHHHHHHHHHHHHHHHHTT-H CS
        YfiO 103 pesarqafedfkklvekyPdseYaadakkrltelrerLArhElevaefylkreayvaainRvkevlknypdtesveeaLaimveayralgle 194
                 +e +  a   fk+l++++P s+Y +da+++l+e+ e+LA++  ++  fy+k+ +y aai+R+ e+++ yp+t+   eaL+   eay+alg +
  AHX11799.1 134 TEFLDRAKDTFKELIRRFPGSKYVSDAREKLREIDEILAEKIFSIGMFYFKEMNYHAAISRFTELINGYPKTKCYSEALSKRREAYKALGID 225
                 9****************************************************************************************975 PP

>> TPR_18  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.6   0.2   1.2e-15   3.6e-12       4     145 .]      33     164 ..      30     164 .. 0.87
   2 !    5.7   0.0    0.0049        15      20     136 ..     182     206 ..     166     216 .. 0.54

  Alignments for each domain:
  == domain 1  score: 46.6 bits;  conditional E-value: 1.2e-15
      TPR_18   4 avpdvpeaelyqeaqkaldegnyltaieqLealdtryPfGaYaeqaqLDLiYakykskdyelavasidrfirlnPahpkiDyvlYlrglanmaldkssl 102
                 +  + +e ++y++a  al++g+ + +    ++l    Pf +  e+a+       y  kd+++a+ s+d +i ++P  + +Dy+l ++g a + + +++ 
  AHX11799.1  33 KGKQASELSVYNDAVSALKQGKLKISKALFRELSDVSPFSPLGEKAKCFYTELLYDGKDFAAAAGSADEYILNYPVGKDLDYMLSIKGNAYFRMLRNFA 131
                 566889999**************999999999999999988888888777777799********************************99998766554 PP

      TPR_18 103 qslvsldrsdrdteaakaafrdfkrLlsryPnseYaaDaakrl 145
                 +          +te   +a   fk+L++r+P s+Y +Da+++l
  AHX11799.1 132 N----------STEFLDRAKDTFKELIRRFPGSKYVSDAREKL 164
                 4..........45556667788*****************9875 PP

  == domain 2  score: 5.7 bits;  conditional E-value: 0.0049
      TPR_18  20 aldegnyltaieqLealdtryPfGaYaeqaqLDLiYakykskdyelavasidrfirlnPahpkiDyvlYlrglanmaldksslqslvsldrsdrdteaa 118
                  ++e ny  ai + ++l + yP                                                                             
  AHX11799.1 182 YFKEMNYHAAISRFTELINGYP----------------------------------------------------------------------------- 203
                 4455555555555555555555............................................................................. PP

      TPR_18 119 kaafrdfkrLlsryPnse 136
                                + +
  AHX11799.1 204 ---------------KTK 206
                 ...............443 PP

>> TPR_6  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.0      0.52   1.5e+03       7      28 ..      46      67 ..      43      72 .. 0.79
   2 ?    2.4   0.1       0.1     3e+02       9      31 ..      85     107 ..      77     107 .. 0.81
   3 !   12.7   0.0   5.2e-05      0.16      17      33 .]     138     154 ..     119     154 .. 0.89
   4 !   13.7   0.0   2.5e-05     0.073       5      33 .]     177     205 ..     175     205 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.52
                HHHHHHHHHHHHHHHHHHHHHH CS
       TPR_6  7 alsyrklgdtdkAlealerlik 28
                a s +k+g+   +++++++l +
  AHX11799.1 46 AVSALKQGKLKISKALFRELSD 67
                6678888899999999998865 PP

  == domain 2  score: 2.4 bits;  conditional E-value: 0.1
                 HHHHHHHHHHHHHHHHHHHHH-T CS
       TPR_6   9 syrklgdtdkAlealerlikeYP 31 
                 +++ ++d ++A    ++ i +YP
  AHX11799.1  85 LLYDGKDFAAAAGSADEYILNYP 107
                 345558****************9 PP

  == domain 3  score: 12.7 bits;  conditional E-value: 5.2e-05
                 HHHHHHHHHHHHH-TT- CS
       TPR_6  17 dkAlealerlikeYPdS 33 
                 d+A++++++li+++P+S
  AHX11799.1 138 DRAKDTFKELIRRFPGS 154
                 79*************98 PP

  == domain 4  score: 13.7 bits;  conditional E-value: 2.5e-05
                 HHHHHHHH.HHHHHHHHHHHHHHHHH-TT- CS
       TPR_6   5 klalsyrk.lgdtdkAlealerlikeYPdS 33 
                  +++ y+k + ++ +A+  + +li+ YP++
  AHX11799.1 177 SIGMFYFKeM-NYHAAISRFTELINGYPKT 205
                 589****99*.*****************86 PP

>> MPS2  Monopolar spindle protein 2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.0   0.2   3.1e-05     0.094      51     109 ..     120     178 ..      85     197 .. 0.84

  Alignments for each domain:
  == domain 1  score: 12.0 bits;  conditional E-value: 3.1e-05
        MPS2  51 selgkdllrtFakekeffkiykeeFkdlfdkLvgksfkevvekifedvDgieaekissl 109
                  +    +lr+Fa+ +ef    k+ Fk+l+ +  g ++ +  ++ + ++D i aeki s 
  AHX11799.1 120 GNAYFRMLRNFANSTEFLDRAKDTFKELIRRFPGSKYVSDAREKLREIDEILAEKIFSI 178
                 55556789******************************999999*********999875 PP

>> TPR_16  Tetratricopeptide repeat
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.7   0.1    0.0019       5.6       4      61 ..      46     103 ..      43     110 .. 0.86
   2 ?    7.3   0.3    0.0025       7.5       6      59 ..      85     139 ..      83     144 .. 0.80
   3 ?    1.1   0.0      0.22   6.6e+02      13      30 ..     137     154 ..     134     164 .. 0.83
   4 ?   -3.6   0.0         6   1.8e+04      12      23 ..     187     198 ..     183     204 .. 0.73

  Alignments for each domain:
  == domain 1  score: 7.7 bits;  conditional E-value: 0.0019
      TPR_16   4 araalragdyddAaaaleaalkrdpssPdaaeAllllgdaalrqgrlaeAaalyraal 61 
                 a +al++g+     a+++++ +  p sP+   A  ++ ++++  +++a+Aa   ++++
  AHX11799.1  46 AVSALKQGKLKISKALFRELSDVSPFSPLGEKAKCFYTELLYDGKDFAAAAGSADEYI 103
                 5689999999999**********999999999999999999999******96666654 PP

  == domain 2  score: 7.3 bits;  conditional E-value: 0.0025
      TPR_16   6 aalragdyddAaaaleaalkrdpssPdaaeAllllgdaal.rqgrlaeAaalyra 59 
                 ++++ +d+++Aa  +++++ ++p+  d   +l  +g+a++  + ++a   +++++
  AHX11799.1  85 LLYDGKDFAAAAGSADEYILNYPVGKDLDYMLSIKGNAYFrMLRNFANSTEFLDR 139
                 6899999***************999999999999999998555666666555555 PP

  == domain 3  score: 1.1 bits;  conditional E-value: 0.22
      TPR_16  13 yddAaaaleaalkrdpss 30 
                  d+A   ++++++r+p+s
  AHX11799.1 137 LDRAKDTFKELIRRFPGS 154
                 689999*********655 PP

  == domain 4  score: -3.6 bits;  conditional E-value: 6
      TPR_16  12 dyddAaaaleaa 23 
                 +y +A+ +++++
  AHX11799.1 187 NYHAAISRFTEL 198
                 577777777665 PP

>> LPAM_1  Prokaryotic membrane lipoprotein lipid attachment site
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   2.4   0.00019      0.57       2      18 .]       3      23 ..       1      23 [. 0.85

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00019
      LPAM_1  2 KKi....llalgalllLsGCs 18
                +Ki    ll+l+ ll++sGC+
  AHX11799.1  3 RKIcdflLLLLCSLLVVSGCT 23
                56677779************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (235 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       561  (0.0312901); expected 358.6 (0.02)
Passed bias filter:                      485  (0.0270511); expected 358.6 (0.02)
Passed Vit filter:                        43  (0.00239835); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.46u 0.25s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1694.98
//
Query:       AHX11800.1  [L=422]
Description: phosphoribosylamine--glycine ligase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    7.6e-62  208.5   0.0      1e-61  208.1   0.0    1.2  1  GARS_A           Phosphoribosylglycinamide synthetase, ATP-gr
    1.5e-24   86.5   0.0    2.8e-24   85.7   0.0    1.4  1  GARS_N           Phosphoribosylglycinamide synthetase, N doma
    1.8e-14   53.8   0.0    6.5e-14   52.0   0.0    1.9  2  GARS_C           Phosphoribosylglycinamide synthetase, C doma
    9.7e-07   28.6   0.0      2e-06   27.6   0.0    1.5  1  RimK             RimK-like ATP-grasp domain
    1.6e-06   27.8   0.0      6e-06   25.9   0.0    1.8  2  ATP-grasp        ATP-grasp domain
    1.9e-05   24.8   0.0    3.2e-05   24.0   0.0    1.4  1  ATP-grasp_3      ATP-grasp domain
    0.00038   20.0   0.0    0.00064   19.3   0.0    1.3  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
    0.00043   19.9   0.0    0.00068   19.3   0.0    1.2  1  ATP-grasp_2      ATP-grasp domain
     0.0043   16.6   0.0     0.0069   15.9   0.0    1.3  1  CPSase_L_D2      Carbamoyl-phosphate synthase L chain, ATP bi
  ------ inclusion threshold ------
      0.018   14.7   0.0      0.032   13.8   0.0    1.4  1  ATP-grasp_4      ATP-grasp domain
      0.079   13.8   0.0       0.32   11.8   0.0    1.9  2  GFO_IDH_MocA     Oxidoreductase family, NAD-binding Rossmann 


Domain annotation for each model (and alignments):
>> GARS_A  Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  208.1   0.0   6.3e-65     1e-61       1     194 []     102     293 ..     102     293 .. 0.97

  Alignments for each domain:
  == domain 1  score: 208.1 bits;  conditional E-value: 6.3e-65
                 HBHHHHHHHHHHTT--B--EEEESSHHHHHHHHHHHSSSEEEEEESC-GGGT-EEEESSHHHHHHHHHHHCTS-TTCCCCSSEEEEE---SEEEEEEEE CS
      GARS_A   1 asKsfakdllkkagiptaeyeaftdpeeakeyieeatakalVvKadglaagKgvivakseeealkavkeilekkkfGeagekvviEelleGeEvsllal 99 
                 +sK fak++ +  g pta+y+  ++p+++++ ie+ ++  +V+Ka+gla+gKgv+++ + +eal++ + +l +  fG a++++++Ee+l+GeE+s ++l
  AHX11800.1 102 SSKFFAKEIAEMQGTPTARYAFCSSPNNLRKQIESIGDFPVVIKANGLASGKGVVMCGTMDEALQVGEAML-NGMFGAASKNIIVEEFLQGEELSYFVL 199
                 59**********************************99888***********************9776666.6************************** PP

                 ECTTEEEE---BEEEEEEECCCEEEEECECEEEES-TTS-HHHHHHHHHHTHHHHHHHHHCTT---EEEEEEEEEEETTEEEEEEEESS--TTCH CS
      GARS_A 100 vdgktvkplplaqdhkrvlegDkgpnTGGmGayspapvvteellekikeeileptveglkkegipfkGvLyaglmlvedgpkvlefnvRfgDpet 194
                 vdg+tv p+  a+dhk+v+   k  nTGGmGayspap+ + +++++i  +i+ pt+ +l++ +i +kGvL+aglml+++gpk+le+nvRfgDpet
  AHX11800.1 200 VDGQTVLPIGYARDHKQVTHQGKTYNTGGMGAYSPAPI-STKVEQEILGRIIYPTISALSSINIRYKGVLFAGLMLTNSGPKLLEYNVRFGDPET 293
                 *************************************9.77899**************************************************8 PP

>> GARS_N  Phosphoribosylglycinamide synthetase, N domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   85.7   0.0   1.7e-27   2.8e-24       2      90 .]       5     101 ..       4     101 .. 0.87

  Alignments for each domain:
  == domain 1  score: 85.7 bits;  conditional E-value: 1.7e-27
                 EEEEEESSHHHHHHHHHHTTSTTESEEEEEE--CGG.........TTHHH...HHHHHHHCTESEEEE-SHHHHHTTHHHHHHHHHT-EEES--CCCCH CS
      GARS_N   2 kvLvvGsGGRehalawklaqspkvekvyvapgNagt.........edlea...lvefakeekidlvvvGpeapLvaGvadaleeekgikvfGpskeaAq 88 
                 kvLvvG+GGRehal+ k+++sp + k+y++    +          +   +   l +++k+e+idlvvvG+e  L +G++dal++e g++vfGp+k+aA+
  AHX11800.1   5 KVLVVGNGGREHALISKIKDSPLLGKIYTTNPEFSRfaehikadpT---NhlyLSSICKSEEIDLVVVGQERYLENGITDALTAE-GVAVFGPTKNAAK 99 
                 8***************************986555556755554332...15559****************************777.************* PP

                 HH CS
      GARS_N  89 lE 90 
                 lE
  AHX11800.1 100 LE 101
                 *9 PP

>> GARS_C  Phosphoribosylglycinamide synthetase, C domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.1       6.3     1e+04      24      40 ..     213     228 ..     200     231 .. 0.64
   2 !   52.0   0.0     4e-17   6.5e-14       2      72 ..     329     415 ..     328     416 .. 0.95

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 6.3
                 TTEEEEESSEEEEE-SS CS
      GARS_C  24 egvkvfhagtklvtsGG 40 
                 ++ +v h g  ++ +GG
  AHX11800.1 213 DHKQVTHQGK-TYNTGG 228
                 4456788884.666665 PP

  == domain 2  score: 52.0 bits;  conditional E-value: 4e-17
                 EEEEEEETTTTSS--ST-EEBS..........TTEEEEESSEE......EEE-SSEEEEEEEEESSHHHHHHHHHHHHTTCB-TTEE CS
      GARS_C   2 vgvvlaskGYPgsyekgkeitg..........egvkvfhagtk......lvtsGGRvlavvavgetleeArakayeavkkikfeglf 72 
                 + vvla +GYP +y++g +i+g          +g ++f ag k      ++++GGRvl++v  g++l++ ++ka +a++ i++++ f
  AHX11800.1 329 LSVVLATQGYPVDYKTGYHINGdnlerainavDGLQIFNAGIKydengnMLSNGGRVLNLVVKGSSLNDCKRKAKQAIDIIDWKEGF 415
                 68******************99**********9999*****999999999********************************98765 PP

>> RimK  RimK-like ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.6   0.0   1.2e-09     2e-06       5      86 ..     100     193 ..      96     225 .. 0.77

  Alignments for each domain:
  == domain 1  score: 27.6 bits;  conditional E-value: 1.2e-09
                 HHHHHHHHHTT.....-----EEEESS-S-HHHHHHTT-.-SSEEEEE-TTTT--EEEEE-SHHHHHHHHHH........GGG--EEEEE--SS- CS
        RimK   5 lkslklLakak.....ikvpntalardeedaekliekiklrfPvvvKsvegsqGikvvlakkeqklkqvlea........lkeailvqeyieeae 86 
                 l s k  ak+       ++ + a+  ++++++k ie i+  fPvv+K      G +vv++ + +++ qv ea          ++i+v e+++ +e
  AHX11800.1 100 LESSKFFAKEIaemqgTPTARYAFCSSPNNLRKQIESIG-DFPVVIKANGLASGKGVVMCGTMDEALQVGEAmlngmfgaASKNIIVEEFLQGEE 193
                 555666665543332367777888999***********9.****************************988876667766677779999987544 PP

>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   3.7e-09     6e-06       4      82 ..     114     198 ..     111     243 .. 0.87
   2 ?   -1.4   0.0      0.93   1.5e+03      72     104 ..     321     353 ..     319     360 .. 0.85

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 3.7e-09
                 TT--B-EEEEECCHHHHHHHHHHH.-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHC.......GTTCEEEEE----SEEEEEEE CS
   ATP-grasp   4 lglpvprflaveskeeleeaaeel.glpvvvKarrlgydGkGqsvvrseedleqaleal.......keekvivEefvpfekElsvlv 82 
                  g p++r+++ +s ++l++ +e++ ++pvv+K + +  +GkG  ++   +++ q+ ea+       +++++ivEef +   Els  v
  AHX11800.1 114 QGTPTARYAFCSSPNNLRKQIESIgDFPVVIK-ANGLASGKGVVMCGTMDEALQVGEAMlngmfgaASKNIIVEEFLQ-GEELSYFV 198
                 689*********************779*****.666678****************9999999**9999********97.45777666 PP

  == domain 2  score: -1.4 bits;  conditional E-value: 0.93
                 ---SEEEEEEEEEETTC-EEE--EEEEEEETTE CS
   ATP-grasp  72 vpfekElsvlvvrsaeGetafypvvetvqedgi 104
                 ++f+  +s+ vv +++G  + y++  +++ d+ 
  AHX11800.1 321 ISFSDDVSLSVVLATQGYPVDYKTGYHINGDNL 353
                 899**************9999999888888875 PP

>> ATP-grasp_3  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   24.0   0.0     2e-08   3.2e-05      18     158 ..     126     288 ..     100     291 .. 0.78

  Alignments for each domain:
  == domain 1  score: 24.0 bits;  conditional E-value: 2e-08
                  --....-EESS--SSSEEEEESS-------B--SS--TTE..................EEEE---SEEEEEEEEE.SSSEEEEEEEEEEEET....TE CS
  ATP-grasp_3  18 vPtkleaeeleeeekklvvKprdGaggesvrvveekeeaeaaieeve...........lvqefieGkplSvsllsdgekvlvlavnrqliekaekefv 104
                   P++l+++  +  + ++v+K    a g++v++    +ea +  e +            +v ef++G++lS  +l+dg++vl++   r + + ++++  
   AHX11800.1 126 SPNNLRKQIESIGDFPVVIKANGLASGKGVVMCGTMDEALQVGEAMLngmfgaaskniIVEEFLQGEELSYFVLVDGQTVLPIGYARDHKQVTHQGKT 223
                  578899999999999999*99999999999999999888877776657999999***********************************999999977 PP

                  EE....EEEES----H...HHHHHHHHHHHHTTST....T--EEEEEEEEESS.SEEEEEEESS- CS
  ATP-grasp_3 105 ya....Gnvtpietel...keevvelaeevvekle....glaGyvGvDlvlkdeepyviEvNPRl 158
                  y+    G  +p++ +    +e + +++  ++++l       +G++   l+l++++p ++E N R+
   AHX11800.1 224 YNtggmGAYSPAPISTkveQEILGRIIYPTISALSsiniRYKGVLFAGLMLTNSGPKLLEYNVRF 288
                  74422255555554443335555566667777777321333455555778999999999999998 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   3.9e-07   0.00064      22     139 ..     125     246 ..     109     285 .. 0.79

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 3.9e-07
                      H-H-HHHHHHHHHC-SSEEEEESSSSTTTTEEEESSGGGH....HHHHHHHH.TT-SCEEEEE--ESEEEEEEEEETSSCEEEEEEEEE-SSSS CS
  Dala_Dala_lig_C  22 eekkellekveeelgypvfVKpareGSSvGvskveseeel....keaieeaf.kydekvlvEeaiegreievavlgneklevsevgeivvkkgf 110
                      +++++l +++e+   +pv++K+  + S  Gv  + +++e     +++++  f    ++++vEe+++g+e+   vl  + ++v+++g  + +k++
       AHX11800.1 125 SSPNNLRKQIESIGDFPVVIKANGLASGKGVVMCGTMDEAlqvgEAMLNGMFgAASKNIIVEEFLQGEELSYFVLV-DGQTVLPIGYARDHKQV 217
                      444556677999999******************9988775122223444444346789*****************9.66789999999999999 PP

                      S-HHHHHC.TT-EEESS----HHHHHHHH CS
  Dala_Dala_lig_C 111 ydyeakysddkaqlevpaklekeveekiq 139
                          + y    +    pa ++++ve++i 
       AHX11800.1 218 THQGKTYNTGGMGAYSPAPISTKVEQEIL 246
                      99999997788888889999999998884 PP

>> ATP-grasp_2  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.3   0.0   4.1e-07   0.00068       5      78 ..     105     174 ..     102     205 .. 0.87

  Alignments for each domain:
  == domain 1  score: 19.3 bits;  conditional E-value: 4.1e-07
                  HHHHHHHHCTT----SEEEESSHHHHHHHHHHHTSSSEEEEE--SSSTCCCTTCEEEESSHHHHHHHHHCCTTS CS
  ATP-grasp_2   5 yqakeilakygvkvpegevaesaeeaeeaakklgekelvvKaQvlaGGRGKagGvklvkskeeakeaakellgk 78 
                  + akei +  g ++++ + ++s+++++++++++g+  +v+Ka  la G+    Gv ++ +++ea ++ +++l+ 
   AHX11800.1 105 FFAKEIAEMQGTPTARYAFCSSPNNLRKQIESIGDFPVVIKANGLASGK----GVVMCGTMDEALQVGEAMLNG 174
                  679***************************************9999876....699*************99975 PP

>> CPSase_L_D2  Carbamoyl-phosphate synthase L chain, ATP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.9   0.0   4.3e-06    0.0069      11     105 ..     113     204 ..     103     258 .. 0.76

  Alignments for each domain:
  == domain 1  score: 15.9 bits;  conditional E-value: 4.3e-06
                  HTT-BBSSEECSSBSSHHHHHHHHHHH-.SSEEEEETTCCTTTTEEEESSHHHHHHHHHHHHHHHHHHHSTS-EEEEE--SSSEEEEEEEEEETTS CS
  CPSase_L_D2  11 kinvpvvpssaapvetleealaiakeig.yPviikaafglGGkGmrvarneeelaelvkkalaeakaafgnkqvlvekslkgpkeiEvevlrDakg 105
                    ++p+++ + +  ++ ++  +  ++ig +Pv+ika     GkG  ++ + +e  ++ + a+ + +   ++k++ ve++l+g  e+ + vl D + 
   AHX11800.1 113 MQGTPTARYAFC--SSPNNLRKQIESIGdFPVVIKANGLASGKGVVMCGTMDEALQVGE-AMLNGMFGAASKNIIVEEFLQG-EELSYFVLVDGQT 204
                  445556555555..667777777788877********************9999887655.4445545566899*******98.5888999988775 PP

>> ATP-grasp_4  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0     2e-05     0.032       3      79 ..     140     205 ..     138     227 .. 0.80

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2e-05
  ATP-grasp_4   3 lPvviKPsvgffSlGVykinneeewkaavaaieeeleqakeeykeevveeesflvEeyieGeEfavdayfdeeGepv 79 
                  +PvviK +  ++  GV ++ + +e  ++ +a+ +       ++ +    +++++vEe+++GeE +  +++d  G++v
   AHX11800.1 140 FPVVIKANGLASGKGVVMCGTMDEALQVGEAMLNG------MFGA---ASKNIIVEEFLQGEELSYFVLVD--GQTV 205
                  89****9999999******9999988877776655......4554...5899************9988884..5454 PP

>> GFO_IDH_MocA  Oxidoreductase family, NAD-binding Rossmann fold
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.8   0.0   0.00019      0.32       3      90 ..       6      91 ..       4      92 .. 0.79
   2 ?   -1.3   0.0       2.4   3.8e+03      50      79 ..     106     135 ..      94     136 .. 0.76

  Alignments for each domain:
  == domain 1  score: 11.8 bits;  conditional E-value: 0.00019
                  EEEETTSHHHHHHHHHHHHTTTTEEEEEEECSSHHHHHHHHHHTTHEEESS..HHHHHTCTTESEEEE-S-GGGHHHHHHHHHHTT-EEE CS
  GFO_IDH_MocA  3 vaiiGaGkigskhlrplnesqrleevvalldpdaeraeavaesfgveaysd..leelladpeidavivatpngtheelakaaleagkhvl 90
                  v+++G    g++h+  + + ++   +  ++ +++e   ++ae+ +++  +   l+ + +++eid+v+v+   ++ + ++ a+++ g++v+
    AHX11800.1  6 VLVVGN--GGREHA-LISKIKDSPLLGKIYTTNPE-FSRFAEHIKADPTNHlyLSSICKSEEIDLVVVGQERYLENGITDALTAEGVAVF 91
                  666666..577776.55555455666667777765.5558999999977777799*********************************98 PP

  == domain 2  score: -1.3 bits;  conditional E-value: 2.4
                   EESSHHHHHTCTTESEEEE-S-GGGHHHHH CS
  GFO_IDH_MocA  50 aysdleelladpeidavivatpngtheela 79 
                   + ++++e+   p +++++  +pn++ ++++
    AHX11800.1 106 FAKEIAEMQGTPTARYAFCSSPNNLRKQIE 135
                   45569999999999999999**99998876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (422 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      400  (0.0223102); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.50u 0.26s 00:00:00.76 Elapsed: 00:00:00.42
# Mc/sec: 3032.05
//
Query:       AHX11801.1  [L=285]
Description: hypothetical protein NHE_0882 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (285 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       451  (0.0251548); expected 358.6 (0.02)
Passed bias filter:                      381  (0.0212505); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.44u 0.24s 00:00:00.68 Elapsed: 00:00:00.39
# Mc/sec: 2166.71
//
Query:       AHX11802.1  [L=133]
Description: biopolymer transport ExbD/TolR family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    3.9e-28   98.2   0.4    4.3e-28   98.1   0.4    1.0  1  ExbD      Biopolymer transport protein ExbD/TolR
  ------ inclusion threshold ------
       0.13   12.3   0.0       0.17   11.9   0.0    1.5  1  DUF2487   Protein of unknown function (DUF2487)
        2.1    8.7   5.7        3.8    7.8   5.7    1.5  1  DUF2149   Uncharacterized conserved protein (DUF2149)


Domain annotation for each model (and alignments):
>> ExbD  Biopolymer transport protein ExbD/TolR
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   98.1   0.4   7.2e-32   4.3e-28       5     129 ..       9     130 ..       5     131 .. 0.94

  Alignments for each domain:
  == domain 1  score: 98.1 bits;  conditional E-value: 7.2e-32
        ExbD   5 saeinltpmiDvvflLLifFlvtaklkkpeplevdlPsssstqkeveekelirisisadgsiyldkkavsveelaqklkerkakppdkltvaikadkdv 103
                  +ein+tpm+Dv+++LL++F++ta++ +p  +e+++P ++s++ +  e+ ++ ++i+++gsiy+++ +v++ +l+ k+ ++ +++  +  + i++d ++
  AHX11802.1   9 ISEINVTPMVDVMLVLLVVFMITAPMLVPG-IEINVPIVQSGSVNNLENIEVVLNITKNGSIYINDTQVNLRDLKGKILQKSDDSGIR--LFIRGDRSA 104
                 689***************************.************88888888888888**********************999998765..********* PP

        ExbD 104 sygklvevldtlkkagiekvslvttl 129
                 +y+ +v+vl+ lk+ g+++++lvt++
  AHX11802.1 105 PYERIVKVLAYLKESGFKHIALVTEN 130
                 ***********************985 PP

>> DUF2487  Protein of unknown function (DUF2487)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.9   0.0   2.9e-05      0.17      62      94 ..      99     131 ..      36     133 .] 0.80

  Alignments for each domain:
  == domain 1  score: 11.9 bits;  conditional E-value: 2.9e-05
     DUF2487  62 eeekeeeverlkeweeelkeegfkhvvfitsde 94 
                 + ++++  er+ ++ + lke+gfkh+ ++t ++
  AHX11802.1  99 RGDRSAPYERIVKVLAYLKESGFKHIALVTENR 131
                 4455666789********************876 PP

>> DUF2149  Uncharacterized conserved protein (DUF2149)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.8   5.7   0.00064       3.8       4      25 ..      14      35 ..      12      89 .. 0.69

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.00064
     DUF2149  4 vaNLfDvalVlavallvalvss 25
                v+ ++Dv+lVl v++++++ + 
  AHX11802.1 14 VTPMVDVMLVLLVVFMITAPML 35
                5669*************97654 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (133 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       576  (0.0321267); expected 358.6 (0.02)
Passed bias filter:                      373  (0.0208043); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.41u 0.24s 00:00:00.64 Elapsed: 00:00:00.41
# Mc/sec: 982.49
//
Query:       AHX11803.1  [L=218]
Description: motA/TolQ/ExbB proton channel family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.4e-34  117.0   2.6    4.9e-34  116.8   1.8    1.5  2  MotA_ExbB  MotA/TolQ/ExbB proton channel family


Domain annotation for each model (and alignments):
>> MotA_ExbB  MotA/TolQ/ExbB proton channel family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.2   0.0      0.19   3.4e+03      54      69 ..      49      64 ..      45      88 .. 0.68
   2 !  116.8   1.8   2.7e-38   4.9e-34      21     126 ..      97     202 ..      76     203 .. 0.92

  Alignments for each domain:
  == domain 1  score: -2.2 bits;  conditional E-value: 0.19
                HHHHHHHHHHHHHHHH CS
   MotA_ExbB 54 slaPllGLlGTVlGli 69
                ++a++ G+l T  Gl 
  AHX11803.1 49 KVATFQGILCTTNGLS 64
                5777777777776664 PP

  == domain 2  score: 116.8 bits;  conditional E-value: 2.7e-38
                 HHHHHHHHHHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSGGCTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH CS
   MotA_ExbB  21 gaepeelrraleealsreeerlekglsilatigslaPllGLlGTVlGlieafqaladagsadlakvapgiaeALiaTalGlvvAipavlaynklkrkve 119
                 +  + +l+ ++  ++++  +r ekg  +lat++++aP++GL+GTV+G++++fqa+++ +s +l++vap+i+eAL+aTa+Gl+vAipa+++yn+ ++++ 
  AHX11803.1  97 QGFERKLQTVMSLEIAKISSRFEKGSDFLATTAGVAPFVGLFGTVWGIMRSFQAIGTLNSVALTVVAPSIGEALLATAVGLFVAIPALIFYNYTSARTA 195
                 4556788999999**********************************************99************************************** PP

                 HHHHHHX CS
   MotA_ExbB 120 rlvlele 126
                 +++++le
  AHX11803.1 196 QITQDLE 202
                 ***9988 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (218 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       508  (0.028334); expected 358.6 (0.02)
Passed bias filter:                      267  (0.0148921); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.38u 0.24s 00:00:00.62 Elapsed: 00:00:00.38
# Mc/sec: 1723.67
//
Query:       AHX11804.1  [L=253]
Description: hypothetical protein NHE_0885 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
      5e-09   36.0   9.5    3.2e-06   27.0   0.3    3.7  4  Mito_carr  Mitochondrial carrier protein
  ------ inclusion threshold ------
       0.33   10.5   0.6        2.9    7.4   0.2    2.2  2  ArfA       Alternative ribosome-rescue factor A


Domain annotation for each model (and alignments):
>> Mito_carr  Mitochondrial carrier protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   27.0   0.3   3.6e-10   3.2e-06       9      95 ..      13      89 ..       6      91 .. 0.85
   2 ?   -1.9   0.0      0.36   3.2e+03       5      26 ..      96     117 ..      93     119 .. 0.78
   3 ?    0.4   0.0     0.067     6e+02      69      89 ..     141     161 ..     137     167 .. 0.87
   4 !   12.2   0.4   1.4e-05      0.13       7      85 ..     170     243 ..     164     252 .. 0.79

  Alignments for each domain:
  == domain 1  score: 27.0 bits;  conditional E-value: 3.6e-10
                HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSTTTSCSSHHHHHHHHHHHHHHHGGGTTHHHHHHHHHHHHHHHHHHHHHHHHHHCT CS
   Mito_carr  9 llaGglagavatlvttPldvvKtrlqtqkksskksksaaildvlkkiykeeGlrglyrGllpnllrvapasalkfvlyetlkrlllk 95
                ++ G++a ava++++ Pl ++K+  q  ++s++k        +   ++++eG+++++rG+lp  ++++  s++ f++ e++ + llk
  AHX11804.1 13 VFFGSFA-AVAAVLMSPLQFLKVIKQQTGESYSK--------IATDTFRTEGVAAFFRGALPYAIMNF-LSSMSFGISEVIADNLLK 89
                5566666.46678899********9999999887........6799**********************.899999999999887765 PP

  == domain 2  score: -1.9 bits;  conditional E-value: 0.36
                 HHHHHHHHHHHHHHHHHHHHHH CS
   Mito_carr   5 vlkellaGglagavatlvttPl 26 
                 +++ ++ ++++g+++tl+  P 
  AHX11804.1  96 LFAVFFRSVFGGCCETLCSLPS 117
                 6777888899999999999886 PP

  == domain 3  score: 0.4 bits;  conditional E-value: 0.067
                 HHHHHHHHHHHHHHHHHHHHH CS
   Mito_carr  69 lpnllrvapasalkfvlyetl 89 
                 lp l+r+++ +++ +++ye  
  AHX11804.1 141 LPILFRNMIFWSASVTSYEIS 161
                 6889**************975 PP

  == domain 4  score: 12.2 bits;  conditional E-value: 1.4e-05
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSTTTSCSSHHHHHHHHHH.HHHHHGGGTTHHHHHHHHHHHHHHHHHH CS
   Mito_carr   7 kellaGglagavatlvttPldvvKtrlqtqkksskksksaaildvlkkiyk.eeGlrglyrGllpnllrvapasalkfvl 85 
                  + ++G   g++a+++  Pldvv tr   + ++        i+  l  i+  ee +  l rG ++++++va  + +++++
  AHX11804.1 170 CTTFTGFSFGVLAAFLSIPLDVVATRDCGALTNRG------IFGHLTAILSgEERINYLLRGTSIRIVQVAMFTLVTVLT 243
                 567899999*****************666655544......66666666655999999*********9999888877665 PP

>> ArfA  Alternative ribosome-rescue factor A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.5   0.0     0.046   4.2e+02      13      33 ..      20      40 ..      19      44 .. 0.84
   2 ?    7.4   0.2   0.00032       2.9       8      23 ..      82      97 ..      82      99 .. 0.93

  Alignments for each domain:
  == domain 1  score: 0.5 bits;  conditional E-value: 0.046
        ArfA 13 alkAlvtskLFrqrvekakKG 33
                a++A++ s+L   +v k++ G
  AHX11804.1 20 AVAAVLMSPLQFLKVIKQQTG 40
                899*******88888887655 PP

  == domain 2  score: 7.4 bits;  conditional E-value: 0.00032
        ArfA  8 kIkDNalkAlvtskLF 23
                +I DN lk  v+s LF
  AHX11804.1 82 VIADNLLKFFVHSTLF 97
                599************* PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (253 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       638  (0.0355848); expected 358.6 (0.02)
Passed bias filter:                      277  (0.0154498); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.39u 0.23s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 2065.63
//
Query:       AHX11805.1  [L=247]
Description: hypothetical protein NHE_0886 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0024   17.8   2.6       0.13   12.2   0.0    3.0  4  Mito_carr  Mitochondrial carrier protein


Domain annotation for each model (and alignments):
>> Mito_carr  Mitochondrial carrier protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   12.2   0.0   7.2e-06      0.13       7      90 ..       8      82 ..       4      86 .. 0.79
   2 ?   -3.7   0.0      0.67   1.2e+04      12      23 ..     100     111 ..      97     114 .. 0.65
   3 ?   -1.8   0.0      0.16   2.9e+03      69      92 ..     138     161 ..     137     166 .. 0.82
   4 !    4.5   0.2    0.0018        33       7      83 ..     167     236 ..     161     245 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.2e-06
                HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSTTTSCSSHHHHHHHHHHHHHHHGGGTTHHHHHHHHHHHHHHHHHHHHHHH CS
   Mito_carr  7 kellaGglagavatlvttPldvvKtrlqtqkksskksksaaildvlkkiykeeGlrglyrGllpnllrvapasalkfvlyetlk 90
                + l+ ++la+ v ++++ P+ +vK+  q  ++s+++     i+    + y+++ lr ++ G+ p +++++  s l f+l +++ 
  AHX11805.1  8 APLVYAALAAFV-AFFVSPVQYVKVVRQDTARSYSS-----IF--RETWYRDDCLRIFFGGAAPYVVMNF-LSNLSFGLSDMVS 82
                556777777776.7999***********99999887.....44..3455689999***************.6667888877765 PP

  == domain 2  score: -3.7 bits;  conditional E-value: 0.67
                 HHHHHHHHHHHH CS
   Mito_carr  12 Gglagavatlvt 23 
                 ++l+ga++tl+t
  AHX11805.1 100 ALLGGAIETLMT 111
                 566777777765 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 0.16
                 HHHHHHHHHHHHHHHHHHHHHHHH CS
   Mito_carr  69 lpnllrvapasalkfvlyetlkrl 92 
                  p++lr+++a+    ++ye   r+
  AHX11805.1 138 FPSFLRNSVAWLGSTSAYEISTRF 161
                 589999999999999999987765 PP

  == domain 4  score: 4.5 bits;  conditional E-value: 0.0018
                 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCSSTTTSCSSHHHHHHHHHHHHHHHGGGTTHHHHHHHHHHHHHHHH CS
   Mito_carr   7 kellaGglagavatlvttPldvvKtrlqtqkksskksksaaildvlkkiykeeGlrglyrGllpnllrvapasalkf 83 
                  ++l +++ g++ ++v  P+dv+ t+  +++++ +      +l+ + +i+++   + +  G ++++l++++ +a+++
  AHX11805.1 167 VSILLSVCMGLIFAIVSIPFDVLVTQSCAAREELT------LLNRVLRIMRDSKNK-FLLGSVIRVLQIVIFTAVTV 236
                 56788999999************999888887755......566666666666554.34466666666666666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (247 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       690  (0.0384851); expected 358.6 (0.02)
Passed bias filter:                      368  (0.0205254); expected 358.6 (0.02)
Passed Vit filter:                        28  (0.00156172); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.45u 0.24s 00:00:00.69 Elapsed: 00:00:00.41
# Mc/sec: 1823.73
//
Query:       AHX11806.1  [L=87]
Description: ribosomal L36 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    4.7e-10   39.5   4.4    4.7e-10   39.5   4.4    1.4  2  Ribosomal_L36  Ribosomal protein L36


Domain annotation for each model (and alignments):
>> Ribosomal_L36  Ribosomal protein L36
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.9   0.1      0.47   8.4e+03       1       5 [.       1       5 [.       1       7 [. 0.75
   2 !   39.5   4.4   2.6e-14   4.7e-10       1      38 []      44      85 ..      44      85 .. 0.99

  Alignments for each domain:
  == domain 1  score: -2.9 bits;  conditional E-value: 0.47
  Ribosomal_L36 1 MKVrs 5
                  MKV  
     AHX11806.1 1 MKVSK 5
                  99976 PP

  == domain 2  score: 39.5 bits;  conditional E-value: 2.6e-14
  Ribosomal_L36  1 MKVrssvkkmc....egCkvvrRkgrvyviCkknPrhKqRQG 38
                   MKV +s+k+ +    ++++v +R +rvyv+++ nPr++ RQG
     AHX11806.1 44 MKVIGSLKSAKkrdaRNSYVAKRGKRVYVYNRRNPRCNVRQG 85
                   *****************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       355  (0.0198003); expected 358.6 (0.02)
Passed bias filter:                      275  (0.0153383); expected 358.6 (0.02)
Passed Vit filter:                        20  (0.00111551); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.35u 0.25s 00:00:00.60 Elapsed: 00:00:00.40
# Mc/sec: 657.90
//
Query:       AHX11807.1  [L=306]
Description: dihydrodipicolinate synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-67  227.2   0.1    1.9e-67  227.0   0.1    1.0  1  DHDPS     Dihydrodipicolinate synthetase family


Domain annotation for each model (and alignments):
>> DHDPS  Dihydrodipicolinate synthetase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  227.0   0.1   1.1e-71   1.9e-67       2     288 ..       7     291 ..       6     292 .. 0.98

  Alignments for each domain:
  == domain 1  score: 227.0 bits;  conditional E-value: 1.1e-71
                 -SEEEEE----B-TTSSB-HHHHHHHHHHHHHCT-SEEEESSCCCTGGGS-HHHHHHHHHHHHHHHTTSSEEEEE---SSHHHHHHHHHCCCCCT-SEE CS
       DHDPS   2 fsgiitalvtpfdedgkldkealrklieflinkgvdglvvaGttGEsatlsteekeqlveiaveaakgripviagvGsnstseaiklakkaeeaGadgv 100
                 f+g++ta+vtpf+++ ++d e  r l+e +i +g+ g+vvaG+tGEs++ls++e+ +l+  av+++k+r+p+i gv   +ts  i+   + +e  + + 
  AHX11807.1   7 FEGVFTAVVTPFKRE-QVDYEGFRILVESQIGNGIHGIVVAGSTGESQLLSHSEYLALIDCAVDVVKERVPLIVGVPHCATSKVIEEIVSLKERSVSAF 104
                 89**********987.6********************************************************************************** PP

                 EEE---SS---HHHHHHHHHHHHHCHSS-EEEEE-HHHHSHHHHHHHHHHHHTSTTEEEEEE-SS-CTHHHHHHCCCSTTSEEEES-GGGHHHHHHTT- CS
       DHDPS 101 lavtPYYnkpsqeglyqhfkaiieatdlpvilYnvpsrtgadlspetvkrLaelenivgvKeavgdleevikikkevgkdlviysGddelllsalslGa 199
                 l+ tPYY+ p+qeg+ +h++ai e+t  ++i+Yn+p r g++++  t+ r++ l+ +v++K+a+g+l e   i k +++++ i+ G d   ++    G+
  AHX11807.1 105 LISTPYYVLPQQEGIFEHYRAITEKTKANIIVYNIPHRCGVNIENSTMLRIMDLPGVVAIKDASGNL-ECPTILKAANERVPILMGNDTQYAAHRLHGG 202
                 *******************************************************************.888999999********************** PP

                 SEEEESCHHCHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHCCCCSCCHHHHHHHHCTTSSSBB.--TTS--S-HHHHHHHHHHHHH CS
       DHDPS 200 dGvisvtsniagermrqlikalkeGdlaeaaelnekllplikilfaepnvilvktalellGlvveatlrkPltpleeeekeeleallka 288
                 dGvis+ sn+++ +m +l +a++ G+ +  ++l++ + pl k +f e+n+ ++k+al ++    ++ +r+Pl++++++ k +++++l++
  AHX11807.1 203 DGVISAVSNLIPSEMLALENAIRSGQYERMKALHKAIFPLAKSIFCETNPGPLKYALSCVNKCITHNVRHPLVNASDSTKRTIQNALEE 291
                 **************************************************************99999***************9999875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (306 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       578  (0.0322383); expected 358.6 (0.02)
Passed bias filter:                      527  (0.0293937); expected 358.6 (0.02)
Passed Vit filter:                        34  (0.00189637); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.48u 0.22s 00:00:00.70 Elapsed: 00:00:00.39
# Mc/sec: 2336.15
//
Query:       AHX11808.1  [L=173]
Description: prokaryotic cytochrome b561 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    8.4e-24   84.2  11.0    1.2e-23   83.7  11.0    1.2  1  Ni_hydr_CYTB  Prokaryotic cytochrome b561
    8.1e-05   23.1   2.7    8.1e-05   23.1   2.7    2.5  2  DUF4405       Domain of unknown function (DUF4405)


Domain annotation for each model (and alignments):
>> Ni_hydr_CYTB  Prokaryotic cytochrome b561
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   83.7  11.0   1.3e-27   1.2e-23       1     180 [.       6     173 .]       6     173 .] 0.89

  Alignments for each domain:
  == domain 1  score: 83.7 bits;  conditional E-value: 1.3e-27
                   -----TTHHHHHHHHHHHHHHHHHHHHHS------S-GGG-HHHHHHHHHHHHHHHHHHHHHHH------------STTTSSSSS------------ CS
  Ni_hydr_CYTB   1 ryslvarllHWlnallvvllllsgllianlhprlywgdsgkaralHklaGlvllalllfrllwlkkakkpspriifrqikrdltlllrgrkpeagkn 97 
                   +ys+ +r++HW++ ++++++++ g+l+++   ++    +  +++ Hk +G+++ +l+++r++++                      l  + p  +  
    AHX11808.1   6 KYSISMRVMHWVLGFAIIAMIVVGFLMTHYMVPPVKF-A--VYNQHKAIGITIGVLMIVRIFVR----------------------LFSKLPGDQFS 77 
                   599**********************998877775533.3..39*********************......................66666666666 PP

                   ----TT...THHHHHHHHHHHHHHHHHHHTHHHHHHHH............HTS-THHHHHHH.HHHHHHHHHHHHHHHHHHHHHH---X.XXXXXX CS
  Ni_hydr_CYTB  98 nplqkl...vhlllyvllvvliltGlllsfaatagfpll.........lddkggaqlarelHellaaallafvvlHiaaallhgpvkkd.tlrrMi 180
                    +   +   +h+llyv ++ ++++G+++s+++ + ++++           d  +a +a+ +H++l++ l +++vlHi+aa+ h  ++k+ ++++Mi
    AHX11808.1  78 KIESIAmqaAHVLLYVTTIGAVISGYVMSYSSGREVSWFncfrlpaliPVDPYIAGSAHKMHQVLVYSLGCLIVLHIFAAIKHLCIDKKnIFKKMI 173
                   6666666689*******************988888888899999999999*********************************************7 PP

>> DUF4405  Domain of unknown function (DUF4405)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    3.4   7.2     0.013   1.2e+02       3      60 ..      15      61 ..      13      65 .. 0.80
   2 !   23.1   2.7     9e-09   8.1e-05       4      63 ..      89     155 ..      86     158 .. 0.84

  Alignments for each domain:
  == domain 1  score: 3.4 bits;  conditional E-value: 0.013
     DUF4405  3 dlllllsflvlaiSGillsfavlpsgrgaywaflglskhqwrdiHeilgllflilvvl 60
                 ++l ++++++++ G+l+     p++           k  + + H+ +g+   +l+++
  AHX11808.1 15 HWVLGFAIIAMIVVGFLMTHYMVPPV-----------KFAVYNQHKAIGITIGVLMIV 61
                5789999***********99988844...........445888888888888888876 PP

  == domain 2  score: 23.1 bits;  conditional E-value: 9e-09
     DUF4405   4 lllllsflvlaiSGillsfavlpsgrgaywa.......flgl...skhqwrdiHeilgllflilvvlHlg 63 
                 +ll ++ ++++iSG ++s++   sgr + w        ++++     + ++++H +l + + +l+vlH++
  AHX11808.1  89 VLLYVTTIGAVISGYVMSYS---SGREVSWFncfrlpaLIPVdpyIAGSAHKMHQVLVYSLGCLIVLHIF 155
                 799***************76...66666666698888844447778999*******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (173 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       806  (0.0449551); expected 358.6 (0.02)
Passed bias filter:                      290  (0.0161749); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.37
# Mc/sec: 1403.53
//
Query:       AHX11809.1  [L=328]
Description: aminotransferase class IV family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-36  126.5   0.0    1.8e-36  126.1   0.0    1.2  1  Aminotran_4  Amino-transferase class IV


Domain annotation for each model (and alignments):
>> Aminotran_4  Amino-transferase class IV
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  126.1   0.0     1e-40   1.8e-36       2     222 ..      50     276 ..      49     277 .. 0.88

  Alignments for each domain:
  == domain 1  score: 126.1 bits;  conditional E-value: 1e-40
  Aminotran_4   2 lfEtmrvyngeiffldeHleRLrksa.ell.glelpfdeeelrkileelleannsen.grlrllvsrgggglg...aatsepsvavyvsalppgpese 93 
                  ++E+  v +g ++ +d H++RLr s+ ++  +l++ f+++el +i++ ll  n+ ++  +l + +srg ++++    +++ p+v+v+++ +  +p  +
   AHX11809.1  50 IYEVTPVIHGVPIDFDLHIARLRDSCeKISiELPWIFYTDELGQIVNRLLSLNGAKKdYKLYIQISRGVAERNhilHEKVRPTVLVMLQQFVRPPRIQ 147
                  79************************5555777888*********************888**************966666666666666665555555 PP

  Aminotran_4  94 kelplvtssdvrrdapsplpgaKtlnyldnvlarreakergadevllvdedgn...vtEgstsNv.fivkggelitPplssgiLpGitrrallelaka 187
                    ++ +       d ++  +++K++++l nvla++ a  +ga e++l+d++ +   vtEgs++N+ +++k +++it p+ s+iL G+tr +++++a a
   AHX11809.1 148 EGMAGF----LVEDCRWAYRDIKSTSILANVLAKKAAFDAGASEAILYDTKPEgkiVTEGSSCNIfIVDKRNRVITHPVNSSILSGVTRHRVIQIAIA 241
                  554444....445777777999***************************998888**********66678**************************** PP

  Aminotran_4 188 lgleveereitlkdleeadeafltntlrgvlpvrs 222
                  ++l+v e+ +t+++l +a e+f t +   ++ +++
   AHX11809.1 242 ENLQVCEQVFTIEELLDANEVFATASGIFIRGIHK 276
                  **************************999999887 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (328 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       488  (0.0272185); expected 358.6 (0.02)
Passed bias filter:                      414  (0.0230911); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.43u 0.25s 00:00:00.68 Elapsed: 00:00:00.40
# Mc/sec: 2482.01
//
Query:       AHX11810.1  [L=188]
Description: HAD hydrolase, IA, variant 1 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.3e-21   77.4   0.0    1.5e-21   77.3   0.0    1.1  1  HAD_2        Haloacid dehalogenase-like hydrolase
    1.4e-07   32.0   0.0    1.8e-07   31.6   0.0    1.3  1  Hydrolase    haloacid dehalogenase-like hydrolase
    1.4e-06   28.9   0.0    1.7e-06   28.6   0.0    1.1  1  HAD          haloacid dehalogenase-like hydrolase
  ------ inclusion threshold ------
       0.17   12.0   0.0       0.41   10.8   0.0    1.6  1  Hydrolase_6  Haloacid dehalogenase-like hydrolase


Domain annotation for each model (and alignments):
>> HAD_2  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   77.3   0.0   3.4e-25   1.5e-21      21     174 ..       7     159 ..       1     163 [. 0.76

  Alignments for each domain:
  == domain 1  score: 77.3 bits;  conditional E-value: 3.4e-25
       HAD_2  21 nelleeyglselseeelrkliglslrellrklgeseeeee..kieellrkyneekkkkevkpydgvkelLeeLkeagyklgivTsksreaveekleqlg 117
                 n++l++ +   + e+++++       e +++++  ++e     ++ +lr+   +   + +++++g  elL++++e+g+  giv++ks e +++++e+lg
  AHX11810.1   7 NKALKQLNK-PIVEDYINTA---GRAEFFKQSFGGDWEYAneVFNNYLRHESIQSI-QDIRIFPGFVELLDYINENGIFTGIVSNKSGELLRKEIEALG 100
                 555544422.3333333332...223456666665553323455555444333333.58**************************************** PP

       HAD_2 118 iesyFdvivtsedvekkKPdpeviekaleklklkkee..viyvGDsptDieaakkagik 174
                 +++ Fdv v+s d+ + KP++++++ al   +++++e  v ++GDs+ D+e+ak+a ++
  AHX11810.1 101 LTNNFDVAVGSGDTDQDKPSAKPLLYALSGSGISPSEndVTFIGDSIIDMECAKNASVR 159
                 ********************************99875559****************987 PP

>> Hydrolase  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   31.6   0.0   4.1e-11   1.8e-07     108     209 ..      53     156 ..       3     157 .. 0.85

  Alignments for each domain:
  == domain 1  score: 31.6 bits;  conditional E-value: 4.1e-11
                 HHHHHHHHTHHBHTTHHHHHHHHHHTTEEEEEEESSEHHHHHHHHHHTT.GGGESEEEEHHCESSTTTSHHHHHHHHHHHTST..GGGEEEEESSHHHH CS
                 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx..xxxxxxxxxxxxxx RF
   Hydrolase 108 lavftiadplkvkpeaaeavasLkaagievvlltgdnpetaeraanqlG.ddyfdaviasdietvakpspegkvaaireLqgk..peevamVGDgvnDa 203
                   +  i+d  +++p+ +e++ +++++gi ++++++ + e  ++ ++ lG  + fd+ ++s ++   kps + +++a+   +++   ++v ++GD++ D+
  AHX11810.1  53 ESIQSIQDI-RIFPGFVELLDYINENGIFTGIVSNKSGELLRKEIEALGlTNNFDVAVGSGDTDQDKPSAKPLLYALSGSGISpsENDVTFIGDSIIDM 150
                 444455555.89*********************************************************************6633677*********** PP

                 HHHHHT CS
                 xxxxxx RF
   Hydrolase 204 aalaaA 209
                 + +++A
  AHX11810.1 151 ECAKNA 156
                 **9998 PP

>> HAD  haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.6   0.0   3.8e-10   1.7e-06      52     188 .]      25     154 ..       4     154 .. 0.70

  Alignments for each domain:
  == domain 1  score: 28.6 bits;  conditional E-value: 3.8e-10
         HAD  52 aglaelleallaglseelaaelerfv.....aevirpklldpgalellaahraaGdrvvvvSgglrplvepllaelgadevlatelevddrltgelgle 145
                 ag+ae++   ++g  e+ ++ ++ ++     ++++  +++ pg++ell+   ++G+ + +vS+   +l++   ++lg    l +       ++      
  AHX11810.1  25 AGRAEFFKQSFGGDWEYANEVFNNYLrhesiQSIQDIRIF-PGFVELLDYINENGIFTGIVSNKSGELLRKEIEALG----LTN------NFDVA---V 109
                 4455666666666666666666666654445555555578.*******9999*************************....999......55555...3 PP

         HAD 146 gkpvrgegkvaalrewlaaegegidlee..vvayGDspsDlpllr 188
                 g+   +++k++a    +a  g gi+++e  v ++GDs+ D+++++
  AHX11810.1 110 GSGDTDQDKPSAKPLLYALSGSGISPSEndVTFIGDSIIDMECAK 154
                 344444445555555555566666666666*************96 PP

>> Hydrolase_6  Haloacid dehalogenase-like hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.0   9.3e-05      0.41      13      56 ..      61     101 ..      58     124 .. 0.80

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 9.3e-05
                  TEE-TTHHHHHHHHHHTT-EEEEEE---SS-HHHHHHHHHHTT- CS
  Hydrolase_6  13 dkaipgaaealnalraagkpvvllTNnsskseeeyakkleklgv 56 
                   +++pg +e+l++++++g+ + +++N+s++  ++ +   e+lg+
   AHX11810.1  61 IRIFPGFVELLDYINENGIFTGIVSNKSGELLRKEI---EALGL 101
                  5789***********************998855444...44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (188 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       429  (0.0239277); expected 358.6 (0.02)
Passed bias filter:                      410  (0.022868); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.40u 0.23s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1508.88
//
Query:       AHX11811.1  [L=256]
Description: uracil-DNA glycosylase, 4 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    4.6e-46  156.6   0.0    6.2e-46  156.2   0.0    1.2  1  UDG       Uracil DNA glycosylase superfamily


Domain annotation for each model (and alignments):
>> UDG  Uracil DNA glycosylase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.2   0.0   3.5e-50   6.2e-46       3     155 .]      95     245 ..      93     245 .. 0.97

  Alignments for each domain:
  == domain 1  score: 156.2 bits;  conditional E-value: 3.5e-50
                 C-CTT-SEEEEESSTCHHHHHHSSSS.-STT--HHHHHHHCCCCCCCHHGCTEEEEESSS....SECGCTTCCCCTCCHHHHHHHHHHHHSSEEEEESH CS
         UDG   3 egppdakvvivGeaPgaeedatglpFsgragnllrkllneaglkrdleseqgvyitnvvkcrppgnrdtptsaeikacaplleeeiellkprlivllGk 101
                  g+pd+ ++++GeaPg++ed+ g+pF gr+gnll+k+l+++ l+r     ++vyitn++++rppgnr  p ++ei+ac+p+le++i+l++p+livllG 
  AHX11811.1  95 DGNPDSGIMLIGEAPGEQEDKLGIPFRGRSGNLLDKMLQAIDLDR-----KKVYITNTIFWRPPGNR-RPLPEEIEACRPFLEHHIRLVSPKLIVLLGS 187
                 599******************************************.....*****************.******************************* PP

                 HHHHH....HHHHSCESCCCSCT........SEEEEES-SSTTTTTTTTSHHHHHHHHHHHHH CS
         UDG 102 taakall..geklgklrgklleak.......irvlplphPsplnrnffksnpelkaeawedLk 155
                 taa+++l  + ++++ r+++++ k       i+ ++++hPs+l+r+     p++k+ awedLk
  AHX11811.1 188 TAASSVLnsQDRVSQMRNRFHQYKndfikeaITTMVTFHPSYLLRQ-----PAQKRLAWEDLK 245
                 ******998779***********77888899***************.....**********97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (256 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       510  (0.0284455); expected 358.6 (0.02)
Passed bias filter:                      490  (0.02733); expected 358.6 (0.02)
Passed Vit filter:                        27  (0.00150594); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.40u 0.22s 00:00:00.62 Elapsed: 00:00:00.35
# Mc/sec: 2160.74
//
Query:       AHX11812.1  [L=254]
Description: vacJ like lipofamily protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.4e-47  162.0   0.0    1.9e-47  161.5   0.0    1.2  1  MlaA      MlaA lipoprotein


Domain annotation for each model (and alignments):
>> MlaA  MlaA lipoprotein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  161.5   0.0     1e-51   1.9e-47       1     191 [.      52     251 ..      52     254 .] 0.94

  Alignments for each domain:
  == domain 1  score: 161.5 bits;  conditional E-value: 1e-51
        MlaA   1 vkDplegfNRavfkfNdkldkyvlkPvakgYrkvvPep...........vrtgvsnffsNlsepvsvvnnlLqgkfkkavkelgRfliNttlGlgGlfD 88 
                 v+DplegfNR++fk+N  l   + ++++k+  kv+ +            v++++ n+++Nlsep+ ++n+lLqg+++++v+el+Rf+iN+tlG++G+fD
  AHX11812.1  52 VYDPLEGFNRKMFKINCSLIAKLQQSANKKLFKVTSRSrpfdnkstvkpVKQALFNIMDNLSEPSMAINHLLQGHPENSVRELWRFFINSTLGIFGTFD 150
                 58***************************99999998888999999999************************************************** PP

        MlaA  89 vasklglekkkedfgqTLgvwgvgeGpYlvlPllGpstlRdavglvvdilldpvlsaeeaevslaltaleavdkraklldaeklleeasldpYafvRda 187
                 +a ++glek+  ++ qTL+ +g+++Gp+l++PllG+++lR++++++++il++p   +     +  + ++ + dk a+ ++  +++ e+ +dpYa +R++
  AHX11812.1 151 IAGTIGLEKRPSSYKQTLALYGIKSGPFLIVPLLGATSLRNSFAAILEILTNPL--NLLVPNRSIIFIMYNCDKIARGIKYRSIVFENNIDPYAKLRTL 247
                 *****************************************************4..245566788899999********9999999***********99 PP

        MlaA 188 ylqr 191
                  ++ 
  AHX11812.1 248 SINA 251
                 8875 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (254 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       496  (0.0276647); expected 358.6 (0.02)
Passed bias filter:                      426  (0.0237604); expected 358.6 (0.02)
Passed Vit filter:                        23  (0.00128284); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.41u 0.26s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1872.90
//
Query:       AHX11813.1  [L=176]
Description: toluene tolerance, Ttg2 family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model       Description
    ------- ------ -----    ------- ------ -----   ---- --  --------    -----------
    1.6e-18   67.0   0.4      2e-18   66.7   0.4    1.0  1  MlaC         MlaC protein
     0.0018   18.2   0.2     0.0018   18.2   0.2    1.7  2  Tox-MPTase4  Metallopeptidase toxin 4


Domain annotation for each model (and alignments):
>> MlaC  MlaC protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.7   0.4   2.2e-22     2e-18      23     159 ..      31     168 ..      17     174 .. 0.87

  Alignments for each domain:
  == domain 1  score: 66.7 bits;  conditional E-value: 2.2e-22
                 HHHHHHHHHHTGGGB-HHHHHHHHHCCHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS-EEEE----S-TTTSSEEEEEEEEEETT.S..EEEEEE CS
        MlaC  23 eelrekveellepyfdfermarlvlGkywrkatpeqrqrfveaFrellvrtYasalaeysgqkievkperpspkgkkdvvVkteiiqag.g..kpikvd 118
                 +++ ek+  l+++++df+ + ++vlG++++ ++pe+ q f++ +++++ ++Ya+ l+    ++++ + +++ +k  +++ V+t ++++g +  + +k++
  AHX11813.1  31 SKKLEKMGALMKENIDFQTVVKFVLGNKIKLLSPEEVQSFTKYYEDTVSKKYAKLLTTE-LKSYKATRQEDLSK--ERYLVHTILEKDGsSagSTLKIA 126
                 678899999********************************************977765.57777777777764..58*******9998646577**** PP

                 EEEEEETTEEEEEEEEETT.EEHHHHHHHHHHHHHHHHCHHH CS
        MlaC 119 YrlrkkggewkiyDviieG.vslvatyrsqfasilrqkgidg 159
                 Y +  k++++ki+D ii+G +s++ + r+++a+ l+++ + +
  AHX11813.1 127 YLIIGKNSDYKIIDAIISGgISMAMADREEIATFLERNTLRQ 168
                 *****************988****************998765 PP

>> Tox-MPTase4  Metallopeptidase toxin 4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.2   0.2     2e-07    0.0018      34     100 ..      49     115 ..      26     124 .. 0.90
   2 ?   -3.2   0.1      0.82   7.4e+03      18      31 ..     160     173 ..     151     175 .. 0.68

  Alignments for each domain:
  == domain 1  score: 18.2 bits;  conditional E-value: 2e-07
  Tox-MPTase4  34 lgikvviDkkdkilpenkaagfdpetgeivlrkepsllsalhesvhaeqwlelGkenYlkqsvlere 100
                  + +k v+ +k k+l  +  ++f  + ++ v +k + ll     s+ a +  +l ke Yl  + le++
   AHX11813.1  49 TVVKFVLGNKIKLLSPEEVQSFTKYYEDTVSKKYAKLLTTELKSYKATRQEDLSKERYLVHTILEKD 115
                  34789999******999999********************************************986 PP

  == domain 2  score: -3.2 bits;  conditional E-value: 0.82
  Tox-MPTase4  18 lmsvkdlkafkkel 31 
                  +++++ l++fkk++
   AHX11813.1 160 FLERNTLRQFKKKF 173
                  45666778888765 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (176 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       759  (0.0423336); expected 358.6 (0.02)
Passed bias filter:                      392  (0.021864); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.37u 0.24s 00:00:00.61 Elapsed: 00:00:00.37
# Mc/sec: 1425.11
//
Query:       AHX11814.1  [L=45]
Description: hypothetical protein NHE_0895 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.9e-11   41.9   0.2    8.1e-11   41.6   0.2    1.1  1  DUF2610   Domain of unknown function (DUF2610)


Domain annotation for each model (and alignments):
>> DUF2610  Domain of unknown function (DUF2610)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.2   4.5e-15   8.1e-11      51      80 ..       1      30 [.       1      31 [. 0.96

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 4.5e-15
     DUF2610 51 veslskLfklakennvsfeeLivyaLenAe 80
                ++slskL++la+ennvsfe+L+vyaL+ Ae
  AHX11814.1  1 MDSLSKLRELAEENNVSFEDLCVYALKIAE 30
                79*************************986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (45 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       506  (0.0282224); expected 358.6 (0.02)
Passed bias filter:                      305  (0.0170115); expected 358.6 (0.02)
Passed Vit filter:                        22  (0.00122706); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.32u 0.21s 00:00:00.53 Elapsed: 00:00:00.34
# Mc/sec: 395.05
//
Query:       AHX11815.1  [L=492]
Description: type I secretion membrane fusion, HlyD family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    4.7e-12   46.6   0.7    7.9e-08   33.0   0.0    3.8  3  HlyD_3           HlyD family secretion protein
    1.1e-09   38.0   1.1    4.6e-08   32.8   0.2    2.7  2  Biotin_lipoyl_2  Biotin-lipoyl like
    3.6e-06   26.4   1.7      0.019   14.2   0.1    2.5  2  HlyD_D23         Barrel-sandwich domain of CusB or HlyD membr
    4.6e-05   23.2   0.2     0.0034   17.2   0.1    2.6  2  Biotin_lipoyl    Biotin-requiring enzyme
    0.00013   21.8   0.0    0.00033   20.5   0.0    1.7  1  HlyD             HlyD membrane-fusion protein of T1SS
     0.0057   16.6   0.5        5.1    7.1   0.0    2.5  2  RnfC_N           RnfC Barrel sandwich hybrid domain
  ------ inclusion threshold ------
      0.049   13.6   2.5       0.36   10.8   0.2    2.9  3  ApoO             Apolipoprotein O
      0.097   12.9   0.3        4.6    7.5   0.0    2.6  2  Peptidase_M23    Peptidase family M23
        0.4   11.4   7.3        1.1    9.9   6.4    2.1  1  AATF-Che1        Apoptosis antagonizing transcription factor
        1.3    9.2   9.5        1.9    8.7   6.7    2.2  2  Fib_alpha        Fibrinogen alpha/beta chain family
        6.2    6.9   8.6        1.1    9.4   1.1    2.7  3  Cob_adeno_trans  Cobalamin adenosyltransferase


Domain annotation for each model (and alignments):
>> HlyD_3  HlyD family secretion protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.8   0.0    0.0033       5.4       8      50 ..     104     145 ..     101     159 .. 0.81
   2 ?   -3.3   0.0         9   1.5e+04       4      14 ..     260     270 ..     252     295 .. 0.63
   3 !   33.0   0.0   4.8e-11   7.9e-08       1     105 [.     327     458 ..     327     459 .. 0.72

  Alignments for each domain:
  == domain 1  score: 7.8 bits;  conditional E-value: 0.0033
      HlyD_3   8 Gvvvelnveegevvqagdelleiippdtllveakvpaadlgsi 50 
                 G+++e+ v eg+ v++g+ l ++ + ++ ++++++ +++ +s+
  AHX11815.1 104 GIIKEILVHEGDHVEEGQILITLNNVNN-KAQLAILEENQASL 145
                 999********************97555.77777777776665 PP

  == domain 2  score: -3.3 bits;  conditional E-value: 9
      HlyD_3   4 ApvdGvvveln 14 
                 A+ dG+++e +
  AHX11815.1 260 ASLDGKINEYK 270
                 56666666543 PP

  == domain 3  score: 33.0 bits;  conditional E-value: 4.8e-11
      HlyD_3   1 tlrApvdGvvvelnv.eegevvqagdelleiipp.dtllveakvpaadlgsik................kkgqkvtlkldqgsdy.tlkgkierisp.. 78 
                 t+rAp +G+v+ l+  + g v+++g+ l+eiip+ +++ +e+kv + ++  i+                +++ kv+l++ ++++   l+g  +++s+  
  AHX11815.1 327 TIRAPQSGTVTGLKSlSIGGVIAPGTLLMEIIPEnEDMFIEVKVMPNNIEAIAsakfiekhvvnidglsGIKTKVRLTAFNSKKVgMLDGVMTYVSAnt 425
                 79*********87655*****************955899999999999999988877777766666744444444444434444488899999998864 PP

      HlyD_3  79 tvdaktg..aykvevslenpe....kksiplkp 105
                  v+++tg  +y + v+++++e    k +++l p
  AHX11815.1 426 IVEPRTGmhYYLAHVRIPKSElariKTRTKLYP 458
                 447888844444566777666766666666665 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   32.8   0.2   2.8e-11   4.6e-08      10      48 ..     102     141 ..      92     144 .. 0.92
   2 ?    2.7   0.0     0.068   1.1e+02       3      16 ..     326     339 ..     322     341 .. 0.88

  Alignments for each domain:
  == domain 1  score: 32.8 bits;  conditional E-value: 2.8e-11
  Biotin_lipoyl_2  10 sG.rVaqlnVkdGqrVkaGdvLaelDsralqlalaqaeaq 48 
                      +G  +++++V++G++V++G++L++l+  + +++la +e++
       AHX11815.1 102 DGgIIKEILVHEGDHVEEGQILITLNNVNNKAQLAILEEN 141
                      566*******************************988886 PP

  == domain 2  score: 2.7 bits;  conditional E-value: 0.068
  Biotin_lipoyl_2   3 vsIaapvsGrVaql 16 
                      ++I ap+sG+V+ l
       AHX11815.1 326 TTIRAPQSGTVTGL 339
                      68*********976 PP

>> HlyD_D23  Barrel-sandwich domain of CusB or HlyD membrane-fusion
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   11.2   0.2   9.3e-05      0.15      23      79 ..      99     153 ..      81     212 .. 0.62
   2 !   14.2   0.1   1.2e-05     0.019      94     169 ..     311     388 ..     228     404 .. 0.79

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.3e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XX CS
    HlyD_D23  23 sarveGwveklyvnatgdkVkkGqpLaelyspelvaaqeeyllalkakkklkkkell 79 
                 +    G ++++ v+ +gd+V++Gq L++l+  +  +aq + l+  +a+  +++++ll
  AHX11815.1  99 QHFDGGIIKEILVH-EGDHVEEGQILITLNNVN-NKAQLAILEENQASLLASEQRLL 153
                 33334667777777.888888888888887755.45555555555544444333322 PP

  == domain 2  score: 14.2 bits;  conditional E-value: 1.2e-05
                 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXX.XXXXXXXXXXXXXXXXXXXXXXXXXXXXX CS
    HlyD_D23  94 eqiaelektgkvqktvtvkapisGvVtekn.vreGqyvqpgdtlftia.dlstVWveaevyeqqlalvkvgqkvevtv 169
                 e+ ++l++  ++  ++t++ap+sG+Vt ++ +  G ++ pg+ l++i  + +++ +e++v+ ++++ ++  + +e +v
  AHX11815.1 311 ENSQKLASAYDAVLRTTIRAPQSGTVTGLKsLSIGGVIAPGTLLMEIIpENEDMFIEVKVMPNNIEAIASAKFIEKHV 388
                 5556777888888899***********9762678***********98626789********99999998877666555 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.2   0.1   2.1e-06    0.0034      50      73 .]     103     126 ..      95     136 .. 0.73
   2 ?    3.2   0.0      0.05        81      43      73 .]     326     357 ..     324     357 .. 0.79

  Alignments for each domain:
  == domain 1  score: 17.2 bits;  conditional E-value: 2.1e-06
                    SEEEEEESSTTTEEE-TTCEEEEE CS
  Biotin_lipoyl  50 aGvvkeilvkeGdtvevgdllaki 73 
                     G++keilv eGd ve+g++l+++
     AHX11815.1 103 GGIIKEILVHEGDHVEEGQILITL 126
                    466777777777777777777654 PP

  == domain 2  score: 3.2 bits;  conditional E-value: 0.05
                    EEEEBSSSEEEEEESS.TTTEEE-TTCEEEEE CS
  Biotin_lipoyl  43 meieapkaGvvkeilv.keGdtvevgdllaki 73 
                    ++i ap++G+v+ ++  + G  +  g+ll++i
     AHX11815.1 326 TTIRAPQSGTVTGLKSlSIGGVIAPGTLLMEI 357
                    6899********99852558888888888876 PP

>> HlyD  HlyD membrane-fusion protein of T1SS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   20.5   0.0     2e-07   0.00033       1      78 [.      66     448 ..      66     450 .. 0.95

  Alignments for each domain:
  == domain 1  score: 20.5 bits;  conditional E-value: 2e-07
                 HSEEEEEEEEEE....................................................................................... CS
                 xxxxxxxxxxxx....................................................................................... RF
        HlyD   1 alavfvawaala....................................................................................... 12 
                 ++++f +waa+a                                                                                       
  AHX11815.1  66 FFGIFGVWAAFApidgasiatgevvissdrrvvqhfdggiikeilvhegdhveegqilitlnnvnnkaqlaileenqasllaseqrllahkekkdemml 164
                 799************************************************************************************************ PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        HlyD  13 ................................................................................................... 12 
                                                                                                                    
  AHX11815.1 165 pdvsqlehvdndkkniaiknqlslfeshresfsnqiriidkkieqirnevlaleaqlqstyenltllqeeltakkalyatrvidktkitnlerekasld 263
                 *************************************************************************************************** PP

                 ................................................................................................... CS
                 ................................................................................................... RF
        HlyD  13 ................................................................................................... 12 
                                                                                                                    
  AHX11815.1 264 gkineykaliargeqriseaeleriqmnnrlnnelatelkevshllhensqklasaydavlrttirapqsgtvtglkslsiggviapgtllmeiipene 362
                 *************************************************************************************************** PP

                 .........................EEEEEEEECEEEEEEEGCGEEECTTTSEEEEEEECTSBEEEEEEEEEEEETTEEEESSSS-TTEEE CS
                 .........................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
        HlyD  13 .........................etdldqvrvgqpvevrfdAfpqtktgkftgvVvgispdrvpvrvvvekaqgpyyplriglkagalv 78 
                                          ++ +d++ +g + +vr++Af+ +k g+  gv +++s+      +v  +++ +yy  ++  +  +l+
  AHX11815.1 363 dmfievkvmpnnieaiasakfiekhVVNIDGL-SGIKTKVRLTAFNSKKVGMLDGVMTYVSAN----TIVEPRTGMHYYLAHVRIPKSELA 448
                 **********************9988888887.5999**************************....999999999999999988777765 PP

>> RnfC_N  RnfC Barrel sandwich hybrid domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    7.1   0.1    0.0033       5.3      39      60 ..     104     125 ..      86     135 .. 0.83
   2 !    7.1   0.0    0.0031       5.1      55      82 ..     313     341 ..     303     352 .. 0.87

  Alignments for each domain:
  == domain 1  score: 7.1 bits;  conditional E-value: 0.0033
      RnfC_N  39 GapakplvkvgdkVlkGqkiae 60 
                 G   ++lv++gd+V++Gq++ +
  AHX11815.1 104 GIIKEILVHEGDHVEEGQILIT 125
                 666799************9755 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.0031
      RnfC_N  55 Gqkiaeaeg.fvsapvhasvsGtVkaiek 82 
                  qk+a+a   ++ + + a+ sGtV+ +++
  AHX11815.1 313 SQKLASAYDaVLRTTIRAPQSGTVTGLKS 341
                 699999955599************98876 PP

>> ApoO  Apolipoprotein O
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.8   0.2   0.00022      0.36      20      66 ..     189     235 ..     181     242 .. 0.89
   2 ?   -0.9   0.1      0.92   1.5e+03      13      53 ..     295     335 ..     284     341 .. 0.81
   3 ?    0.8   0.0      0.27   4.4e+02      40      75 ..     431     465 ..     416     467 .. 0.87

  Alignments for each domain:
  == domain 1  score: 10.8 bits;  conditional E-value: 0.00022
        ApoO  20 vrslRkslepytsavqdelnkvkskvetaeqsvtdtiasLkeppedl 66 
                 ++s R+s+++++  ++++++++++ v  +e ++++t+++L   +e+l
  AHX11815.1 189 FESHRESFSNQIRIIDKKIEQIRNEVLALEAQLQSTYENLTLLQEEL 235
                 7899***********************************98666555 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 0.92
        ApoO  13 tdrLeegvrslRkslepytsavqdelnkvkskvetaeqsvt 53 
                  ++L++  +++ + l+++++++ ++++ v      a qs+t
  AHX11815.1 295 NNELATELKEVSHLLHENSQKLASAYDAVLRTTIRAPQSGT 335
                 46788889999999999999999999999888888777776 PP

  == domain 3  score: 0.8 bits;  conditional E-value: 0.27
        ApoO  40 kvkskvetaeqsvtdtiasLkeppedllPrlgyilv 75 
                 + ++++   ++  ++++a +k    +l+P++ +i++
  AHX11815.1 431 TGMHYYLAHVRIPKSELARIKTR-TKLYPGMPAIVF 465
                 67889999999999*******96.*******99998 PP

>> Peptidase_M23  Peptidase family M23
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    7.5   0.0    0.0028       4.6      34      74 ..      87     128 ..      75     143 .. 0.72
   2 ?    2.5   0.0       0.1   1.7e+02      11      30 ..     323     342 ..     315     350 .. 0.74

  Alignments for each domain:
  == domain 1  score: 7.5 bits;  conditional E-value: 0.0028
                    EEEEEEEECTCEEEEEEE.ESEESS-TTEEE-TTCEEEEEBS CS
  Peptidase_M23  34 Gnvviidhgdgystlyah.lskisvkegqkVkaGqvIGtvgs 74 
                    G+vvi  +   +++  +  +++i v+eg++V++Gq++ t  +
     AHX11815.1  87 GEVVISSDRRVVQHFDGGiIKEILVHEGDHVEEGQILITLNN 128
                    555555555555555444367899***********9877665 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.1
                    TTT-EEEESSSEEEEEEEEE CS
  Peptidase_M23  11 pkgtpVlAaadGtVvfagkk 30 
                       t+++A+++GtV+  +  
     AHX11815.1 323 VLRTTIRAPQSGTVTGLKSL 342
                    55689*********876654 PP

>> AATF-Che1  Apoptosis antagonizing transcription factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    9.9   6.4   0.00069       1.1      33     133 ..     184     324 ..     175     329 .. 0.62

  Alignments for each domain:
  == domain 1  score: 9.9 bits;  conditional E-value: 0.00069
   AATF-Che1  33 nqLpqpetl.kefles.......seefeealeeaekalkklleslleLreelleqne.ikkla...................................e 87 
                 nqL+  e++ ++f ++        e++++++ ++e++l++++e+l+ L+eel++++   ++ +                                   +
  AHX11815.1 184 NQLSLFESHrESFSNQiriidkkIEQIRNEVLALEAQLQSTYENLTLLQEELTAKKAlYAT-RvidktkitnlerekasldgkineykaliargeqriS 281
                 677733333033433366777777799999**********************777774443.3577777877778887787777777777777664432 PP

   AATF-Che1  88 skeeeekkkskrkrkkkkkeetsleelwkeleklekalkpfrnatl 133
                 +    e ++ + +++ +++ +t+l+e+++ l ++ ++l++  +a+l
  AHX11815.1 282 E---AELERIQMNNRLNNELATELKEVSHLLHENSQKLASAYDAVL 324
                 2...222222233333345556666655555555555555554444 PP

>> Fib_alpha  Fibrinogen alpha/beta chain family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.7   6.7    0.0012       1.9      26     106 ..     196     282 ..     192     296 .. 0.78
   2 ?    0.1   0.1       0.5   8.2e+02      29      59 ..     294     324 ..     287     333 .. 0.75

  Alignments for each domain:
  == domain 1  score: 8.7 bits;  conditional E-value: 0.0012
                 CCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHHHCCCHHHHHHHCCHHHHHH CS
   Fib_alpha  26 llkyekdvkkdlekleneleeisnstkeaeelvkeikdslrekqkskkdn......dnvikksskeleeeilrlketidaqesnirv 106
                 ++++ + ++k++e+++ne+  ++ + ++++e  + +++ l++k++ ++         + +++ + +l+ +i+++k+ i + e++i +
  AHX11815.1 196 FSNQIRIIDKKIEQIRNEVLALEAQLQSTYENLTLLQEELTAKKALYATRvidktkITNLEREKASLDGKINEYKALIARGEQRISE 282
                 67888999**********************************999998744432113334455667888888888888888888864 PP

  == domain 2  score: 0.1 bits;  conditional E-value: 0.5
                 CCCCCCHHHCCCCCCCCCCCCHHHHHHHHHH CS
   Fib_alpha  29 yekdvkkdlekleneleeisnstkeaeelvk 59 
                  ++++ ++l+++ + l+e+s++  +a++ v 
  AHX11815.1 294 LNNELATELKEVSHLLHENSQKLASAYDAVL 324
                 5677788888888888888888888887765 PP

>> Cob_adeno_trans  Cobalamin adenosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.8   0.3      0.93   1.5e+03      50      93 ..     131     172 ..     116     207 .. 0.67
   2 ?    9.4   1.1   0.00067       1.1      50     117 ..     214     281 ..     180     290 .. 0.72
   3 ?    1.2   0.1      0.23   3.7e+02      49      74 ..     294     319 ..     281     338 .. 0.59

  Alignments for each domain:
  == domain 1  score: -0.8 bits;  conditional E-value: 0.93
                      THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--.HHHHHHHHH CS
  Cob_adeno_trans  50 eeelkeaLeeiqneLfdlgaelatpekkkekkkit.eeeveelek 93 
                      +++  + Lee q +L+   + l ++  k++k ++   + v++le+
       AHX11815.1 131 NKAQLAILEENQASLLASEQRLLAH--KEKKDEMMlPD-VSQLEH 172
                      4455677888888888888887644..33444444244.666665 PP

  == domain 2  score: 9.4 bits;  conditional E-value: 0.00067
                      THHHHHHHHHHHHHHHHHHHHHHT.-BTCCG-S--HHHHHHHHHHHHHHHHHS--EESEEES-SSHHH CS
  Cob_adeno_trans  50 eeelkeaLeeiqneLfdlgaelatpekkkekkkiteeeveelekeideleaelpplksfilpggspaa 117
                        +l+++L++  ++L  l++el ++++ ++++ i++ ++++le+e  +l+ ++++ k  i  g+++ +
       AHX11815.1 214 VLALEAQLQSTYENLTLLQEELTAKKALYATRVIDKTKITNLEREKASLDGKINEYKALIARGEQRIS 281
                      33456666666666666666665557777777788889*****************9999998876655 PP

  == domain 3  score: 1.2 bits;  conditional E-value: 0.23
                      TTHHHHHHHHHHHHHHHHHHHHHHT. CS
  Cob_adeno_trans  49 eeeelkeaLeeiqneLfdlgaelatp 74 
                       ++el+++L+e+ + L++  ++la+ 
       AHX11815.1 294 LNNELATELKEVSHLLHENSQKLASA 319
                      25666777777777777777766644 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (492 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1498  (0.0835518); expected 358.6 (0.02)
Passed bias filter:                      569  (0.0317363); expected 358.6 (0.02)
Passed Vit filter:                        61  (0.00340231); expected 17.9 (0.001)
Passed Fwd filter:                        15  (0.000836633); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.62u 0.31s 00:00:00.93 Elapsed: 00:00:00.43
# Mc/sec: 3424.30
//
Query:       AHX11816.1  [L=377]
Description: 3-dehydroquinate synthase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    9.6e-46  156.5   0.0    1.3e-45  156.1   0.0    1.1  1  Fe-ADH_2      Iron-containing alcohol dehydrogenase
    4.6e-10   38.9   0.0    6.2e-10   38.4   0.0    1.1  1  Fe-ADH        Iron-containing alcohol dehydrogenase
    3.1e-08   33.1   0.5    0.00087   18.5   0.1    2.8  2  DHQ_synthase  3-dehydroquinate synthase


Domain annotation for each model (and alignments):
>> Fe-ADH_2  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  156.1   0.0   2.1e-49   1.3e-45      20     250 .]      33     269 ..      18     269 .. 0.85

  Alignments for each domain:
  == domain 1  score: 156.1 bits;  conditional E-value: 2.1e-49
    Fe-ADH_2  20 kkvllvadentkka..agekveeslkeagikvevveeveeeadleeveklvealreketdlvvavGgGtiiDiakyvsaklnvpyvsvpTaaSvDGfas 116
                 +  ll+ dent+ +  ++ ++e++lk+  + +      + ++++ e+++lv+  +  + +l++a+G+Gti Di+k ++  +n++++++pTa+Sv+ ++s
  AHX11816.1  33 RSSLLICDENTQYFipLTLRMERNLKRI-VLP-----RDVQPTELEIRRLVKHTQ--DRELIIALGAGTITDICKCLAKITNREFIIFPTAPSVNAYTS 123
                 5678899999998834455566666555.222.....346789999999998886..999*************************************** PP

    Fe-ADH_2 117 pgaslvvd..gkkrtvakaaaPlaviaDldvlaeAPrrllasGvGDllgkytaladwklan.evseplaklsaamvqeaaeklve.....dkketeale 207
                 p+as++    +kk + +ka++P+++++D  +l++AP r++ sG+ Dl+  +t  +d  +a+ ++++++a  +++++++  + l++      k+++ ++e
  AHX11816.1 124 PTASIMPIgsNKKYS-IKAKMPIGIYIDRGILKKAPTRMIVSGLCDLVCSSTIKVDCLIASiALKQEYATIIFEELKHYEKILLKyskllVKGDIMLIE 221
                 *****9873345555.5*****************************************99988899999999999865555555543333466999*** PP

    Fe-ADH_2 208 ellealalsgigi.....srpaSGsEHliSHaldmlalkqalHGeqVG 250
                  l++al+lsg+g+     sr+aS sEH ++H l+++++++ lHGe V+
  AHX11816.1 222 LLMQALILSGLGMwlhgdSRTASQSEHVVAHILERKYSRHFLHGEMVA 269
                 *********************************************996 PP

>> Fe-ADH  Iron-containing alcohol dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   38.4   0.0     1e-13   6.2e-10       3     299 ..      15     295 ..      14     324 .. 0.77

  Alignments for each domain:
  == domain 1  score: 38.4 bits;  conditional E-value: 1e-13
                 EEEEETTGGGGHHHHHTTT-..EEEEEEEHHHH.HH.THHHHHHHHHCTT-EEEE.EEE-S---HHHHHHHHTTS-TT.--EEEEEESHHHHHHHHHHH CS
      Fe-ADH   3 rivfgkgaleelgellkklgakralivtdkgslkksglldkvlesleeagievtvfdgvepnptleeveeaaalareegadvviavGGGsviDtAKaia 101
                 +i+f+++ l +l++l++     + l+++d+++    +++  ++  +e++  ++++  +v   pt+ e++++++  ++   +++ia+G G+  D++K++a
  AHX11816.1  15 QIIFENDLLINLQDLISHR---SSLLICDENT----QYFIPLTLRMERNLKRIVLPRDV--QPTELEIRRLVKHTQDR--ELIIALGAGTITDICKCLA 102
                 7999999999*****9654...78******94....58999999998888888888888..89**********77776..8****************** PP

                 HHTT..................--EEEEESS-S-S-TT-SEEEEE.-TTSEEEEE-..SS--SEEEEEHHHHHHS-HHHHHHHHHHHHHHHHHHHHH.H CS
      Fe-ADH 102 lllanpevedylgegkakkkkalpliaiPTtaGtGsevtplavitdeeegeklsifdpellPdlaivDpeltltlPkrvtaatglDalahalEayvs.k 199
                  +++                   ++i+ PT ++  + ++p+a i    +++k+si     +P  + +D  ++ ++P r+++++  D ++       +  
  AHX11816.1 103 KITN------------------REFIIFPTAPSVNAYTSPTASIMPIGSNKKYSIK--AKMPIGIYIDRGILKKAPTRMIVSGLCDLVCSSTIKVDClI 181
                 ****..................78*********************66678999**9..99*****************************9988888866 PP

                 T---TTSSB--HHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHH.....HHHSS---.........HHHHHHHHHHC.CGGGGGS-HHHHHH CS
      Fe-ADH 200 kanplsdalaleairliaknleravadge.....dleareqmllastlagl.....afsnaglg.........avHalahalgalfgiphglanaillp 279
                  +  l + +a  +++ + ++ + +++  +     d+   e +++a +l+gl     +      +         ++H l+++ + +f     +a++i+l 
  AHX11816.1 182 ASIALKQEYATIIFEELKHYEKILLKYSKllvkgDIMLIELLMQALILSGLgmwlhG-----DSrtasqsehvVAHILERKYSRHFLHGEMVAVGIILV 275
                 677788888888888888888888877544444477888888999999998444442.....2222355444466666666666432224445555777 PP

                 HHH..........HHHHHHT CS
      Fe-ADH 280 avlrfnaeaaperlaqlara 299
                 + ++  + +++ ++  + +a
  AHX11816.1 276 SMIQEKLFRKEGKITFMTKA 295
                 77665555555555555555 PP

>> DHQ_synthase  3-dehydroquinate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   10.9   0.0   3.1e-05      0.19      25     135 ..      78     184 ..      66     218 .. 0.68
   2 !   18.5   0.1   1.5e-07   0.00087     183     251 ..     248     313 ..     235     322 .. 0.71

  Alignments for each domain:
  == domain 1  score: 10.9 bits;  conditional E-value: 3.1e-05
                   HTT--TT-EEEEEESHHHHHHHHHHHHHBTT--EEEEEE-S..HHHHHTTTSSSEEEEEETTEEEEEEEE---SEEEEEGGGGGGS-HHHHHHHHHH CS
  DHQ_synthase  25 eakleRksllialGGGvvgDlaGfvAatylRGvrfvqvPtt..llaqvDssvGgKtainlplgKNliGafaqPkavlidlevLktLperelraGlaE 119
                   ++ ++ ++l+ialG G+++D++   A +  R  +f+  Pt+  + a   s       i   ++K  i    +P  ++id  +Lk  p+r + +Gl +
    AHX11816.1  78 KH-TQDRELIIALGAGTITDICKCLAKITNR--EFIIFPTApsVNAYT-SPTASIMPIGS-NKKYSI-KAKMPIGIYIDRGILKKAPTRMIVSGLCD 168
                   44.445579*********************9..788888861022322.33333344443.334445.44788899999999999999999999988 PP

                   HHHHHHHT-HHHHHHH CS
  DHQ_synthase 120 viKyalikdeelfell 135
                   ++  + ik   l++++
    AHX11816.1 169 LVCSSTIKVDCLIASI 184
                   8888887765555544 PP

  == domain 2  score: 18.5 bits;  conditional E-value: 1.5e-07
                   HHHHHHHHHHHTTTTS-HHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHTT---STTTT.-HHHH CS
  DHQ_synthase 183 HtigHaiEallgyekllHGeaVaiGmvlaaelseklgllkkeeverllkllkklglpvslkelleveel 251
                   H ++H +E+  +  ++lHGe Va+G++l   + ekl + k+ +++ ++k ++ ++ + s ++l ++e++
    AHX11816.1 248 HVVAHILERKYSR-HFLHGEMVAVGIILVSMIQEKL-FRKEGKITFMTKAFELYKKQKSSSSL-TPETF 313
                   9*********999.**************99999888.44556666555555555544444444.44444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (377 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       582  (0.0324614); expected 358.6 (0.02)
Passed bias filter:                      446  (0.0248759); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.50u 0.27s 00:00:00.77 Elapsed: 00:00:00.42
# Mc/sec: 2696.23
//
Query:       AHX11817.1  [L=87]
Description: flavinator of succinate dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.9e-20   72.6   0.0    2.1e-20   72.4   0.0    1.1  1  Sdh5      Flavinator of succinate dehydrogenase


Domain annotation for each model (and alignments):
>> Sdh5  Flavinator of succinate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   72.4   0.0   1.2e-24   2.1e-20       1      66 [.       7      72 ..       7      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 72.4 bits;  conditional E-value: 1.2e-24
                HHHHHHHH.--SSHHHHHTTTTHHHHHTTT--HHHHHHHHHHHTS--HHHHHHHHT-.---S-HHH CS
        Sdh5  1 raRllyrsrrRGmlElDllLgrFaekhlatlseeeldaferLLdleDpdLldwltgrkeepedael 66
                r+R+lyrs++RG++E+D+lLg+Faek++ +l+++e+++fer+L+l D+ ++d+  gr ++ped el
  AHX11817.1  7 RKRILYRSTHRGCKETDILLGGFAEKNFGNLTDHEVEQFERILELTDSFIFDCYQGRVNPPEDLEL 72
                79************************************************************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (87 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       293  (0.0163422); expected 358.6 (0.02)
Passed bias filter:                      270  (0.0150594); expected 358.6 (0.02)
Passed Vit filter:                        18  (0.00100396); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.34u 0.24s 00:00:00.58 Elapsed: 00:00:00.37
# Mc/sec: 700.19
//
Query:       AHX11818.1  [L=39]
Description: putative membrane protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (39 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       420  (0.0234257); expected 358.6 (0.02)
Passed bias filter:                      239  (0.0133304); expected 358.6 (0.02)
Passed Vit filter:                        13  (0.000725082); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.33u 0.24s 00:00:00.57 Elapsed: 00:00:00.40
# Mc/sec: 293.07
//
Query:       AHX11819.1  [L=205]
Description: cytidylyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    3.7e-44  151.5  15.3      1e-40  140.2   9.8    2.0  2  CTP_transf_1  Cytidylyltransferase family
     0.0082   16.1   1.3     0.0082   16.1   1.3    2.1  2  CarS-like     CDP-archaeol synthase


Domain annotation for each model (and alignments):
>> CTP_transf_1  Cytidylyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.8   0.8   9.8e-07    0.0088       1      59 [.       8      68 ..       8      83 .. 0.83
   2 !  140.2   9.8   1.2e-44     1e-40     124     262 ..      71     204 ..      57     205 .] 0.90

  Alignments for each domain:
  == domain 1  score: 15.8 bits;  conditional E-value: 9.8e-07
                  HHHHHHHHHHHHHHHHTTTSH.HHHHHHHHHHHHHHHHHHHHTT--SHHHHHHHHH..... CS
  CTP_transf_1  1 kqRvitalvlilivliilllgglvflllvavvvilalkElirlvrlkkrekrllll..lls 59
                  k+R i+++vl+ + +++++ g++v+   v+++++l ++E+i ++  + +   ll l  ++ 
    AHX11819.1  8 KVRAISSIVLLFLCALAIYGGEYVVCSGVLLLAVLSYREWIDMTVDRGKILGLLGLlvVIL 68
                  689*****************************************99999888877743333 PP

  == domain 2  score: 140.2 bits;  conditional E-value: 1.2e-44
                   THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH---B-S-TTS---BHHHHHHHHHHHHHHHHHHHHHHHCTS---TTSHHHHHHHHHHHHHHHH CS
  CTP_transf_1 124 lllienikeglllvllllalvvaaDigaYffGklfGktkllpkiSPkKTveGfigGlvaavvvglllalvlskalalsllhllllslllslvavfGD 220
                    +li+   e+  ++++ll++vv++DigaY +G+++G  kll +iSP+KT+ Gf+gGl++a++ g+ +a v + +     + ++ll++ ++++a+ GD
    AHX11819.1  71 SALISIYAEDPEIFIWLLICVVSNDIGAYCIGRVIGGPKLLESISPNKTLGGFFGGLLSALIGGSTFAIVSGLS-----MNFVLLTVPVAIFATAGD 162
                   445555566667899*******************************************************9985.....78999************* PP

                   HHHHHHHHHHT-SSS-S-SSSSS-HHHHHHHHHHHHHHHHHH CS
  CTP_transf_1 221 LveSglKRafgiKDsGkliPGhGGilDRlDsllfaapvvyll 262
                   L+eS +KR+   KDsG+liPGhGG+lDR+D+++f+ap++ +l
    AHX11819.1 163 LFESFIKRKCSAKDSGSLIPGHGGVLDRVDGFIFSAPFLLYL 204
                   **************************************9876 PP

>> CarS-like  CDP-archaeol synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    0.2   0.2      0.07   6.3e+02     113     147 ..      51      85 ..      40     106 .. 0.63
   2 !   16.1   1.3   9.2e-07    0.0082      53     132 ..     119     198 ..      95     205 .] 0.71

  Alignments for each domain:
  == domain 1  score: 0.2 bits;  conditional E-value: 0.07
   CarS-like 113 kierGkpalildqldfvlgalllaypvkllpieli 147
                  ++rGk   +l  l  +l   +l ++++  p  +i
  AHX11819.1  51 TVDRGKILGLLGLLVVILPNSALISIYAEDPEIFI 85 
                 56778777777777777766666555554443222 PP

  == domain 2  score: 16.1 bits;  conditional E-value: 9.2e-07
   CarS-like  53 tvaGvlvGvlvgliqglleklsilaldssgsvlefvilalllafGallGdavGsfikrrlki.erGkpal....ildqld.fvlga 132
                 t++G ++G+l +li g        a+ s +s ++fv+l++ +a+ a  Gd+  sfikr+    + G+ ++    +ld++d f+++a
  AHX11819.1 119 TLGGFFGGLLSALIGGST-----FAIVSGLS-MNFVLLTVPVAIFATAGDLFESFIKRKCSAkDSGSLIPghggVLDRVDgFIFSA 198
                 566777777777777755.....56655555.6799**********************9865256665544444666665455555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (205 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       574  (0.0320152); expected 358.6 (0.02)
Passed bias filter:                      323  (0.0180155); expected 358.6 (0.02)
Passed Vit filter:                        31  (0.00172904); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.44u 0.27s 00:00:00.71 Elapsed: 00:00:00.42
# Mc/sec: 1461.07
//
Query:       AHX11820.1  [L=230]
Description: di-trans,poly-cis-decaprenylcistransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    6.2e-75  251.6   0.0      7e-75  251.4   0.0    1.0  1  Prenyltransf    Putative undecaprenyl diphosphate synthase
  ------ inclusion threshold ------
      0.061   12.4   0.0      0.097   11.7   0.0    1.3  1  Ferrochelatase  Ferrochelatase


Domain annotation for each model (and alignments):
>> Prenyltransf  Putative undecaprenyl diphosphate synthase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  251.4   0.0   7.8e-79     7e-75       1     224 []      13     229 ..      13     229 .. 0.94

  Alignments for each domain:
  == domain 1  score: 251.4 bits;  conditional E-value: 7.8e-79
                   EE--HHHHHHHTT.S-HHHHHHHHHHHHHHHHHHHHHTT-SEEEEEEEEGGGGGS-HHHHHHHHHHHHHHHHHHHHHHHHHTTEEEEEESSGGGS-H CS
  Prenyltransf   1 imDGNrRwAkkrgleereeGhkaGaealkeilelclelgvkvvtvYafSteNfkRskeevdalmellkeellkeelkellkegvrvrviGdlellpe 97 
                   imDGN RwA++rg +++ +G+++G++a  ++++++ elg++++t++ fSteN++Rs+e+v+ +++l++e +++++l+e+ + g++++viGd+e l++
    AHX11820.1  13 IMDGNARWARSRG-LQNFDGYRKGVDAAVSVVKAACELGISYLTLFLFSTENWSRSSEDVNLVFNLFQE-TCTSRLEEVCRAGAKIKVIGDREALNQ 107
                   9************.55556************************************************65.888889********************* PP

                   HHHHHHHHHHHHHT.TTTSEEEEEEEEE-HHHHHHHHHHHHHHTT..SSSGGGHSHHHHHCTSTT..TSSS-SEEEEESS--S-TTSSTTTTTT-EE CS
  Prenyltransf  98 dvlealekaeeatkknnkklvlniavnYgsrdeiveavrelvkekseekkkeeideetlekhlytakalpdpDlliRtsGeeRlSnFllwqlaysel 194
                   +v++ ++ +e++t+ +n+++++ +a+nYg+r+ei++av+ +v+e+      +eid+++++++lyt k+lpdpDl+iRt+Ge+RlSnFllwq++yse+
    AHX11820.1 108 NVRQVIALLEAETA-QNEGIQVYLAMNYGGRAEILRAVSMMVSEG---VPVAEIDAKKFSAYLYT-KDLPDPDLIIRTAGEKRLSNFLLWQSSYSEF 199
                   **************.6666***********************998...33445799********9.556**************************** PP

                   EEESSSGGG--HHHHHHHHHHHHHCHHHTT CS
  Prenyltransf 195 yfldvlWPdfskedllealleyqkrerrfg 224
                   yf+d+lWPdf+ked++ al +y++r+r++g
    AHX11820.1 200 YFCDTLWPDFEKEDFILALDDYRRRDRKYG 229
                   ***************************987 PP

>> Ferrochelatase  Ferrochelatase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.7   0.0   1.1e-05     0.097      49      99 ..      84     136 ..      70     155 .. 0.78

  Alignments for each domain:
  == domain 1  score: 11.7 bits;  conditional E-value: 1.1e-05
                     HHHHHHHHHHHHT...TSS-SHHHHHHHHHHHHHHHHHHH---EEEEEEESSSS CS
  Ferrochelatase  49 erlekvaekYeki...gggSPlneitrkqaealekelaergidvkvylamrywe 99 
                     +rle+v ++ +ki   g++  ln+  r+ ++ le+e a++   ++vylam+y+ 
      AHX11820.1  84 SRLEEVCRAGAKIkviGDREALNQNVRQVIALLEAETAQN-EGIQVYLAMNYGG 136
                     566777666666666699*******************975.9**********63 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       457  (0.0254894); expected 358.6 (0.02)
Passed bias filter:                      423  (0.0235931); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.43u 0.22s 00:00:00.65 Elapsed: 00:00:00.38
# Mc/sec: 1809.26
//
Query:       AHX11821.1  [L=185]
Description: ribosome recycling factor [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.2e-48  163.4   1.0    4.8e-48  163.2   1.0    1.0  1  RRF        Ribosome recycling factor
  ------ inclusion threshold ------
      0.079   13.4   1.5       0.19   12.2   0.1    2.1  2  EF-hand_7  EF-hand domain pair


Domain annotation for each model (and alignments):
>> RRF  Ribosome recycling factor
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  163.2   1.0   5.4e-52   4.8e-48       1     162 []      20     183 ..      20     183 .. 0.98

  Alignments for each domain:
  == domain 1  score: 163.2 bits;  conditional E-value: 5.4e-52
                 HHHHHHHSS-SSSSCGGGTTSEEEETTEEEEGGGTEEEEESSTTEEEEEESSCCHHHHHHHHHHHSCC-SEEEEESSEEEEE--SSSHHHHHHHHHHHH CS
         RRF   1 lkkelsklrtgranpslldnikVeyygkktpLnqlAqvsvkeartllitpfdkslvkaiekaIlksdlglnpqqdgevlrvpipplTeErrkelvkeak 99 
                 ++++ls +r+g ++ s+ld i V++   k++Lnq+A+ sv ++++l+++++dk +v a++ aI++sdlg+np  +g+vlr+p+p lTeErrkelvk+++
  AHX11821.1  20 FSSDLSGIRSGSLSVSILDGIVVSTAMGKLRLNQVASLSVVNNKMLSVQVWDKGNVGAVKDAIISSDLGMNPIVEGTVLRLPVPDLTEERRKELVKVLR 118
                 5789*********************************************************************************************** PP

                 HHHHHHHHHHHHHHHHHHHHHHHHHH.C.S-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT CS
         RRF 100 kaaekakvairniRrdankklkklek.k.iseDdvkkaekeiqkltdkyikeidellkakekell 162
                 k++++akva+rniRrd   k+k+lek k iseD+++   k+i+kl+ +   +id ++++ke+++l
  AHX11821.1 119 KYGDRAKVAVRNIRRDSIAKVKALEKnKeISEDEMHVCVKKIDKLISEEDTRIDGVVSKKEADIL 183
                 **************************669*********************************996 PP

>> EF-hand_7  EF-hand domain pair
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.3   0.1      0.17   1.5e+03      46      55 ..       2      11 ..       1      13 [. 0.77
   2 ?   12.2   0.1   2.2e-05      0.19      22      65 ..     111     179 ..     109     180 .. 0.78

  Alignments for each domain:
  == domain 1  score: -0.3 bits;  conditional E-value: 0.17
   EF-hand_7 46 lellfkefDt 55
                le++fke+D+
  AHX11821.1  2 LEDIFKEIDL 11
                6788888886 PP

  == domain 2  score: 12.2 bits;  conditional E-value: 2.2e-05
   EF-hand_7  22 eellrllrkifqga..................gegsklsdee.......lellfkefDtdkdGvisfdE 65 
                  el ++lrk  + a                  + ++++s++e       +++l+ e Dt+ dGv+s  E
  AHX11821.1 111 KELVKVLRKYGDRAkvavrnirrdsiakvkalEKNKEISEDEmhvcvkkIDKLISEEDTRIDGVVSKKE 179
                 677788888877778888888888899999997777777755555555599**************9877 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       983  (0.0548274); expected 358.6 (0.02)
Passed bias filter:                      520  (0.0290033); expected 358.6 (0.02)
Passed Vit filter:                        41  (0.0022868); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.36u 0.24s 00:00:00.60 Elapsed: 00:00:00.35
# Mc/sec: 1569.77
//
Query:       AHX11822.1  [L=233]
Description: UMP kinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
    4.9e-23   82.0   0.9    5.8e-23   81.7   0.9    1.1  1  AA_kinase  Amino acid kinase family


Domain annotation for each model (and alignments):
>> AA_kinase  Amino acid kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   81.7   0.9   3.2e-27   5.8e-23       2     240 ..       3     209 ..       2     210 .. 0.92

  Alignments for each domain:
  == domain 1  score: 81.7 bits;  conditional E-value: 3.2e-27
                 EEEEEE-TTCCC.CTCC....HHHHHHHHHHHHHHHHTTEEEEEE--HHHHHHHHHHTCCCCCHHHC....E..HHHHHHHHHHHHHHHHHHHHHHHHH CS
   AA_kinase   2 rvVvKlGGsslt.dkee....aslrrlaeqiaalkesgnklvvVhGggsftdgllalksglssgelaaglrstleeagevatrdalaslgerlvaalla 95 
                 rv +K+ G  l+ d++     a +  lae +++ +  g+++ +V+Ggg++ +g + +  ++++  +                 d++++l++ ++a  l+
  AHX11822.1   3 RVLLKISGERLAgDGSSvhdaAIIGMLAEGVKRVHDTGIQVCLVVGGGNIYRGSSGI-PNIERATS-----------------DYMGMLATVINALALQ 83 
                 67889999977767777888888999999999999**********************.88888887.................9*************** PP

                 TTHGEEEE-GGGTCEECCCE..HHHTTTCEEECCHHHHHHHTT-EEEEESEEEEETTTEEEEE-HHHHHHHHHHHCTSSEEEEEESSSSCESSTTTTCC CS
   AA_kinase  96 aglpavglsaaaldateagrdegsdgnvesvdaeaieelleagvvpvltgfigldeegelgrgssDtiaallAealgAdkliiltdVdGVydadpkkvp 194
                  ++++ g+ ++   a+  +        +e +++++    +e++ v++++ +    ++    ++++Dt+a+l A+++++d ++  t VdGVy++dpkk++
  AHX11822.1  84 GAISNLGIVSRVQSAIPMRS------ICEPYTRQKAISHMEKNRVVIFAAGT--GNP----FFTTDTAAVLRAVEMNCDVMLKGTLVDGVYSDDPKKNS 170
                 ***********999998888......99999999999999999888877744..344....99************************************ PP

                 TTCECCEEEHHHCHHCSSS.TTTHHHHCHHHHHHHHHCTT-EEEEE CS
   AA_kinase 195 darllpeisvdeaeesaselatgGmkvkhpaalaaarrggipvvIt 240
                 +a++++++s+ ++++          +v++ +a+ +ar++ +p++I+
  AHX11822.1 171 NAERISRLSYTDVLS-------RKLRVLDSSAVSVARENSMPIIIF 209
                 ***************.......**********************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (233 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       394  (0.0219756); expected 358.6 (0.02)
Passed bias filter:                      349  (0.0194657); expected 358.6 (0.02)
Passed Vit filter:                        30  (0.00167327); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.24s 00:00:00.63 Elapsed: 00:00:00.37
# Mc/sec: 1866.04
//
Query:       AHX11823.1  [L=282]
Description: translation elongation factor Ts [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.3e-58  198.0   0.4    1.7e-58  197.7   0.4    1.1  1  EF_TS     Elongation factor TS
  ------ inclusion threshold ------
      0.024   13.6   0.0      0.032   13.2   0.0    1.1  1  Orbi_VP7  Orbivirus inner capsid protein VP7
      0.074   13.0   0.0        5.1    7.1   0.0    2.8  3  RBD-FIP   FIP domain


Domain annotation for each model (and alignments):
>> EF_TS  Elongation factor TS
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  197.7   0.4   2.8e-62   1.7e-58       1     207 [.      65     279 ..      65     280 .. 0.97

  Alignments for each domain:
  == domain 1  score: 197.7 bits;  conditional E-value: 2.8e-62
       EF_TS   1 avivevnsETDFVAknekFqelvkkvaeaaleekakdleellalkled.etveealkekiakigEkielrrfaklea.ekevvasYiHgn.....grig 92 
                 +v++e+n+ETDFVA+n+kFq++++ v++a++e+kak++ee+la++l++ +tv++a+ e+i++ +E+i+l +++ +e   +++v+ YiH++     g+ig
  AHX11823.1  65 GVMIELNCETDFVARNDKFQQFADLVLQAVCENKAKTVEECLAVTLSGgQTVRDAIMEQISIFRENIVLSKCTAFELsGSGLVGVYIHNKytenlGKIG 163
                 69*************************************************************************998899****************** PP

       EF_TS  93 vlvalegksdealkelakqiAmhiaAmnPqylsedevdaevlekekeilkeqakeegkpekiiekiveGrlekflkevcLleQeyvkddkktVeqvlke 191
                 v+vale++ + al+++ak+iA++i +  Pq++s +++d e+l  eke ++e+++  gkp++++ekiv+G+l+kf+k+++LleQ+   d++ +V+q+l++
  AHX11823.1 164 VVVALESNAA-ALQDVAKNIAIQIMSECPQAISIQDIDPELLSGEKEKYREETQ--GKPDSVAEKIVQGKLNKFYKRIVLLEQPLFADPEISVKQYLDN 259
                 *******988.6**********************************99998876..8****************************************** PP

       EF_TS 192 aske....lkvvkfvrfevG 207
                 +++e    +kv  +  f++G
  AHX11823.1 260 VAAElsgvIKVLWYRVFTLG 279
                 ****99999*****999998 PP

>> Orbi_VP7  Orbivirus inner capsid protein VP7
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.2   0.0   5.4e-06     0.032      34     100 ..     105     171 ..      76     191 .. 0.81

  Alignments for each domain:
  == domain 1  score: 13.2 bits;  conditional E-value: 5.4e-06
                 HHHHHHHHHHH-----SS--SHHHHHHHHHHHHHHHHHHHT----S--SS----TTHHHHHT-TTS- CS
    Orbi_VP7  34 giainryngltlrgvtmrptslaqrnemffmcldmmlsaaginvgpispdytqhmatigvlatpeip 100
                  +a+    g t+r   m   s+ + n ++  c  + ls +g+    i   yt+ +  igv+ + e  
  AHX11823.1 105 CLAVTLSGGQTVRDAIMEQISIFRENIVLSKCTAFELSGSGLVGVYIHNKYTENLGKIGVVVALESN 171
                 356667789*********************************9999**************9887654 PP

>> RBD-FIP  FIP domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.4   0.0     0.026   1.5e+02      18      33 ..      79      97 ..      66      98 .. 0.77
   2 ?    7.1   0.0   0.00085       5.1      12      36 ..     168     192 ..     162     194 .. 0.87
   3 ?   -2.3   0.0      0.73   4.3e+03      20      25 ..     254     259 ..     250     260 .. 0.87

  Alignments for each domain:
  == domain 1  score: 2.4 bits;  conditional E-value: 0.026
                H...HHHHHHHHHHHHHHC CS
     RBD-FIP 18 r...LedYiDnlLlrvmEh 33
                r    ++++D  L++v E+
  AHX11823.1 79 RndkFQQFADLVLQAVCEN 97
                344489**********997 PP

  == domain 2  score: 7.1 bits;  conditional E-value: 0.00085
                 HHHHHHHHHHHHHHHHHHHHHC-GG CS
     RBD-FIP  12 qEeenrrLedYiDnlLlrvmEhnPs 36 
                  E  ++ L+d + n+  ++m ++P+
  AHX11823.1 168 LESNAAALQDVAKNIAIQIMSECPQ 192
                 6778888*****************8 PP

  == domain 3  score: -2.3 bits;  conditional E-value: 0.73
                 HHHHHH CS
     RBD-FIP  20 edYiDn 25 
                 ++Y+Dn
  AHX11823.1 254 KQYLDN 259
                 79***9 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (282 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       538  (0.0300073); expected 358.6 (0.02)
Passed bias filter:                      450  (0.025099); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.23s 00:00:00.66 Elapsed: 00:00:00.37
# Mc/sec: 2300.57
//
Query:       AHX11824.1  [L=310]
Description: ribosomal protein S2 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    1.3e-84  282.8   0.0    1.6e-84  282.5   0.0    1.1  1  Ribosomal_S2  Ribosomal protein S2


Domain annotation for each model (and alignments):
>> Ribosomal_S2  Ribosomal protein S2
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  282.5   0.0   8.9e-89   1.6e-84       1     213 [.      13     226 ..      13     228 .. 0.97

  Alignments for each domain:
  == domain 1  score: 282.5 bits;  conditional E-value: 8.9e-89
  Ribosomal_S2   1 LLeagvhfGhqtrrwnpkmkpyIygern.gihiidlektlaalrraykvvkevaakggkilfvgtkkqakeavkeaakrangyyvnerWlgGtLTNf 96 
                   L e g+h+Gh+tr wnpkm +yIyg+ n ++hiidl+kt+++++ a+k ++ev+a+ g++lfvgtk qa +++ke+a+r++++yvn rW  G++TN+
    AHX11824.1  13 LFEVGAHLGHKTRFWNPKMVSYIYGASNtKTHIIDLQKTVPMMKAALKEINEVVANSGRVLFVGTKMQACDIIKEEASRCGQHYVNLRWPSGMFTNW 109
                   7899********************998758******************************************************************* PP

  Ribosomal_S2  97 ktikksikklkeleeleedgeldltkkealklkkekekleknlggikkmkklPdlvvvldpkkekiavkEakklgipviaivDtnvdpdlvdypIpa 193
                   +t++ksikkl ++e+l e++   l+kke+l++++++e+++k+lgg+++m  lP++v+v+dpkke+iav+Ea+kl+ipv+aivDtn+dp++++ypIp+
    AHX11824.1 110 NTVSKSIKKLAHYEKLLEQEGEVLSKKERLSINRKRERIDKYLGGVRRMGGLPSIVFVIDPKKEYIAVEEANKLNIPVVAIVDTNCDPSKITYPIPG 206
                   ***************98766666************************************************************************** PP

  Ribosomal_S2 194 Nddsirsiklilgvladaie 213
                   Ndds+++i  +++++ada+ 
    AHX11824.1 207 NDDSLKCIGYYCKLVADAVL 226
                   ******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (310 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       877  (0.0489152); expected 358.6 (0.02)
Passed bias filter:                      590  (0.0329076); expected 358.6 (0.02)
Passed Vit filter:                        39  (0.00217525); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 2231.34
//
Query:       AHX11825.1  [L=230]
Description: ubiquinone/menaquinone biosynthesis methyltransferase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.6e-75  252.7   0.1    2.9e-75  252.6   0.1    1.0  1  Ubie_methyltran  ubiE/COQ5 methyltransferase family
    2.4e-19   69.8   0.0    8.5e-19   68.1   0.0    1.8  2  Methyltransf_25  Methyltransferase domain
    1.1e-17   64.5   0.0    9.9e-17   61.4   0.0    2.1  2  Methyltransf_11  Methyltransferase domain
    6.2e-15   55.3   0.0    7.8e-15   55.0   0.0    1.2  1  Methyltransf_31  Methyltransferase domain
    6.4e-10   39.7   0.0      1e-09   39.0   0.0    1.3  1  Methyltransf_12  Methyltransferase domain
    6.1e-07   29.4   0.0      8e-07   29.0   0.0    1.1  1  Methyltransf_23  Methyltransferase domain
    2.2e-06   27.3   0.0    3.4e-06   26.7   0.0    1.3  1  MTS              Methyltransferase small domain
    3.3e-05   23.5   0.0      0.025   14.1   0.0    2.9  3  Methyltransf_5   MraW methylase family
    0.00057   19.8   0.1     0.0013   18.7   0.0    1.7  2  Methyltransf_8   Hypothetical methyltransferase
     0.0026   17.5   0.0     0.0054   16.5   0.0    1.5  2  Met_10           Met-10+ like-protein
  ------ inclusion threshold ------
      0.026   14.4   0.0      0.042   13.8   0.0    1.3  1  Methyltransf_18  Methyltransferase domain


Domain annotation for each model (and alignments):
>> Ubie_methyltran  ubiE/COQ5 methyltransferase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  252.6   0.1   1.8e-78   2.9e-75       9     233 .]       6     229 ..       1     229 [. 0.98

  Alignments for each domain:
  == domain 1  score: 252.6 bits;  conditional E-value: 1.8e-78
                      XXXXXX-HHHHHHHHHHHHHTTTHHHHHHHHHHH--S--TTEEEEES-TT-HHHHHHHHHHHHHHEEEEEES-HHHHHHHHHHHHHHTSSTEEE CS
  Ubie_methyltran   9 vkevfesvaskyDlmndvlslgihrlWkkfveklvavkrgakvlDvagGtgDlafklsdsvgekgkvvvlDinenmLkvgekklkeegkinief 102
                      v+ +f+sv+++yDl nd++s gihr Wk+   k  +  + + vlD+a+GtgD++++l+++ +++ +v+++D n++mL++++++l ++g+ +++ 
       AHX11825.1   6 VDGIFSSVSKRYDLTNDLMSAGIHRRWKRNFVKSIGLIPNQLVLDMAAGTGDITLRLLET-DKSPDVIMCDRNPEMLQIAKDRLLDNGYLSVKI 98 
                      999**************************99999999********************986.78899**************************** PP

                      EE--TTT-TTS-T-EEEEEEES-GGG-S-HHHHHHHHHHHEEEEEEEEEEEE----SHHHHHHHHHHHH.HHHHHHHHHHS-HHHHHHHHHHHH CS
  Ubie_methyltran 103 lqanaeeLpfeddsfDvvtvsfGlrnvtDklkaLkeayrvlkpGGrlvvlefskvelpllsqayelyskevlPvlGkllakdldsyryLvesir 196
                      + a+a eLpfed++fD + v+fG+rn++D++k++ ea+rvl+ GG++ +lefs+v +  +++ y  ys +++P +G+ + ++ d y yLvesi+
       AHX11825.1  99 VRAEAAELPFEDNTFDHYVVAFGVRNFSDIQKSISEAHRVLRTGGKFSCLEFSNVDNSYINMIYGYYSRNFIPWIGEKVTQNRDAYVYLVESIK 192
                      ********************************************************************************************** PP

                      HS--HHHHHHHHHHTTEEEEEEEEEGGGTEEEEEEEE CS
  Ubie_methyltran 197 afPdqetlkeliedaGfksveyesltgGvvaihigvk 233
                      +fPd+e +k+++ d Gf+ v+ye+ t+Gvvaih+++k
       AHX11825.1 193 NFPDAESFKQILSDTGFTRVKYEKATFGVVAIHTALK 229
                      **********************************987 PP

>> Methyltransf_25  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   68.1   0.0   5.2e-22   8.5e-19       1      97 []      48     143 ..      48     143 .. 0.96
   2 ?   -0.9   0.0       1.7   2.7e+03      50      78 ..     186     213 ..     165     229 .. 0.58

  Alignments for each domain:
  == domain 1  score: 68.1 bits;  conditional E-value: 5.2e-22
                      EEEET-TTSHHHHHHHCTSTSSEEEEEESSHHHHHHHHHHHHHTTT.TEEEEESBCCGBSSSTTTEEEEEEESTGGGSSHHHHHHHHHHHHHHE CS
  Methyltransf_25   1 vLdlGcGtGrltlalakrlgkakvtgvDiseemleaareraeeegl.nvefvqgdaedlpfedgsfDlvvssgalhhlsdedlekalkeiarvL 93 
                      vLd+++GtG++tl+l++  ++ +v+++D ++eml++a+ r+ ++g+ +v++v+++a +lpfed++fD  v+++++  +s  d++k ++e++rvL
       AHX11825.1  48 VLDMAAGTGDITLRLLETDKSPDVIMCDRNPEMLQIAKDRLLDNGYlSVKIVRAEAAELPFEDNTFDHYVVAFGVRNFS--DIQKSISEAHRVL 139
                      9***************997699*********************9999************************98888887..899********** PP

                      EEEE CS
  Methyltransf_25  94 kpgG 97 
                      + gG
       AHX11825.1 140 RTGG 143
                      ***9 PP

  == domain 2  score: -0.9 bits;  conditional E-value: 1.7
                      EEESBCCGBSSSTTTEEEEEEESTGGGSS CS
  Methyltransf_25  50 fvqgdaedlpfedgsfDlvvssgalhhls 78 
                      +++ +++++p + +sf  ++s  ++  ++
       AHX11825.1 186 YLVESIKNFPDA-ESFKQILSDTGFTRVK 213
                      556666666644.4777777743354444 PP

>> Methyltransf_11  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.4   0.0   6.1e-20   9.9e-17       1      95 [.      49     146 ..      49     147 .. 0.95
   2 ?    0.9   0.0      0.45   7.3e+02      33      75 ..     172     213 ..     155     229 .. 0.65

  Alignments for each domain:
  == domain 1  score: 61.4 bits;  conditional E-value: 6.1e-20
                      EEET-TTSHHHHHHHHTT..SEEEEEES-HHHHHHHHHHCCHHT-.EEEETTEECCCTSS-TT-EEEEEEES-CCC-CCHHHHHHHHHHHEEEE CS
  Methyltransf_11   1 LdvGcGtGrlaealakrg..arvvgvDlskemlklakekaseegl.kvefvvadaeklpfednsfDlvvssevlhhvedpekalkeiaRvLkpg 91 
                      Ld+++GtG ++  l ++    +v+ +D ++eml++ak++  ++g  +v++v+a+a +lpfedn+fD  v+ + + ++ d +k ++e++RvL+ g
       AHX11825.1  49 LDMAAGTGDITLRLLETDksPDVIMCDRNPEMLQIAKDRLLDNGYlSVKIVRAEAAELPFEDNTFDHYVVAFGVRNFSDIQKSISEAHRVLRTG 142
                      89*************665669*********************9999************************************************ PP

                      EEEE CS
  Methyltransf_11  92 Gllv 95 
                      G++ 
       AHX11825.1 143 GKFS 146
                      *986 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.45
                      HHHHHCCHHT-EEEETTEECCCTSS-T.T-EEEEEEES-CCC-C CS
  Methyltransf_11  33 lakekaseeglkvefvvadaeklpfed.nsfDlvvssevlhhve 75 
                      +  ek+ +++    ++v+++++  f+d +sf  ++s   ++ v+
       AHX11825.1 172 WIGEKVTQNRDAYVYLVESIKN--FPDaESFKQILSDTGFTRVK 213
                      5555555555445566777776..66656887777776666664 PP

>> Methyltransf_31  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   55.0   0.0   4.8e-18   7.8e-15       7     114 ..      48     156 ..      44     216 .. 0.81

  Alignments for each domain:
  == domain 1  score: 55.0 bits;  conditional E-value: 4.8e-18
  Methyltransf_31   7 vlDlGCGtGeltfelaeelgpkaevvGiDiseeaielArenaqklgldnveFeqgdieeleklledekfDl.ilsnevlnaladpdkileeier 99 
                      vlD ++GtG++t++l  e  +  +v+  D+++e+++ A+ ++ ++g+  v+  ++++ el+  +ed++fD  +++++v   ++d +k + e++r
       AHX11825.1  48 VLDMAAGTGDITLRLL-ETDKSPDVIMCDRNPEMLQIAKDRLLDNGYLSVKIVRAEAAELP--FEDNTFDHyVVAFGVR-NFSDIQKSISEAHR 137
                      9***************.6667789*************************************..*******736666665.9************* PP

  Methyltransf_31 100 vlkpggilliedpr....l 114
                      vl++gg + + +++     
       AHX11825.1 138 VLRTGGKFSCLEFSnvdnS 156
                      **********999944440 PP

>> Methyltransf_12  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.0   0.0   6.2e-13     1e-09       1      99 []      49     145 ..      49     145 .. 0.91

  Alignments for each domain:
  == domain 1  score: 39.0 bits;  conditional E-value: 6.2e-13
  Methyltransf_12   1 LeiGcGtGsllralleklpdieytgvDispsaiedakeklakrennnnnnvelealdlldldggssfDl.vvasnvlhhlkdirevldnirklL 93 
                      L+  +GtG+++ +lle  +  +++ +D +p++++ ak +l +++ ++++ v+ ea +l  +d   +fD  vva++v + + di++++++++++L
       AHX11825.1  49 LDMAAGTGDITLRLLETDKSPDVIMCDRNPEMLQIAKDRLLDNGYLSVKIVRAEAAELPFEDN--TFDHyVVAFGVRN-FSDIQKSISEAHRVL 139
                      8999*****************************************************998776..9**8355556655.58************* PP

  Methyltransf_12  94 kpgGrl 99 
                      + gG++
       AHX11825.1 140 RTGGKF 145
                      ****86 PP

>> Methyltransf_23  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   29.0   0.0   4.9e-10     8e-07      20     163 ..      42     212 ..      20     214 .. 0.78

  Alignments for each domain:
  == domain 1  score: 29.0 bits;  conditional E-value: 4.9e-10
  Methyltransf_23  20 lraggrvLdiGcGtG.illevlren.gfsvtgvDlspeaveiae.........kakkaqkdqfdeqeaaepqgkfdlIvlrevlehvpdppell 102
                      l +++ vLd+++GtG i+l++l++    +v++ D +pe+ +ia+         + k  + + +   e ++++++fd  v  ++  ++ d  + +
       AHX11825.1  42 LIPNQLVLDMAAGTGdITLRLLETDkSPDVIMCDRNPEMLQIAKdrlldngylSVKIVRAEAA---ELPFEDNTFDHYVVAFGVRNFSDIQKSI 132
                      566779*********99*****666266*******************9986663333333333...6788999***99999999********** PP

  Methyltransf_23 103 rqiatllkpgGylllseplasl.....................kedrllldwlylvpagrhisffsarslkelleeaGlevv 163
                      + +++ l+ gG + ++e+ + +                     k ++  + + ylv+     +f +a+s+k++l + G++ v
       AHX11825.1 133 SEAHRVLRTGGKFSCLEFSNVDnsyinmiygyysrnfipwigeKVTQNRDAYVYLVES--IKNFPDAESFKQILSDTGFTRV 212
                      ************9999975544677999999888887777766566666666677755..559****************866 PP

>> MTS  Methyltransferase small domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.7   0.0   2.1e-09   3.4e-06      31     138 ..      44     148 ..       8     164 .. 0.87

  Alignments for each domain:
  == domain 1  score: 26.7 bits;  conditional E-value: 2.1e-09
                 TCSEEEEET-TTSHHHHHHHHHTTC.EEEEEESBHHHHHHHHHHHHHTTGC.EEEEE-STTT.TSTTS-EEEEEE---STTTCHCHHHHHHHHHHHHHH CS
         MTS  31 lsgkvlDlGcGaGvlgaalakespeaevtlvdvdarAlesakenleankle.vevvasdvle.eveekkfdlivsNPPfhagkatelavaeeliaeAke 127
                  ++ vlD+++G+G +++ l++  ++ +v ++d + + l++ak  l +n+   v++v  ++ e  +e++ fd+ v    +++ ++     +++ i eA++
  AHX11825.1  44 PNQLVLDMAAGTGDITLRLLETDKSPDVIMCDRNPEMLQIAKDRLLDNGYLsVKIVRAEAAElPFEDNTFDHYVVAFGVRNFSD-----IQKSISEAHR 137
                 45679*******************************************98779999888887367899****999877777777.....8888999*** PP

                 HEEEEEEEEEE CS
         MTS 128 aLkegGeLliV 138
                 +L++gG++ + 
  AHX11825.1 138 VLRTGGKFSCL 148
                 ******99875 PP

>> Methyltransf_5  MraW methylase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   14.1   0.0   1.5e-05     0.025      14      77 ..      38     102 ..      33     120 .. 0.83
   2 ?    4.0   0.0     0.018        29     217     251 ..     126     160 ..     122     172 .. 0.82
   3 ?    2.1   0.0      0.07   1.1e+02      68     113 ..     174     220 ..     165     226 .. 0.85

  Alignments for each domain:
  == domain 1  score: 14.1 bits;  conditional E-value: 1.5e-05
                     HHT---TT-EEEES--TTSHHHHHHHTT--TTEEEEEES-HHHHHHHTT.....---.EEEEES- CS
  Methyltransf_5  14 ellepkedgvyiDaTlGaggHsealLeqlselrligidrDksalarakerLkefekr.ltlvkgn 77 
                     + +   ++++ +D+  G+g  + +lLe  ++  +i++dr +++l++ak+rL +     +++v+++
      AHX11825.1  38 KSIGLIPNQLVLDMAAGTGDITLRLLETDKSPDVIMCDRNPEMLQIAKDRLLDNGYLsVKIVRAE 102
                     555666788999**************************************988654336666555 PP

  == domain 2  score: 4.0 bits;  conditional E-value: 0.018
                     HHHHHHHHHHHHHEEEEEEEEEEESSHHHHHHHHH CS
  Methyltransf_5 217 eeleelleaalellakggrlavisFhSledrivkk 251
                     + +++++++a ++l++gg+++ + F  +++  +  
      AHX11825.1 126 SDIQKSISEAHRVLRTGGKFSCLEFSNVDNSYINM 160
                     57899********************9998877655 PP

  == domain 3  score: 2.1 bits;  conditional E-value: 0.07
                     ---EEEEES-GGGHHHHHHHTT.TT-EEEEEEE-S--HHHHH-GGG- CS
  Methyltransf_5  68 ekrltlvkgnfkelkealaean.vtkvdgillDLGvSslqldkaerG 113
                      +++t  ++ +  l e +++ + +++++ il D G   ++++ka  G
      AHX11825.1 174 GEKVTQNRDAYVYLVESIKNFPdAESFKQILSDTGFTRVKYEKATFG 220
                     5778999999999999999998899***************9998755 PP

>> Methyltransf_8  Hypothetical methyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   7.8e-07    0.0013     104     159 ..      94     150 ..      48     163 .. 0.87
   2 ?   -2.2   0.0       1.9     3e+03     155     183 ..     186     214 ..     176     222 .. 0.76

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 7.8e-07
                     SSTTEEES-TTS-S--TT-EEEEEEES---S.S-HHHHHHHHHHHEEEEEEEEEEEE CS
  Methyltransf_8 104 vnervvacdlakvPledesvdvavfclslmg.tnladflkeanrvlkvGGllkvaev 159
                     +  ++v  + a++P ed++ d  v+ + +    ++++ + ea+rvl++GG +   e 
      AHX11825.1  94 LSVKIVRAEAAELPFEDNTFDHYVVAFGVRNfSDIQKSISEAHRVLRTGGKFSCLEF 150
                     56678888999**********9999999865389****************9987765 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 1.9
                     EEEEEGGG-S-HHHHHHHHHCTTEEEEEE CS
  Methyltransf_8 155 kvaevksrfesvklfaraltklGfevksk 183
                     ++ e    f++ + f++ l+  Gf  ++ 
      AHX11825.1 186 YLVESIKNFPDAESFKQILSDTGFTRVKY 214
                     55555667899999999999999987655 PP

>> Met_10  Met-10+ like-protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   16.5   0.0   3.3e-06    0.0054      99     186 ..      43     130 ..      16     144 .. 0.79
   2 ?   -2.9   0.0       2.8   4.6e+03     133     159 ..     180     206 ..     176     214 .. 0.73

  Alignments for each domain:
  == domain 1  score: 16.5 bits;  conditional E-value: 3.3e-06
                 -TT-EEEETT-TTTCCHHHCCHHTTSSEEEEEES-HHHHHHHHHHHHHTT-TTCEEEEES-GGG---.TT-EEEEEE--TTTGGGGHHH CS
      Met_10  99 eegevVvdvfAGiGpfaipiakyskakrvlaidlnPesvkylkeniklNkvekvvkpileDgrevir.eqladrvvmnlpksaieFldk 186
                  ++++V+d+ AG G  ++ +    k   v+  d nPe  +  k+ +  N     vk + ++++e+   ++++d++v  +  +  + ++k
  AHX11825.1  43 IPNQLVLDMAAGTGDITLRLLETDKSPDVIMCDRNPEMLQIAKDRLLDNGY-LSVKIVRAEAAELPFeDNTFDHYVVAFGVRNFSDIQK 130
                 589***********************************9998888766654.4566677777777655888999998776665555555 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 2.8
                 -HHHHHHHHHHHHHTT-TTCEEEEES- CS
      Met_10 133 nPesvkylkeniklNkvekvvkpileD 159
                 n +++ yl e ik    ++  k il+D
  AHX11825.1 180 NRDAYVYLVESIKNFPDAESFKQILSD 206
                 778899999999876666666666666 PP

>> Methyltransf_18  Methyltransferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.8   0.0   2.6e-05     0.042      12      73 ..      43     103 ..      36     140 .. 0.77

  Alignments for each domain:
  == domain 1  score: 13.8 bits;  conditional E-value: 2.6e-05
  Methyltransf_18  12 vekgsrvaDiGtDHgylpiylvkegkakkviasDinegplekakeniekagledkievrlsd 73 
                      ++ ++ v+D  +  g +++ l++++k + vi++D n++ l+ ak+ + ++g+ +   vr   
       AHX11825.1  43 IP-NQLVLDMAAGTGDITLRLLETDKSPDVIMCDRNPEMLQIAKDRLLDNGYLSVKIVRAEA 103
                      55.78899*************************************99998886544444444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (230 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      366  (0.0204139); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                        11  (0.000613531); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              11  [number of targets reported over threshold]
# CPU time: 0.46u 0.27s 00:00:00.73 Elapsed: 00:00:00.44
# Mc/sec: 1573.04
//
Query:       AHX11826.1  [L=441]
Description: hypothetical protein NHE_0907 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model     Description
    ------- ------ -----    ------- ------ -----   ---- --  --------  -----------
     0.0014   18.8  35.2      0.028   14.7   0.5    6.0  5  Gag_p6     Gag protein p6
  ------ inclusion threshold ------
       0.17   11.9   0.3    1.3e+02    2.6   0.0    3.3  3  CHB_HEX_C  Chitobiase/beta-hexosaminidase C-terminal domain


Domain annotation for each model (and alignments):
>> Gag_p6  Gag protein p6
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -1.6   0.1      0.38   3.4e+03       1       6 [.     104     109 ..     104     114 .. 0.92
   2 ?    0.9   3.1     0.064   5.7e+02       2      29 ..     124     162 ..     118     164 .. 0.84
   3 !   13.0   2.1     1e-05      0.09       1      28 [.     165     217 ..     165     220 .. 0.77
   4 !   14.7   0.5   3.1e-06     0.028       1      28 [.     221     273 ..     221     276 .. 0.77
   5 !    8.2   3.5   0.00032       2.9       1      12 [.     277     288 ..     277     334 .. 0.75

  Alignments for each domain:
  == domain 1  score: -1.6 bits;  conditional E-value: 0.38
      Gag_p6   1 lQsRpE 6  
                 +QsR+E
  AHX11826.1 104 PQSRLE 109
                 8***99 PP

  == domain 2  score: 0.9 bits;  conditional E-value: 0.064
      Gag_p6   2 QsRpEPTAPPA...........EsfgfgeeitpspKqeq 29 
                 Q  pE  APP+           E+    + itp++  e+
  AHX11826.1 124 QAVPEANAPPEslqieltldqsEDSSEKQPITPPQQTEP 162
                 44578899**999999999999999977889**999987 PP

  == domain 3  score: 13.0 bits;  conditional E-value: 1e-05
      Gag_p6   1 lQsRpEPTAPPA.........................EsfgfgeeitpspKqe 28 
                 lQ + EPTAPP+                         E+    + itp++  e
  AHX11826.1 165 LQHQIEPTAPPEphktepvivnappeslqieltldqsEDSSEKQPITPPQQTE 217
                 799*********99999999999997777766666666666555566666666 PP

  == domain 4  score: 14.7 bits;  conditional E-value: 3.1e-06
      Gag_p6   1 lQsRpEPTAPPA.........................EsfgfgeeitpspKqe 28 
                 lQ + EPTAPP+                         E+    + itp++  e
  AHX11826.1 221 LQHQIEPTAPPEphktepvivnalpeslqieltldqsEDSSEKQPITPPQQTE 273
                 799*********99999999999997777777776666666555567766666 PP

  == domain 5  score: 8.2 bits;  conditional E-value: 0.00032
      Gag_p6   1 lQsRpEPTAPPA 12 
                 lQ + EPTAPP+
  AHX11826.1 277 LQHQIEPTAPPE 288
                 799********8 PP

>> CHB_HEX_C  Chitobiase/beta-hexosaminidase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    2.6   0.0     0.015   1.3e+02      29      65 ..     130     166 ..     126     170 .. 0.78
   2 ?    2.5   0.0     0.017   1.5e+02      32      65 ..     189     222 ..     179     226 .. 0.77
   3 ?    2.4   0.0     0.018   1.6e+02      33      65 ..     246     278 ..     236     282 .. 0.78

  Alignments for each domain:
  == domain 1  score: 2.6 bits;  conditional E-value: 0.015
   CHB_HEX_C  29 nvalPGltieYsldggetwqkytayepvavsgkvklr 65 
                 n     l+ie +ld++e  ++ +  +p + +++v+l+
  AHX11826.1 130 NAPPESLQIELTLDQSEDSSEKQPITPPQQTEPVSLQ 166
                 5556789**********99888866777777777775 PP

  == domain 2  score: 2.5 bits;  conditional E-value: 0.017
   CHB_HEX_C  32 lPGltieYsldggetwqkytayepvavsgkvklr 65 
                    l+ie +ld++e  ++ +  +p + +++v+l+
  AHX11826.1 189 PESLQIELTLDQSEDSSEKQPITPPQQTEPVSLQ 222
                 56799*********99888866777777777775 PP

  == domain 3  score: 2.4 bits;  conditional E-value: 0.018
   CHB_HEX_C  33 PGltieYsldggetwqkytayepvavsgkvklr 65 
                   l+ie +ld++e  ++ +  +p + +++v+l+
  AHX11826.1 246 ESLQIELTLDQSEDSSEKQPITPPQQTEPVSLQ 278
                 5799*********99888866777777777775 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (441 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       464  (0.0258799); expected 358.6 (0.02)
Passed bias filter:                      284  (0.0158403); expected 358.6 (0.02)
Passed Vit filter:                        33  (0.00184059); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.54u 0.29s 00:00:00.83 Elapsed: 00:00:00.42
# Mc/sec: 3178.37
//
Query:       AHX11827.1  [L=394]
Description: pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    5.2e-84  281.3   0.6    7.1e-84  280.9   0.6    1.1  1  2-oxoacid_dh     2-oxoacid dehydrogenases acyltransferase (ca
    2.7e-15   55.9   2.1    7.4e-15   54.6   1.4    2.1  2  Biotin_lipoyl    Biotin-requiring enzyme
    8.6e-13   48.4   0.1    1.8e-12   47.4   0.1    1.6  1  E3_binding       e3 binding domain
    0.00038   20.2   0.0     0.0011   18.7   0.0    1.8  1  Biotin_lipoyl_2  Biotin-lipoyl like


Domain annotation for each model (and alignments):
>> 2-oxoacid_dh  2-oxoacid dehydrogenases acyltransferase (catalytic domain)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  280.9   0.6   1.6e-87   7.1e-84       5     231 ..     173     393 ..     170     394 .] 0.98

  Alignments for each domain:
  == domain 1  score: 280.9 bits;  conditional E-value: 1.6e-87
                   XXXXXXXXXXXXXXXXXXXX.XXXEEEEEEEEE-HHHHHHHHHHHHHHHHTT-----HHHHHHHHHHHHHHH-GGGG-EE.EESEEEE--SS--EEE CS
  2-oxoacid_dh   5 ervplsgirkaiakrlteskqeiphftlsdevdvtallelrkelkekeakeekakltlldflikavalAlkefPelnasvdeeekeivvkkhvniGv 101
                   ++  +s++r++ia+rl eskq+iphf+ls+++ + +ll+ r+e++  +      k+t++df++ka+a Al ++P++n s++++   i ++++++++v
    AHX11827.1 173 TELAISPMRRVIAERLVESKQNIPHFYLSVDCHLGNLLKTREEINGYLG----EKITINDFVVKATAFALGKHPDMNVSWNGDV--IKQHQAIDVSV 263
                   67789*****************************************996....39*****************************..*********** PP

                   E--------EEEE--GGG--HHHHHHHHHHHHHHHTTT---GGGTSS-SEEEE---------------TT-SEEEEE---.B--TTSTT-HT---EE CS
  2-oxoacid_dh 102 AvatprGLlvPviknadkkslleiakelkelaekaregklkpedleggtftisNlGmlGvtsftPiinppqvaIlgvgrikerpvvkegelvvrkvm 198
                   Ava p+GL++P+++ adk+sl+ i++e+k+l++ka+++kl+p +++gg+ftisNlGm+G+++ft+iinppq+aIl+vg+ ++ pv++++++vvr++m
    AHX11827.1 264 AVAIPDGLITPIVHAADKLSLSRISTEVKKLVQKAKDNKLQPIEFQGGSFTISNLGMYGIKEFTAIINPPQAAILAVGAGRKAPVIVDDAIVVRNIM 360
                   ************************************************************************************************* PP

                   EEEEEEETTT--HHHHHHHHHHHHHTT-HHXXX CS
  2-oxoacid_dh 199 tlslsaDHRvidGaeaarFlntlkkllenpeel 231
                   tl+ls+DHRvidGa aarFl+tlk+ +e+p+ +
    AHX11827.1 361 TLTLSCDHRVIDGALAARFLQTLKQAIEKPAIM 393
                   ******************************866 PP

>> Biotin_lipoyl  Biotin-requiring enzyme
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   54.6   1.4   1.6e-18   7.4e-15      12      73 .]       1      64 [.       1      64 [. 0.94
   2 ?   -2.9   0.0       1.4   6.1e+03      30      42 ..      87      99 ..      86     105 .. 0.83

  Alignments for each domain:
  == domain 1  score: 54.6 bits;  conditional E-value: 1.6e-18
                   EEE..ECSESSSTTCEE-TTSEEEEEECTTEEEEEEBSSSEEEEEESSTTTEE.E-TTCEEEEE CS
  Biotin_lipoyl 12 veeg.vvevlvkvGdkVkagqvlaeveamKmemeieapkaGvvkeilvkeGdt.vevgdllaki 73
                   ++eg   ++lv++G+k+kagqv+ae+e++K+++e+ea ++G++++il+++ +t ++v++++ ++
     AHX11827.1  1 MKEGtLSKWLVSEGEKIKAGQVMAEIETDKATVEFEAVDEGTLAKILIPDKATnIKVNEPIGVL 64
                   57888999*****************************************99888******9875 PP

  == domain 2  score: -2.9 bits;  conditional E-value: 1.4
                   TSEEEEEECTTEE CS
  Biotin_lipoyl 30 gqvlaeveamKme 42
                   g+++  ve +K++
     AHX11827.1 87 GEPIKSVEPDKLS 99
                   7889999999987 PP

>> E3_binding  e3 binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.4   0.1     4e-16   1.8e-12       1      35 [.     120     155 ..     120     156 .. 0.95

  Alignments for each domain:
  == domain 1  score: 47.4 bits;  conditional E-value: 4e-16
                 SBE-HHHHHHHHHCT--TTTS-.--CTTTBE-HHHH CS
  E3_binding   1 vlAsPaaRklAkelGidLsdvk.GtGpgGRItkeDV 35 
                 +lA+P+a+k+A  ++idLs ++ G+Gp+GRI+k+D 
  AHX11827.1 120 ILATPLAKKIASINNIDLSLIQtGSGPNGRIVKDDL 155
                 79*******************77************6 PP

>> Biotin_lipoyl_2  Biotin-lipoyl like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.7   0.0   2.6e-07    0.0011      11      37 ..       4      30 ..       2      41 .. 0.89

  Alignments for each domain:
  == domain 1  score: 18.7 bits;  conditional E-value: 2.6e-07
  Biotin_lipoyl_2 11 GrVaqlnVkdGqrVkaGdvLaelDsra 37
                     G++++++V +G  +kaG+v ae+++++
       AHX11827.1  4 GTLSKWLVSEGEKIKAGQVMAEIETDK 30
                     99*********************9876 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (394 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       537  (0.0299515); expected 358.6 (0.02)
Passed bias filter:                      454  (0.0253221); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.49u 0.20s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 3112.75
//
Query:       AHX11828.1  [L=255]
Description: phosphomethylpyrimidine kinase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
      2e-70  237.0   0.1    2.2e-70  236.9   0.1    1.0  1  Phos_pyr_kin  Phosphomethylpyrimidine kinase
    3.2e-06   26.7   0.0    4.3e-06   26.3   0.0    1.2  1  PfkB          pfkB family carbohydrate kinase
      0.007   15.8   1.5        1.2    8.5   0.0    2.5  3  HK            Hydroxyethylthiazole kinase family


Domain annotation for each model (and alignments):
>> Phos_pyr_kin  Phosphomethylpyrimidine kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  236.9   0.1   3.6e-74   2.2e-70       1     238 [.      15     250 ..      15     255 .] 0.97

  Alignments for each domain:
  == domain 1  score: 236.9 bits;  conditional E-value: 3.6e-74
                   ETTSSSHHHHHHHHHHHTTEEEEEEEEEEEEEETTCEEEEEE--HHHHHHHHHHHHHTS--SEEEE-S--SHHHHHHHHHHHHHTTSSEEEE---SS CS
  Phos_pyr_kin   1 DssGGAGiqADlktfsalgvygmsvitaltaqntkgvkevhplpaelveaqleavledvkvdavKiGmlasaeiievvaeklkkykvpvVlDPVmva 97 
                   Ds GGAG+qADl+ ++ l++ +  v+t++taq+ kgv+++h l+ ++v+aql   l+  k++a+KiGml+s+eii+++ ++lk  k+p+VlDPV++a
    AHX11828.1  15 DSIGGAGLQADLRIAALLDCSASNVVTCITAQDLKGVHAIHYLDGSMVSAQLACALSG-KPQAIKIGMLGSSEIISAIWNTLKISKIPIVLDPVLIA 110
                   99***************************************************99987.9************************************* PP

                   CTSSSBSSHHHHHHHHHHTGGG-SEEE-BHHHHHHHHT---SSHHHHHHHHHHHHHTT-SEEEEEEGGS-SSSEEEEEEEE.TSSEEEEEEEE---- CS
  Phos_pyr_kin  98 ksgselleeeavealkeeLlplatvitPNlpEaeaLlgekikteedmkeaakkllklgakaVlikGghlegeeavvtdvly.dgeeveeleaeriet 193
                   +s  +l+++ a+++l e+L+pl+ +itPNl+Eae+++geki ++++mk aa k+l+lga++VlikG h+   e+ + d+l+ ++++++e++ ++i+ 
    AHX11828.1 111 TSKFSLTKDGAFSVLLEKLIPLSYLITPNLFEAEMISGEKIYSTDTMKVAAGKILALGARNVLIKGFHC--GEDSLLDLLMtEDQRFVEFRYDKIKV 205
                   ********************************************************************8..566678****999************* PP

                   S--BTHHHHHHHHHHHHHHCTSSHHHHHHHHHHHHHHHHHCG-BS CS
  Phos_pyr_kin 194 knthGtGCtlssaiaaelakgesleeAvkkAkeyvteaikealel 238
                   ++thGtGC lssaia++ a g+slee+++ A + v++ i + l+l
    AHX11828.1 206 ETTHGTGCRLSSAIACYTAIGKSLEESITLASSLVSKEILRMLSL 250
                   ***********************************9999776665 PP

>> PfkB  pfkB family carbohydrate kinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   26.3   0.0   7.1e-10   4.3e-06     172     284 ..     119     238 ..      60     248 .. 0.81

  Alignments for each domain:
  == domain 1  score: 26.3 bits;  conditional E-value: 7.1e-10
                 H..HHHHHHHHHCTESEEEEEHHHHHHHHTSCTHSHHHHHHHHHHHHHTTSSEEEEE...EGGGEEEEEE.TTEEEEEEE..SSSS-SBGTTHHHHHHH CS
        PfkB 172 q..fkeallellaladllkpneeElealtgekledieealaalhklkakgaktvvvt...lGkeGalvve.kdgelkvpav.pkvkvvDttGAGDsfvg 263
                 +  f   l++l++l+ l++pn  E+e ++gek+ + +  + a+ k++a ga++v+++   +G++  l    ++++ +v+    k+kv  t G+G    +
  AHX11828.1 119 DgaFSVLLEKLIPLSYLITPNLFEAEMISGEKIYSTDTMKVAAGKILALGARNVLIKgfhCGEDSLLDLLmTEDQRFVEFRyDKIKVETTHGTGCRLSS 217
                 1557778999***********************9999999999999*********986657888877666544444444335999999999***88888 PP

                 HHHHHHHTTHHHHHHHHHHHH CS
        PfkB 264 gflaallegksleealrfana 284
                 +++   + gkslee++ +a+ 
  AHX11828.1 218 AIACYTAIGKSLEESITLASS 238
                 87777777********99975 PP

>> HK  Hydroxyethylthiazole kinase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    8.5   0.0    0.0002       1.2      54      94 ..      76     114 ..      61     128 .. 0.83
   2 ?   -2.2   0.0      0.36   2.2e+03     109     136 ..     155     182 ..     150     209 .. 0.67
   3 !    5.6   0.4    0.0015       8.7     184     207 ..     209     232 ..     188     244 .. 0.80

  Alignments for each domain:
  == domain 1  score: 8.5 bits;  conditional E-value: 0.0002
                 EEE-TT--HHHHHHHHHHHHHHHHTT--EEEE-TTBTTBHH CS
          HK  54 llNiGtleekaiealkaAvksakevnrPvvlDPVgvgAtel 94 
                 ++ iG l +   e++ a  ++ k +++P+vlDPV ++ +++
  AHX11828.1  76 AIKIGMLGS--SEIISAIWNTLKISKIPIVLDPVLIATSKF 114
                 588999998..7778888899999**********8877665 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 0.36
                 SEEEEEHHHHHHHHTSSCCSCSSSSSS- CS
          HK 109 avikGNasEilslaglelkvkGvDskea 136
                 + +k  a+ il+l   ++ +kG    e 
  AHX11828.1 155 DTMKVAAGKILALGARNVLIKGFHCGED 182
                 5566667777777777777777766655 PP

  == domain 3  score: 5.6 bits;  conditional E-value: 0.0015
                 TTHHHHHHHHHHHHHTTBSSHHHH CS
          HK 184 tasGCllgsvvaaflavkkdklla 207
                  ++GC l+s++a   a+ k   ++
  AHX11828.1 209 HGTGCRLSSAIACYTAIGKSLEES 232
                 59************9997654444 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (255 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       367  (0.0204696); expected 358.6 (0.02)
Passed bias filter:                      320  (0.0178482); expected 358.6 (0.02)
Passed Vit filter:                        21  (0.00117129); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.42u 0.26s 00:00:00.68 Elapsed: 00:00:00.41
# Mc/sec: 1881.20
//
Query:       AHX11829.1  [L=166]
Description: crossover junction endodeoxyribonuclease RuvC [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    2.5e-38  131.3   0.0    2.8e-38  131.1   0.0    1.0  1  RuvC      Crossover junction endodeoxyribonuclease RuvC
  ------ inclusion threshold ------
      0.057   13.5   0.0      0.089   12.9   0.0    1.3  1  DUF3882   Lactococcus phage M3 protein


Domain annotation for each model (and alignments):
>> RuvC  Crossover junction endodeoxyribonuclease RuvC
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  131.1   0.0   3.1e-42   2.8e-38       1     145 [.       5     152 ..       5     157 .. 0.94

  Alignments for each domain:
  == domain 1  score: 131.1 bits;  conditional E-value: 3.1e-42
                 EEEEE--SSEEEEEEEEE.ETTEEEEEEEEEEE---S.-HHHHHHHHHHHHHHHHHHH--SEEEEEE-S----HHHHHHHHHHHHHHHHHHHTTT--EE CS
        RuvC   1 ilGiDPGsrktGygviee.agrklslltsgvirtksd.plserlkavfdaveelldayepdalaieqvffaknvdsvlklaqarGvvilaalereisva 97 
                 +lGiDPG+ +tG++v+e  + +++ +++sgvi t++  +ls+r++++ ++v+e++d+++p++  +e++f++ n+ s lkla  rG+++l ++ + ++v 
  AHX11829.1   5 VLGIDPGLARTGWAVVEYkNPSEMCYIASGVISTNAReELSKRIRKIHEGVTEVIDNFDPNVSVLEKIFVNSNPCSSLKLAYCRGALMLTLALKSLPVL 103
                 79***************867899************998************************************************************* PP

                 EEEHHHHHHHHTSSTT--HHHHHHHHHHHTT----S.S.S-THHHHHHH CS
        RuvC  98 eytpsqvkkavtGigkaekeqvqalvkrlLklkakp.kpadaaDalava 145
                 e +p+++kk +tG g+a k q+ ++v++lL l+ +  k  d  Dala+a
  AHX11829.1 104 EIAPNAIKKRITGSGHATKLQIRYMVEKLLGLNLNLsKYSDLYDALALA 152
                 ******************************9997752668*******98 PP

>> DUF3882  Lactococcus phage M3 protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.9   0.0     1e-05     0.089      28      93 ..      28      92 ..       3     100 .. 0.71

  Alignments for each domain:
  == domain 1  score: 12.9 bits;  conditional E-value: 1e-05
                EEEEEE.E----TTS-HHHHHHHHHHHHHHHHHHTT-TT-EEEEE-----SSHHHHHHHHHHHHHHH CS
     DUF3882 28 evvvGs.ikaynkkkdalerakdivdaikevieeydlkdyflaieepiitrkrkgsisliranGsfl 93
                  ++ s + + n + +  +r  +i ++++evi+++d      ++e+  +  +   s+ l+ + G ++
  AHX11829.1 28 MCYIASgVISTNAREELSKRIRKIHEGVTEVIDNFDPNV--SVLEKIFVNSNPCSSLKLAYCRGALM 92
                3333332448888888999****************9654..45677788888899999999998776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (166 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       646  (0.036031); expected 358.6 (0.02)
Passed bias filter:                      588  (0.032796); expected 358.6 (0.02)
Passed Vit filter:                        54  (0.00301188); expected 17.9 (0.001)
Passed Fwd filter:                         2  (0.000111551); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               2  [number of targets reported over threshold]
# CPU time: 0.42u 0.25s 00:00:00.67 Elapsed: 00:00:00.41
# Mc/sec: 1220.13
//
Query:       AHX11830.1  [L=315]
Description: malate dehydrogenase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    5.1e-40  136.8   0.5    8.2e-40  136.2   0.5    1.3  1  Ldh_1_N         lactate/malate dehydrogenase, NAD binding dom
    1.2e-26   93.6   0.1    1.8e-26   93.1   0.1    1.2  1  Ldh_1_C         lactate/malate dehydrogenase, alpha/beta C-te
    0.00037   20.1   0.5     0.0016   18.1   0.5    1.9  1  UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family,
     0.0015   18.4   1.4      0.014   15.3   0.2    2.4  2  3HCDH_N         3-hydroxyacyl-CoA dehydrogenase, NAD binding 
     0.0047   16.5   0.2      0.026   14.1   0.0    2.1  2  Glyco_hydro_4   Family 4 glycosyl hydrolase
     0.0067   17.0   3.0       0.02   15.5   0.9    2.5  2  F420_oxidored   NADP oxidoreductase coenzyme F420-dependent
  ------ inclusion threshold ------
       0.11   12.6   0.1       0.26   11.4   0.1    1.6  1  DUF357          Protein of unknown function (DUF357)
       0.25   10.7   3.8        0.2   11.0   1.0    2.1  3  ThiF            ThiF family


Domain annotation for each model (and alignments):
>> Ldh_1_N  lactate/malate dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  136.2   0.5   3.7e-43   8.2e-40       1     141 []       1     141 [.       1     141 [. 0.98

  Alignments for each domain:
  == domain 1  score: 136.2 bits;  conditional E-value: 3.7e-43
                 EEEEEETTTSHHHHHHHHHHHHTTSSSEEEEE-SSHHHHHHHHHHHHHCHCCSTS-EEEEE.SSGGGGTTESEEEE--S-SS-TTTTHHHHHHHHHHHH CS
     Ldh_1_N   1 vkvavvGaaGgiGqslalllankkladelaLlDiakekleGvaldlshistflsvkvkvse.keeealkdadvvvitagvprkpGetRddLlkvNakIv 98 
                 +k++++Ga G+iG +la+l+a k+la+e++L+D++ + ++G+ald+s+   ++ + +k+s+ ++ e l++++v+++tag+prkpG++R++Ll+vNa ++
  AHX11830.1   1 MKISLIGA-GNIGGTLAHLIALKGLASEVELIDVNGDTAKGKALDISQSLPIIGRTMKISGsSKMERLQGSSVIIVTAGIPRKPGMSREELLDVNALVM 98 
                 69******.*******************************************9999999998999********************************** PP

                 HHHHHHHHHHTTTSEEEE-SSSHHHHHHHHHHHHTS-GGGEEE CS
     Ldh_1_N  99 keiveaiakvapnaivlvvsNPvdiltevlkkasglpkkrvig 141
                 ke++e+i+++ap+a+v+v++NP d ++ vlk+asg+++++++g
  AHX11830.1  99 KEVGEKIKQFAPEAFVIVITNPLDAMVWVLKQASGISPAKIVG 141
                 ****************************************997 PP

>> Ldh_1_C  lactate/malate dehydrogenase, alpha/beta C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   93.1   0.1     8e-30   1.8e-26       2     158 ..     145     306 ..     144     313 .. 0.94

  Alignments for each domain:
  == domain 1  score: 93.1 bits;  conditional E-value: 8e-30
                 HHHHHHHHHHHHHHHTS-GGGEE--EEBSSST..........ETTEEHHHHHTTSTTSTHHHHHHHHHHHHHHHHHHHHHHTTSSSS-HHHHHHHHHHH CS
     Ldh_1_C   2 tLDivRaktflaekagvtprsvkvtViGgHsg..........vtiipllsqvkellklsekqleeliervqnggdevvkakkGagsatlsmAvAgakfv 90 
                  LD+ R++ fla++ +v+ ++vk +V+G H++          v ++ l + ++  + +s+++++ +ier++ gg+e+v   k +gsa++  A+++ +++
  AHX11830.1 145 VLDSSRMNLFLAQELDVSVSDVKSMVLGSHGDsmvplirystVSGVSLKELIDM-DLISQEKVDSIIERTKAGGAEIVALLK-NGSAYYTPAASALEMA 241
                 59**************************************99999999888888.88999******************9865.6*************** PP

                 HHHHTTHTEEEEEEEEEESCCCECCSSEEEEEEEEEEETTEEEEE-------HHHHHHHHHHHHHHHH CS
     Ldh_1_C  91 eallrdtkeilsagvyldgevglkdqeieyfsvPvvlgknGvekvleilklndfeeekleksvkeLkk 158
                 e+ ++d k+ l+ +v+++g + ++d+  ++ ++Pvv+g nGve+v+e l+l+++e+ ++e+s +  +k
  AHX11830.1 242 ESYIEDQKKTLICSVIMKGRYLVEDD--IFSGIPVVIGSNGVERVVE-LNLTNEERRMFEASLDAARK 306
                 *************************9..9******************.************99876555 PP

>> UDPG_MGDP_dh_N  UDP-glucose/GDP-mannose dehydrogenase family, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.1   0.5   7.1e-07    0.0016       1     118 [.       1     116 [.       1     129 [. 0.69

  Alignments for each domain:
  == domain 1  score: 18.1 bits;  conditional E-value: 7.1e-07
                     SEEEEE--STTHHHHHHHHHHCT..SEEEEE-S-HHHHHHHCTTS-SS--TTHHHHHHHHCHTTTEEEES-HHHHHHC-SEEEE-----B-T... CS
  UDPG_MGDP_dh_N   1 mkisviGlGYvGlvtaavlaeig..hevigvDideekvdklnsgkipiyepgLeelvkkavesgrlsfttdvekaveeadvifiaVgTPskk... 90 
                     mkis iG+G +G++ a ++a +g   ev ++D++  +    + + + i  + L  ++ + +   ++s+++++e+ ++ + vi+++ g P k    
      AHX11830.1   1 MKISLIGAGNIGGTLAHLIALKGlaSEVELIDVNGDTA---KGKALDIS-QSLP-IIGRTM---KISGSSKMER-LQGSSVIIVTAGIPRKPgms 86 
                     89*********************9899*****998653...33444443.3343.444444...6889999988.99999999999999998544 PP

                     TTTCB-THH..HHHHHHHHHHHHHCEEEEE CS
  UDPG_MGDP_dh_N  91 kgkaaDlky..vesaarsiaealkkgkvvv 118
                     +++  D+++  ++++ ++i++++ +  v+v
      AHX11830.1  87 REELLDVNAlvMKEVGEKIKQFAPEAFVIV 116
                     444444443112444455555554455555 PP

>> 3HCDH_N  3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.3   0.2   6.1e-06     0.014       1      56 [.       2      59 ..       2      76 .. 0.80
   2 ?    1.7   0.1     0.091     2e+02       4      66 ..     139     212 ..     137     223 .. 0.67

  Alignments for each domain:
  == domain 1  score: 15.3 bits;  conditional E-value: 6.1e-06
                EEEEE--SCCHHHHHHHHHHTT-..EEEEE-S-HHHHHHHHHHHHHHHHCCTTTTSS- CS
     3HCDH_N  1 kvaviGaGtmGagiaavfasagl..eVvlvdiseealekalekieksleklvekgklk 56
                k+  iGaG +G  +a+++a +gl  eV l+d++ ++++  +  i++sl    +  k++
  AHX11830.1  2 KISLIGAGNIGGTLAHLIALKGLasEVELIDVNGDTAKGKALDISQSLPIIGRTMKIS 59
                5789*****************97558**********9999988888876665555554 PP

  == domain 2  score: 1.7 bits;  conditional E-value: 0.091
                 EE-.-SCCHHHHHHHHHHTT-EEEEE-S-HHHHHHHHHHHHH..........HHHCCTTTTSS-HHHHCCCHHC CS
     3HCDH_N   4 viG.aGtmGagiaavfasagleVvlvdiseealekalekiek..........sleklvekgklkeeeveaalar 66 
                 ++G aG++ ++  ++f++++l+V + d+++  l +  +++            sl++l+    +++e+v+++++r
  AHX11830.1 139 IVGmAGVLDSSRMNLFLAQELDVSVSDVKSMVLGSHGDSMVPlirystvsgvSLKELIDMDLISQEKVDSIIER 212
                 56635999999999999999999999997766655444333223333344456666666666666666666666 PP

>> Glyco_hydro_4  Family 4 glycosyl hydrolase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -0.7   0.0      0.39   8.7e+02       1      38 [.       2      35 ..       2      66 .. 0.63
   2 !   14.1   0.0   1.2e-05     0.026     124     166 ..      98     142 ..      90     157 .. 0.83

  Alignments for each domain:
  == domain 1  score: -0.7 bits;  conditional E-value: 0.39
                   EEEEETTTSSSHHHHHHHHHHTTTTCTE..EEEEEE-SSH CS
  Glyco_hydro_4  1 kiviiGgGStifaklllgdlkkteelsv..selaLvDide 38
                   ki +iG+G       + g l +  +l++  se+ L+D++ 
     AHX11830.1  2 KISLIGAGN------IGGTLAHLIALKGlaSEVELIDVNG 35
                   566666664......4444444444443225888888876 PP

  == domain 2  score: 14.1 bits;  conditional E-value: 1.2e-05
                    HHHHHHHHHHH-TTSEEEE-SSSHHHHHHHHHHHSTT..SEEEEE CS
  Glyco_hydro_4 124 lleIakdieelcPdawvlnytNPaavvteallrlvpn..ikavgl 166
                    + e+ ++i++++P+a+v+  tNP+  + ++l + ++    k+vg+
     AHX11830.1  98 MKEVGEKIKQFAPEAFVIVITNPLDAMVWVLKQASGIspAKIVGM 142
                    668999************************998765311577776 PP

>> F420_oxidored  NADP oxidoreductase coenzyme F420-dependent
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.5   0.9     9e-06      0.02       1      68 [.       2      76 ..       2      97 .. 0.77
   2 ?    0.8   0.1      0.34   7.6e+02      54      91 ..     104     140 ..      81     140 .. 0.78

  Alignments for each domain:
  == domain 1  score: 15.5 bits;  conditional E-value: 9e-06
                   EEEEETTSHHHHHHHHHHHHTTS-GGCEEEEEESSCCCHHHHHHHHC.........-EEECECHHHHHHH-SEEEE- CS
  F420_oxidored  1 kigiiGaGnmgealasgllaagaqpheivvansrnpekaeelaeelg.........vkvtavdneeaaeeadvvvla 68
                   ki +iGaGn+g +la+ ++ +g  ++e+ ++ + n ++a+  a +++          k++++++ e ++ + v++++
     AHX11830.1  2 KISLIGAGNIGGTLAHLIALKG-LASEVELI-DVNGDTAKGKALDISqslpiigrtMKISGSSKMERLQGSSVIIVT 76
                   799*******************.55555544.444444444444444445599999999999999999999999987 PP

  == domain 2  score: 0.8 bits;  conditional E-value: 0.34
                    CHHHHHHH-SEEEE-S-HHHHHHHHHHCGHHHHTTSEE CS
  F420_oxidored  54 dneeaaeeadvvvlavkpedveevlselakdalkgklv 91 
                    + ++ a ea v+v++ +  ++  vl+++ +  +  k+v
     AHX11830.1 104 KIKQFAPEAFVIVITNPLDAMVWVLKQA-SGISPAKIV 140
                    4566777888999999999999999998.777777776 PP

>> DUF357  Protein of unknown function (DUF357)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   0.00012      0.26      18      42 ..     225     249 ..     210     252 .. 0.84

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 0.00012
                 ..TS---HHHHHHHHHHHHHHHHHH CS
      DUF357  18 deesplgeaaeevlemaesYleDak 42 
                 +++s +++ a + lemaesY+eD k
  AHX11830.1 225 KNGSAYYTPAASALEMAESYIEDQK 249
                 6899******************965 PP

>> ThiF  ThiF family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.0   1.0   8.8e-05       0.2      20      49 ..       2      32 ..       1      35 [. 0.91
   2 ?   -3.5   0.0       2.4   5.3e+03       8      27 ..      59      78 ..      54      78 .. 0.77
   3 ?   -1.1   0.0      0.43   9.6e+02      12      54 ..     159     202 ..     148     205 .. 0.66

  Alignments for each domain:
  == domain 1  score: 11.0 bits;  conditional E-value: 8.8e-05
                EEEEE--SHHHHHHHHHHHHHTTT.EEEEEE CS
                xxxxxxxxxxxxxxxxxxxxxxxx.xxxxxx RF
        ThiF 20 kvllvGaGglGsellknLalsGvg.kltlvD 49
                k+ l+GaG +G  l++++al G+  +++l+D
  AHX11830.1  2 KISLIGAGNIGGTLAHLIALKGLAsEVELID 32
                899********************55999999 PP

  == domain 2  score: -3.5 bits;  conditional E-value: 2.4
                HHHHHHHHHHTSEEEEE--S CS
                xxxxxxxxxxxxxxxxxxxx RF
        ThiF  8 lgedgqekLrdskvllvGaG 27
                 g+  +e+L+ s+v +v aG
  AHX11830.1 59 SGSSKMERLQGSSVIIVTAG 78
                45588999*****9999666 PP

  == domain 3  score: -1.1 bits;  conditional E-value: 0.43
                 HHHHHHTSEEEEE--SH.HHHHHHHHHHHHTTTEEEEEESSB-- CS
                 xxxxxxxxxxxxxxxxx.xxxxxxxxxxxxxxxxxxxxxxxxxx RF
        ThiF  12 gqekLrdskvllvGaGg.lGsellknLalsGvgkltlvDnDkie 54 
                  +  ++d+k +++G  g    +l+++   sGv+  +l+D+D i+
  AHX11830.1 159 LDVSVSDVKSMVLGSHGdSMVPLIRYSTVSGVSLKELIDMDLIS 202
                 55555666666666533133466777777888888999999997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (315 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       546  (0.0304535); expected 358.6 (0.02)
Passed bias filter:                      464  (0.0258799); expected 358.6 (0.02)
Passed Vit filter:                        42  (0.00234257); expected 17.9 (0.001)
Passed Fwd filter:                         8  (0.000446204); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               8  [number of targets reported over threshold]
# CPU time: 0.48u 0.24s 00:00:00.72 Elapsed: 00:00:00.39
# Mc/sec: 2417.55
//
Query:       AHX11831.1  [L=149]
Description: dUTP diphosphatase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    8.4e-34  116.0   0.0    9.7e-34  115.8   0.0    1.0  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  115.8   0.0   5.4e-38   9.7e-34       2     129 .]      15     147 ..      14     147 .. 0.93

  Alignments for each domain:
  == domain 1  score: 115.8 bits;  conditional E-value: 5.4e-38
                 TCTBEBESSTT-SSEEEE-SSSEEEET..TEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEE...EEEETTBTSEEEEEEEE-SSS-EEE-TT-E CS
     dUTPase   2 eaeiptrkspesAgyDlsaakdltvkp..getvlvptdisiklpdglaalilpRSglaakglivvp...gvidsdyrGevkvvlfnltkkdvkikkgdR 95 
                 e eip+++s++s+g Dl+aa + tv+   ge +l+pt+i+i+lp+++ a i pRSglaak +i v    g id+dyrGe+kv l+nl+k++++i +gdR
  AHX11831.1  15 ELEIPKYASEGSSGMDLRAAVPATVTLkeGEFKLIPTGICIELPENMEAQIRPRSGLAAKFGITVLnspGTIDQDYRGEIKVCLINLSKEPFTIVRGDR 113
                 5689**************9988877777699*****************************766553366****************************** PP

                 EEEEEEEEBECGEEEEESSTTTESSBTTXTTTTX CS
     dUTPase  96 iAqLifariltaeleevetlkatergeggfgssg 129
                 iAq+++ari    l+e++++++t+r +ggfgs+g
  AHX11831.1 114 IAQMVMARISRVALKETKEVEETKRSSGGFGSTG 147
                 *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (149 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       298  (0.0166211); expected 358.6 (0.02)
Passed bias filter:                      276  (0.0153941); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.26s 00:00:00.65 Elapsed: 00:00:00.42
# Mc/sec: 1061.29
//
Query:       AHX11832.1  [L=48]
Description: hypothetical protein NHE_0913 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (48 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       144  (0.00803168); expected 358.6 (0.02)
Passed bias filter:                      107  (0.00596798); expected 358.6 (0.02)
Passed Vit filter:                         6  (0.000334653); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.30u 0.24s 00:00:00.54 Elapsed: 00:00:00.37
# Mc/sec: 389.06
//
Query:       AHX11833.1  [L=870]
Description: DNA gyrase, A subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
   5.9e-145  483.4   0.3   5.9e-145  483.4   0.3    1.4  2  DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
    4.2e-60  199.0  13.2      7e-12   44.6   0.1    6.5  6  DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
  ------ inclusion threshold ------
      0.062   12.6   0.0       0.15   11.4   0.0    1.5  1  Aldose_epim    Aldose 1-epimerase


Domain annotation for each model (and alignments):
>> DNA_topoisoIV  DNA gyrase/topoisomerase IV, subunit A
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  483.4   0.3  9.8e-149  5.9e-145       1     425 [.      28     490 ..      28     491 .. 0.97
   2 ?   -3.4   0.0      0.56   3.4e+03     249     312 ..     743     806 ..     731     811 .. 0.58

  Alignments for each domain:
  == domain 1  score: 483.4 bits;  conditional E-value: 9.8e-149
  DNA_topoisoIV   1 RaiPsvrDGlKPvqRriLyamfkl.lnldkkekKvaqlvGevlgkYhPHGdaslydaivrlaqdfvgniplldpqGnfGsildgdkdAaaRYietr 95 
                    RaiP+vrDGlKPv+RriL++m++l    +k+++K+a+++Gev+gkYhPHGd+++yda+vr+aqdf++ +pl+d+qGnfGsi dgd++Aa+RY+e+r
     AHX11833.1  28 RAIPDVRDGLKPVHRRILHSMNELgFYWNKPYRKSARVIGEVIGKYHPHGDSAIYDALVRMAQDFSLLVPLIDGQGNFGSI-DGDPAAAMRYTEVR 122
                    9************************999*****************************************************.************** PP

  DNA_topoisoIV  96 LskiarellkeidketvdyqenyDgsekEPevlppiiPnlLvnGaeGIavGmatkipphnlkeiidaliallkgeea...ellelvlgPdfptggg 188
                    L+ i++ ll+++ ++ vd+++nyD se+EP+vlp+++Pn+LvnG+ G+avGmat++p hnl+e+ida++ +l+++++   ell++++gPdfptgg 
     AHX11833.1 123 LEYISKFLLDDLYENSVDFRPNYDTSENEPVVLPAKFPNILVNGTAGVAVGMATNVPTHNLAEVIDACKLFLENKDVqtdELLKVIKGPDFPTGGF 218
                    ***************************************************************************9999***************** PP

  DNA_topoisoIV 189 iigkeeikeayetgrGkikvrakveie...e.ktivitElPigvntskliekieelvkkkkik.isdirdesdr.gvrivielkrgaseekvlekl 278
                    iig+e+i++a+etgrG+i +r+++++e   + k i++ ElP++vn++klie+i+ lvk+k+++ isd+rdes++ g+rivielkrg s e+vl++l
     AHX11833.1 219 IIGEEGIRSAFETGRGSIIIRSRTHFEetdTrKVIIVDELPYQVNKAKLIENIALLVKEKRLDsISDLRDESNKdGIRIVIELKRGFSCEVVLNQL 314
                    *************************999984599*************************************8888********************* PP

  DNA_topoisoIV 279 ykktkLessisvnnlvlfdkkpkylslkeilkeflevrlevyerrkeyllekleerleilegllkalnkidevievirkskkekkakkeLiee... 371
                    +++t+L++s+s+n+++l++ kp+++ lk++l +f+++r+ev++rr+e++l+k++er+++l ++++a+ +ide++ ++++sk++++a  +L+++   
     AHX11833.1 315 FQMTQLQTSYSTNMMLLHKMKPTLMPLKDVLAAFIDHRREVISRRTEFRLAKARERASVLIAVYVAILNIDEIVPILKSSKDNETAVLSLCSKkwn 410
                    *******************************************************************************************99888 PP

  DNA_topoisoIV 372 lse.......................eqaeyllemrlrrLtkeeveklekeieelekeikelekllak...lkklikeel 425
                    ++e                       +q +++lem+++r+t  e+e+l +ei++  + i+e+ ++l +   l ++i +el
     AHX11833.1 411 IDEdlkklveiisniqlenseyelsrSQSKAILEMKMQRITGVEKEQLVREIHSEIEVINECISILGSdavLVNVIVQEL 490
                    7779999*******************9*************************************9999777777777766 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.56
  DNA_topoisoIV 249 sdirdesdrgvrivielkrgaseekvleklykktkLessisvnnlvlfdk.kpkylslkeilkef 312
                    ++i+d ++++ ++v++++++   + + +  y+ t+ +  + + n++  ++ ++ + s + +l+++
     AHX11833.1 743 ERIKDPTNKDEQFVLSVTENGYGKITSSYEYRITN-RGGVGIINIATSKRnGKVVSSFRVLLDNH 806
                    46777777777777777766666655554444333.45666666666666346666666666555 PP

>> DNA_gyraseA_C  DNA gyrase C-terminal domain, beta-propeller
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   39.1   0.2   6.4e-14   3.8e-10       3      48 .]     525     570 ..     523     570 .. 0.95
   2 !   30.6   0.0   2.9e-11   1.8e-07       1      47 [.     573     622 ..     573     623 .. 0.97
   3 !   23.1   0.0   6.1e-09   3.7e-05       2      45 ..     629     670 ..     628     673 .. 0.92
   4 !   28.6   0.0   1.2e-10     7e-07       3      48 .]     678     724 ..     676     724 .. 0.95
   5 !   36.7   0.5   3.6e-13   2.2e-09       2      45 ..     755     799 ..     754     801 .. 0.93
   6 !   44.6   0.1   1.2e-15     7e-12       2      44 ..     806     848 ..     805     851 .. 0.96

  Alignments for each domain:
  == domain 1  score: 39.1 bits;  conditional E-value: 6.4e-14
                    EEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEEEES CS
  DNA_gyraseA_C   3 llliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvlvvs 48 
                    ++++T  Gy+kr+++s +++q+Rg+kG+++ ++k++d l  ++v+s
     AHX11833.1 525 VVTVTYSGYIKRVSISNYRVQKRGGKGKIAQNIKPEDQLAQIFVLS 570
                    789999**********************************999975 PP

  == domain 2  score: 30.6 bits;  conditional E-value: 2.9e-11
                    SEEEEEETTSEEEEEEGGGS-BT-TTSCTEEGS...ETTTTSSEEEEEEE CS
  DNA_gyraseA_C   1 dellliTsnGyvkrfplselpeqgRgakGvkgi...klkegdklvsvlvv 47 
                    de+l+++++G+v+++++++lp+    a+G  ++    l+eg++++s+l++
     AHX11833.1 573 DEILFFSNRGKVYKIKAYKLPVGDPQARGRALVnifELSEGESITSILPL 622
                    89*********************************************986 PP

  == domain 3  score: 23.1 bits;  conditional E-value: 6.1e-09
                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEEE CS
  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsvl 45 
                    +l++ T +G++kr + s++     +  G+ +ikl+e+d+l++v 
     AHX11833.1 629 NLIFLTAQGKIKRNSMSDFNYVPTN--GKVAIKLNEDDRLIAVK 670
                    89*****************999966..***************96 PP

  == domain 4  score: 28.6 bits;  conditional E-value: 1.2e-10
                    EEEEETTSEEEEEEGGGS-B.T-TTSCTEEGSETTTTSSEEEEEEES CS
  DNA_gyraseA_C   3 llliTsnGyvkrfplselpe.qgRgakGvkgiklkegdklvsvlvvs 48 
                    +++ T+ G+++rf +++l++ ++R + Gvk+ +l++gd+ +s+ +++
     AHX11833.1 678 IFISTRDGKCIRFLVDDLRVlKSRSSEGVKALTLSNGDEAISLSILN 724
                    6888**************************************99875 PP

  == domain 5  score: 36.7 bits;  conditional E-value: 3.6e-13
                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTT.SSEEEEE CS
  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkeg.dklvsvl 45 
                     +l +T+nGy+k ++ +e++ ++Rg+ G++ i ++++ +k+vs +
     AHX11833.1 755 FVLSVTENGYGKITSSYEYRITNRGGVGIINIATSKRnGKVVSSF 799
                    5899**************************************966 PP

  == domain 6  score: 44.6 bits;  conditional E-value: 1.2e-15
                    EEEEEETTSEEEEEEGGGS-BT-TTSCTEEGSETTTTSSEEEE CS
  DNA_gyraseA_C   2 ellliTsnGyvkrfplselpeqgRgakGvkgiklkegdklvsv 44 
                    +++liT++G+v+r+ +s +p++gR ++Gv++ + k+++++ sv
     AHX11833.1 806 HIMLITNRGQVIRIAASNIPVLGRSTQGVRLFTVKDDERVASV 848
                    8***************************************998 PP

>> Aldose_epim  Aldose 1-epimerase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.0   2.4e-05      0.15     198     260 ..     627     694 ..     611     717 .. 0.82

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 2.4e-05
                  TCCC.CCCSSEEHCSSETEEEEEEEESSCSEEEEEETTTTEEEEEEEETTSSEEEEEECTTTT......S CS
  Aldose_epim 198 gtpf.dfrqpkaigedlkglDhayllksklkaviidpdkksgiklevsttepalvvytgnflk......k 260
                  ++++ ++++  +i++++   D +y+ ++  k +i++ ++++ i +++s++e ++ + t ++++       
   AHX11833.1 627 DENLiFLTAQGKIKRNS-MSDFNYVPTN-GKVAIKLNEDDRLIAVKTSKNEDCIFISTRDGKCirflvdD 694
                  44554668899999998.9*********.******************************99997555550 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (870 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       604  (0.0336884); expected 358.6 (0.02)
Passed bias filter:                      356  (0.0198561); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.61u 0.33s 00:00:00.94 Elapsed: 00:00:00.45
# Mc/sec: 5830.27
//
Query:       AHX11834.1  [L=307]
Description: GTP-binding protein Era [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
    4.1e-24   84.9   1.3    2.1e-23   82.6   0.3    2.1  2  MMR_HSR1      50S ribosome-binding GTPase
    6.4e-17   61.2   1.0    6.4e-17   61.2   1.0    1.9  2  KH_2          KH domain
    9.6e-13   47.9   0.2    1.7e-12   47.1   0.2    1.4  1  FeoB_N        Ferrous iron transport protein B
    2.9e-11   43.3   0.3    9.4e-11   41.6   0.3    1.8  1  PduV-EutP     Ethanolamine utilisation - propanediol utilisat
    1.2e-09   38.3   4.1    1.7e-06   28.1   0.2    2.5  3  RsgA_GTPase   RsgA GTPase
    2.1e-08   33.7   1.0    3.3e-08   33.1   0.1    1.6  2  AIG1          AIG1 family
    3.4e-07   30.5   4.7    0.00077   19.6   1.2    3.1  3  Dynamin_N     Dynamin family
    3.6e-07   29.9   0.4    5.9e-05   22.7   0.3    2.7  1  GTP_EFTU      Elongation factor Tu GTP binding domain
    3.6e-05   23.7   0.3    3.6e-05   23.7   0.3    2.3  3  MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
    6.2e-05   22.7   1.9    0.00093   18.8   0.0    2.8  3  cobW          CobW/HypB/UreG, nucleotide-binding domain
    0.00047   20.4   1.1     0.0027   17.9   1.1    2.2  1  Roc           Ras of Complex, Roc, domain of DAPkinase
    0.00075   19.1   0.6    0.00075   19.1   0.6    2.2  2  Ras           Ras family
  ------ inclusion threshold ------
      0.011   16.2   1.3      0.018   15.6   0.3    1.8  2  ABC_tran      ABC transporter
      0.017   14.9   0.4      0.041   13.7   0.4    1.7  1  KH_1          KH domain
      0.025   13.7   0.3      0.052   12.7   0.0    1.6  2  DNApol_Exo    DNA mitochondrial polymerase exonuclease domain
      0.045   13.5   0.0        0.1   12.3   0.0    1.6  1  AAA_29        P-loop containing region of AAA domain
      0.059   12.8   0.6        1.6    8.1   0.0    2.2  2  TniB          Bacterial TniB protein
      0.076   12.2   0.2      0.076   12.2   0.2    1.9  2  NB-ARC        NB-ARC domain


Domain annotation for each model (and alignments):
>> MMR_HSR1  50S ribosome-binding GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   82.6   0.3   2.1e-26   2.1e-23       2     114 .]      25     136 ..      24     136 .. 0.88
   2 ?    1.0   0.0      0.44   4.4e+02      68      98 ..     232     271 ..     217     300 .. 0.62

  Alignments for each domain:
  == domain 1  score: 82.6 bits;  conditional E-value: 2.1e-26
                 EEEEESTTSSHHHHHHHHHTS.TEEESSSTTSSSSEEEEEEEETTEEEEEEECGGCS.SHHHHHH.HHHHHHHHHHCTSEEEEEEETTTTCSHHHHHHH CS
    MMR_HSR1   2 vaivGrpNvGKStLinaltge.kaivsdkpgtTrdinegrvklkgkeielvDtpGli.egaseek.glgkaflaleeadlillvvdaseeklkpldeel 97 
                 va++G++NvGKStL+n+++g+ ++iv++k +tTr+ ++g ++++++++++vDtpG++  + s e+  +++a++a   ad++++vvd +   + ++ e++
  AHX11834.1  25 VALIGNSNVGKSTLLNTIVGSkVSIVTHKVQTTRTRIRGIYTKNETQLVFVDTPGIFiPKRSLERyIVRNAWKAFSGADIFCFVVDPR---Y-EITESM 119
                 89******************9678****************99889**********753356666669*******999*********44...4.456888 PP

                 HHHHHHTTSEEEEEEES CS
    MMR_HSR1  98 eelleeakkplilvlnk 114
                 e++l++  +++ilv+nk
  AHX11834.1 120 ENILKKVYDNVILVINK 136
                 8888888899*****98 PP

  == domain 2  score: 1.0 bits;  conditional E-value: 0.44
                 HHHHHHHCTSEEEEEEETT.........TTCSHHHHHHHH CS
    MMR_HSR1  68 kaflaleeadlillvvdas.........eeklkpldeele 98 
                 +++++ ++++ i++v++ s          e++k ++++ e
  AHX11834.1 232 ETLQDRIKVSQIIHVISDShkkmvigakGETIKTIRQQAE 271
                 5556667788889999755554444443222333333333 PP

>> KH_2  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -3.1   0.0       7.2   7.2e+03      61      74 ..      42      55 ..      37      59 .. 0.69
   2 !   61.2   1.0   6.4e-20   6.4e-17       1      78 []     219     295 ..     219     295 .. 0.94

  Alignments for each domain:
  == domain 1  score: -3.1 bits;  conditional E-value: 7.2
                HHTTCEEEEEEEET CS
        KH_2 61 legkkVklnivkVk 74
                + g+kV++  +kV+
  AHX11834.1 42 IVGSKVSIVTHKVQ 55
                45788888777886 PP

  == domain 2  score: 61.2 bits;  conditional E-value: 6.4e-20
                 HHHHHHHHHTECETEEEEEEECCSCEEEEEEEESCHHHHHTGGGHHHHHHHHHHHHHHHHHHTTCEEEEEE.EETTTGG CS
        KH_2   1 eipeslaveikkagvskveIertanrviiviresqpgivIGkgGsnikkigkelrkdieklegkkVklniv.kVkkpel 78 
                 e+p+sl+ve+++ ++ + +I+    ++i vi +s++++vIG +G++ik+i++++++++e+++gk+V+l ++ +V k+++
  AHX11834.1 219 ELPYSLTVETENVETLQDRIKV--SQIIHVISDSHKKMVIGAKGETIKTIRQQAEREMEEFFGKRVSLLVFvRVSKNWQ 295
                 79********999977767744..9*****************************************************6 PP

>> FeoB_N  Ferrous iron transport protein B
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   47.1   0.2   1.7e-15   1.7e-12       3     154 ..      25     177 ..      23     179 .. 0.83

  Alignments for each domain:
  == domain 1  score: 47.1 bits;  conditional E-value: 1.7e-15
                 EEEEESTTSSHHHHHHHHHTTSEEEEESTTSSS.EEEEEEEEETTEEEEEEE----SSSSSSSHHHHHHHHHHH.CTSSSEEEEEEEGGGHHHHHHHHH CS
      FeoB_N   3 valvGnpnvGkttlfnaltgakqkvgNwpGvtv.ekkegklklkgkeveivDlPGiYslsayseeekvardfll.eeepdvvvnvvdatnlernLyLtl 99 
                 val+Gn nvGk+tl+n++ g+k ++  +   t   + +g ++ +++++ +vD PGi+ + + s e  ++r+     + +d+   vvd    e +  +  
  AHX11834.1  25 VALIGNSNVGKSTLLNTIVGSKVSIVTHKVQTTrTRIRGIYTKNETQLVFVDTPGIF-IPKRSLERYIVRNAWKaFSGADIFCFVVDPR-YEITESMEN 121
                 89********************99999987666267788888888***********9.688999*999999987367899*******75.344445566 PP

                 HHHHTTSSEEEEEETHHHHHHTTEEE-HHHHHHHHTS.-EEEEBTTTTBTHHHHHH CS
      FeoB_N 100 qllelgvpvvlalnmideaekkgieidlkkLsekLgv.pvvktsakkkegieellk 154
                  l  +  +v+l++n+id +ek ++   ++kL+++  + +   +sa k++g+++l++
  AHX11834.1 122 ILKKVYDNVILVINKIDLIEKFRLLEVARKLNDIKRFkETFMISALKNRGVDDLKN 177
                 6788999**************99877778888776652578889999999999875 PP

>> PduV-EutP  Ethanolamine utilisation - propanediol utilisation
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   41.6   0.3   9.4e-14   9.4e-11       4     141 ..      25     179 ..      22     181 .. 0.80

  Alignments for each domain:
  == domain 1  score: 41.6 bits;  conditional E-value: 9.4e-14
   PduV-EutP   4 illiGkvgsGKttLtqalkg..eelkYkktqai...........efsdeviDtPGeylenrklysalivtsae....advialvqdateeesvfppgfa 85 
                 + liG++++GK tL +++ g   ++  +k q++           e +  ++DtPG ++ +r+l + ++  + +    ad+  +v+d   e +   +++ 
  AHX11834.1  25 VALIGNSNVGKSTLLNTIVGskVSIVTHKVQTTrtrirgiytknETQLVFVDTPGIFIPKRSLERYIVRNAWKafsgADIFCFVVDPRYEITESMENIL 123
                 679***************994434556777765222222111112223459***********9999988876522237999999999999999999999 PP

   PduV-EutP  86 svfnkeviGiitkidlaedeenieaveelLksaGaekifevsavekegieellkyl 141
                 + +  +vi +i kidl e+   +e++++l      ++ f +sa+++ g+++l+++l
  AHX11834.1 124 KKVYDNVILVINKIDLIEKFRLLEVARKLNDIKRFKETFMISALKNRGVDDLKNFL 179
                 99999************99999999999989999*******************997 PP

>> RsgA_GTPase  RsgA GTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   28.1   0.2   1.7e-09   1.7e-06      88     161 ..       9      80 ..       1      84 [. 0.61
   2 !   11.3   0.1   0.00024      0.24      48      97 ..     129     179 ..     110     183 .. 0.80
   3 ?   -2.6   0.0       4.5   4.5e+03      66      75 ..     241     250 ..     207     280 .. 0.51

  Alignments for each domain:
  == domain 1  score: 28.1 bits;  conditional E-value: 1.7e-09
                  TTHHHHHHHCTT..SEEEEECSTTSSHHHHHHHHCTT.-----S--------------SEEEEEETT.TEEEESS-SS CS
  RsgA_GTPase  88 egleelkellkd..ktsvlvGqSGvGKStLinallpe.lelktgevseklgrGkhTTtavellelae.gglliDtPGf 161
                   +l+++ke+ +    +++l+G+S vGKStL+n+++++  ++ t++v+++       T+ + ++  +e + + +DtPG+
   AHX11834.1   9 IALDQMKEKSETrsAFVALIGNSNVGKSTLLNTIVGSkVSIVTHKVQTTR------TRIRGIYTKNEtQLVFVDTPGI 80 
                  556666655544337899******************70344444444332......3444444443313345788886 PP

  == domain 2  score: 11.3 bits;  conditional E-value: 0.00024
                  EEEEEEE-GGG--HHHHHHHHHHHHHHTT..SEEEE--TTTHTTHHHHHHHC CS
  RsgA_GTPase  48 epvivlnKiDlleeeeeleelkeelealg..yevllvsaktkegleelkell 97 
                  ++++v+nKiDl+e+ + l e++ +l+++    e++++sa +++g+++lk+ l
   AHX11834.1 129 NVILVINKIDLIEKFR-LLEVARKLNDIKrfKETFMISALKNRGVDDLKNFL 179
                  689***********99.555555555554337899999**9*******9977 PP

  == domain 3  score: -2.6 bits;  conditional E-value: 4.5
                  HHHHHHHHHT CS
  RsgA_GTPase  66 eelkeeleal 75 
                  +++ + +++ 
   AHX11834.1 241 SQIIHVISDS 250
                  3333333333 PP

>> AIG1  AIG1 family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   33.1   0.1   3.3e-11   3.3e-08       4     107 ..      26     126 ..      24     141 .. 0.84
   2 ?   -2.2   0.1       2.1   2.1e+03      95     115 ..     262     282 ..     231     296 .. 0.71

  Alignments for each domain:
  == domain 1  score: 33.1 bits;  conditional E-value: 3.3e-11
                 EEESSTTSSHHHHHHHHHTS--SS--TTTS---SS-EEEEEEETTEEEEEEE--SCCCTTCCHHCHHHHHHHHHHHCTT-ESEEEEEEETT.B-SHHHH CS
        AIG1   4 vlvGktgnGkSaTgNsilgkkaFesklsaqsvtkkcqkksrtwdgkkinViDTPglfdlsvsadkiskeivrclllseegihalllvlslg.rfteede 101
                  l+G + +GkS+  N+i+g+k+     ++ + t++  +   t+++++++ +DTPg+f  + s +   + ivr    +  g +++ +v++ + ++te  e
  AHX11834.1  26 ALIGNSNVGKSTLLNTIVGSKVSIVT-HKVQTTRTRIRGIYTKNETQLVFVDTPGIFIPKRSLE---RYIVRNAWKAFSGADIFCFVVDPRyEITESME 120
                 69*******************96666.455556666666669***************8888765...678888888999*********99999998888 PP

                 HHHHHH CS
        AIG1 102 kalktl 107
                 ++lk++
  AHX11834.1 121 NILKKV 126
                 887776 PP

  == domain 2  score: -2.2 bits;  conditional E-value: 2.1
                 B-SHHHHHHHHHHHHHHCGGG CS
        AIG1  95 rfteedekalktlkelFGeki 115
                  +++  ++a ++++e+FG+++
  AHX11834.1 262 TIKTIRQQAEREMEEFFGKRV 282
                 455556777788888888876 PP

>> Dynamin_N  Dynamin family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.6   1.2   7.7e-07   0.00077       1      34 [.      25      59 ..      25      62 .. 0.82
   2 !   10.2   0.0   0.00058      0.58      95     155 ..      64     128 ..      59     137 .. 0.76
   3 ?    0.3   0.1      0.65   6.5e+02      27      80 ..     223     278 ..     209     297 .. 0.58

  Alignments for each domain:
  == domain 1  score: 19.6 bits;  conditional E-value: 7.7e-07
                EEEEEBTTTTHHHHHHHHHTS--S---SS.S---S CS
   Dynamin_N  1 iavvGsqSsGKSSvlnaLlgedilprgpn.ptTrr 34
                +a++G+ + GKS++ln ++g+++  +     tTr+
  AHX11834.1 25 VALIGNSNVGKSTLLNTIVGSKVSIVTHKvQTTRT 59
                799********************996555156654 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.00058
                 EEETTS-SEEEEE---B-SSSGTTS....HHHHHHHSTTEEEEEEEETTS-CCC-CHHHHHHHHS CS
   Dynamin_N  95 ilsllvkgltlvDlPGldsvnkrdq....elvkeyikkadiilavtsanhdlsnsealflarevd 155
                 i++ ++ +l++vD+PG+   +   +    + + ++   adi+ +v++   ++++s    l++ +d
  AHX11834.1  64 IYTKNETQLVFVDTPGIFIPKRSLEryivRNAWKAFSGADIFCFVVDPRYEITESMENILKKVYD 128
                 6888999**********997777777666555556688999999999999999777766666555 PP

  == domain 3  score: 0.3 bits;  conditional E-value: 0.65
                 -SSS---S-EEEEECCT---CCS...SSEEEE...T-EB--CHHHHHHHHHHHHHHH CS
   Dynamin_N  27 gpnptTrrplelqlgeeeeaseravkeelkek...ekkledfsevreeieketekia 80 
                 + ++ T ++ +lq + + +   +  +++ k k    +k e ++ +r++ e+e+e+  
  AHX11834.1 223 SLTVETENVETLQDRIKVSQIIHVISDSHK-KmviGAKGETIKTIRQQAEREMEEFF 278
                 555555555555554444322222222222.23566666666666666666666655 PP

>> GTP_EFTU  Elongation factor Tu GTP binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   22.7   0.3     6e-08   5.9e-05      55     189 ..      51     180 ..      20     212 .. 0.70

  Alignments for each domain:
  == domain 1  score: 22.7 bits;  conditional E-value: 6e-08
                 CSSCEEEEEE....TTCSSEEEEEEEESS.......SGGG.HHHHHHHHHT-SEEEEEEETTTBSTHHHHHHHHHHHHTTTEEEEEEESCGST.HHHHH CS
    GTP_EFTU  55 Tiksaaisle....ketkkylinliDtPG.......HvdF.skevirglrvlDgavlvvdaveGvepqteevlrlalkegvpiivfiNKmDrl.kaelk 140
                 T k++++ +      +++++++ ++DtPG        + + +++  ++ + +D+ ++vvd +  +++  e++l+ +     ++i++iNK+D + k +l 
  AHX11834.1  51 THKVQTTRTRirgiYTKNETQLVFVDTPGifipkrsLERYiVRNAWKAFSGADIFCFVVDPRYEITESMENILKKVY---DNVILVINKIDLIeKFRLL 146
                 33333333333333367899999******5555443234426788899*************9888777777776665...579**********878888 PP

                 HHHHHHHHHHHHHHHHHHHHHHTTTTTEEEEEEBTTTTBTHHHHHHHHH CS
    GTP_EFTU 141 eiveevkqklsrkeeklekygekgekevpvvfgSalkgegvktllealv 189
                 e++++++ ++         +      + + +++Salk+ gv++l + l 
  AHX11834.1 147 EVARKLN-DI---------KR-----FKETFMISALKNRGVDDLKNFLL 180
                 8888888.44.........12.....23467888888888887666554 PP

>> MMR_HSR1_Xtn  C-terminal region of MMR_HSR1 domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   -2.5   0.0       5.2   5.1e+03      84      99 ..       2      17 ..       1      18 [. 0.82
   2 !   23.7   0.3   3.6e-08   3.6e-05      52      98 ..     124     177 ..     112     182 .. 0.86
   3 ?   -1.8   0.1       3.2   3.2e+03      36      52 ..     234     250 ..     223     256 .. 0.70

  Alignments for each domain:
  == domain 1  score: -2.5 bits;  conditional E-value: 5.2
  MMR_HSR1_Xtn 84 viSaekelnldeLkek 99
                   iS +k++ ld++kek
    AHX11834.1  2 LISPRKDIALDQMKEK 17
                  6888999999999986 PP

  == domain 2  score: 23.7 bits;  conditional E-value: 3.6e-08
  MMR_HSR1_Xtn  52 nrvYipclyvlNKiDlisleeldelare.......pnsvviSaekelnldeLke 98 
                   ++vY ++++v+NKiDli++  l e+ar+       +++++iSa k+ ++d+Lk+
    AHX11834.1 124 KKVYDNVILVINKIDLIEKFRLLEVARKlndikrfKETFMISALKNRGVDDLKN 177
                   579*************99999888888777888778****************97 PP

  == domain 3  score: -1.8 bits;  conditional E-value: 3.2
  MMR_HSR1_Xtn  36 iredvtvDdlidviegn 52 
                   ++++++v ++i vi+++
    AHX11834.1 234 LQDRIKVSQIIHVISDS 250
                   45667777777777664 PP

>> cobW  CobW/HypB/UreG, nucleotide-binding domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    1.3   0.2      0.23   2.3e+02      11      22 ..      33      44 ..      24      58 .. 0.74
   2 !   18.8   0.0   9.3e-07   0.00093      75     168 ..      63     154 ..      45     162 .. 0.73
   3 ?    0.1   0.0      0.53   5.3e+02     103     125 ..     231     264 ..     220     285 .. 0.66

  Alignments for each domain:
  == domain 1  score: 1.3 bits;  conditional E-value: 0.23
                CCHHHHHHHHHC CS
        cobW 11 sGKTtLlnhlle 22
                 GK+tLln+++ 
  AHX11834.1 33 VGKSTLLNTIVG 44
                6********983 PP

  == domain 2  score: 18.8 bits;  conditional E-value: 9.3e-07
                 HHHHHHTT-SEEEEEECTTTTHHHH...HTTSHHHHHCCCECEEEEEEETTTH.CCHCCHHHHHHHHHHTSSEEEEE-HHHHCHC..HHHHHHHHHH CS
        cobW  75 aleereerldviliEttGlaePapv...afteeelksdltldavvavvDaknleaeeekieekaedqlaaadllvlnKtDlldeeallekleerlrq 168
                  + +++ + +++++ t G+  P+ +    +  + +k+   +d+  +vvD  ++  e +++ e++ +++    +lv+nK+Dl+++ +ll +++++l++
  AHX11834.1  63 GIYTKN-ETQLVFVDTPGIFIPKRSlerYIVRNAWKAFSGADIFCFVVDP-RY--EITESMENILKKVYDNVILVINKIDLIEKFRLL-EVARKLND 154
                 444455.899***************554444999****************.43..4455555555666677799********998663.33444444 PP

  == domain 3  score: 0.1 bits;  conditional E-value: 0.53
                 SHHHHHCCCECEEEEEEETTTH............ CS
        cobW 103 eeelksdltldavvavvDaknl...........e 125
                  e+l+++++++ ++ v++ ++            +
  AHX11834.1 231 VETLQDRIKVSQIIHVISDSHKkmvigakgetiK 264
                 6788999999999999987665566655444431 PP

>> Roc  Ras of Complex, Roc, domain of DAPkinase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   17.9   1.1   2.7e-06    0.0027       2     119 ..      25     138 ..      25     139 .. 0.56

  Alignments for each domain:
  == domain 1  score: 17.9 bits;  conditional E-value: 2.7e-06
                 EEEESSTTSSHHHHHHCHCT-CCC-EEETTTTEEEEEEECGGSGGCTTBTTTTCEEEEEEEE-SGGCTTTT-HHHH.CTSCEEEEEEEGHHH..HCHHH CS
         Roc   2 vvlvGdsgvGKtsllkrfvedkfsekekstigvdfltkevtkikgvendkkvkkvklniWDtaGqerfrslhplyl.reaalailvydsrss..enlke 97 
                 v l+G+s+vGK++ll+ +v +k+s     t+ v++++++   i+g+ ++   ++ +l + Dt G    +   + y+ r+a  a+   d   +  +   e
  AHX11834.1  25 VALIGNSNVGKSTLLNTIVGSKVS---IVTHKVQTTRTR---IRGIYTK---NETQLVFVDTPGIFIPKRSLERYIvRNAWKAFSGADIFCFvvDPRYE 114
                 679****************99986...445555554444...5666544...35679999999987666555555414333333333322211122222 PP

                 HHHHHHHHCSS..S-EEEEEE-TT CS
         Roc  98 Wlkelkkvagk..spvilvgnkiD 119
                   +++++  +k  ++vilv+nkiD
  AHX11834.1 115 ITESMENILKKvyDNVILVINKID 138
                 333333333331146888888888 PP

>> Ras  Ras family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   19.1   0.6   7.5e-07   0.00075       2     152 ..      25     175 ..      24     184 .. 0.67
   2 ?   -0.7   0.1      0.94   9.3e+02      94     119 ..     240     267 ..     222     297 .. 0.62

  Alignments for each domain:
  == domain 1  score: 19.1 bits;  conditional E-value: 7.5e-07
                 EEEEESTTSSHHHHHHHHHHSSCSSSCTTTSSEEEEEEEEEETTEEEEEEEEEETTSGG.GHHHHHHHHTTESEE.....EEEEETTBHHHHHTHHHHH CS
         Ras   2 lvlvGdsavGKtslllrfvkdkFkeeyesTigvdfytkeievdgkevkleiwDTAGqee.fkslrelyyrdaegi.....llvyditsresfenvkkwv 94 
                 + l+G+s+vGK++ll+  v +k +   ++       ++ i + ++e +l   DT G     +sl++  +r+a  +     + ++ ++ r    ++++ +
  AHX11834.1  25 VALIGNSNVGKSTLLNTIVGSKVSIVTHKVQTTRTRIRGI-YTKNETQLVFVDTPGIFIpKRSLERYIVRNAWKAfsgadIFCFVVDPR---YEITESM 119
                 579****************998766655554334444444.5577889********743134555555555533312223788888776...3567777 PP

                 HHHHHHSTTTSEEEEEEETTTGGGG.-SS-HHHHHHHHHHHTSEEEEEBTTTTCTHHHH CS
         Ras  95 eeikrvaeenvpivLvGnKvDleek.ravsteegeelakelglkfletSAktnenveea 152
                 e+i +++ +  +++Lv nK+Dl ek r ++ ++  +  k+++ +f+ +SA +n +v+++
  AHX11834.1 120 ENILKKVYD--NVILVINKIDLIEKfRLLEVARKLNDIKRFKETFM-ISALKNRGVDDL 175
                 788777776..799*******9875255555554444555555555.899999999875 PP

  == domain 2  score: -0.7 bits;  conditional E-value: 0.94
                 HHHHHHHSTTTSEEEEEEETTTGGG..G CS
         Ras  94 veeikrvaeenvpivLvGnKvDlee..k 119
                 v++i +v +++ + +++G K    +  +
  AHX11834.1 240 VSQIIHVISDSHKKMVIGAKGETIKtiR 267
                 5677777778888889998877654332 PP

>> ABC_tran  ABC transporter
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   15.6   0.3   1.8e-05     0.018      11      35 ..      22      46 ..      18     126 .. 0.84
   2 ?   -2.3   0.0       5.7   5.7e+03      89      89 ..     244     244 ..     200     283 .. 0.54

  Alignments for each domain:
  == domain 1  score: 15.6 bits;  conditional E-value: 1.8e-05
                TSEEEEEESTTSSHHHHHHHHTTSS CS
                xxxxxxxxxxxxxxxxxxxxxxxxx RF
    ABC_tran 11 gekvaivGenGaGKStLlkllagll 35
                +  va++G++  GKStLl+++ g  
  AHX11834.1 22 SAFVALIGNSNVGKSTLLNTIVGSK 46
                5679*****************9975 PP

  == domain 2  score: -2.3 bits;  conditional E-value: 5.7
                 H CS
                 x RF
    ABC_tran  89 l 89 
                 +
  AHX11834.1 244 I 244
                 1 PP

>> KH_1  KH domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.7   0.4   4.1e-05     0.041       6      28 ..     247     269 ..     241     272 .. 0.84

  Alignments for each domain:
  == domain 1  score: 13.7 bits;  conditional E-value: 4.1e-05
                 EGGGHHHHHHTGGGHHHHHHHHH CS
        KH_1   6 vPsslvgriIGkgGsnIkeIree 28 
                 +  s+   +IG +G++Ik Ir++
  AHX11834.1 247 ISDSHKKMVIGAKGETIKTIRQQ 269
                 56677889*************96 PP

>> DNApol_Exo  DNA mitochondrial polymerase exonuclease domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.7   0.0   5.2e-05     0.052     132     174 ..      46      88 ..      12     103 .. 0.79
   2 ?   -2.7   0.1       2.5   2.5e+03     116     137 ..     236     257 ..     224     259 .. 0.78

  Alignments for each domain:
  == domain 1  score: 12.7 bits;  conditional E-value: 5.2e-05
  DNApol_Exo 132 ervvvGhnvsyDRarikeeYslessktrflDTmsLhvavsGlt 174
                 +  +v h+v+  R+ri+  Y+ ++++++f+DT  + ++ ++l 
  AHX11834.1  46 KVSIVTHKVQTTRTRIRGIYTKNETQLVFVDTPGIFIPKRSLE 88 
                 45699***************************88877776665 PP

  == domain 2  score: -2.7 bits;  conditional E-value: 2.5
  DNApol_Exo 116 eklelkeLiplesskkervvvG 137
                 ++++ +++i + s++++++v+G
  AHX11834.1 236 DRIKVSQIIHVISDSHKKMVIG 257
                 6788899999999999999999 PP

>> AAA_29  P-loop containing region of AAA domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.3   0.0    0.0001       0.1      23      41 ..      22      41 ..      11      44 .. 0.79

  Alignments for each domain:
  == domain 1  score: 12.3 bits;  conditional E-value: 0.0001
      AAA_29 23 g.atlltGpsGsGKSTllDA 41
                + ++ l+G+s +GKSTll  
  AHX11834.1 22 SaFVALIGNSNVGKSTLLNT 41
                34789************965 PP

>> TniB  Bacterial TniB protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?    8.1   0.0    0.0016       1.6      28      56 ..      15      43 ..       9      76 .. 0.79
   2 ?    2.9   0.1     0.062        62     114     157 ..     122     166 ..     105     184 .. 0.79

  Alignments for each domain:
  == domain 1  score: 8.1 bits;  conditional E-value: 0.0016
        TniB 28 eypkrkrmpnlllvGdsnnGKtmivekFa 56
                +  +++r   + l+G+sn+GK+++++   
  AHX11834.1 15 KEKSETRSAFVALIGNSNVGKSTLLNTIV 43
                455678888999************98765 PP

  == domain 2  score: 2.9 bits;  conditional E-value: 0.062
        TniB 114 llrel.kvrvLiiDEihnllagsarkqreflnalksLgnelkipi 157
                 +l+++ +  +L+i  i+ +++ +  +  + ln +k++++++ i+ 
  AHX11834.1 122 ILKKVyDNVILVINKIDLIEKFRLLEVARKLNDIKRFKETFMISA 166
                 55554145589******************************9986 PP

>> NB-ARC  NB-ARC domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   12.2   0.2   7.6e-05     0.076       9      43 ..      11      45 ..       5     130 .. 0.87
   2 ?   -1.6   0.1       1.3   1.3e+03      33      71 ..     263     303 ..     239     306 .. 0.66

  Alignments for each domain:
  == domain 1  score: 12.2 bits;  conditional E-value: 7.6e-05
                HHHHHCTTTSCSEEEEEEESTTSSHHHHHHHHCCS CS
      NB-ARC  9 iekLlekdelqslvvalvGmgGvGKttlakqilnk 43
                 +++ ek e  s +val G   vGK+tl++ i+ +
  AHX11834.1 11 LDQMKEKSETRSAFVALIGNSNVGKSTLLNTIVGS 45
                567889999*********************99865 PP

  == domain 2  score: -1.6 bits;  conditional E-value: 1.3
                 HHHHHHHHCCSHCCCCC.CBTEEEEEEEESXXHHH.HHHHX CS
      NB-ARC  33 Kttlakqilnksdeveg.rFdsvawvvvsktdkse.eilet 71 
                   t+ +q+ ++++e  g r   +++v vsk+ +++ +il+t
  AHX11834.1 263 IKTIRQQAEREMEEFFGkRVSLLVFVRVSKNWQEKpDILNT 303
                 45777788777777766577778888888877654245555 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (307 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       918  (0.051202); expected 358.6 (0.02)
Passed bias filter:                      537  (0.0299515); expected 358.6 (0.02)
Passed Vit filter:                        57  (0.00317921); expected 17.9 (0.001)
Passed Fwd filter:                        18  (0.00100396); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):              18  [number of targets reported over threshold]
# CPU time: 0.55u 0.23s 00:00:00.78 Elapsed: 00:00:00.39
# Mc/sec: 2357.56
//
Query:       AHX11835.1  [L=311]
Description: malonyl CoA-acyl carrier protein transacylase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model          Description
    ------- ------ -----    ------- ------ -----   ---- --  --------       -----------
    8.7e-38  130.6   0.2      1e-37  130.3   0.2    1.0  1  Acyl_transf_1   Acyl transferase domain
     0.0041   16.9   1.5       0.46   10.2   0.0    2.3  2  SAT             Starter unit:ACP transacylase in aflatoxin bi
  ------ inclusion threshold ------
      0.078   12.5   0.0       0.15   11.6   0.0    1.4  1  DUF2974         Protein of unknown function (DUF2974)
       0.23   10.7   0.0       0.33   10.2   0.0    1.2  1  Glyco_hydro_97  Glycoside hydrolase 97


Domain annotation for each model (and alignments):
>> Acyl_transf_1  Acyl transferase domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  130.3   0.2   2.3e-41     1e-37       3     274 ..       5     284 ..       3     296 .. 0.89

  Alignments for each domain:
  == domain 1  score: 130.3 bits;  conditional E-value: 2.3e-41
                    EE--TT---TTTTCCHHHC-HHHHHHHHHHHHHCCHHHT--HHHHHHS--TTGGGSHHHHHHHHHHHHHHHHHHH.HHTT....-TTSEEEE-TTH CS
  Acyl_transf_1   3 vfsGqGsQwaGMGmeLlktskafaaviaradeafksqygfsvldvlrnnpeglldaiqfvqpaLaavqialaell.kskG....vrpaavvGHSlG 93 
                    vf+GqGsQ  GMG+eL++  +++++v ++ d a++     ++++++   pe+ll++++ +qpaL++  ia+  +l +  G         ++GHSlG
     AHX11835.1   5 VFPGQGSQYVGMGRELYDAFPVAREVFEEVDDALNM----KLSEIIFRGPESLLSSTENTQPALMVTSIAALRTLlRESGktiaDVSKYLAGHSLG 96 
                    9*******************************9988....*****************************9998877999*6533334578****** PP

                    HHHHHHHCCSSSHHHHHHHHHHHHHHHHHHT..S-EECCEECS....HHHHHHH...TT.EEEEEEECCCCECCEEHHHHHHHHHHHHHCC..CCE CS
  Acyl_transf_1  94 ElAaavvagalsseeallavvlrsrlmmqla..gpgdmaavel...aeeeeklr.cqddvvgavansprrvvisgsqealrelvervskeg.vgal 182
                    E+ a+ + ga ++   ++++ +r+  m+++   g+g maa+     +e++  +   + d   +  ns ++vv+sg++++++++ +  + +g   + 
     AHX11835.1  97 EYTALCASGAATPSQIAKVLKIRGSAMQEAVplGEGSMAALLKvtcEEVQNLIVeSNADCEISNDNSNEQVVVSGKTAEIEKITKYAKNKGiKHVI 192
                    *****************************9988999***99986433333333346677888888999**************99999999944555 PP

                    EECCCEECTTCCCCCCCCHHHHHHHHCCCHHCHHTTBEHCCCHHHHHHCHHHHHHHHHHHCHCCHCCHHTTSSSECC-CCEECSSSSCCHCC CS
  Acyl_transf_1 183 venvnvavhspqvdaiadalasaladiaprkpkvakisstsldesserelsaeywvanlrspvrfaeavlsaaetiplvfveispHslllaa 274
                    + nv+  +h + ++++ ++ + al +    +p v+  s +++ + + +    e  v+ +  ++r +e +l a++ + ++f+ei +  +l + 
     AHX11835.1 193 RLNVSAPFHCRLMQPAVQQVSDALSTAEIGTPAVPIVSNVTATPINDPSEIRELLVKQVTGCIRWRESILFAINAGVRTFIEIGAGNVLSKM 284
                    66777789************************************99999999999****************************987777655 PP

>> SAT  Starter unit:ACP transacylase in aflatoxin biosynthesis
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !    5.7   0.3    0.0023        10      77     130 ..      61     113 ..      40     130 .. 0.83
   2 !   10.2   0.0    0.0001      0.46     190     240 .]     150     201 ..     123     201 .. 0.81

  Alignments for each domain:
  == domain 1  score: 5.7 bits;  conditional E-value: 0.0023
         SAT  77 sallciaqlaqfivyleenpeeypspestylvGlCtGllaAaavacskslseLv 130
                  + l+++ +a +   l e+++++++  s yl+G++ G   A +++ + + s++ 
  AHX11835.1  61 QPALMVTSIAALRTLLRESGKTIADV-SKYLAGHSLGEYTALCASGAATPSQIA 113
                 56788999999999999999988875.66***************9998887765 PP

  == domain 2  score: 10.2 bits;  conditional E-value: 0.0001
         SAT 190 lppasrvyisavssss.vtisGpPstleallksskakkkkkksklpiyapyH 240
                 +++ +   is  +s++ v++sG    +e++ k  k k  k+  +l ++ap+H
  AHX11835.1 150 VESNADCEISNDNSNEqVVVSGKTAEIEKITKYAKNKGIKHVIRLNVSAPFH 201
                 344477889*****999**********************************9 PP

>> DUF2974  Protein of unknown function (DUF2974)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.6   0.0   3.2e-05      0.15      36     128 ..      40     127 ..      27     198 .. 0.74

  Alignments for each domain:
  == domain 1  score: 11.6 bits;  conditional E-value: 3.2e-05
     DUF2974  36 edtlvvaFRGTddtlvgWkedfnmafrsevpaqesAlkYlnkileesegk.iylgGhSkGGnlAvyaamnaeddlqeriskiysfDgpGfskev 128
                  + + ++FRG+ ++l++  e+ + a +  v++  +    l++  +++ +   yl+GhS G   A+ a+  a ++    i+k++ + g  ++++v
  AHX11835.1  40 MKLSEIIFRGP-ESLLSSTENTQPALM--VTSIAALRTLLRESGKTIADVsKYLAGHSLGEYTALCASGAATPSQ---IAKVLKIRGSAMQEAV 127
                 566779*****.899999*****9988..44433334456666667766557************99999866654...5555555566666555 PP

>> Glyco_hydro_97  Glycoside hydrolase 97
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   10.2   0.0   7.5e-05      0.33      64     104 ..     158     198 ..     142     223 .. 0.70

  Alignments for each domain:
  == domain 1  score: 10.2 bits;  conditional E-value: 7.5e-05
  Glyco_hydro_97  64 kkkkekefdftkpypdfdleelvaYakekgvgvelwlhset 104
                      ++++++ +++ + ++ ++e++++Yak+kg++ ++ l+ ++
      AHX11835.1 158 ISNDNSNEQVVVSGKTAEIEKITKYAKNKGIKHVIRLNVSA 198
                     3456678889999999**************98777776665 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (311 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       676  (0.0377043); expected 358.6 (0.02)
Passed bias filter:                      553  (0.0308439); expected 358.6 (0.02)
Passed Vit filter:                        55  (0.00306766); expected 17.9 (0.001)
Passed Fwd filter:                         4  (0.000223102); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               4  [number of targets reported over threshold]
# CPU time: 0.48u 0.26s 00:00:00.74 Elapsed: 00:00:00.39
# Mc/sec: 2364.55
//
Query:       AHX11836.1  [L=582]
Description: DNA primase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.1e-31  108.5   0.0    3.3e-31  107.0   0.0    1.9  1  zf-CHC2   CHC2 zinc finger
    8.6e-31  106.7   0.0    2.2e-30  105.3   0.0    1.7  1  Toprim_N  DNA primase catalytic core, N-terminal domain
    1.4e-17   63.9   0.0    6.5e-17   61.7   0.0    2.2  2  Toprim_2  Toprim-like
    2.3e-16   60.0   0.0      5e-16   58.9   0.0    1.6  1  Toprim_4  Toprim domain
    2.4e-06   27.7   0.0    8.7e-06   25.9   0.0    2.0  1  Toprim    Toprim domain
     0.0092   16.3   0.0      0.018   15.4   0.0    1.5  1  Toprim_3  Toprim domain


Domain annotation for each model (and alignments):
>> zf-CHC2  CHC2 zinc finger
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  107.0   0.0   1.1e-34   3.3e-31       3      96 ..       3      96 ..       1      98 [. 0.97

  Alignments for each domain:
  == domain 1  score: 107.0 bits;  conditional E-value: 1.1e-34
     zf-CHC2  3 eevidelkeridivdvveeyvkLkkkgkdyvalCPFHeektpsftvspekqfyyCfgCgagGdaikFlmeieklsfveaveklakklgleleae 96
                ++ i+ +keri +++vv++ +kL+k g+  ++ CPFHeektpsf+v+++ +f+yCfgCg++Gd+i+F++e+++l+ ++ave+la+++g+++e++
  AHX11836.1  3 KKYIELIKERIPLSEVVGRTIKLRKVGTRLIGRCPFHEEKTPSFSVNDSGKFFYCFGCGKSGDVIDFISETKHLNLNDAVEELAASIGIKIEKR 96
                578999************************************************************************************9875 PP

>> Toprim_N  DNA primase catalytic core, N-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  105.3   0.0   7.3e-34   2.2e-30       1     127 [.     116     235 ..     116     236 .. 0.91

  Alignments for each domain:
  == domain 1  score: 105.3 bits;  conditional E-value: 7.3e-34
                 HHHHHHHCSCHHHHHHHHHCTT--HHHHHHCT-EEE-SHSCHHHHHHHHCT-HHHHHCCTTCEECSTTT-EEETTTTEEEEEEE-TTS-EEEEEEEESS CS
    Toprim_N   1 fykeelkseegekaleYLkkRglseetiekFqlGyapkswdnllkllkkkkvseeelleagllskkekgklydrFrnRimfPikdakgkvvgFgGRale 99 
                 ++ ++l+s+ g +a++YL++R l++++i++F+lGy p++ +++ k   k ++++++++e+g+l k       ++F+nRi+fPi++++gkv++Fg+Ra++
  AHX11836.1 116 WFCDNLHSKIGLNARAYLESR-LKKDVITEFKLGYCPSDINSFIKG--KCNFQRSVMMESGVLDKGG----RCYFKNRIIFPINNRQGKVIAFGSRAIK 207
                 577899**************9.899************997666543..467999*********7764....688************************* PP

                 S-SS.SEEE--SBTTB-CCC-EETHHHH CS
    Toprim_N 100 eeekaKYlNspetelFkKselLYgldea 127
                 +++ +KY+Ns et++FkKse+LY+ld+a
  AHX11836.1 208 DDSVPKYINSCETPFFKKSEVLYNLDKA 235
                 *************************987 PP

>> Toprim_2  Toprim-like
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   61.7   0.0   2.2e-20   6.5e-17       1      89 [.     244     333 ..     244     334 .. 0.93
   2 ?   -1.8   0.0       1.4   4.2e+03      41      72 ..     552     581 ..     542     582 .] 0.80

  Alignments for each domain:
  == domain 1  score: 61.7 bits;  conditional E-value: 2.2e-20
    Toprim_2   1 vvfEgaiDalSlaqlgikektnvvalgGtalteaalkllerypekkvvlalDnDkaGrkaakrlaellreag.....vrekirelpegkDwnel 89 
                 vv+Eg++D++Sl+q+g k   nv+ ++Gt++t+++lk l++   kkv +++D D aG+kaa r+ el+ ++      +r  ++ lp gkD++el
  AHX11836.1 244 VVVEGYMDVISLHQHGYK---NVLGVLGTSITPHHLKTLNQL-GKKVQFCFDGDLAGIKAAGRVLELIMSEFievldIRIDFAFLPAGKDPDEL 333
                 79***************9...*********************.888*********************9877788877788888999******96 PP

  == domain 2  score: -1.8 bits;  conditional E-value: 1.4
    Toprim_2  41 rypekkvvlalDnDkaGrkaakrlaellreag 72 
                 +y  ++++   D D++  + a+++ e++reag
  AHX11836.1 552 EY--RNLIKSPDLDEKKMEEANKILEKIREAG 581
                 34..7788888999999999999999999987 PP

>> Toprim_4  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   58.9   0.0   1.7e-19     5e-16       2      78 ..     242     307 ..     241     318 .. 0.89

  Alignments for each domain:
  == domain 1  score: 58.9 bits;  conditional E-value: 1.7e-19
    Toprim_4   2 eiiiVEgyaDvlalekagiknvvavlggalspldgirpeklktenlveaekkvkevilaldgDaeGeataerlaell 78 
                 ++++VEgy+Dv++l++ g+knv  vlg+++ ++++++   l++          k+v +++dgD +G ++a r++el+
  AHX11836.1 242 TLVVVEGYMDVISLHQHGYKNVLGVLGTSI-TPHHLK--TLNQL--------GKKVQFCFDGDLAGIKAAGRVLELI 307
                 79****************************.******..88882........49*******************9954 PP

>> Toprim  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   25.9   0.0   2.9e-09   8.7e-06       1      91 [.     242     312 ..     242     323 .. 0.89

  Alignments for each domain:
  == domain 1  score: 25.9 bits;  conditional E-value: 2.9e-09
                 EEEEESSHHHHHHHHHTHTSTEEEEEEESSSSEEEHSTTEEEEEECTTTHHHHHHHHHHHHHHSEEEEECSSSHHHHHHHHHHHHHHT.HHH CS
      Toprim   1 elvivEgpsdaktiakalgsgfqavtaslGhildletefkpvyeeiedkkkvlkalkelakradeiilatDpDreGeaiawellevlk.ell 91 
                 +lv+vEg++d++++++    g+++v+ +lG+ ++  +                  lk l +  +++ +++D+D +G ++a ++le++  e++
  AHX11836.1 242 TLVVVEGYMDVISLHQH---GYKNVLGVLGTSITPHH------------------LKTLNQLGKKVQFCFDGDLAGIKAAGRVLELIMsEFI 312
                 59***************...9****************..................99999999*********************87765444 PP

>> Toprim_3  Toprim domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   15.4   0.0   6.2e-06     0.018       2      86 ..     243     331 ..     242     337 .. 0.74

  Alignments for each domain:
  == domain 1  score: 15.4 bits;  conditional E-value: 6.2e-06
    Toprim_3   2 liivEGietaLsileartgaaviAllsa....anlkaiawpergkrvviaaDnDaandGreaaeklaerleaagieavllep.....aegeDwn 86 
                 l++vEG+ +++s+ ++     v+ +l++     +lk  ++ + gk+v  ++D+D a  G +aa ++ e + ++ ie+  +       ++g+D +
  AHX11836.1 243 LVVVEGYMDVISL-HQHGYKNVLGVLGTsitpHHLK--TLNQLGKKVQFCFDGDLA--GIKAAGRVLELIMSEFIEVLDIRIdfaflPAGKDPD 331
                 89***********.7777777777777744666777..6668**************..*******99998876666543333344446666655 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (582 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       717  (0.0399911); expected 358.6 (0.02)
Passed bias filter:                      451  (0.0251548); expected 358.6 (0.02)
Passed Vit filter:                        38  (0.00211947); expected 17.9 (0.001)
Passed Fwd filter:                         6  (0.000334653); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               6  [number of targets reported over threshold]
# CPU time: 0.58u 0.30s 00:00:00.87 Elapsed: 00:00:00.48
# Mc/sec: 3682.41
//
Query:       AHX11837.1  [L=121]
Description: holo-[acyl-carrier-protein] synthase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    1.7e-18   66.8   0.0    1.9e-18   66.6   0.0    1.0  1  ACPS      4'-phosphopantetheinyl transferase superfamily


Domain annotation for each model (and alignments):
>> ACPS  4'-phosphopantetheinyl transferase superfamily
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.6   0.0   1.1e-22   1.9e-18       2     114 .]       7     115 ..       6     115 .. 0.93

  Alignments for each domain:
  == domain 1  score: 66.6 bits;  conditional E-value: 1.1e-22
                 EEEEEEEHHHHH.HHH-----HHHHHS-HHHHHHHTT--HHHHHHHHHHHHHHHHHHHHHTTS-SSSS--GGG-EEEE-TTS-EEEE-S-SSEEEEEEE CS
        ACPS   2 vGiDieklsrlrkrvkrrgakilkrifteeErkllkssdeearaelfarlWaaKEAllKalgpglrklldfksievledstgrptlellseakkkawkl 100
                 +G Di+++sr+++ +++  +++lkr+f+  E++  +    ++r+ ++a+++aaKEA++Ka g+++   l++k+i+++++  g+p +++ ++  ++++ +
  AHX11837.1   7 IGADIVQVSRISRILESYQSRFLKRFFNSWEIEESQLHCGKTRISYLAKRFAAKEAIIKARGHAM--GLELKQISIRNNCRGKPFIYFKGRMLRNSQIS 103
                 9***********99999999**************999999999**********************..********************999998888766 PP

                 E-....SSEEEEEE CS
        ACPS 101 eslkidkdyviavv 114
                  s+  d+dy++a+v
  AHX11837.1 104 LSD--DGDYALAFV 115
                 444..499999986 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (121 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       413  (0.0230353); expected 358.6 (0.02)
Passed bias filter:                      371  (0.0206927); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.37u 0.23s 00:00:00.60 Elapsed: 00:00:00.38
# Mc/sec: 950.80
//
Query:       AHX11838.1  [L=393]
Description: hypothetical protein NHE_0919 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
  ------ inclusion threshold ------
        0.1   11.9   0.0       0.17   11.2   0.0    1.4  1  CbiD      CbiD


Domain annotation for each model (and alignments):
>> CbiD  CbiD
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.2   0.0   9.5e-06      0.17      46     109 ..      35     108 ..       8     134 .. 0.80

  Alignments for each domain:
  == domain 1  score: 11.2 bits;  conditional E-value: 9.5e-06
        CbiD  46 ekvalleee...aavikdaGddpDvTngaeivaeve.......eeieiegGeGvGrvtkpgLevevgeaAInpv 109
                 e++++l+e+    +    +G ++Dv ++ +i a+ +       +++e++  +G+ r+  +g++++vg+ A n++
  AHX11838.1  35 EELKKLQESfeeKSKSEASGANIDVSENDDIAADQKaeqlkleRRVEVSRKKGILRIIAEGFSLSVGKTAWNKI 108
                 3333333334447778889**************99999*****88*************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (393 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                      1796  (0.100173); expected 358.6 (0.02)
Passed bias filter:                      720  (0.0401584); expected 358.6 (0.02)
Passed Vit filter:                        65  (0.00362541); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.56u 0.24s 00:00:00.80 Elapsed: 00:00:00.39
# Mc/sec: 3018.63
//
Query:       AHX11839.1  [L=449]
Description: UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.2e-82  277.8   0.2    1.4e-82  277.7   0.2    1.0  1  EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvin


Domain annotation for each model (and alignments):
>> EPSP_synthase  EPSP synthase (3-phosphoshikimate 1-carboxyvinyltransferase)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  277.7   0.2   7.7e-87   1.4e-82       3     417 .]      39     441 ..      37     441 .. 0.94

  Alignments for each domain:
  == domain 1  score: 277.7 bits;  conditional E-value: 7.7e-87
                    CSS--EEEEE--B-HHHHHHHHHHHGGGBSS.EEEES---SHHHHHHHHHHHHTT.EEEEEECTSEEEEEGTT..--EE-HHHHTT-GGGGGGHHH CS
  EPSP_synthase   3 kgkrlegevkvpGsksisnralllAaLaege.stitnlLdseDvrsmlealreLgaeiikldeekevviveglggsfeapeelvldlgnsgtalrl 97 
                    +g +l+ge++++G  ++s +++++A+L+++e + +++++ ++Dv +m+ ++ +Lg     ++e+  ++i   + ++ ++++ l + +++s +a+++
     AHX11839.1  39 GGLELNGEITISG-SKNSSLPIIAASLLTDEeVVLKGIPAIRDVSNMIMVVSSLGKRCDFIEENTLRIIPDDKFEERSVDKSLHIWIRASCLAMGP 133
                    56689********.789***********9999***********************99999987777777666667777778999************ PP

                    HHHHHSEESSEEEEE-SBTTCGS--HHHHHHHHHTT-EEEEETTEEEEEESEETSS-BEEEEETSSTTHHHHHHHHHHHTTSBSEEEEES-TTHHH CS
  EPSP_synthase  98 LtallalasgevvLtGdesirkRPidrlldaLrqlGaeieveegenkaplkvkglklkgveikaevsSqqvtsllllaallaegtteleelaseps 193
                     +a+ +++   + ++G+++i+ RPid +++a++++Ga+ e+e++++++ ++     l g++i+++ +S+++t++ ++aa+l+egtt+++++  ep+
     AHX11839.1 134 TLARKGKI--SMYFPGGCAIGRRPIDFHISAFEKMGAKTEIESEKVTLTAT----SLHGADIEFPRVSVGATQNAIMAAVLSEGTTTISNASTEPE 223
                    ****9987..899*******************************8888887....9**************************************** PP

                    HHHHHHHHHHTT-EEEETTSSEEEEEE--SSB--EEEE--B-HHHHHHHHHHHHHTT-EEEEES--GGGGHHH..HHHHHHHHTTEEEEEESTSEE CS
  EPSP_synthase 194 iddtlkmlkkfgikietsgteesitvkGkeklpgteyvvegDassAayflvaAaitggevtvenvginslqGdiealdeilekmgaeitqeedasi 289
                    i+d++++l+ +g+ki   g+ + ++++++ +l+g ++ v++D+++A+++++  a+ gg+++++nv+ ++++    +l++il+  +++i+  ed +i
     AHX11839.1 224 INDLISFLNGIGAKIYWIGDRK-LKINPVSRLKGITHKVIPDRIEASTYMIMSAVVGGRIVLRNVDVSQMT---CLLEQILKTESVRIESSEDYII 315
                    *****************88887.***********************************************9...57999*************8888 PP

                    EEEETTS--BEEEEEBGSTTSBHGGGHHHHHHHHHTSBSEEEEEGSSSTTCCHHHHHHHTTT-EEEE.ETTEEEEEEEEE.EB-EEEE-TTSTTTT CS
  EPSP_synthase 290 vvgpsglklkdvdietlpdeaptlavlaafaegttviegiaelrvketdrlaamateLrklGaevee.eedgliiipaekqlkgaevesydDhRia 384
                    v++    k+++ +++t ++++++++v+ +++++ + +eg + +r+++++++++++ eL+k+Ga++e  ++d + i++++  l++++    +D+R++
     AHX11839.1 316 VEKI--GKIRPLEVATDVYPGLPTDVQPQLTTLLSFAEGRSIIRETIFENRFTHVPELKKMGAQIESmGPDCISIVGSRH-LNPSKGLRANDLRAG 408
                    8888..68999999***************************************************962679999999986.****998889***** PP

                    HHHHHHHHHSBSEEEEETTHHHHHHSSSHHHHH CS
  EPSP_synthase 385 malalaglvaegeveiddiectdksfpefeekL 417
                    +al++a+l a+g+ +id  + +++++++f  kL
     AHX11839.1 409 AALIIAALQANGKSIIDGSDNVERGYEDFRVKL 441
                    *****************************8776 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (449 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       339  (0.0189079); expected 358.6 (0.02)
Passed bias filter:                      311  (0.0173462); expected 358.6 (0.02)
Passed Vit filter:                        19  (0.00105974); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.49u 0.25s 00:00:00.74 Elapsed: 00:00:00.42
# Mc/sec: 3205.63
//
Query:       AHX11840.1  [L=185]
Description: deoxycytidine triphosphate deaminase [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------
    6.6e-05   22.6   0.0    0.00012   21.7   0.0    1.4  1  dUTPase   dUTPase


Domain annotation for each model (and alignments):
>> dUTPase  dUTPase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.7   0.0   6.8e-09   0.00012      24     112 ..      78     166 ..      71     180 .. 0.86

  Alignments for each domain:
  == domain 1  score: 21.7 bits;  conditional E-value: 6.8e-09
                 EEEETTEEEEEEEEEEEE--TTEEEEEEE-HHHHHHHEEEEEEEEETTBTSEEEEEEEE-SSS-EEE-TT-EEEEEEEEEBECGEEEEE CS
     dUTPase  24 ltvkpgetvlvptdisiklpdglaalilpRSglaakglivvpgvidsdyrGevkvvlfnltkkdvkikkgdRiAqLifariltaeleev 112
                 ++++p++  l  t  ++ +p+++  + l++S  a+ g++v ++ +   ++G v + + n t  + ki +++ i+qLif + +   +  +
  AHX11840.1  78 CIIPPNGFMLGCTVEYFRIPRDVIVICLGKSTYARCGIVVNVTPLEPGWEGFVTLEFSNTTPLPAKIYANEGICQLIFLKGESECMTSY 166
                 57778999999******************************999**********************************97666444445 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (185 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       261  (0.0145574); expected 358.6 (0.02)
Passed bias filter:                      241  (0.0134419); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.38
# Mc/sec: 1465.54
//
Query:       AHX11841.1  [L=317]
Description: thiC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
      7e-69  232.6   0.0    9.7e-69  232.1   0.0    1.1  1  ThiC_Rad_SAM     Radical SAM ThiC family
    1.3e-11   44.1   0.0      4e-11   42.6   0.0    1.9  1  ThiC-associated  ThiC-associated domain
  ------ inclusion threshold ------
       0.16   12.1   0.1       0.28   11.4   0.1    1.3  1  Pox_A9           A9 protein conserved region


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  232.1   0.0   1.6e-72   9.7e-69       1     183 [.     123     311 ..     123     314 .. 0.98

  Alignments for each domain:
  == domain 1  score: 232.1 bits;  conditional E-value: 1.6e-72
  ThiC_Rad_SAM   1 tqleaarkgiiteemeevaeken.......vepefvreevaeGrivipanknhkek.pvaiGkglrtkvnaniGtsadasdieeEveKlkvalkaga 89 
                   tql++a+kgiit+eme++a +en       v++efvr+e+a+Gr++ip+n+nh+e+ p++iGk++ +kvnaniG+s+ +s i++E+ K+ +a+k+ga
    AHX11841.1 123 TQLYYAKKGIITPEMEYAAIRENcgrtngrVTAEFVRDEIASGRAIIPCNINHPESePMVIGKNFLVKVNANIGKSSVTSGIKDELYKMLWACKWGA 219
                   89***************************************************7777**************************************** PP

  ThiC_Rad_SAM  90 dtvmdLstggdideirekileespvpvgtvpiYqaleekekkveelteeellevieeqaedGvdfltiHagvtlellellkkekRltgivSrgG 183
                   dtvmdLstg++++++re+i+++s vpvgtvpiYqale+++++ve+lt+e +++++ eqae+Gvd++tiHag+ +++++l+   +R+tgivSrg 
    AHX11841.1 220 DTVMDLSTGENLHNVREWIVRNSLVPVGTVPIYQALEKVKGNVEKLTWEIYRDTLIEQAEQGVDYFTIHAGLLKNYIQLTF--DRVTGIVSRGA 311
                   *******************************************************************************99..*********95 PP

>> ThiC-associated  ThiC-associated domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   42.6   0.0   6.7e-15     4e-11       1      80 [.      14      78 ..      14      79 .. 0.95

  Alignments for each domain:
  == domain 1  score: 42.6 bits;  conditional E-value: 6.7e-15
                     S-TT-EEEEEE-SS.TT-EEEEEEE---GG.........G----EEEE---GGGG-TTS---TTT-S--TTHHHHHHTS-E CS
  ThiC-associated  1 pfpnsrkvyvegsr.pdirVpmreiklsptvlketkekeeenepvrvYDtSGpYtdpeveidvrkGLprlReaWieergdv 80
                     pfpns+ v+ +g+  p+i+V mr+i+ls+             e ++vYDt G      +++ v++GLp+lR++Wie+r+d+
       AHX11841.1 14 PFPNSEVVHERGKLfPEIEVRMRKINLSNG------------ESLTVYDTLGQ----IMKVTVEEGLPKLRKSWIENREDT 78
                     69**************************99............689*******6....689*******************97 PP

>> Pox_A9  A9 protein conserved region
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   11.4   0.1   4.6e-05      0.28       2      23 ..      86     107 ..      85     109 .. 0.93

  Alignments for each domain:
  == domain 1  score: 11.4 bits;  conditional E-value: 4.6e-05
      Pox_A9   2 IdllrHlfMyfcEnrlRpNsfa 23 
                 I+++ H++ ++ E++l++ sf 
  AHX11841.1  86 INIIDHCLTHYNEHKLKSDSFM 107
                 8999****************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (317 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       493  (0.0274974); expected 358.6 (0.02)
Passed bias filter:                      445  (0.0248201); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.46u 0.23s 00:00:00.69 Elapsed: 00:00:00.38
# Mc/sec: 2473.93
//
Query:       AHX11842.1  [L=251]
Description: thiC family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model        Description
    ------- ------ -----    ------- ------ -----   ---- --  --------     -----------
   5.7e-112  374.5   0.0   6.5e-112  374.4   0.0    1.0  1  ThiC_Rad_SAM  Radical SAM ThiC family


Domain annotation for each model (and alignments):
>> ThiC_Rad_SAM  Radical SAM ThiC family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  374.4   0.0  3.6e-116  6.5e-112     190     417 ..       1     233 [.       1     234 [. 0.98

  Alignments for each domain:
  == domain 1  score: 374.4 bits;  conditional E-value: 3.6e-116
  ThiC_Rad_SAM 190 mlanekenplyeefdelleilkeydvtlSlgdglRpGsiaDatdeaqlaelivlgelvkrareagvqvmveGPGHvpldeieanvklqkklckeaPf 286
                   m+ ++ken+ly++fde+++i+++ydv++SlgdglRpG+i+Da+d+aq+ael +lgel+  a+e+++qvmveGPGH+pl+++++n++ + ++c ++Pf
    AHX11842.1   1 MMIHKKENFLYTNFDEICKIMSRYDVSFSLGDGLRPGCINDANDKAQFAELRTLGELTLIAHEHDCQVMVEGPGHIPLHKVRENMERHAEYCYGVPF 97 
                   789********************************************************************************************** PP

  ThiC_Rad_SAM 287 yvlGplvtDiapgYDhitsaiGaalaaaaGadllCyvtpaEHlglPdeedvkeGviaakiaahaadlakglkkarerdkalskaRkeldwekqfela 383
                   y+lGplvtDiapgYDhitsaiGa+ +a++G++llCyvtp+EHlglP+++dv++G+ia+kiaahaadlakg+++ ++rd+alskaR++++we+qf+l+
    AHX11842.1  98 YTLGPLVTDIAPGYDHITSAIGATNIAYYGTALLCYVTPKEHLGLPNVDDVRDGMIAYKIAAHAADLAKGNENSVARDNALSKARFDFRWEDQFNLS 194
                   ************************************************************************************************* PP

  ThiC_Rad_SAM 384 ldpekareireeklpe....eeeaCsmCgek.Cavkive 417
                   ldp +are+++e+lp     +++ CsmCg+k C +++++
    AHX11842.1 195 LDPFRAREFHDETLPGsgskKAHYCSMCGPKfCPMELMN 233
                   *************98777779*********99***9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (251 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       416  (0.0232026); expected 358.6 (0.02)
Passed bias filter:                      359  (0.0200234); expected 358.6 (0.02)
Passed Vit filter:                        29  (0.00161749); expected 17.9 (0.001)
Passed Fwd filter:                         1  (5.57756e-05); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.39u 0.22s 00:00:00.61 Elapsed: 00:00:00.36
# Mc/sec: 2074.27
//
Query:       AHX11843.1  [L=342]
Description: phosphoribosylaminoimidazole carboxylase, ATPase subunit [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model           Description
    ------- ------ -----    ------- ------ -----   ---- --  --------        -----------
    2.2e-42  144.5   0.0    3.2e-42  144.0   0.0    1.2  1  ATP-grasp        ATP-grasp domain
    1.2e-12   47.3   0.0    2.4e-12   46.4   0.0    1.5  1  PurK_C           Phosphoribosylaminoimidazole carboxylase C-t
    2.4e-05   24.0   0.0    0.00013   21.6   0.0    2.1  1  Dala_Dala_lig_C  D-ala D-ala ligase C-terminus


Domain annotation for each model (and alignments):
>> ATP-grasp  ATP-grasp domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  144.0   0.0   5.3e-46   3.2e-42       2     171 .]     107     270 ..     106     270 .. 0.96

  Alignments for each domain:
  == domain 1  score: 144.0 bits;  conditional E-value: 5.3e-46
                 HTTT--B-EEEEECCHHHHHHHHHHH-SCEEEEESSS-CTTTTEEEECTCCGHHCHHHHCGTTCEEEEE----SEEEEEEEEEETTC-EEE--EEEEEE CS
   ATP-grasp   2 eklglpvprflaveskeeleeaaeelglpvvvKarrlgydGkGqsvvrseedleqalealkeekvivEefvpfekElsvlvvrsaeGetafypvvetvq 100
                 +++++p+++++ +++  +l    e+l++p+++K+ r+gydG+Gq++++++e+ e+ +  l e ++i+E+ v+ +kE s++v+r++ G    +p+ e+v+
  AHX11843.1 107 KQNQIPTTPYWPIAQIGDL----EDLEFPIILKTTRGGYDGRGQFLLKNREEYESKVPSL-EFPLIAEKLVDIKKEFSIIVARNETG-KIHFPIAENVH 199
                 7899*********999665....567**********************************.9*************************.5668******* PP

                 ETTEEEEEEECEE-SCHHHHHHHHHHHHHHHHHTSSEEEEEEEEEETTCTEEEEEEESS--GGGGGHHHHB CS
   ATP-grasp 101 edgilrlsvapaevsekaqkkaeeiakkiveeLggvGvfavElFvledgellvnElapRpHnsGhvtldaa 171
                 ++gilr+s +pa++s +   ++ +i  +i + L++ G++ +E+F+ + ++l+vnElapRpHnsGh+++d++
  AHX11843.1 200 SNGILRTSKVPAKLSPTLSDEVVKIGLQISDLLNIKGLICIEFFLDHMDRLMVNELAPRPHNSGHWSMDCC 270
                 **********************************************9999*******************98 PP

>> PurK_C  Phosphoribosylaminoimidazole carboxylase C-terminal domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   46.4   0.0   3.9e-16   2.4e-12       1      46 [.     296     340 ..     296     342 .] 0.96

  Alignments for each domain:
  == domain 1  score: 46.4 bits;  conditional E-value: 3.9e-16
      PurK_C   1 avMvNlLGedaeekleellaipgahlHlYgKeearpgRKmGHitvv 46 
                 ++M N+LGe+  + ++++ a ++++++ YgK+earp RKmGH++++
  AHX11843.1 296 CIMKNVLGEEI-SLWSDMIAEKNLRFYNYGKDEARPERKMGHFNIL 340
                 69*********.99******************************98 PP

>> Dala_Dala_lig_C  D-ala D-ala ligase C-terminus
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   21.6   0.0   2.1e-08   0.00013      75     176 ..     166     259 ..     105     264 .. 0.69

  Alignments for each domain:
  == domain 1  score: 21.6 bits;  conditional E-value: 2.1e-08
                      EEEEE--.ESEEEEEEEEETSSCEEE.EEEEEE-SSSSS-HHHHHC.TT-EEESS----HHHHHHHHHHHHHHHHHTT--SEEEEEEEEETTTE CS
  Dala_Dala_lig_C  75 vlvEeai.egreievavlgneklevs.evgeivvkkgfydyeakysddkaqlevpaklekeveekiqelalkaykaldlrGlaRvDfflteege 166
                       + E+ +   +e+ + v  ne+ +++ ++ e v ++g+            + +vpakl++  ++++ ++ l++ ++l+++Gl  + ffl++ ++
       AHX11843.1 166 LIAEKLVdIKKEFSIIVARNETGKIHfPIAENVHSNGIL----------RTSKVPAKLSPTLSDEVVKIGLQISDLLNIKGLICIEFFLDHMDR 249
                      555555533345555555555555441333334444443..........34689**************************************** PP

                      EEEEEEESS- CS
  Dala_Dala_lig_C 167 ivlnEvNtlP 176
                      +++nE+ + P
       AHX11843.1 250 LMVNELAPRP 259
                      *****98777 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (342 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       322  (0.0179597); expected 358.6 (0.02)
Passed bias filter:                      292  (0.0162865); expected 358.6 (0.02)
Passed Vit filter:                        32  (0.00178482); expected 17.9 (0.001)
Passed Fwd filter:                         3  (0.000167327); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               3  [number of targets reported over threshold]
# CPU time: 0.43u 0.21s 00:00:00.64 Elapsed: 00:00:00.45
# Mc/sec: 2296.33
//
Query:       AHX11844.1  [L=210]
Description: short chain dehydrogenase family protein [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------      -----------
    1.8e-18   66.7   0.0    2.2e-18   66.4   0.0    1.0  1  adh_short      short chain dehydrogenase
    6.7e-13   48.7   0.0    8.1e-13   48.5   0.0    1.0  1  adh_short_C2   Enoyl-(Acyl carrier protein) reductase
    0.00084   19.3   0.0     0.0011   18.9   0.0    1.2  1  KR             KR domain
  ------ inclusion threshold ------
      0.011   15.2   0.0      0.021   14.3   0.0    1.4  1  Epimerase      NAD dependent epimerase/dehydratase family
      0.033   13.6   0.0       0.05   13.0   0.0    1.2  1  GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase


Domain annotation for each model (and alignments):
>> adh_short  short chain dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   66.4   0.0   6.2e-22   2.2e-18       1     182 [.       3     185 ..       3     190 .. 0.89

  Alignments for each domain:
  == domain 1  score: 66.4 bits;  conditional E-value: 6.2e-22
                 SEEEEESTTSHHHHHHHHHHHHTT-EEEE.EESCHHHHHHHHHHHHHT.TSEEEEEE-TTTSHHHHHHHHHHHHHHHSSESEEEE---SS--SSGGGCS CS
   adh_short   1 kvvlvtGassGIGraiakelakeGakvvv.vdrseekleevakelkee.gakalaiqvDvtdreevealvekavkklgkldvLvnNAGitgsgpfsels 97 
                 k++l+tG ++ +G  ia+ la  G+++v+ ++rs e++  + ++l+++ g ++  +q D   ++++++++e   + + +l +LvnNA+   + +f    
  AHX11844.1   3 KAALITGSAKRLGAYIANVLAMHGYDIVIhYNRSCEDAFSLREKLRNDyGISVELYQEDFLASNDLSKIIEYSFQIFPHLCLLVNNASFFLQDNF---- 97 
                 789**************************************************************************************433333.... PP

                 HHHHHHHHHHHTHHHHHHHHHHHHHHH..HCTTEEEEEEEEGGG.TSB-TTBHHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEESSB CS
   adh_short  98 eeewervievNltgvflltravlpaml..kqssGrIvnvsSvag.kvpvagvaaYsAsKaavagltrslakelaptgirvnavaPGlv 182
                  +++er+++v ++  + +  ++++++   + ++G+I+n+      +++++ + +Y  sK  + +lt+ + + ++++g +v a++PG+v
  AHX11844.1  98 GSDVERLFDVYYKIHVRVPLSLMRHFSkrEPKNGKIINIIDKLInRKSSNKYFSYLFSKKCLFQLTQMVDDYMSSKGMKVYAIHPGIV 185
                 34466666666666666666666666655899******9987654899999***********************************98 PP

>> adh_short_C2  Enoyl-(Acyl carrier protein) reductase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   48.5   0.0   2.3e-16   8.1e-13       1     176 [.       9     187 ..       9     208 .. 0.90

  Alignments for each domain:
  == domain 1  score: 48.5 bits;  conditional E-value: 2.3e-16
                   TTTTSHHHHHHHHHHHTT-EEEEEESSGGH..HHHHHHHHHHTTSEE..EE--TTSHHHHHHHHHHHHHHHSSEEEEEE-----EGCSS-GGGH-HH CS
  adh_short_C2   1 GaasgIGraiAkalaeeGaevvltdlneea..kkrveelaeelgaev..lecDVtdeeqvealveevvekfgklDilvnnagiapklkgpfletsre 93 
                   G a+ +G+ iA  la +G+++v+++ +  +   +  e+l +++g +v  ++ D    +++ +++e   + f +l  lvnna +  +   +f +  + 
    AHX11844.1   9 GSAKRLGAYIANVLAMHGYDIVIHYNRSCEdaFSLREKLRNDYGISVelYQEDFLASNDLSKIIEYSFQIFPHLCLLVNNASFFLQ--DNFGSDVER 103
                   55677899*****************998886457788999999966566************************************9..99999999* PP

                   HHHHHHHHHTHHHHHHHHHHHHHCTSCCEEEEE.EEGGGTSBSTTTTHHHHHHHHHHHHHHHHHHHHGGGTEEEEEEEE--BHC CS
  adh_short_C2  94 efdraldvnlyslfllakaalplmkeggsivnl.ssvgaervvpnynaygaaKaalealtrylAvelgpkgiRvNavspgpikT 176
                    fd   ++ ++  ++l++++ +   ++g+i+n+   +  +++ ++y  y  +K  l +lt+ +   + +kg++v a++pg++  
    AHX11844.1 104 LFDVYYKIHVRVPLSLMRHFSKREPKNGKIINIiDKLINRKSSNKYFSYLFSKKCLFQLTQMVDDYMSSKGMKVYAIHPGIVIM 187
                   ********************************8788899999**************************************9864 PP

>> KR  KR domain
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !   18.9   0.0   3.1e-07    0.0011       4      90 ..       6      90 ..       4     126 .. 0.84

  Alignments for each domain:
  == domain 1  score: 18.9 bits;  conditional E-value: 3.1e-07
                EEETTTSHHHHHHHHHHHHHHS-EEEEE-SS..--HHHHHHHHHHHHT.T-EEEE----TT-HHHHHHHHHHHHHHSS---EEEE--- CS
          KR  4 litGGlGgLGlelarwlaekgarhlvllsRsaaadedskaliaeleal.gaevevvaaDvsdkdavealleeikaeeppikGvihaAg 90
                litG +  LG  +a+ la +g   ++   Rs    ed+ +l ++l++  g++ve+++ D   ++++++++e   + +p +   ++ A 
  AHX11844.1  6 LITGSAKRLGAYIANVLAMHGYDIVIHYNRSC---EDAFSLREKLRNDyGISVELYQEDFLASNDLSKIIEYSFQIFPHLCLLVNNAS 90
                9******************************3...44455677777655********************9988877777776666665 PP

>> Epimerase  NAD dependent epimerase/dehydratase family
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   14.3   0.0   5.7e-06     0.021       1      61 [.       5      73 ..       5      85 .. 0.92

  Alignments for each domain:
  == domain 1  score: 14.3 bits;  conditional E-value: 5.7e-06
                EEEETTTSHHHHHHHHHHHHCTSEEEEEES-STTTTCHHCHHC........EEEE--TT-HHHHHHHHH CS
   Epimerase  1 ilVtGatGfiGsalvkallekgyevigldrlssasntarledl........elveldltdrsalerlfk 61
                +l+tG +  +G+++++ l+ +gy+++   ++s +++++++e+l        el++ d++ +++l ++++
  AHX11844.1  5 ALITGSAKRLGAYIANVLAMHGYDIVIHYNRSCEDAFSLREKLrndygisvELYQEDFLASNDLSKIIE 73
                59**********************99999999999999999999******9999999999999999987 PP

>> GDP_Man_Dehyd  GDP-mannose 4,6 dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ?   13.0   0.0   1.4e-05      0.05       1      72 [.       6      73 ..       6      79 .. 0.91

  Alignments for each domain:
  == domain 1  score: 13.0 bits;  conditional E-value: 1.4e-05
                   EEETTTSHHHHHHHHHHHHCT-CCEEEEEEESS-TTHHHHHCTTT...TTGCCEEEEE--TT-HHHHHHHHH CS
  GDP_Man_Dehyd  1 LiTGiaGfiGsylaelLlekgyevhgivrrsssfntgriehlakdpkeeleenlklhkgDltDssslerlla 72
                   LiTG a   G+y+a+ L   gy++++  +rs + +++  e+l++d       +++l++ D   s+ l ++++
     AHX11844.1  6 LITGSAKRLGAYIANVLAMHGYDIVIHYNRSCEDAFSLREKLRNDYG----ISVELYQEDFLASNDLSKIIE 73
                   8*******************************999999999987654....4799********999999996 PP



Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (210 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       727  (0.0405488); expected 358.6 (0.02)
Passed bias filter:                      515  (0.0287244); expected 358.6 (0.02)
Passed Vit filter:                        40  (0.00223102); expected 17.9 (0.001)
Passed Fwd filter:                         5  (0.000278878); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               5  [number of targets reported over threshold]
# CPU time: 0.42u 0.24s 00:00:00.65 Elapsed: 00:00:00.39
# Mc/sec: 1619.85
//
Query:       AHX11845.1  [L=42]
Description: hypothetical protein NHE_0926 [Neorickettsia helminthoeca str. Oregon]
Scores for complete sequence (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Model    Description
    ------- ------ -----    ------- ------ -----   ---- --  -------- -----------

   [No hits detected that satisfy reporting thresholds]


Domain annotation for each model (and alignments):

   [No targets detected that satisfy reporting thresholds]


Internal pipeline statistics summary:
-------------------------------------
Query sequence(s):                         1  (42 residues searched)
Target model(s):                       17929  (3037991 nodes)
Passed MSV filter:                       183  (0.0102069); expected 358.6 (0.02)
Passed bias filter:                      130  (0.00725082); expected 358.6 (0.02)
Passed Vit filter:                        10  (0.000557756); expected 17.9 (0.001)
Passed Fwd filter:                         0  (0); expected 0.2 (1e-05)
Initial search space (Z):              17929  [actual number of targets]
Domain search space  (domZ):               0  [number of targets reported over threshold]
# CPU time: 0.29u 0.24s 00:00:00.53 Elapsed: 00:00:00.35
# Mc/sec: 359.35
//
[ok]
